@article{wagnerj.tig.2024.05.007,
  author = {Wagner, Viktoria and Meese, Eckart and Keller, Andreas},
  year = {2024},
  month = {06},
  pages = {},
  title = {The intricacies of isomiRs: from classification to clinical relevance},
  journal = {Trends in genetics : TIG},
  doi = {10.1016/j.tig.2024.05.007}
}

@article{engel15476286,
  author = {Engel, Annika and Ludwig, Nicole and Grandke, Friederike and Wagner, Viktoria and Kern, Fabian and Fehlmann, Tobias and Schmartz, Georges and Aparicio-Puerta, Ernesto and Henn, Dominic and Walch-Rückheim, Barbara and Hannig, Matthias and Rupf, Stefan and Meese, Eckart and Laschke, Matthias and Keller, Andreas},
  year = {2024},
  month = {06},
  pages = {31-44},
  title = {Skin treatment with non-thermal plasma modulates the immune system through miR-223-3p and its target genes},
  volume = {21},
  journal = {RNA Biology},
  doi = {10.1080/15476286.2024.2361571}
}

@article{lehmannS2589-7500,
  author = {Lehmann, and Reich, Christoph and Kayvanpour, Elham and Sedaghat-Hamedani, Farbod and Meder, Manuela and Haas, Jan and Gomes, Bruna and Ashley, Euan and Lehmann, David and Gomes, Bruna and Vetter, Niklas and Braun, Olivia and Amr, Ali and Hilbel, Thomas and Müller, Jens and Köthe, Ulrich and Reich, Christoph and Kayvanpour, Elham and Sedaghat-Hamedani, Farbod and Meder, Benjamin},
  year = {2024},
  month = {05},
  pages = {e407-e417},
  title = {Prediction of diagnosis and diastolic filling pressure by AI-enhanced cardiac MRI: a modelling study of hospital data},
  volume = {6},
  journal = {The Lancet Digital Health},
  doi = {10.1016/S2589-7500(24)00063-3}
}

@article{hirsch2401,
  author = {Hirsch, Pascal and Molano, Leidy-Alejandra and Engel, Annika and Zentgraf, Jens and Rahmann, Sven and Hannig, Matthias and Müller, Rolf and Kern, Fabian and Keller, Andreas and Schmartz, Georges},
  year = {2024},
  month = {05},
  pages = {},
  title = {Mibianto: ultra-efficient online microbiome analysis through k-mer based metagenomics},
  journal = {Nucleic acids research},
  doi = {10.1093/nar/gkae364}
}

@article{pedro2401,
  author = {Guimarães, Pedro and Keller, Andreas and Böhm, Michael and Lauder, Lucas and Fehlmann, Tobias and Ruilope, Luis and Vinyoles, Ernest and Gorostidi, Manuel and Segura, Julian and Ruiz-Hurtado, Gema and Staplin, Natalie and Williams, Bryan and Sierra, Alejandro and Mahfoud, Felix},
  year = {2024},
  month = {04},
  pages = {},
  title = {Artificial Intelligence-Derived Risk Prediction: A Novel Risk Calculator Using Office and Ambulatory Blood Pressure},
  journal = {Hypertension (Dallas, Tex. : 1979)},
  doi = {10.1161/HYPERTENSIONAHA.123.22529}
}

@article{engel2401,
  author = {Engel, Annika and Rishik, Shusruto and Hirsch, Pascal and Keller, Verena and Fehlmann, Tobias and Kern, Fabian and Keller, Andreas},
  year = {2024},
  month = {04},
  pages = {},
  title = {SingmiR: a single-cell miRNA alignment and analysis tool},
  journal = {Nucleic acids research},
  doi = {10.1093/nar/gkae225}
}

@article{hms12276,
  author = {Hart, Martin and Kern, Fabian and Fecher-Trost, Claudia and Krammes, Lena and Aparicio, Ernesto and Engel, Annika and Hirsch, Pascal and Wagner, Viktoria and Keller, Verena and Schmartz, Georges and Rheinheimer, Stefanie and Diener, Caroline and Fischer, Ulrike and Mayer, Jens and Meyer, Markus and Flockerzi, Veit and Keller, Andreas and Meese, Eckart},
  year = {2024},
  month = {04},
  pages = {},
  title = {Experimental capture of miRNA targetomes: disease-specific 3'UTR library-based miRNA targetomics for Parkinson's disease},
  volume = {56},
  journal = {Experimental & molecular medicine},
  doi = {10.1038/s12276-024-01202-5}
}

@article{tal2401,
  author = {Iram, Tal and Garcia, Miguel and Amand, Jérémy and Kaur, Achint and Atkins, Micaiah and Iyer, Manasi and Lam, Mable and Ambiel, Nicholas and Jorgens, Danielle and Keller, Andreas and Wyss-Coray, Tony and Kern, Fabian and Zuchero, J},
  year = {2024},
  month = {03},
  pages = {e2307250121},
  title = {SRF transcriptionally regulates the oligodendrocyte cytoskeleton during CNS myelination},
  volume = {121},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  doi = {10.1073/pnas.2307250121}
}

@article{caro23x01,
  author = {Diener, Caroline and Keller, Andreas and Meese, Eckart},
  year = {2023},
  month = {11},
  pages = {},
  title = {The miRNA–target interactions: An underestimated intricacy},
  volume = {52},
  journal = {Nucleic Acids Research},
  doi = {10.1093/nar/gkad1142}
}

@article{hirsch0123,
    	author = {Hirsch, Pascal and Tagirdzhanov, Azat and Kushnareva, Aleksandra and Olkhovskii, Ilia and Graf, Simon and Schmartz, Georges and Hegemann, Julian and Bozhueyuek, Kenan and Müller, Rolf and Keller, Andreas and Gurevich, Alexey},
    	year = {2023},
    	month = {11},
	abstract = "{The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.}",
    	pages = {},
    	title = {ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome},
    	volume = {52},
    	journal = {Nucleic Acids Research},
    	doi = {10.1093/nar/gkad1086},
    	url = {https://doi.org/10.1093/nar/gkad1086}
}

The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.

@article{flotho0123,
    	author = {Flotho, Matthias and Amand, Jérémy and Hirsch, Pascal and Grandke, Friederike and Wyss-Coray, Tony and Keller, Andreas and Kern, Fabian},
    	year = {2023},
    	month = {11},
	abstract = "{The molecular causes and mechanisms of neurodegenerative diseases remain poorly understood. A growing number of single-cell studies have implicated various neural, glial, and immune cell subtypes to affect the mammalian central nervous system in many age-related disorders. Integrating this body of transcriptomic evidence into a comprehensive and reproducible framework poses several computational challenges. Here, we introduce ZEBRA, a large single-cell and single-nucleus RNA-seq database. ZEBRA integrates and normalizes gene expression and metadata from 33 studies, encompassing 4.2 million human and mouse brain cells sampled from 39 brain regions. It incorporates samples from patients with neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, and Multiple sclerosis, as well as samples from relevant mouse models. We employed scVI, a deep probabilistic auto-encoder model, to integrate the samples and curated both cell and sample metadata for downstream analysis. ZEBRA allows for cell-type and disease-specific markers to be explored and compared between sample conditions and brain regions, a cell composition analysis, and gene-wise feature mappings. Our comprehensive molecular database facilitates the generation of data-driven hypotheses, enhancing our understanding of mammalian brain function during aging and disease. The data sets, along with an interactive database are freely available at https://www.ccb.uni-saarland.de/zebra.}",
    	pages = {},
    	title = {ZEBRA: a hierarchically integrated gene expression atlas of the murine and human brain at single-cell resolution},
    	volume = {52},
    	journal = {Nucleic acids research},
    	doi = {10.1093/nar/gkad990},
    	url = {https://doi.org/10.1093/nar/gkad990}
}

The molecular causes and mechanisms of neurodegenerative diseases remain poorly understood. A growing number of single-cell studies have implicated various neural, glial, and immune cell subtypes to affect the mammalian central nervous system in many age-related disorders. Integrating this body of transcriptomic evidence into a comprehensive and reproducible framework poses several computational challenges. Here, we introduce ZEBRA, a large single-cell and single-nucleus RNA-seq database. ZEBRA integrates and normalizes gene expression and metadata from 33 studies, encompassing 4.2 million human and mouse brain cells sampled from 39 brain regions. It incorporates samples from patients with neurodegenerative diseases like Alzheimer's disease, Parkinson's disease, and Multiple sclerosis, as well as samples from relevant mouse models. We employed scVI, a deep probabilistic auto-encoder model, to integrate the samples and curated both cell and sample metadata for downstream analysis. ZEBRA allows for cell-type and disease-specific markers to be explored and compared between sample conditions and brain regions, a cell composition analysis, and gene-wise feature mappings. Our comprehensive molecular database facilitates the generation of data-driven hypotheses, enhancing our understanding of mammalian brain function during aging and disease. The data sets, along with an interactive database are freely available at https://www.ccb.uni-saarland.de/zebra.

@article{gkad1142,
	author = {Diener, Caroline and Keller, Andreas and Meese, Eckart},
	year = {2023},
	month = {11},
	abstract = "{MicroRNAs (miRNAs) play indispensable roles in posttranscriptional gene regulation. Their cellular regulatory impact is determined not solely by their sheer number, which likely amounts to >2000 individual miRNAs in human, than by the regulatory effectiveness of single miRNAs. Although, one begins to develop an understanding of the complex mechanisms underlying miRNA-target interactions (MTIs), the overall knowledge of MTI functionality is still rather patchy. In this critical review, we summarize key features of mammalian MTIs. We especially highlight latest insights on (i) the dynamic make-up of miRNA binding sites including non-canonical binding sites, (ii) the cooperativity between miRNA binding sites, (iii) the adaptivity of MTIs through sequence modifications, (iv) the bearing of intra-cellular miRNA localization changes and (v) the role of cell type and cell status specific miRNA interaction partners. The MTI biology is discussed against the background of state-of-the-art approaches with particular emphasis on experimental strategies for evaluating miRNA functionality.}",
	pages = {},
	title = {The miRNA–target interactions: An underestimated intricacy},
	journal = {Nucleic Acids Research},
	doi = {10.1093/nar/gkad1142},
    	url = {https://doi.org/10.1093/nar/gkad1142}
}

MicroRNAs (miRNAs) play indispensable roles in posttranscriptional gene regulation. Their cellular regulatory impact is determined not solely by their sheer number, which likely amounts to >2000 individual miRNAs in human, than by the regulatory effectiveness of single miRNAs. Although, one begins to develop an understanding of the complex mechanisms underlying miRNA-target interactions (MTIs), the overall knowledge of MTI functionality is still rather patchy. In this critical review, we summarize key features of mammalian MTIs. We especially highlight latest insights on (i) the dynamic make-up of miRNA binding sites including non-canonical binding sites, (ii) the cooperativity between miRNA binding sites, (iii) the adaptivity of MTIs through sequence modifications, (iv) the bearing of intra-cellular miRNA localization changes and (v) the role of cell type and cell status specific miRNA interaction partners. The MTI biology is discussed against the background of state-of-the-art approaches with particular emphasis on experimental strategies for evaluating miRNA functionality.

@article{hen0123,
	author = {Henn, Dominic and Zhao, Dehua and Sivaraj, Dharshan and Trotsyuk, Artem and Bonham, Clark and Fischer, Katharina and Kehl, Tim and Fehlmann, Tobias and Greco, Autumn and Kussie, Hudson and Illouz, Sylvia and Padmanabhan, Jagannath and Barrera, Janos and Kneser, Ulrich and Lenhof, Hans-Peter and Januszyk, Michael and Levi, Benjamin and Keller, Andreas and Longaker, Michael and Gurtner, Geoffrey},
	year = {2023},
	month = {08},
	abstract = "{Chronic wounds impose a significant healthcare burden to a broad patient population. Cell-based therapies, while having shown benefits for the treatment of chronic wounds, have not yet achieved widespread adoption into clinical practice. We developed a CRISPR/Cas9 approach to precisely edit murine dendritic cells to enhance their therapeutic potential for healing chronic wounds. Using single-cell RNA sequencing of tolerogenic dendritic cells, we identified N-myc downregulated gene 2 (Ndrg2), which marks a specific population of dendritic cell progenitors, as a promising target for CRISPR knockout. Ndrg2-knockout alters the transcriptomic profile of dendritic cells and preserves an immature cell state with a strong pro-angiogenic and regenerative capacity. We then incorporated our CRISPR-based cell engineering within a therapeutic hydrogel for in vivo cell delivery and developed an effective translational approach for dendritic cell-based immunotherapy that accelerated healing of full-thickness wounds in both non-diabetic and diabetic mouse models. These findings could open the door to future clinical trials using safe gene editing in dendritic cells for treating various types of chronic wounds.}",
	pages = {},
	title = {Cas9-mediated knockout of Ndrg2 enhances the regenerative potential of dendritic cells for wound healing},
	volume = {14},
	journal = {Nature Communications},
	doi = {10.1038/s41467-023-40519-z},
    	url = {https://doi.org/10.1038/s41467-023-40519-z}
}

Chronic wounds impose a significant healthcare burden to a broad patient population. Cell-based therapies, while having shown benefits for the treatment of chronic wounds, have not yet achieved widespread adoption into clinical practice. We developed a CRISPR/Cas9 approach to precisely edit murine dendritic cells to enhance their therapeutic potential for healing chronic wounds. Using single-cell RNA sequencing of tolerogenic dendritic cells, we identified N-myc downregulated gene 2 (Ndrg2), which marks a specific population of dendritic cell progenitors, as a promising target for CRISPR knockout. Ndrg2-knockout alters the transcriptomic profile of dendritic cells and preserves an immature cell state with a strong pro-angiogenic and regenerative capacity. We then incorporated our CRISPR-based cell engineering within a therapeutic hydrogel for in vivo cell delivery and developed an effective translational approach for dendritic cell-based immunotherapy that accelerated healing of full-thickness wounds in both non-diabetic and diabetic mouse models. These findings could open the door to future clinical trials using safe gene editing in dendritic cells for treating various types of chronic wounds.

@article{hahn0123,
	author = {Hahn, Oliver and Foltz, Aulden and Atkins, Micaiah and Kedir, Blen and Moran Losada, Patricia and Guldner, Ian and Munson, Christy and Kern, Fabian and Pálovics, Róbert and Lu, Nannan and Zhang, Hui and Kaur, Achint and Hull, Jacob and Huguenard, John and Groenke, Sebastian and Lehallier, Benoit and Partridge, Linda and Keller, Andreas and Wyss-Coray, Tony},
	year = {2023},
	month = {08},
	abstract = "{Aging is the key risk factor for cognitive decline, yet the molecular changes underlying brain aging remain poorly understood. Here, we conducted spatiotemporal RNA sequencing of the mouse brain, profiling 1,076 samples from 15 regions across 7 ages and 2 rejuvenation interventions. Our analysis identified a brain-wide gene signature of aging in glial cells, which exhibited spatially defined changes in magnitude. By integrating spatial and single-nucleus transcriptomics, we found that glial aging was particularly accelerated in white matter compared with cortical regions, whereas specialized neuronal populations showed region-specific expression changes. Rejuvenation interventions, including young plasma injection and dietary restriction, exhibited distinct effects on gene expression in specific brain regions. Furthermore, we discovered differential gene expression patterns associated with three human neurodegenerative diseases, highlighting the importance of regional aging as a potential modulator of disease. Our findings identify molecular foci of brain aging, providing a foundation to target age-related cognitive decline.}",
	pages = {},
	title = {Atlas of the aging mouse brain reveals white matter as vulnerable foci},
	volume = {186},
	journal = {Cell},
	doi = {10.1016/j.cell.2023.07.027},
    	url = {https://doi.org/10.1016/j.cell.2023.07.027}
}

Aging is the key risk factor for cognitive decline, yet the molecular changes underlying brain aging remain poorly understood. Here, we conducted spatiotemporal RNA sequencing of the mouse brain, profiling 1,076 samples from 15 regions across 7 ages and 2 rejuvenation interventions. Our analysis identified a brain-wide gene signature of aging in glial cells, which exhibited spatially defined changes in magnitude. By integrating spatial and single-nucleus transcriptomics, we found that glial aging was particularly accelerated in white matter compared with cortical regions, whereas specialized neuronal populations showed region-specific expression changes. Rejuvenation interventions, including young plasma injection and dietary restriction, exhibited distinct effects on gene expression in specific brain regions. Furthermore, we discovered differential gene expression patterns associated with three human neurodegenerative diseases, highlighting the importance of regional aging as a potential modulator of disease. Our findings identify molecular foci of brain aging, providing a foundation to target age-related cognitive decline.

@article{kern0723,
	author = {Kern, Fabian and Kuhn, Thomas and Ludwig, Nicole and Simon, Martin and Gröger, Laura and Fabis, Natalie and Aparicio-Puerta, Ernesto and Salhab, Abdulrahman and Fehlmann, Tobias and Hahn, Oliver and Engel, Annika and Wagner, Viktoria and Koch, Marcus and Winek, Katarzyna and Soreq, Hermona and Nazarenko, Irina and Fuhrmann, Gregor and Wyss-Coray, Tony and Meese, Eckart and Keller, Andreas},
	year = {2023},
	month = {07},
	abstract = "{Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2-18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR.}",
	pages = {482-494},
	title = {Ageing-associated small RNA cargo of extracellular vesicles},
	volume = {20},
	journal = {RNA biology},
	doi = {10.1080/15476286.2023.2234713},
    	url = {https://doi.org/10.1080/15476286.2023.2234713}
}

Previous work on murine models and humans demonstrated global as well as tissue-specific molecular ageing trajectories of RNAs. Extracellular vesicles (EVs) are membrane vesicles mediating the horizontal transfer of genetic information between different tissues. We sequenced small regulatory RNAs (sncRNAs) in two mouse plasma fractions at five time points across the lifespan from 2-18 months: (1) sncRNAs that are free-circulating (fc-RNA) and (2) sncRNAs bound outside or inside EVs (EV-RNA). Different sncRNA classes exhibit unique ageing patterns that vary between the fcRNA and EV-RNA fractions. While tRNAs showed the highest correlation with ageing in both fractions, rRNAs exhibited inverse correlation trajectories between the EV- and fc-fractions. For miRNAs, the EV-RNA fraction was exceptionally strongly associated with ageing, especially the miR-29 family in adipose tissues. Sequencing of sncRNAs and coding genes in fat tissue of an independent cohort of aged mice up to 27 months highlighted the pivotal role of miR-29a-3p and miR-29b-3p in ageing-related gene regulation that we validated in a third cohort by RT-qPCR.

@article{herp123,
	author = {Herppich, Susanne and Hönicke, Lisa and Kern, Fabian and Kruse, Friederike and Smout, Justine and Greweling‐Pils, Marina and Geffers, Robert and Burton, Oliver and Liston, Adrian and Keller, Andreas and Floess, Stefan and Huehn, Jochen},
	year = {2023},
	month = {06},
	abstract = "{Mucosal barrier integrity and pathogen clearance is a complex process influenced by both Th17 and Treg cells. Previously, we had described the DNA methylation profile of Th17 cells and identified Zinc finger protein (Zfp)362 to be uniquely demethylated. Here, we generated Zfp362−/− mice to unravel the role of Zfp362 for Th17 cell biology. Zfp362−/− mice appeared clinically normal, showed no phenotypic alterations in the T‐cell compartment, and upon colonization with segmented filamentous bacteria, no effect of Zfp362 deficiency on Th17 cell differentiation was observed. By contrast, Zfp362 deletion resulted in increased frequencies of colonic Foxp3⁺ Treg cells and IL‐10⁺ and RORγt⁺ Treg cell subsets in mesenteric lymph nodes. Adoptive transfer of naïve CD4⁺ T cells from Zfp362−/− mice into Rag2−/− mice resulted in a significantly lower weight loss when compared with controls receiving cells from Zfp362+/+ littermates. However, this attenuated weight loss did not correlate with alterations of Th17 cells but instead was associated with an increase of effector Treg cells in mesenteric lymph nodes. Together, these results suggest that Zfp362 plays an important role in promoting colonic inflammation; however, this function is derived from constraining the effector function of Treg cells rather than directly promoting Th17 cell differentiation.}",
	pages = {},
	title = {Zfp362 potentiates murine colonic inflammation by constraining Treg cell function rather than promoting Th17 cell differentiation},
	journal = {European Journal of Immunology},
    	url = {https://doi.org/10.1002/eji.202250270},
	doi = {10.1002/eji.202250270}
}

Mucosal barrier integrity and pathogen clearance is a complex process influenced by both Th17 and Treg cells. Previously, we had described the DNA methylation profile of Th17 cells and identified Zinc finger protein (Zfp)362 to be uniquely demethylated. Here, we generated Zfp362−/− mice to unravel the role of Zfp362 for Th17 cell biology. Zfp362−/− mice appeared clinically normal, showed no phenotypic alterations in the T‐cell compartment, and upon colonization with segmented filamentous bacteria, no effect of Zfp362 deficiency on Th17 cell differentiation was observed. By contrast, Zfp362 deletion resulted in increased frequencies of colonic Foxp3⁺ Treg cells and IL‐10⁺ and RORγt⁺ Treg cell subsets in mesenteric lymph nodes. Adoptive transfer of naïve CD4⁺ T cells from Zfp362−/− mice into Rag2−/− mice resulted in a significantly lower weight loss when compared with controls receiving cells from Zfp362+/+ littermates. However, this attenuated weight loss did not correlate with alterations of Th17 cells but instead was associated with an increase of effector Treg cells in mesenteric lymph nodes. Together, these results suggest that Zfp362 plays an important role in promoting colonic inflammation; however, this function is derived from constraining the effector function of Treg cells rather than directly promoting Th17 cell differentiation.

@article{puerta123,
	author = {Aparicio-Puerta, Ernesto and Hirsch, Pascal and Schmartz, Georges and Kern, Fabian and Fehlmann, Tobias and Keller, Andreas},
	year = {2023},
	month = {05},
	abstract = "{MicroRNAs (miRNAs) are small non-coding RNAs that play a critical role in regulating diverse biological processes. Extracting functional insights from a list of miRNAs is challenging, as each miRNA can potentially interact with hundreds of genes. To address this challenge, we developed miEAA, a flexible and comprehensive miRNA enrichment analysis tool based on direct and indirect miRNA annotation. The latest release of miEAA includes a data warehouse of 19 miRNA repositories, covering 10 different organisms and 139 399 functional categories. We have added information on the cellular context of miRNAs, isomiRs, and high-confidence miRNAs to improve the accuracy of the results. We have also improved the representation of aggregated results, including interactive Upset plots to aid users in understanding the interaction among enriched terms or categories. Finally, we demonstrate the functionality of miEAA in the context of ageing and highlight the importance of carefully considering the miRNA input list. MiEAA is free to use and publicly available at https://www.ccb.uni-saarland.de/mieaa/.}",
	pages = {},
	title = {miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations},
	journal = {Nucleic Acids Research},
    	url = {https://doi.org/10.1093/nar/gkad392},
	doi = {10.1093/nar/gkad392}
}

MicroRNAs (miRNAs) are small non-coding RNAs that play a critical role in regulating diverse biological processes. Extracting functional insights from a list of miRNAs is challenging, as each miRNA can potentially interact with hundreds of genes. To address this challenge, we developed miEAA, a flexible and comprehensive miRNA enrichment analysis tool based on direct and indirect miRNA annotation. The latest release of miEAA includes a data warehouse of 19 miRNA repositories, covering 10 different organisms and 139 399 functional categories. We have added information on the cellular context of miRNAs, isomiRs, and high-confidence miRNAs to improve the accuracy of the results. We have also improved the representation of aggregated results, including interactive Upset plots to aid users in understanding the interaction among enriched terms or categories. Finally, we demonstrate the functionality of miEAA in the context of ageing and highlight the importance of carefully considering the miRNA input list. MiEAA is free to use and publicly available at https://www.ccb.uni-saarland.de/mieaa/.

@article{reh123,
	author = {Rehner, Jacqueline and Schmartz, Georges and Kramer, Tabea and Keller, Verena and Keller, Andreas and Becker, Soeren Leif},
	year = {2023},
	month = {04},
	abstract = "{In 2019, researchers from the EAT-Lancet Commission developed the ‘Planetary Health (PH) diet’. Specifically, they provided recommendations pertaining to healthy diets derived from sustainable food systems. Thus far, it has not been analysed how such a diet affects the human intestinal microbiome, which is important for health and disease development. Here, we present longitudinal genome-wide metagenomic sequencing and mass spectrometry data on the gut microbiome of healthy volunteers adhering to the PH diet, as opposed to vegetarian or vegan (VV) and omnivorous (OV) diets. We obtained basic epidemiological information from 41 healthy volunteers and collected stool samples at inclusion and after 2, 4, and 12 weeks. Individuals opting to follow the PH diet received detailed instructions and recipes, whereas individuals in the control groups followed their habitual dietary pattern. Whole-genome DNA was extracted from stool specimens and subjected to shotgun metagenomic sequencing (~3 GB per patient). Conventional bacterial stool cultures were performed in parallel and bacterial species were identified with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. We analysed samples from 16 PH, 16 OV, and 9 VV diet patterns. The α-diversity remained relatively stable for all dietary groups. In the PH group, we observed a constant increase from 3.79% at inclusion to 4.9% after 12 weeks in relative abundance of Bifidobacterium adolescentis. Differential PH abundance analysis highlighted a non-significant increase in possible probiotics such as Paraprevotella xylaniphila and Bacteroides clarus. The highest abundance of these bacteria was observed in the VV group. Dietary modifications are associated with rapid alterations to the human gut microbiome, and the PH diet led to a slight increase in probiotic-associated bacteria at ≥4 weeks. Additional research is required to confirm these findings.}",
	pages = {1924},
	title = {The Effect of a Planetary Health Diet on the Human Gut Microbiome: A Descriptive Analysis},
	volume = {15},
	journal = {Nutrients},
    	url = {https://doi.org/10.3390/nu15081924},
	doi = {10.3390/nu15081924}
}

In 2019, researchers from the EAT-Lancet Commission developed the ‘Planetary Health (PH) diet’. Specifically, they provided recommendations pertaining to healthy diets derived from sustainable food systems. Thus far, it has not been analysed how such a diet affects the human intestinal microbiome, which is important for health and disease development. Here, we present longitudinal genome-wide metagenomic sequencing and mass spectrometry data on the gut microbiome of healthy volunteers adhering to the PH diet, as opposed to vegetarian or vegan (VV) and omnivorous (OV) diets. We obtained basic epidemiological information from 41 healthy volunteers and collected stool samples at inclusion and after 2, 4, and 12 weeks. Individuals opting to follow the PH diet received detailed instructions and recipes, whereas individuals in the control groups followed their habitual dietary pattern. Whole-genome DNA was extracted from stool specimens and subjected to shotgun metagenomic sequencing ( 3 GB per patient). Conventional bacterial stool cultures were performed in parallel and bacterial species were identified with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. We analysed samples from 16 PH, 16 OV, and 9 VV diet patterns. The α-diversity remained relatively stable for all dietary groups. In the PH group, we observed a constant increase from 3.79% at inclusion to 4.9% after 12 weeks in relative abundance of Bifidobacterium adolescentis. Differential PH abundance analysis highlighted a non-significant increase in possible probiotics such as Paraprevotella xylaniphila and Bacteroides clarus. The highest abundance of these bacteria was observed in the VV group. Dietary modifications are associated with rapid alterations to the human gut microbiome, and the PH diet led to a slight increase in probiotic-associated bacteria at ≥4 weeks. Additional research is required to confirm these findings.

@article{wag123,
	author = {Wagner, Viktoria and Kern, Fabian and Hahn, Oliver and Schaum,  Nicholas and Ludwig, Nicole and Fehlmann, Tobias and Engel, Annika and Henn, Dominic and Rishik, Shusruto and Isakova, Alina and Tan, Michelle and Sit, Rene and Neff, Norma and Hart, Martin and Meese, Eckart and Quake, Steve and Wyss-Coray, Tony and Keller, Andreas},
	year = {2023},
	month = {04},
	abstract = "{Molecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map of noncoding RNA (ncRNA) expression in aging (16 organs at ten timepoints from 1 to 27 months) and rejuvenated mice. We found molecular aging trajectories are largely tissue-specific except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence in circulating plasma and extracellular vesicles (EVs) whereas tissue-specific ncRNAs were less present. For miR-29c-3p, we observe the largest correlation with aging in solid organs, plasma and EVs. In mice rejuvenated by heterochronic parabiosis, miR-29c-3p was the most prominent miRNA restored to similar levels found in young liver. miR-29c-3p targets the extracellular matrix and secretion pathways, known to be implicated in aging. We provide a map of organism-wide expression of ncRNAs with aging and rejuvenation and identify a set of broadly deregulated miRNAs, which may function as systemic regulators of aging via plasma and EVs.}",
	pages = {1-10},
	title = {Characterizing expression changes in noncoding RNAs during aging and heterochronic parabiosis across mouse tissues},
	journal = {Nature Biotechnology},
    	url = {https://doi.org/10.1038/s41587-023-01751-6},
	doi = {10.1038/s41587-023-01751-6}
}

Molecular mechanisms of organismal and cell aging remain incompletely understood. We, therefore, generated a body-wide map of noncoding RNA (ncRNA) expression in aging (16 organs at ten timepoints from 1 to 27 months) and rejuvenated mice. We found molecular aging trajectories are largely tissue-specific except for eight broadly deregulated microRNAs (miRNAs). Their individual abundance mirrors their presence in circulating plasma and extracellular vesicles (EVs) whereas tissue-specific ncRNAs were less present. For miR-29c-3p, we observe the largest correlation with aging in solid organs, plasma and EVs. In mice rejuvenated by heterochronic parabiosis, miR-29c-3p was the most prominent miRNA restored to similar levels found in young liver. miR-29c-3p targets the extracellular matrix and secretion pathways, known to be implicated in aging. We provide a map of organism-wide expression of ncRNAs with aging and rejuvenation and identify a set of broadly deregulated miRNAs, which may function as systemic regulators of aging via plasma and EVs.

@article{ber123,
	author = {Berger, Fabian and Schmartz, Georges and Fritz, Tobias and Veith, Nils and Alhussein, Farah and Roth, Sophie and Schneitler, Sophie and Gilcher, Thomas and Gärtner, Barbara and Pirpilashvili, Vakhtang and Pohlemann, Tim and Keller, Andreas and Rehner, Jacqueline and Becker, Soeren Leif},
	year = {2023},
	month = {04},
	abstract = "{We analysed consecutive clinical cases of infections due to carbapenemase-producing Gram-negative bacteria detected in war-wounded patients from Ukraine who were treated at one University medical centre in southwest Germany between June and December 2022. Isolates of multiresistant Gram-negative bacteria were subjected to a thorough microbiological characterisation and whole-genome sequencing. We identified five war-wounded Ukrainian patients who developed infections with NDM-1-positive Klebsiella pneumoniae. Two isolates also carried OXA-48 carbapenemases. The bacteria were resistant to novel antibiotics such as ceftazidime/avibactam and cefiderocol. Employed treatment strategies included combinations of ceftazidime/avibactam + aztreonam, colistin, or tigecycline. Whole-genome sequencing suggested transmission during primary care in Ukraine. We conclude that there is an urgent need for thorough surveillance of multiresistant pathogens in patients from war zones.}",
	pages = {},
	title = {Occurrence, resistance patterns and management of carbapenemase-producing bacteria in war-wounded refugees from Ukraine},
	volume = {132},
	journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases},
    	url = {https://doi.org/10.1016/j.ijid.2023.04.394},
	doi = {10.1016/j.ijid.2023.04.394}
}

We analysed consecutive clinical cases of infections due to carbapenemase-producing Gram-negative bacteria detected in war-wounded patients from Ukraine who were treated at one University medical centre in southwest Germany between June and December 2022. Isolates of multiresistant Gram-negative bacteria were subjected to a thorough microbiological characterisation and whole-genome sequencing. We identified five war-wounded Ukrainian patients who developed infections with NDM-1-positive Klebsiella pneumoniae. Two isolates also carried OXA-48 carbapenemases. The bacteria were resistant to novel antibiotics such as ceftazidime/avibactam and cefiderocol. Employed treatment strategies included combinations of ceftazidime/avibactam + aztreonam, colistin, or tigecycline. Whole-genome sequencing suggested transmission during primary care in Ukraine. We conclude that there is an urgent need for thorough surveillance of multiresistant pathogens in patients from war zones.

@article{ha123,
	author = {Hart, Martin and Diener, Caroline and Lunkes, Laetitia and Rheinheimer, Stefanie and Krammes, Lena and Keller, Andreas and Meese, Eckart},
	year = {2023},
	month = {04},
	pages = {},
	title = {miR-34a-5p as molecular hub of pathomechanisms in Huntington’s disease},
	abstract = "{Background Although a pivotal role of microRNA (miRNA, miR) in the pathogenesis of Huntington’s disease (HD) is increasingly recognized, the molecular functions of miRNAs in the pathomechanisms of HD await further elucidation. One of the miRNAs that have been associated with HD is miR-34a-5p, which was deregulated in the mouse R6/2 model and in human HD brain tissues. Methods The aim of our study was to demonstrate interactions between miR-34a-5p and HD associated genes. By computational means we predicted 12 801 potential target genes of miR-34a-5p. An in-silico pathway analysis revealed 22 potential miR-34a-5p target genes in the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway “Huntington’s disease”. Results Using our high-throughput miRNA interaction reporter assay (HiTmIR) we identified NDUFA9, TAF4B, NRF1, POLR2J2, DNALI1, HIP1, TGM2 and POLR2G as direct miR-34a-5p target genes. Direct binding of miR-34a-5p to target sites in the 3’UTRs of TAF4B, NDUFA9, HIP1 and NRF1 was verified by a mutagenesis HiTmIR assay and by determining endogenous protein levels for HIP1 and NDUFA9 . STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) analysis identified protein–protein interaction networks associated with HD like “Glutamine Receptor Signaling Pathway” and “Calcium Ion Transmembrane Import Into Cytosol”. Conclusion Our study demonstrates multiple interactions between miR-34a-5p and HD associated target genes and thereby lays the ground for future therapeutic interventions using this miRNA.}",
	volume = {29},
	journal = {Molecular Medicine},
    	url = {https://doi.org/10.1186/s10020-023-00640-7},
	doi = {10.1186/s10020-023-00640-7}
}

Background Although a pivotal role of microRNA (miRNA, miR) in the pathogenesis of Huntington’s disease (HD) is increasingly recognized, the molecular functions of miRNAs in the pathomechanisms of HD await further elucidation. One of the miRNAs that have been associated with HD is miR-34a-5p, which was deregulated in the mouse R6/2 model and in human HD brain tissues. Methods The aim of our study was to demonstrate interactions between miR-34a-5p and HD associated genes. By computational means we predicted 12 801 potential target genes of miR-34a-5p. An in-silico pathway analysis revealed 22 potential miR-34a-5p target genes in the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway “Huntington’s disease”. Results Using our high-throughput miRNA interaction reporter assay (HiTmIR) we identified NDUFA9, TAF4B, NRF1, POLR2J2, DNALI1, HIP1, TGM2 and POLR2G as direct miR-34a-5p target genes. Direct binding of miR-34a-5p to target sites in the 3’UTRs of TAF4B, NDUFA9, HIP1 and NRF1 was verified by a mutagenesis HiTmIR assay and by determining endogenous protein levels for HIP1 and NDUFA9 . STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) analysis identified protein–protein interaction networks associated with HD like “Glutamine Receptor Signaling Pathway” and “Calcium Ion Transmembrane Import Into Cytosol”. Conclusion Our study demonstrates multiple interactions between miR-34a-5p and HD associated target genes and thereby lays the ground for future therapeutic interventions using this miRNA.

@article{apahi22,
	author = {Aparicio-Puerta, Ernesto and Hirsch, Pascal and Schmartz, Georges and Fehlmann, Tobias and Keller, Verena and Engel, Annika and Kern, Fabian and Hackenberg, Michael and Keller, Andreas},
	year = {2023},
	month = {01},
	pages = {},
	title = {isomiRdb: microRNA expression at isoform resolution},
	volume = {51},
    	abstract = "{A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients' samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9 × 1011 sequencing reads) and consistently analyzed them using miRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (>1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence/absence of a particular miRNA/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https://www.ccb.uni-saarland.de/isomirdb.}",
	journal = {Nucleic acids research},
    	url = {https://doi.org/10.1093/nar/gkac884},
	doi = {10.1093/nar/gkac884}
}

A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients' samples. Not surprisingly, multiple studies describe a physiological and pathophysiological role. Despite their importance, systematically collected and annotated isomiR information available in databases remains limited. We thus developed isomiRdb, a comprehensive resource that compiles miRNA expression data at isomiR resolution from various sources. We processed 42 499 human miRNA-seq datasets (5.9 × 1011 sequencing reads) and consistently analyzed them using miRMaster and sRNAbench. Our database provides online access to the 90 483 most abundant isomiRs (>1 RPM in at least 1% of the samples) from 52 tissues and 188 cell types. Additionally, the full set of over 3 million detected isomiRs is available for download. Our resource can be queried at the sample, miRNA or isomiR level so users can quickly answer common questions about the presence/absence of a particular miRNA/isomiR in tissues of interest. Further, the database facilitates to identify whether a potentially interesting new isoform has been detected before and its frequency. In addition to expression tables, isomiRdb can generate multiple interactive visualisations including violin plots and heatmaps. isomiRdb is free to use and publicly available at: https://www.ccb.uni-saarland.de/isomirdb.

@article{dc12023,
	author = {Diener, Caroline and Hart, Martin and Kehl, Tim and Becker-Dorison, Anouck and Tänzer, Tanja and Schub, David and Krammes, Lena and Sester, Martina and Keller, Andreas and Unger, Marcus and Walch-Rückheim, Barbara and Lenhof, Hans-Peter and Meese, Eckart},
	year = {2023},
	month = {01},
	pages = {18},
	title = {Time-resolved RNA signatures of CD4+ T cells in Parkinson’s disease},
	abstract = "{Parkinson’s disease (PD) emerges as a complex, multifactorial disease. While there is increasing evidence that dysregulated T cells play a central role in PD pathogenesis, elucidation of the pathomechanical changes in related signaling is still in its beginnings. We employed time-resolved RNA expression upon the activation of peripheral CD4+ T cells to track and functionally relate changes on cellular signaling in representative cases of patients at different stages of PD. While only few miRNAs showed time-course related expression changes in PD, we identified groups of genes with significantly altered expression for each different time window. Towards a further understanding of the functional consequences, we highlighted pathways with decreased or increased activity in PD, including the most prominent altered IL-17 pathway. Flow cytometric analyses showed not only an increased prevalence of Th17 cells but also a specific subtype of IL-17 producing γδ-T cells, indicating a previously unknown role in PD pathogenesis.}",
	volume = {9},
	journal = {Cell Death Discovery},
    	url = {https://doi.org/10.1038/s41420-023-01333-0},
	doi = {10.1038/s41420-023-01333-0}
}

Parkinson’s disease (PD) emerges as a complex, multifactorial disease. While there is increasing evidence that dysregulated T cells play a central role in PD pathogenesis, elucidation of the pathomechanical changes in related signaling is still in its beginnings. We employed time-resolved RNA expression upon the activation of peripheral CD4+ T cells to track and functionally relate changes on cellular signaling in representative cases of patients at different stages of PD. While only few miRNAs showed time-course related expression changes in PD, we identified groups of genes with significantly altered expression for each different time window. Towards a further understanding of the functional consequences, we highlighted pathways with decreased or increased activity in PD, including the most prominent altered IL-17 pathway. Flow cytometric analyses showed not only an increased prevalence of Th17 cells but also a specific subtype of IL-17 producing γδ-T cells, indicating a previously unknown role in PD pathogenesis.

@article{gui123,
	author = {Guimarães, Pedro and Finkler, Helen and Reichert, Matthias and Zimmer, Vincent and Gruenhage, Frank and Krawczyk, Marcin and Lammert, Frank and Keller, Andreas and Casper, Mary},
	year = {2023},
	month = {01},
	abstract = "{Background: Whereas Artificial Intelligence (AI) based tools have recently been introduced in the field of gastroenterology, application in inflammatory bowel disease (IBD) is in its infancies. We established AI-based algorithms to distinguish IBD from infectious and ischemic colitis using endoscopic images and clinical data. Methods: Firstly, we trained and tested a Convolutional Neural Network (CNN) using 1,796 real-world images from 494 patients, presenting with three diseases (IBD [n=212], ischemic colitis [n=157], infectious colitis [n=125]). Moreover, we evaluated a Gradient Boosted Decision Trees (GBDT) algorithm using five clinical parameters as well as a hybrid approach (CNN+GBDT). Patients and images were randomly split into two completely independent datasets. The proposed approaches were benchmarked against each other and three expert endoscopists on the test set. Results: For the image-based CNN, the GBDT algorithm and the hybrid approach global accuracies were 0.709, 0.792, and 0.766, respectively. Positive predictive values were 0.602, 0.702, and 0.657. Global areas under the receiver operating characteristics (ROC) and precision recall (PR) curves were 0.727/0.585, 0.888/0.823, and 0.838/0.733, respectively. Global accuracy did not differ between CNN and endoscopists (0.721), but the clinical parameter-based GBDT algorithm outperformed CNN and expert image classification. Conclusions: Decision support systems exclusively based on endoscopic image analysis for the differential diagnosis of colitis, representing a complex clinical challenge, seem not yet to be ready for primetime and more diverse image datasets may be necessary to improve performance in future development. The clinical value of the proposed clinical parameters algorithm should be evaluated in prospective cohorts.}",
	pages = {e13960},
	title = {Artificial-intelligence-based decision support tools for the differential diagnosis of colitis},
	volume = {53},
	journal = {European journal of clinical investigation},
    	url = {https://doi.org/10.1111/eci.13960},
	doi = {10.1111/eci.13960}
}

Background: Whereas Artificial Intelligence (AI) based tools have recently been introduced in the field of gastroenterology, application in inflammatory bowel disease (IBD) is in its infancies. We established AI-based algorithms to distinguish IBD from infectious and ischemic colitis using endoscopic images and clinical data. Methods: Firstly, we trained and tested a Convolutional Neural Network (CNN) using 1,796 real-world images from 494 patients, presenting with three diseases (IBD [n=212], ischemic colitis [n=157], infectious colitis [n=125]). Moreover, we evaluated a Gradient Boosted Decision Trees (GBDT) algorithm using five clinical parameters as well as a hybrid approach (CNN+GBDT). Patients and images were randomly split into two completely independent datasets. The proposed approaches were benchmarked against each other and three expert endoscopists on the test set. Results: For the image-based CNN, the GBDT algorithm and the hybrid approach global accuracies were 0.709, 0.792, and 0.766, respectively. Positive predictive values were 0.602, 0.702, and 0.657. Global areas under the receiver operating characteristics (ROC) and precision recall (PR) curves were 0.727/0.585, 0.888/0.823, and 0.838/0.733, respectively. Global accuracy did not differ between CNN and endoscopists (0.721), but the clinical parameter-based GBDT algorithm outperformed CNN and expert image classification. Conclusions: Decision support systems exclusively based on endoscopic image analysis for the differential diagnosis of colitis, representing a complex clinical challenge, seem not yet to be ready for primetime and more diverse image datasets may be necessary to improve performance in future development. The clinical value of the proposed clinical parameters algorithm should be evaluated in prospective cohorts.

@article{die223,
	author = {Diener, Caroline and Hart, Martin and Fecher-Trost, Claudia and Knittel, Jessica and Rheinheimer, Stefanie and Meyer, Markus and Mayer, Jens and Flockerzi, Veit and Keller, Andreas and Meese, Eckart},
	year = {2023},
	month = {01},
	abstract = "{Among the concepts in biology that are widely taken granted is a potentiated cooperative effect of multiple miRNAs on the same target. This strong hypothesis contrasts insufficient experimental evidence. The quantity as well as the quality of required side constraints of cooperative binding remain largely hidden. For miR-21-5p and miR-155-5p, two commonly investigated regulators across diseases, we selected 15 joint target genes. These were chosen to represent various neighboring 3′UTR binding site constellations, partially exceeding the distance rules that have been established for over a decade. We identified different cooperative scenarios with the binding of one miRNA enhancing the binding effects of the other miRNA and vice versa. Using both, reporter assays and whole proteome analyses, we observed these cooperative miRNA effects for genes that bear 3′UTR binding sites at distances greater than the previously defined limits. Astonishingly, the experiments provide even stronger evidence for cooperative miRNA effects than originally postulated. In the light of these findings the definition of targetomes specified for single miRNAs need to be refined by a concept that acknowledges the cooperative effects of miRNAs.}",
	pages = {},
	title = {Outside the limit: questioning the distance restrictions for cooperative miRNA binding sites},
	volume = {28},
	journal = {Cellular & Molecular Biology Letters},
    	url = {https://doi.org/10.1186/s11658-023-00421-4},
	doi = {10.1186/s11658-023-00421-4}
}

Among the concepts in biology that are widely taken granted is a potentiated cooperative effect of multiple miRNAs on the same target. This strong hypothesis contrasts insufficient experimental evidence. The quantity as well as the quality of required side constraints of cooperative binding remain largely hidden. For miR-21-5p and miR-155-5p, two commonly investigated regulators across diseases, we selected 15 joint target genes. These were chosen to represent various neighboring 3′UTR binding site constellations, partially exceeding the distance rules that have been established for over a decade. We identified different cooperative scenarios with the binding of one miRNA enhancing the binding effects of the other miRNA and vice versa. Using both, reporter assays and whole proteome analyses, we observed these cooperative miRNA effects for genes that bear 3′UTR binding sites at distances greater than the previously defined limits. Astonishingly, the experiments provide even stronger evidence for cooperative miRNA effects than originally postulated. In the light of these findings the definition of targetomes specified for single miRNAs need to be refined by a concept that acknowledges the cooperative effects of miRNAs.

@article{ahal123,
	author = {Abu-Halima, Masood and Keller, Andreas and Becker, Lea and Fischer, Ulrike and Engel, Annika and Ludwig, Nicole and Kern, Fabian and Rounge, Trine and Langseth, Hilde and Meese, Eckart and Keller, Verena},
	year = {2022},
	month = {12},
	pages = {1-9},
	title = {Dynamic and static circulating cancer microRNA biomarkers – a validation study},
	abstract = "{For cancers and other pathologies, early diagnosis remains the most promising path to survival. Profiling of longitudinal cohorts facilitates insights into trajectories of biomarkers. We measured microRNA expression in 240 serum samples from patients with colon, lung, and breast cancer and from cancer-free controls. Each patient provided at least two serum samples, one prior to diagnosis and one following diagnosis. The median time interval between the samples was 11.6 years. Using computational models, we evaluated the circulating profiles of 21 microRNAs. The analysis yielded two sets of biomarkers, static ones that show an absolute difference between certain cancer types and controls and dynamic ones where the level over time provided higher diagnostic information content. In the first group, miR-99a-5p stands out for all three cancer types. In the second group, miR-155-5p allows to predict lung cancers and colon cancers. Classification in samples from cancer and non-cancer patients using gradient boosted trees reached an average accuracy of 79.9%. The results suggest that individual change over time or an absolute value at one time point may predict a disease with high specificity and sensitivity.}",
	volume = {20},
	journal = {RNA Biology},
    	url = {https://doi.org/10.1080/15476286.2022.2154470},
	doi = {10.1080/15476286.2022.2154470}
}

For cancers and other pathologies, early diagnosis remains the most promising path to survival. Profiling of longitudinal cohorts facilitates insights into trajectories of biomarkers. We measured microRNA expression in 240 serum samples from patients with colon, lung, and breast cancer and from cancer-free controls. Each patient provided at least two serum samples, one prior to diagnosis and one following diagnosis. The median time interval between the samples was 11.6 years. Using computational models, we evaluated the circulating profiles of 21 microRNAs. The analysis yielded two sets of biomarkers, static ones that show an absolute difference between certain cancer types and controls and dynamic ones where the level over time provided higher diagnostic information content. In the first group, miR-99a-5p stands out for all three cancer types. In the second group, miR-155-5p allows to predict lung cancers and colon cancers. Classification in samples from cancer and non-cancer patients using gradient boosted trees reached an average accuracy of 79.9%. The results suggest that individual change over time or an absolute value at one time point may predict a disease with high specificity and sensitivity.

@article{nima2022,
	author = {Müller, Marion and Eghbalian, Rose and Boeckel, Jes-Niels and Frese, Karen and Haas, Jan and Kayvanpour, Elham and Sedaghat-Hamedani, Farbod and Lackner, Maximilian and Tugrul, Oguz and Ruppert, Thomas and Tappu, Rewati and Bordalo, Diana and Kneuer, Jasmin and Piekarek, Annika and Herch, Sabine and Schudy, Sarah and Keller, Andreas and Grammes, Nadja and Bischof, Cornelius and Meder, Benjamin},
	year = {2022},
	month = {10},
    	abstract = "{To adapt to changing hemodynamic demands, regulatory mechanisms modulate actin-myosin-kinetics by calcium-dependent and -independent mechanisms. We investigate the posttranslational modification of human essential myosin light chain (ELC) and identify NIMA-related kinase 9 (NEK9) to interact with ELC. NEK9 is highly expressed in the heart and the interaction with ELC is calcium-dependent. Silencing of NEK9 results in blunting of calcium-dependent ELC-phosphorylation. CRISPR/Cas9-mediated disruption of NEK9 leads to cardiomyopathy in zebrafish. Binding to ELC is mediated via the protein kinase domain of NEK9. A causal relationship between NEK9 activity and ELC-phosphorylation is demonstrated by genetic sensitizing in-vivo. Finally, we observe significantly upregulated ELC-phosphorylation in dilated cardiomyopathy patients and provide a unique map of human ELC-phosphorylation-sites. In summary, NEK9-mediated ELC-phosphorylation is a calcium-dependent regulatory system mediating cardiac contraction and inotropy. Phosphorylation of the essential myosin light chain (ELC) influence actin-myosin crossbridge cycling in the heart. Here, the authors show upregulated ELC-phosphorylation in systolic heart failure and identify NIMArelated kinase 9 to bind to ELC mediating its calcium-dependent phosphorylation.}",
	pages = {6209},
	title = {NIMA-related kinase 9 regulates the phosphorylation of the essential myosin light chain in the heart},
	volume = {13},
	journal = {Nature Communications},
    	url = {https://doi.org/10.1038/s41467-022-33658-23},
	doi = {10.1038/s41467-022-33658-2}
}

To adapt to changing hemodynamic demands, regulatory mechanisms modulate actin-myosin-kinetics by calcium-dependent and -independent mechanisms. We investigate the posttranslational modification of human essential myosin light chain (ELC) and identify NIMA-related kinase 9 (NEK9) to interact with ELC. NEK9 is highly expressed in the heart and the interaction with ELC is calcium-dependent. Silencing of NEK9 results in blunting of calcium-dependent ELC-phosphorylation. CRISPR/Cas9-mediated disruption of NEK9 leads to cardiomyopathy in zebrafish. Binding to ELC is mediated via the protein kinase domain of NEK9. A causal relationship between NEK9 activity and ELC-phosphorylation is demonstrated by genetic sensitizing in-vivo. Finally, we observe significantly upregulated ELC-phosphorylation in dilated cardiomyopathy patients and provide a unique map of human ELC-phosphorylation-sites. In summary, NEK9-mediated ELC-phosphorylation is a calcium-dependent regulatory system mediating cardiac contraction and inotropy. Phosphorylation of the essential myosin light chain (ELC) influence actin-myosin crossbridge cycling in the heart. Here, the authors show upregulated ELC-phosphorylation in systolic heart failure and identify NIMArelated kinase 9 to bind to ELC mediating its calcium-dependent phosphorylation.

@article{rew2022,
	author = {Tappu, Rewati and Haas, Jan and Lehmann, David and Sedaghat-Hamedani, Farbod and Kayvanpour, Elham and Keller, Andreas and Katus, Hugo and Frey, Norbert and Meder, Benjamin},
	year = {2022},
	month = {08},
    	abstract = "{Dilated cardiomyopathy (DCM), a myocardial disease, is heterogeneous and often results in heart failure and sudden cardiac death. Unavailability of cardiac tissue has hindered the comprehensive exploration of gene regulatory networks and nodal players in DCM. In this study, we carried out integrated analysis of transcriptome and methylome data using non-negative matrix factorization from a cohort of DCM patients to uncover underlying latent factors and covarying features between whole-transcriptome and epigenome omics datasets from tissue biopsies of living patients. DNA methylation data from Infinium HM450 and mRNA Illumina sequencing of n = 33 DCM and n = 24 control probands were filtered, analyzed and used as input for matrix factorization using R NMF package. Mann-Whitney U test showed 4 out of 5 latent factors are significantly different between DCM and control probands ( P <0.05). Characterization of top 10% features driving each latent factor showed a significant enrichment of biological processes known to be involved in DCM pathogenesis, including immune response ( P = 3.97E-21), nucleic acid binding ( P = 1.42E-18), extracellular matrix ( P = 9.23E-14) and myofibrillar structure ( P = 8.46E-12). Correlation network analysis revealed interaction of important sarcomeric genes like Nebulin, Tropomyosin alpha-3 and ERC-protein 2 with CpG methylation of ATPase Phospholipid Transporting 11A0, Solute Carrier Family 12 Member 7 and Leucine Rich Repeat Containing 14B, all with significant P values associated with correlation coefficients >0.7. Using matrix factorization, multi-omics data derived from human tissue samples can be integrated and novel interactions can be identified. Hypothesis generating nature of such analysis could help to better understand the pathophysiology of complex traits such as DCM.}",
	pages = {e0272093},
	title = {Multi-omics assessment of dilated cardiomyopathy using non-negative matrix factorization},
	volume = {17},
	journal = {PLOS ONE},
    	url = {https://doi.org/10.1371/journal.pone.0272093},
	doi = {10.1371/journal.pone.0272093}
}

Dilated cardiomyopathy (DCM), a myocardial disease, is heterogeneous and often results in heart failure and sudden cardiac death. Unavailability of cardiac tissue has hindered the comprehensive exploration of gene regulatory networks and nodal players in DCM. In this study, we carried out integrated analysis of transcriptome and methylome data using non-negative matrix factorization from a cohort of DCM patients to uncover underlying latent factors and covarying features between whole-transcriptome and epigenome omics datasets from tissue biopsies of living patients. DNA methylation data from Infinium HM450 and mRNA Illumina sequencing of n = 33 DCM and n = 24 control probands were filtered, analyzed and used as input for matrix factorization using R NMF package. Mann-Whitney U test showed 4 out of 5 latent factors are significantly different between DCM and control probands ( P <0.05). Characterization of top 10% features driving each latent factor showed a significant enrichment of biological processes known to be involved in DCM pathogenesis, including immune response ( P = 3.97E-21), nucleic acid binding ( P = 1.42E-18), extracellular matrix ( P = 9.23E-14) and myofibrillar structure ( P = 8.46E-12). Correlation network analysis revealed interaction of important sarcomeric genes like Nebulin, Tropomyosin alpha-3 and ERC-protein 2 with CpG methylation of ATPase Phospholipid Transporting 11A0, Solute Carrier Family 12 Member 7 and Leucine Rich Repeat Containing 14B, all with significant P values associated with correlation coefficients >0.7. Using matrix factorization, multi-omics data derived from human tissue samples can be integrated and novel interactions can be identified. Hypothesis generating nature of such analysis could help to better understand the pathophysiology of complex traits such as DCM.

@article{REHNER2022,
	title = {Systematic cross-biospecimen evaluation of DNA extraction kits for long- and short-read multi-metagenomic sequencing studies},
	journal = {Genomics, Proteomics & Bioinformatics},
	year = {2022},
	issn = {1672-0229},
	month = {06},
	doi = {10.1016/j.gpb.2022.05.006},
	url = {https://www.sciencedirect.com/science/article/pii/S1672022922000729},
	author = {Rehner, Jacqueline and Schmartz , Georges Pierre and Groeger, Laura and Dastbaz, Jan and Ludwig, Nicole and Hannig, Matthias and Rupf, Stefan and Seitz, Berthold and Flockerzi, Elias and Berger, Tim and Reichert, Matthias Christian and Krawczyk, Marcin and Meese, Eckart and Herr, Christian and Bals, Robert and Becker, Sören L. and Keller, Andreas and Müller, Rolf },
	keywords = {Whole-genome analysis, Comparative genomics, Short-read sequencing, Long-read sequencing, DNA extraction, Metagenomics},
	abstract = {High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across data sets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of specimen type and DNA extraction, 20 GB metagenomic data were generated using short-read sequencing. While profiles of the specimen type showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kit. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 GB of sequencing data are required to achieve sufficient resolution, but DNA-based identification was superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.}
}

High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across data sets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of specimen type and DNA extraction, 20 GB metagenomic data were generated using short-read sequencing. While profiles of the specimen type showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kit. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 GB of sequencing data are required to achieve sufficient resolution, but DNA-based identification was superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.

@article{doi:10.1080/24733938.2022.2095006,
	author = {Hecksteden, Anne and Schmartz, Georges Pierre and Egyptien, Yanni and Aus der Fünten, Karen and Keller, Andreas and Meyer, Tim},
	title = {Forecasting football injuries by combining screening, monitoring and machine learning},
	journal = {Science and Medicine in Football},
	volume = {0},
	number = {0},
	month = {06},
	pages = {1-15},
	year  = {2022},
	publisher = {Routledge},
	doi = {10.1080/24733938.2022.2095006},
	note ={PMID: 35757889},
	URL = { https://doi.org/10.1080/24733938.2022.2095006},
	eprint = { https://doi.org/10.1080/24733938.2022.2095006},
	abstract = {ABSTRACT Identifying players or circumstances associated with an increased risk of injury is fundamental for successful risk management in football. So far, time-constant and volatile risk factors are generally considered separately in either a screening (constant) or a monitoring (volatile) approach each resulting in a restricted set of explanatory variables. Consequently, improvements in predictive accuracy may be expected when screening and monitoring data are combined, especially when analysed with current machine learning (ML) techniques.This trial was designed as a prospective observational cohort study aiming to forecast non-contact time-loss injuries in male professional football (soccer). Injuries were registered according to the Fuller consensus. Gradient boosting with ROSE upsampling within a leave-one-out cross-validation was used for data analysis. The hierarchical data structure was considered throughout. Different splits of the original dataset were used to probe the robustness of results.Data of 88 players from 4 teams and 51 injuries could be analysed. The cross-validated performance of the gradient boosted model (ROC area under the curve 0.61) was promising and higher compared to models without integration of screening data. Importantly, holdout test set performance was similar (ROC area under the curve 0.62) indicating prospect of generalizability to new cases. However, the variation of predictive accuracy and feature importance with different splits of the original dataset reflects the relatively low number of events.It is concluded that ML-based injury forecasting based on the integration of screening and monitoring data is promising. However, external prospective verification and continued model development are required. }
}

ABSTRACT Identifying players or circumstances associated with an increased risk of injury is fundamental for successful risk management in football. So far, time-constant and volatile risk factors are generally considered separately in either a screening (constant) or a monitoring (volatile) approach each resulting in a restricted set of explanatory variables. Consequently, improvements in predictive accuracy may be expected when screening and monitoring data are combined, especially when analysed with current machine learning (ML) techniques.This trial was designed as a prospective observational cohort study aiming to forecast non-contact time-loss injuries in male professional football (soccer). Injuries were registered according to the Fuller consensus. Gradient boosting with ROSE upsampling within a leave-one-out cross-validation was used for data analysis. The hierarchical data structure was considered throughout. Different splits of the original dataset were used to probe the robustness of results.Data of 88 players from 4 teams and 51 injuries could be analysed. The cross-validated performance of the gradient boosted model (ROC area under the curve 0.61) was promising and higher compared to models without integration of screening data. Importantly, holdout test set performance was similar (ROC area under the curve 0.62) indicating prospect of generalizability to new cases. However, the variation of predictive accuracy and feature importance with different splits of the original dataset reflects the relatively low number of events.It is concluded that ML-based injury forecasting based on the integration of screening and monitoring data is promising. However, external prospective verification and continued model development are required.

@article{j.tig.2022.02.006,
	author = {Iram, Tal and Kern, Fabian and Kaur, Achint and Myneni, Saket and Morningstar, Allison R. and Shin, Heather and Garcia, Miguel A. and Yerra, Lakshmi and Palovics, Robert and Yang, Andrew C. and Hahn, Oliver and Lu, Nannan and Shuken, Steven R. and Haney, Michael S. and Lehallier, Benoit and Iyer, Manasi and Luo, Jian and Zetterberg, Henrik and Keller, Andreas and Zuchero, J. Bradley and Wyss-Coray, Tony},
	title = {Young CSF restores oligodendrogenesis and memory in aged mice via Fgf17},
	journal = {Nature},
	month = {05},
	year  = {2022},
	publisher = {},
	doi = {10.1038/s41586-022-04722-0},
	URL = {https://doi.org/10.1038/s41586-022-04722-0},
	abstract = {Recent understanding of how the systemic environment shapes the brain throughout life has led to numerous intervention strategies to slow brain ageing1–3. Cerebrospinal fluid (CSF) makes up the immediate environment of brain cells, providing them with nourishing compounds4,5. We discovered that infusing young CSF directly into aged brains improves memory function. Unbiased transcriptome analysis of the hippocampus identified oligodendrocytes to be most responsive to this rejuvenated CSF environment. We further showed that young CSF boosts oligodendrocyte progenitor cell (OPC) proliferation and differentiation in the aged hippocampus and in primary OPC cultures. Using SLAMseq to metabolically label nascent mRNA, we identified serum response factor (SRF), a transcription factor that drives actin cytoskeleton rearrangement, as a mediator of OPC proliferation following exposure to young CSF. With age, SRF expression decreases in hippocampal OPCs, and the pathway is induced by acute injection with young CSF. We screened for potential SRF activators in CSF and found that fibroblast growth factor 17 (Fgf17) infusion is sufficient to induce OPC proliferation and long-term memory consolidation in aged mice while Fgf17 blockade impairs cognition in young mice. These findings demonstrate the rejuvenating power of young CSF and identify Fgf17 as a key target to restore oligodendrocyte function in the ageing brain.}
}

Recent understanding of how the systemic environment shapes the brain throughout life has led to numerous intervention strategies to slow brain ageing1–3. Cerebrospinal fluid (CSF) makes up the immediate environment of brain cells, providing them with nourishing compounds4,5. We discovered that infusing young CSF directly into aged brains improves memory function. Unbiased transcriptome analysis of the hippocampus identified oligodendrocytes to be most responsive to this rejuvenated CSF environment. We further showed that young CSF boosts oligodendrocyte progenitor cell (OPC) proliferation and differentiation in the aged hippocampus and in primary OPC cultures. Using SLAMseq to metabolically label nascent mRNA, we identified serum response factor (SRF), a transcription factor that drives actin cytoskeleton rearrangement, as a mediator of OPC proliferation following exposure to young CSF. With age, SRF expression decreases in hippocampal OPCs, and the pathway is induced by acute injection with young CSF. We screened for potential SRF activators in CSF and found that fibroblast growth factor 17 (Fgf17) infusion is sufficient to induce OPC proliferation and long-term memory consolidation in aged mice while Fgf17 blockade impairs cognition in young mice. These findings demonstrate the rejuvenating power of young CSF and identify Fgf17 as a key target to restore oligodendrocyte function in the ageing brain.

@article{10.1093/nar/gkac363,
    author = {Aparicio-Puerta, Ernesto and Gómez-Martín, Cristina and Giannoukakos, Stavros and Medina, José María and Scheepbouwer, Chantal and García-Moreno, Adrián and Carmona-Saez, Pedro and Fromm, Bastian and Pegtel, Michiel and Keller, Andreas and Marchal, Juan Antonio and Hackenberg, Michael},
    title = "{sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms}",
    journal = {Nucleic Acids Research},
    volume = {50},
    number = {W1},
    pages = {W710-W717},
    year = {2022},
    month = {05},
    abstract = "{The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkac363},
    url = {https://doi.org/10.1093/nar/gkac363},
    eprint = {https://academic.oup.com/nar/article-pdf/50/W1/W710/44379497/gkac363.pdf},
}

The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples per miRNA-seq study continues to increase resulting in a vast amount of data that requires accurate, fast and user-friendly analysis methods. Since the previous release of sRNAtoolbox in 2019, 55 000 sRNAbench jobs have been submitted which has motivated many improvements in its usability and the scope of the underlying annotation database. With this update, users can upload an unlimited number of samples or import them from Google Drive, Dropbox or URLs. Micro- and small RNA profiling can now be carried out using high-confidence Metazoan and plant specific databases, MirGeneDB and PmiREN respectively, together with genome assemblies and libraries from 441 Ensembl species. The new results page includes straightforward sample annotation to allow downstream differential expression analysis with sRNAde. Unassigned reads can also be explored by means of a new tool that performs mapping to microbial references, which can reveal contamination events or biologically meaningful findings as we describe in the example. sRNAtoolbox is available at: https://arn.ugr.es/srnatoolbox/.

@article{scitranslmed.abj9152,
	doi = {10.1126/scitranslmed.abj9152},
	author = {Chen,  Kellen and Henn, Dominic and Januszyk, Michael and Barrera, Janos A. and Noishiki, Chikage and Bonham, Clark A. and Griffin, Michelle and Tevlin, Ruth and Carlomagno, Theresa and Shannon, Tara and Fehlmann, Tobias and Trotsyuk, Artem A. and Padmanabhan, Jagannath and Sivaraj, Dharshan and Perrault, David P. and Zamaleeva, Alsu I. and Mays, Chyna J. and Greco, Autumn H. and Kwon, Sun Hyung and Leeolou, Melissa C. and Huskins, Savana L. and Steele, Sydney R. and Fischer, Katharina S. and Kussie, Hudson C. and Mittal, Smiti and Mermin-Bunnell, Alana M. and Deleon, Nestor M. Diaz and Lavin, Christopher and Keller, Andreas and Longaker, Michael T. and Gurtner, Geoffrey C.},
	title = {Disrupting mechanotransduction decreases fibrosis and contracture in split-thickness skin grafting},
	journal = {Science Translational Medicine},
	volume = {14},
	number = {645},
	pages = {eabj9152},
	month = {05},
	year = {2022},
	doi = {10.1126/scitranslmed.abj9152},
	URL = {https://www.science.org/doi/abs/10.1126/scitranslmed.abj9152},
	eprint = {https://www.science.org/doi/pdf/10.1126/scitranslmed.abj9152},
	abstract = {Burns and other traumatic injuries represent a substantial biomedical burden. The current standard of care for deep injuries is autologous split-thickness skin grafting (STSG), which frequently results in contractures, abnormal pigmentation, and loss of biomechanical function. Currently, there are no effective therapies that can prevent fibrosis and contracture after STSG. Here, we have developed a clinically relevant porcine model of STSG and comprehensively characterized porcine cell populations involved in healing with single-cell resolution. We identified an up-regulation of proinflammatory and mechanotransduction signaling pathways in standard STSGs. Blocking mechanotransduction with a small-molecule focal adhesion kinase (FAK) inhibitor promoted healing, reduced contracture, mitigated scar formation, restored collagen architecture, and ultimately improved graft biomechanical properties. Acute mechanotransduction blockade up-regulated myeloid CXCL10-mediated anti-inflammation with decreased CXCL14-mediated myeloid and fibroblast recruitment. At later time points, mechanical signaling shifted fibroblasts toward profibrotic differentiation fates, and disruption of mechanotransduction modulated mesenchymal fibroblast differentiation states to block those responses, instead driving fibroblasts toward proregenerative, adipogenic states similar to unwounded skin. We then confirmed these two diverging fibroblast transcriptional trajectories in human skin, human scar, and a three-dimensional organotypic model of human skin. Together, pharmacological blockade of mechanotransduction markedly improved large animal healing after STSG by promoting both early, anti-inflammatory and late, regenerative transcriptional programs, resulting in healed tissue similar to unwounded skin. FAK inhibition could therefore supplement the current standard of care for traumatic and burn injuries. Use of a FAK inhibitor to target mechanotransduction pathways reduces scarring and promotes healing after traumatic injuries requiring skin grafting. Split-thickness skin grafting (STSG) is used to treat deep burns and other traumatic skin injuries. However, STSG is complicated by hypertrophic scar formation, contractures, and potentially loss of biomechanical function. Here, Chen and colleagues developed a porcine model of STSG and, through single-cell RNA sequencing, identified up-regulation of mechanotransduction signaling pathways in the healing grafts. Applying a hydrogel containing a focal adhesion kinase (FAK) inhibitor to the grafts to disrupt mechanotransduction improved healing and reduced contracture and scar formation, with anti-inflammatory effects in the acute setting and proregenerative effects at later time points. These findings suggest that FAK inhibition could be beneficial for treatment of injuries requiring STSG.}
}

Burns and other traumatic injuries represent a substantial biomedical burden. The current standard of care for deep injuries is autologous split-thickness skin grafting (STSG), which frequently results in contractures, abnormal pigmentation, and loss of biomechanical function. Currently, there are no effective therapies that can prevent fibrosis and contracture after STSG. Here, we have developed a clinically relevant porcine model of STSG and comprehensively characterized porcine cell populations involved in healing with single-cell resolution. We identified an up-regulation of proinflammatory and mechanotransduction signaling pathways in standard STSGs. Blocking mechanotransduction with a small-molecule focal adhesion kinase (FAK) inhibitor promoted healing, reduced contracture, mitigated scar formation, restored collagen architecture, and ultimately improved graft biomechanical properties. Acute mechanotransduction blockade up-regulated myeloid CXCL10-mediated anti-inflammation with decreased CXCL14-mediated myeloid and fibroblast recruitment. At later time points, mechanical signaling shifted fibroblasts toward profibrotic differentiation fates, and disruption of mechanotransduction modulated mesenchymal fibroblast differentiation states to block those responses, instead driving fibroblasts toward proregenerative, adipogenic states similar to unwounded skin. We then confirmed these two diverging fibroblast transcriptional trajectories in human skin, human scar, and a three-dimensional organotypic model of human skin. Together, pharmacological blockade of mechanotransduction markedly improved large animal healing after STSG by promoting both early, anti-inflammatory and late, regenerative transcriptional programs, resulting in healed tissue similar to unwounded skin. FAK inhibition could therefore supplement the current standard of care for traumatic and burn injuries. Use of a FAK inhibitor to target mechanotransduction pathways reduces scarring and promotes healing after traumatic injuries requiring skin grafting. Split-thickness skin grafting (STSG) is used to treat deep burns and other traumatic skin injuries. However, STSG is complicated by hypertrophic scar formation, contractures, and potentially loss of biomechanical function. Here, Chen and colleagues developed a porcine model of STSG and, through single-cell RNA sequencing, identified up-regulation of mechanotransduction signaling pathways in the healing grafts. Applying a hydrogel containing a focal adhesion kinase (FAK) inhibitor to the grafts to disrupt mechanotransduction improved healing and reduced contracture and scar formation, with anti-inflammatory effects in the acute setting and proregenerative effects at later time points. These findings suggest that FAK inhibition could be beneficial for treatment of injuries requiring STSG.

@article{10.1093/nar/gkac298,
	author = {Schmartz, Georges P and Hirsch, Pascal and Amand, Jérémy and Dastbaz, Jan and Fehlmann, Tobias and Kern, Fabian and Müller, Rolf and Keller, Andreas},
	title = "{BusyBee Web: towards comprehensive and differential composition-based metagenomic binning}",
	journal = {Nucleic Acids Research},
	year = {2022},
	month = {04},
	abstract = "{Despite recent methodology and reference database improvements for taxonomic profiling tools, metagenomic assembly and genomic binning remain important pillars of metagenomic analysis workflows. In case reference information is lacking, genomic binning is considered to be a state-of-the-art method in mixed culture metagenomic data analysis. In this light, our previously published tool BusyBee Web implements a composition-based binning method efficient enough to function as a rapid online utility. Handling assembled contigs and long nanopore generated reads alike, the webserver provides a wide range of supplementary annotations and visualizations. Half a decade after the initial publication, we revisited existing functionality, added comprehensive visualizations, and increased the number of data analysis customization options for further experimentation. The webserver now allows for visualization-supported differential analysis of samples, which is computationally expensive and typically only performed in coverage-based binning methods. Further, users may now optionally check their uploaded samples for plasmid sequences using PLSDB as a reference database. Lastly, a new application programming interface with a supporting python package was implemented, to allow power users fully automated access to the resource and integration into existing workflows. The webserver is freely available under: https://www.ccb.uni-saarland.de/busybee.}",
	issn = {0305-1048},
	doi = {10.1093/nar/gkac298},
	url = {https://doi.org/10.1093/nar/gkac298},
}

Despite recent methodology and reference database improvements for taxonomic profiling tools, metagenomic assembly and genomic binning remain important pillars of metagenomic analysis workflows. In case reference information is lacking, genomic binning is considered to be a state-of-the-art method in mixed culture metagenomic data analysis. In this light, our previously published tool BusyBee Web implements a composition-based binning method efficient enough to function as a rapid online utility. Handling assembled contigs and long nanopore generated reads alike, the webserver provides a wide range of supplementary annotations and visualizations. Half a decade after the initial publication, we revisited existing functionality, added comprehensive visualizations, and increased the number of data analysis customization options for further experimentation. The webserver now allows for visualization-supported differential analysis of samples, which is computationally expensive and typically only performed in coverage-based binning methods. Further, users may now optionally check their uploaded samples for plasmid sequences using PLSDB as a reference database. Lastly, a new application programming interface with a supporting python package was implemented, to allow power users fully automated access to the resource and integration into existing workflows. The webserver is freely available under: https://www.ccb.uni-saarland.de/busybee.

@article{milld2022,
	author = {Millenaar, Dominic and Ragoschke-Schumm, Andreas and Fehlmann, Tobias and Raible, Maximilian and Lochner, Piergiorgio and Böhm, Michael and Fassbender, Klaus and Keller, Andreas and Mahfoud, Felix and Ukena, Christian},
	year = {2022},
	month = {04},
    	abstract = "{Background Stroke is the second leading cause of death world-wide. A comprehensive scientometric study regarding ischemic stroke research has not been performed yet. This study aims at investigating the global research output on ischemic stroke research. Methods All 21,115 articles regarding ischemic stroke were retrieved from the Web-of-Science-Core-Collection and analyzed regarding regional differences, the authors' sex, subtopics of stroke, as well as international research collaborations. Results A total of 132 different countries participated, with the USA contributing most publications with 4,614 (21.9%), followed by China with 3,872 (18.3%), and Germany with 1,120 (5.3%). Analyzing the scientific quality of different countries by H-index, the USA ranked first with an H-index of 202, followed by Germany (H-index 135) and the United Kingdom (UK;H-index 129). The most frequently used topic was “Clinical Neurology” with 9,028 publications. Among all first authors attributed to their sex, 32.3% of all first authors were female and 67.7% were male (4,335 vs. 9,097). The proportion of female last authors was comparatively lower at 22.4% (3,083 publications) compared with 77.6% male authors (10,658 publications). There was a broad network of international collaborations. Conclusions Research in ischemic stroke has substantially increased over time. Scientists from the USA have the highest number of publications, followed by China and Germany. Measured by the H-index, the USA held the highest publication quality, followed by Germany and the UK. The scientific landscape was male-dominated with 67.7% of all first authors being male. Worldwide international collaborations play a major role in ischemic stroke research.}",
	pages = {893121},
	title = {Ischemic Stroke–A Scientometric Analysis},
	volume = {13},
	journal = {Frontiers in Neurology},
    	url = {https://doi.org/10.3389/fneur.2022.893121},
	doi = {10.3389/fneur.2022.893121}
}

Background Stroke is the second leading cause of death world-wide. A comprehensive scientometric study regarding ischemic stroke research has not been performed yet. This study aims at investigating the global research output on ischemic stroke research. Methods All 21,115 articles regarding ischemic stroke were retrieved from the Web-of-Science-Core-Collection and analyzed regarding regional differences, the authors' sex, subtopics of stroke, as well as international research collaborations. Results A total of 132 different countries participated, with the USA contributing most publications with 4,614 (21.9%), followed by China with 3,872 (18.3%), and Germany with 1,120 (5.3%). Analyzing the scientific quality of different countries by H-index, the USA ranked first with an H-index of 202, followed by Germany (H-index 135) and the United Kingdom (UK;H-index 129). The most frequently used topic was “Clinical Neurology” with 9,028 publications. Among all first authors attributed to their sex, 32.3% of all first authors were female and 67.7% were male (4,335 vs. 9,097). The proportion of female last authors was comparatively lower at 22.4% (3,083 publications) compared with 77.6% male authors (10,658 publications). There was a broad network of international collaborations. Conclusions Research in ischemic stroke has substantially increased over time. Scientists from the USA have the highest number of publications, followed by China and Germany. Measured by the H-index, the USA held the highest publication quality, followed by Germany and the UK. The scientific landscape was male-dominated with 67.7% of all first authors being male. Worldwide international collaborations play a major role in ischemic stroke research.

@article{cells11061060,
	author = {Minet, Marie and Abu-Halima, Masood and Du, Yiqing and Doerr, Julia and Isted, Christina and Ludwig, Nicole and Keller, Andreas and Meese, Eckart and Fischer, Ulrike},
	title = "{A Temporary Pause in the Replication Licensing Restriction Leads to Rereplication during Early Human Cell Differentiation}",
	journal = {Cells},
	year = {2022},
	month = {03},
	url = {https://www.mdpi.com/2073-4409/11/6/1060},
	issn = {2073-4409},
	abstract = "{Gene amplifications in amphibians and flies are known to occur during development and have been well characterized, unlike in mammalian cells, where they are predominantly investigated as an attribute of tumors. Recently, we first described gene amplifications in human and mouse neural stem cells, myoblasts, and mesenchymal stem cells during differentiation. The mechanism leading to gene amplifications in amphibians and flies depends on endocycles and multiple origin-firings. So far, there is no knowledge about a comparable mechanism in normal human cells. Here, we describe rereplication during the early myotube differentiation of human skeletal myoblast cells, using fiber combing and pulse-treatment with EdU (5′-Ethynyl-2′-deoxyuridine)/CldU (5-Chlor-2′-deoxyuridine) and IdU (5-Iodo-2′-deoxyuridine)/CldU. We found rereplication during a restricted time window between 2 h and 8 h after differentiation induction. Rereplication was detected in cells simultaneously with the amplification of the MDM2 gene. Our findings support rereplication as a mechanism enabling gene amplification in normal human cells.}",
	doi = {10.3390/cells11061060},
	url = {https://www.mdpi.com/2073-4409/11/6/1060},
}

Gene amplifications in amphibians and flies are known to occur during development and have been well characterized, unlike in mammalian cells, where they are predominantly investigated as an attribute of tumors. Recently, we first described gene amplifications in human and mouse neural stem cells, myoblasts, and mesenchymal stem cells during differentiation. The mechanism leading to gene amplifications in amphibians and flies depends on endocycles and multiple origin-firings. So far, there is no knowledge about a comparable mechanism in normal human cells. Here, we describe rereplication during the early myotube differentiation of human skeletal myoblast cells, using fiber combing and pulse-treatment with EdU (5′-Ethynyl-2′-deoxyuridine)/CldU (5-Chlor-2′-deoxyuridine) and IdU (5-Iodo-2′-deoxyuridine)/CldU. We found rereplication during a restricted time window between 2 h and 8 h after differentiation induction. Rereplication was detected in cells simultaneously with the amplification of the MDM2 gene. Our findings support rereplication as a mechanism enabling gene amplification in normal human cells.

@article{jtjet2567,
	author = {Diener, Caroline and Keller, Andreas and Meese, Eckart},
	year = {2022},
	month = {03},
	title = {Emerging concepts of miRNA therapeutics: from cells to clinic},
	abstract = {MicroRNAs (miRNAs) are very powerful genetic regulators, as evidenced by the fact that a single miRNA can direct entire cellular pathways via interacting with a broad spectrum of target genes. This property renders miRNAs as highly interesting therapeutic tools to restore cell functions that are altered as part of a disease phenotype. However, this strength of miRNAs is also a weakness because their cellular effects are so numerous that off-target effects can hardly be avoided. In this review, we point out the main challenges and the strategies to specifically address the problems that need to be surmounted in the push toward a therapeutic application of miRNAs. Particular emphasis is given to approaches that have already found their way into clinical studies.},
	journal = {Trends in Genetics},
	doi = {10.1016/j.tig.2022.02.006},
	URL = {https://doi.org/10.1016/j.tig.2022.02.006},
}

MicroRNAs (miRNAs) are very powerful genetic regulators, as evidenced by the fact that a single miRNA can direct entire cellular pathways via interacting with a broad spectrum of target genes. This property renders miRNAs as highly interesting therapeutic tools to restore cell functions that are altered as part of a disease phenotype. However, this strength of miRNAs is also a weakness because their cellular effects are so numerous that off-target effects can hardly be avoided. In this review, we point out the main challenges and the strategies to specifically address the problems that need to be surmounted in the push toward a therapeutic application of miRNAs. Particular emphasis is given to approaches that have already found their way into clinical studies.

@article{safjrt5362,
	author = {Pálovics, Róbert and Keller, Andreas and Schaum, Nick and Tan, Weilun and Fehlmann, Tobias and Borja, Michael and Kern, Fabian and Bonanno, Liana and Calcuttawala, Kruti and Webber, James and Mcgeever, Aaron and The Tabula Muris Consortium and Luo, Jian and Pisco, Angela Oliveira and Karkanias, Jim and Neff, Norma F. and Darmanis, Spyros and Quake, Stephen R. and Wyss-Coray, Tony},
	year = {2022},
	month = {03},
	pages = {1-6},
	title = "{Molecular hallmarks of heterochronic parabiosis at single-cell resolution}",
	abstract = "{The ability to slow or reverse biological ageing would have major implications for mitigating disease risk and maintaining vitality1. Although an increasing number of interventions show promise for rejuvenation2, their effectiveness on disparate cell types across the body and the molecular pathways susceptible to rejuvenation remain largely unexplored. Here we performed single-cell RNA sequencing on 20 organs to reveal cell-type-specific responses to young and aged blood in heterochronic parabiosis. Adipose mesenchymal stromal cells, haematopoietic stem cells and hepatocytes are among those cell types that are especially responsive. On the pathway level, young blood invokes new gene sets in addition to reversing established ageing patterns, with the global rescue of genes encoding electron transport chain subunits pinpointing a prominent role of mitochondrial function in parabiosis-mediated rejuvenation. We observed an almost universal loss of gene expression with age that is largely mimicked by parabiosis: aged blood reduces global gene expression, and young blood restores it in select cell types. Together, these data lay the groundwork for a systemic understanding of the interplay between blood-borne factors and cellular integrity.}",
	volume = {603},
	journal = {Nature},
	doi = {10.1038/s41586-022-04461-2},
	URL = {https://www.nature.com/articles/s41586-022-04461-2},
}

The ability to slow or reverse biological ageing would have major implications for mitigating disease risk and maintaining vitality1. Although an increasing number of interventions show promise for rejuvenation2, their effectiveness on disparate cell types across the body and the molecular pathways susceptible to rejuvenation remain largely unexplored. Here we performed single-cell RNA sequencing on 20 organs to reveal cell-type-specific responses to young and aged blood in heterochronic parabiosis. Adipose mesenchymal stromal cells, haematopoietic stem cells and hepatocytes are among those cell types that are especially responsive. On the pathway level, young blood invokes new gene sets in addition to reversing established ageing patterns, with the global rescue of genes encoding electron transport chain subunits pinpointing a prominent role of mitochondrial function in parabiosis-mediated rejuvenation. We observed an almost universal loss of gene expression with age that is largely mimicked by parabiosis: aged blood reduces global gene expression, and young blood restores it in select cell types. Together, these data lay the groundwork for a systemic understanding of the interplay between blood-borne factors and cellular integrity.

@article{jders352,
	author = {Yang, Andrew and Vest, Ryan and Kern, Fabian and Lee, Davis and Agam, Maayan and Maat, Christina and Moran Losada, Patricia and Chen, Michelle and Schaum, Nick and Khoury, Nathalie and Toland, Angus and Calcuttawala, Kruti and Shin, Heather and Pálovics, Róbert and Shin, Andrew and Wang, Elizabeth and Luo, Jian and Gate, David and Schulz-Schaeffer, Walter and Chu, Pauline and Siegenthaler, Julie A. and McNerney, M. Windy and Keller, Andreas and Wyss-Coray, Tony},
	year = {2022},
	month = {02},
	pages = {1-8},
	title = "{A human brain vascular atlas reveals diverse mediators of Alzheimer’s risk}",
	abstract = "{The human brain vasculature is of great medical importance: its dysfunction causes disability and death¹, and the specialized structure it forms—the blood–brain barrier—impedes the treatment of nearly all brain disorders2,3. Yet so far, we have no molecular map of the human brain vasculature. Here we develop vessel isolation and nuclei extraction for sequencing (VINE-seq) to profile the major vascular and perivascular cell types of the human brain through 143,793 single-nucleus transcriptomes from 25 hippocampus and cortex samples of 9 individuals with Alzheimer’s disease and 8 individuals with no cognitive impairment. We identify brain-region- and species-enriched genes and pathways. We reveal molecular principles of human arteriovenous organization, recapitulating a gradual endothelial and punctuated mural cell continuum. We discover two subtypes of human pericytes, marked by solute transport and extracellular matrix (ECM) organization; and define perivascular versus meningeal fibroblast specialization. In Alzheimer’s disease, we observe selective vulnerability of ECM-maintaining pericytes and gene expression patterns that implicate dysregulated blood flow. With an expanded survey of brain cell types, we find that 30 of the top 45 genes that have been linked to Alzheimer’s disease risk by genome-wide association studies (GWASs) are expressed in the human brain vasculature, and we confirm this by immunostaining. Vascular GWAS genes map to endothelial protein transport, adaptive immune and ECM pathways. Many are microglia-specific in mice, suggesting a partial evolutionary transfer of Alzheimer’s disease risk. Our work uncovers the molecular basis of the human brain vasculature, which will inform our understanding of overall brain health, disease and therapy.}",
	volume = {603},
	journal = {Nature},
	doi = {10.1038/s41586-021-04369-3},
	URL = {https://www.nature.com/articles/s41586-021-04369-3},
}

The human brain vasculature is of great medical importance: its dysfunction causes disability and death¹, and the specialized structure it forms—the blood–brain barrier—impedes the treatment of nearly all brain disorders2,3. Yet so far, we have no molecular map of the human brain vasculature. Here we develop vessel isolation and nuclei extraction for sequencing (VINE-seq) to profile the major vascular and perivascular cell types of the human brain through 143,793 single-nucleus transcriptomes from 25 hippocampus and cortex samples of 9 individuals with Alzheimer’s disease and 8 individuals with no cognitive impairment. We identify brain-region- and species-enriched genes and pathways. We reveal molecular principles of human arteriovenous organization, recapitulating a gradual endothelial and punctuated mural cell continuum. We discover two subtypes of human pericytes, marked by solute transport and extracellular matrix (ECM) organization; and define perivascular versus meningeal fibroblast specialization. In Alzheimer’s disease, we observe selective vulnerability of ECM-maintaining pericytes and gene expression patterns that implicate dysregulated blood flow. With an expanded survey of brain cell types, we find that 30 of the top 45 genes that have been linked to Alzheimer’s disease risk by genome-wide association studies (GWASs) are expressed in the human brain vasculature, and we confirm this by immunostaining. Vascular GWAS genes map to endothelial protein transport, adaptive immune and ECM pathways. Many are microglia-specific in mice, suggesting a partial evolutionary transfer of Alzheimer’s disease risk. Our work uncovers the molecular basis of the human brain vasculature, which will inform our understanding of overall brain health, disease and therapy.

@article{10.1093/ecco-jcc/jjac003,
    author = {Juzenas, Simonas and Hübenthal, Matthias and Lindqvist, Carl Mårten and Kruse, Robert and Steiert, Tim Alexander and Degenhardt, Frauke and Schulte, Dominik and Nikolaus, Susanna and Zeissig, Sebastian and Bergemalm, Daniel and Almer, Sven and Hjortswang, Henrik and Bresso, Francesca and SIC IBD Working Group and Strüning, Nina and Kupcinskas, Juozas and Keller, Andreas and Lieb, Wolfgang and Rosenstiel, Philip and Schreiber, Stefan and D’Amato, Mauro and Halfvarson, Jonas and Hemmrich-Stanisak, Georg and Franke, Andre},
    title = "{Detailed Transcriptional Landscape of Peripheral Blood Points to Increased Neutrophil Activation in Treatment-Naïve Inflammatory Bowel Disease}",
    journal = {Journal of Crohn's and Colitis},
    year = {2022},
    month = {01},
    abstract = "{Inflammatory bowel disease [IBD] is a chronic relapsing disorder of the gastrointestinal tract, which generally manifests as Crohn’s disease [CD] or ulcerative colitis [UC]. These subtypes are heterogeneous in terms of disease location and histological features, while sharing common clinical presentation, genetic associations and, thus, common immune regulatory pathways.Using miRNA and mRNA coupled transcriptome profiling and systems biology approaches, we report a comprehensive analysis of blood transcriptomes from treatment-naïve [n = 110] and treatment-exposed [n = 177] IBD patients as well as symptomatic [n = 65] and healthy controls [n = 95].Broadly, the peripheral blood transcriptomes of CD and UC patients were similar. However, there was an extensive gene deregulation in the blood of IBD patients, while only a slight deregulation in symptomatic controls, when compared with healthy controls. The deregulated mRNAs and miRNAs are mainly involved in the innate immunity and are especially enriched in neutrophil activation-related pathways. Oxidative phosphorylation and neutrophil activation-related modules were found to be differentially co-expressed among treatment-naïve IBD as compared to healthy controls. In the deregulated neutrophil activation-related co-expression module, IL1B was identified as the central gene. Levels of co-expression among IL1B and chemosensing receptor [CXCR1/2 and FPR1/2] genes were reduced in the blood of IBD patients when compared with healthy controls.Immune dysregulation seen in peripheral blood transcriptomes of treatment-naïve IBD patients is mainly driven by neutrophil activation.}",
    issn = {1873-9946},
    doi = {10.1093/ecco-jcc/jjac003},
    url = {https://doi.org/10.1093/ecco-jcc/jjac003},
    note = {jjac003},
    eprint = {https://academic.oup.com/ecco-jcc/advance-article-pdf/doi/10.1093/ecco-jcc/jjac003/42601153/jjac003.pdf},
}

Inflammatory bowel disease [IBD] is a chronic relapsing disorder of the gastrointestinal tract, which generally manifests as Crohn’s disease [CD] or ulcerative colitis [UC]. These subtypes are heterogeneous in terms of disease location and histological features, while sharing common clinical presentation, genetic associations and, thus, common immune regulatory pathways.Using miRNA and mRNA coupled transcriptome profiling and systems biology approaches, we report a comprehensive analysis of blood transcriptomes from treatment-naïve [n = 110] and treatment-exposed [n = 177] IBD patients as well as symptomatic [n = 65] and healthy controls [n = 95].Broadly, the peripheral blood transcriptomes of CD and UC patients were similar. However, there was an extensive gene deregulation in the blood of IBD patients, while only a slight deregulation in symptomatic controls, when compared with healthy controls. The deregulated mRNAs and miRNAs are mainly involved in the innate immunity and are especially enriched in neutrophil activation-related pathways. Oxidative phosphorylation and neutrophil activation-related modules were found to be differentially co-expressed among treatment-naïve IBD as compared to healthy controls. In the deregulated neutrophil activation-related co-expression module, IL1B was identified as the central gene. Levels of co-expression among IL1B and chemosensing receptor [CXCR1/2 and FPR1/2] genes were reduced in the blood of IBD patients when compared with healthy controls.Immune dysregulation seen in peripheral blood transcriptomes of treatment-naïve IBD patients is mainly driven by neutrophil activation.

@article{article,
    author = {Becker, Anouck and Schmartz, Georges and Gröger, Laura and Grammes, Nadja and Galata, Valentina and Philippeit, Hannah and Weiland, Jacqueline and Ludwig, Nicole and Meese, Eckart and Tierling, Sascha and Walter, Jörn and Schwiertz, Andreas and Spiegel, Jörg and Wagenpfeil, Gudrun and Faßbender, Klaus and Keller, Andreas and Unger, Marcus},
    year = {2021},
    month = {11},
    pages = {},
    abstract = {The composition of the gut microbiome is linked to multiple diseases, including Parkinson’s disease (PD). Bacteria producing short-chain fatty acids (SCFAs) and fecal SCFA concentrations are reduced in PD. SCFAs exert various beneficial functions in humans. In the interventional, monocentric, open-label clinical trial “The Effects of Resistant Starch on Bowel Habits, Short Chain Fatty Acids and Gut Microbiota in Parkinson Disease” (RESISTA-PD, NCT02784145), we aimed at altering fecal SCFAs by an 8-week prebiotic intervention with resistant starch (RS). We enrolled 87 subjects in three study-arms: 32 PD patients received RS (PD + RS), 30 control subjects received RS, and 25 PD patients received solely dietary instructions. We performed paired-end 100 base-pair length metagenomic sequencing of fecal samples using the BGISEQ platform at an average of 9.9 GB. RS was well-tolerated. In PD + RS, fecal butyrate concentrations increased significantly, and fecal calprotectin concentrations dropped significantly after 8 weeks of RS. Clinically, we observed a reduction in non-motor symptoms load in PD + RS. The reference-based analysis of metagenomes highlighted stable alpha-diversity and beta-diversity across the three groups, including bacteria producing SCFAs. Reference-free analysis suggested punctual, yet pronounced differences in the metagenomic signature in PD + RS. RESISTA-PD highlights that a prebiotic treatment with RS is safe and well-tolerated in PD. The stable alpha-diversity and beta-diversity alongside altered fecal butyrate and calprotectin concentrations call for long-term studies, also investigating whether RS is able to modify the clinical course of PD.},
    title = {Effects of Resistant Starch on Symptoms, Fecal Markers and Gut Microbiota in Parkinson’s Disease – the RESISTA-PD Trial},
    journal = {Genomics, Proteomics & Bioinformatics},
    doi = {10.1016/j.gpb.2021.08.009}
}

The composition of the gut microbiome is linked to multiple diseases, including Parkinson’s disease (PD). Bacteria producing short-chain fatty acids (SCFAs) and fecal SCFA concentrations are reduced in PD. SCFAs exert various beneficial functions in humans. In the interventional, monocentric, open-label clinical trial “The Effects of Resistant Starch on Bowel Habits, Short Chain Fatty Acids and Gut Microbiota in Parkinson Disease” (RESISTA-PD, NCT02784145), we aimed at altering fecal SCFAs by an 8-week prebiotic intervention with resistant starch (RS). We enrolled 87 subjects in three study-arms: 32 PD patients received RS (PD + RS), 30 control subjects received RS, and 25 PD patients received solely dietary instructions. We performed paired-end 100 base-pair length metagenomic sequencing of fecal samples using the BGISEQ platform at an average of 9.9 GB. RS was well-tolerated. In PD + RS, fecal butyrate concentrations increased significantly, and fecal calprotectin concentrations dropped significantly after 8 weeks of RS. Clinically, we observed a reduction in non-motor symptoms load in PD + RS. The reference-based analysis of metagenomes highlighted stable alpha-diversity and beta-diversity across the three groups, including bacteria producing SCFAs. Reference-free analysis suggested punctual, yet pronounced differences in the metagenomic signature in PD + RS. RESISTA-PD highlights that a prebiotic treatment with RS is safe and well-tolerated in PD. The stable alpha-diversity and beta-diversity alongside altered fecal butyrate and calprotectin concentrations call for long-term studies, also investigating whether RS is able to modify the clinical course of PD.

@article{article,
    author = {Schmartz, Georges and Hartung, Anna and Hirsch, Pascal and Kern, Fabian and Fehlmann, Tobias and Müller, Rolf and Keller, Andreas},
    year = {2021},
    month = {11},
    pages = {},
    abstract = {Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb.},
    title = {PLSDB: advancing a comprehensive database of bacterial plasmids},
    volume = {50},
    journal = {Nucleic Acids Research},
    doi = {10.1093/nar/gkab1111}
}

Plasmids are known to contain genes encoding for virulence factors and antibiotic resistance mechanisms. Their relevance in metagenomic data processing is steadily growing. However, with the increasing popularity and scale of metagenomics experiments, the number of reported plasmids is rapidly growing as well, amassing a considerable number of false positives due to undetected misassembles. Here, our previously published database PLSDB provides a reliable resource for researchers to quickly compare their sequences against selected and annotated previous findings. Within two years, the size of this resource has more than doubled from the initial 13,789 to now 34,513 entries over the course of eight regular data updates. For this update, we aggregated community feedback for major changes to the database featuring new analysis functionality as well as performance, quality, and accessibility improvements. New filtering steps, annotations, and preprocessing of existing records improve the quality of the provided data. Additionally, new features implemented in the web-server ease user interaction and allow for a deeper understanding of custom uploaded sequences, by visualizing similarity information. Lastly, an application programming interface was implemented along with a python library, to allow remote database queries in automated workflows. The latest release of PLSDB is freely accessible under https://www.ccb.uni-saarland.de/plsdb.

@article{article,
    author = {Amr, Ali and Hinderer, Marc and Griebel, Lena and Deuber, Dominic and Egger, Christoph and Sedaghat-Hamedani, Farbod and Kayvanpour, Elham and Huhn, Daniel and Haas, Jan and Frese, Karen and Schweig, Marc and Marnau, Ninja and Krämer, Annika and Durand, Claudia and Battke, Florian and Prokosch, Hans-Ulrich and Backes, Michael and Keller, Andreas and Schröder, Dominique and Katus, Hugo A. and Frey, Norbert and Meder, Benjamin},
    year = {2021},
    month = {10},
    pages = {1-13},
    abstract = {"Background The development of Precision Medicine strategies requires high-dimensional phenotypic and genomic data, both of which are highly privacy-sensitive data types. Conventional data management systems lack the capabilities to sufficiently handle the expected large quantities of such sensitive data in a secure manner. PROMISE is a genetic data management concept that implements a highly secure platform for data exchange while preserving patient interests, privacy, and autonomy. Methods The concept of PROMISE to democratize genetic data was developed by an interdisciplinary team. It integrates a sophisticated cryptographic concept that allows only the patient to grant selective access to defined parts of his genetic information with single DNA base-pair resolution cryptography. The PROMISE system was developed for research purposes to evaluate the concept in a pilot study with nineteen cardiomyopathy patients undergoing genotyping, questionnaires, and longitudinal follow-up. Results The safety of genetic data was very important to 79%, and patients generally regarded the data as highly sensitive. More than half the patients reported that their attitude towards the handling of genetic data has changed after using the PROMISE app for 4 months (median). The patients reported higher confidence in data security and willingness to share their data with commercial third parties, including pharmaceutical companies (increase from 5 to 32%). Conclusion PROMISE democratizes genomic data by a transparent, secure, and patient-centric approach. This clinical pilot study evaluating a genetic data infrastructure is unique and shows that patient’s acceptance of data sharing can be increased by patient-centric decision-making."},
    title = {Controlling my genome with my smartphone: first clinical experiences of the PROMISE system},
    journal = {Clinical Research in Cardiology},
    doi = {10.1007/s00392-021-01942-8}
}

"Background The development of Precision Medicine strategies requires high-dimensional phenotypic and genomic data, both of which are highly privacy-sensitive data types. Conventional data management systems lack the capabilities to sufficiently handle the expected large quantities of such sensitive data in a secure manner. PROMISE is a genetic data management concept that implements a highly secure platform for data exchange while preserving patient interests, privacy, and autonomy. Methods The concept of PROMISE to democratize genetic data was developed by an interdisciplinary team. It integrates a sophisticated cryptographic concept that allows only the patient to grant selective access to defined parts of his genetic information with single DNA base-pair resolution cryptography. The PROMISE system was developed for research purposes to evaluate the concept in a pilot study with nineteen cardiomyopathy patients undergoing genotyping, questionnaires, and longitudinal follow-up. Results The safety of genetic data was very important to 79%, and patients generally regarded the data as highly sensitive. More than half the patients reported that their attitude towards the handling of genetic data has changed after using the PROMISE app for 4 months (median). The patients reported higher confidence in data security and willingness to share their data with commercial third parties, including pharmaceutical companies (increase from 5 to 32%). Conclusion PROMISE democratizes genomic data by a transparent, secure, and patient-centric approach. This clinical pilot study evaluating a genetic data infrastructure is unique and shows that patient’s acceptance of data sharing can be increased by patient-centric decision-making."

@article{Millenaar4623621,
    author = {Millenaar, Dominic and Dillmann, Markus and Fehlmann, Tobias and Flohr, Alexander and Mehran, Roxana and Al-Lamee, Rasha and Lauder, Lucas and Ukena, Christian and Böhm, Michael and Keller, Andreas and Mahfoud, Felix},
    year = {2021},
    month = {10},
    pages = {},
    abstract = {"Background We sought to investigate sex‐specific differences in authorship of cardiovascular research over the past decade. Methods and Results All 387 463 cardiovascular publications between 2010 and 2019 were retrieved from Web of Science. Articles increased from 19 960 to 29 604 articles per year ( P >0.001). The number of articles written by female first authors increased by 76.3% (6434–11 343 articles) and by 35.0% for male first authors (13 526–18 261) ( P <0.001). The first author was more likely to be a female author in articles with female last authors. The median impact factor (IF) for articles by female first authors was lower (2.46 [interquartile range, 7 1.11–4.03] versus 2.51 [interquartile range, 1.17–4.10]; P <0.001). Female authorship articles reached the highest IF in North America (average IF, 3.7), with the lowest in Africa (average IF, 1.8). Conclusions Publications in cardiovascular research have increased over the past decade, particularly by female authors. Female researchers are cited less often compared with their male peers. The IF remains lower for articles by female researchers."},
    title = {Sex Differences in Cardiovascular Research: A Scientometric Analysis},
    journal = {Journal of the American Heart Association},
    doi = {10.1161/JAHA.121.021522}
}

"Background We sought to investigate sex‐specific differences in authorship of cardiovascular research over the past decade. Methods and Results All 387 463 cardiovascular publications between 2010 and 2019 were retrieved from Web of Science. Articles increased from 19 960 to 29 604 articles per year ( P >0.001). The number of articles written by female first authors increased by 76.3% (6434–11 343 articles) and by 35.0% for male first authors (13 526–18 261) ( P <0.001). The first author was more likely to be a female author in articles with female last authors. The median impact factor (IF) for articles by female first authors was lower (2.46 [interquartile range, 7 1.11–4.03] versus 2.51 [interquartile range, 1.17–4.10]; P <0.001). Female authorship articles reached the highest IF in North America (average IF, 3.7), with the lowest in Africa (average IF, 1.8). Conclusions Publications in cardiovascular research have increased over the past decade, particularly by female authors. Female researchers are cited less often compared with their male peers. The IF remains lower for articles by female researchers."

@article{keller24146822,
    author = {Keller, Andreas and Gröger, Laura and Tschernig, Thomas and Solomon, Jeffrey and Laham, Omar and Schaum, Nick and Wagner, Viktoria and Kern, Fabian and Schmartz, Georges and Li, Yongping and Borcherding, Adam and Meier, Carola and Wyss-Coray, Tony and Meese, Eckart and Fehlmann, Tobias and Ludwig, Nicole},
    year = {2021},
    month = {09},
    pages = {},
    abstract = {Small non-coding RNAs (sncRNAs) are pervasive regulators of physiological and pathological processes. We previously developed the human miRNA Tissue Atlas, detailing the expression of miRNAs across organs in the human body. Here, we present an updated resource containing sequencing data of 188 tissue samples comprising 21 organ types retrieved from six humans. Sampling the organs from the same bodies minimizes intra-individual variability and facilitates the making of a precise high-resolution body map of the non-coding transcriptome. The data allow shedding light on the organ- and organ system-specificity of piwi-interacting RNAs (piRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs) and other non-coding RNAs. As use case of our resource, we describe the identification of highly specific ncRNAs in different organs. The update also contains 58 samples from six tissues of the Tabula Muris collection, allowing to check if the tissue specificity is evolutionary conserved between Homo sapiens and Mus musculus. The updated resource of 87 252 non-coding RNAs from nine non-coding RNA classes for all organs and organ systems is available online without any restrictions (https://www.ccb.uni-saarland.de/tissueatlas2).},
    title = {miRNATissueAtlas2: an update to the human miRNA tissue atlas},
    volume = {50},
    journal = {Nucleic Acids Research},
    doi = {10.1093/nar/gkab808}
}

Small non-coding RNAs (sncRNAs) are pervasive regulators of physiological and pathological processes. We previously developed the human miRNA Tissue Atlas, detailing the expression of miRNAs across organs in the human body. Here, we present an updated resource containing sequencing data of 188 tissue samples comprising 21 organ types retrieved from six humans. Sampling the organs from the same bodies minimizes intra-individual variability and facilitates the making of a precise high-resolution body map of the non-coding transcriptome. The data allow shedding light on the organ- and organ system-specificity of piwi-interacting RNAs (piRNAs), transfer RNAs (tRNAs), microRNAs (miRNAs) and other non-coding RNAs. As use case of our resource, we describe the identification of highly specific ncRNAs in different organs. The update also contains 58 samples from six tissues of the Tabula Muris collection, allowing to check if the tissue specificity is evolutionary conserved between Homo sapiens and Mus musculus. The updated resource of 87 252 non-coding RNAs from nine non-coding RNA classes for all organs and organ systems is available online without any restrictions (https://www.ccb.uni-saarland.de/tissueatlas2).

@article{Gerstner25555521,
    author = {Gerstner, Nico and Kehl, Tim and Lenhof, Kerstin and Eckhart, Lea and Schneider, Lara and Stöckel, Daniel and Backes, Christina and Meese, Eckart and Keller, Andreas and Lenhof, Hans-Peter},
    year = {2021},
    month = {09},
    pages = {},
    abstract = {Experimental high-throughput techniques, like next-generation sequencing or microarrays, are nowadays routinely applied to create detailed molecular profiles of cells. In general, these platforms generate high-dimensional and noisy data sets. For their analysis, powerful bioinformatics tools are required to gain novel insights into the biological processes under investigation. Here, we present an overview of the GeneTrail tool suite that offers rich functionality for the analysis and visualization of (epi-)genomic, transcriptomic, miRNomic, and proteomic profiles. Our framework enables the analysis of standard bulk, time-series, and single-cell measurements and includes various state-of-the-art methods to identify potentially deregulated biological processes and to detect driving factors within those deregulated processes. We highlight the capabilities of our web service with an analysis of a single-cell COVID-19 data set that demonstrates its potential for uncovering complex molecular mechanisms. GeneTrail can be accessed freely and without login requirements at http://genetrail.bioinf.uni-sb.de .},
    title = {GeneTrail: A Framework for the Analysis of High-Throughput Profiles},
    volume = {8},
    journal = {Frontiers in Molecular Biosciences},
    doi = {10.3389/fmolb.2021.716544}
}

Experimental high-throughput techniques, like next-generation sequencing or microarrays, are nowadays routinely applied to create detailed molecular profiles of cells. In general, these platforms generate high-dimensional and noisy data sets. For their analysis, powerful bioinformatics tools are required to gain novel insights into the biological processes under investigation. Here, we present an overview of the GeneTrail tool suite that offers rich functionality for the analysis and visualization of (epi-)genomic, transcriptomic, miRNomic, and proteomic profiles. Our framework enables the analysis of standard bulk, time-series, and single-cell measurements and includes various state-of-the-art methods to identify potentially deregulated biological processes and to detect driving factors within those deregulated processes. We highlight the capabilities of our web service with an analysis of a single-cell COVID-19 data set that demonstrates its potential for uncovering complex molecular mechanisms. GeneTrail can be accessed freely and without login requirements at http://genetrail.bioinf.uni-sb.de .

@article{herr532513421,
    author = {Herr, Christian and Mang, Sebastian and Mozafari, Bahareh and Guenther, Katharina and Speer, Thimoteus and Seibert, Martina and Srikakulam, Sanjay Kumar and Beisswenger, Christoph and Ritzmann, Felix and Keller, Andreas and Müller, Rolf and Smola, Sigrun and Eisinger, Dominic and Zemlin, Michael and Danziger, Guy and Volk, Thomas and Hörsch, Sabrina and Krawczyk, Marcin and Lammert, Frank and Adams, Thomas and Wagenpfeil, Gudrun and Kindermann, Michael and Marcu, Constantin and Ataya, Zuhair Wolf Dietrich and Mittag, Marc and Schwarzkopf, Konrad and Custodis, Florian and Grandt, Daniel and Schaefer, Harald and Eltges, Kai and Lepper, Philipp M and Bals, Robert},
    year = {2021},
    month = {09},
    pages = {4651-4667},
    abstract = {Background: COVID-19 comprises several severity stages ranging from oligosymptomatic disease to multi-organ failure and fatal outcomes. The mechanisms why COVID-19 is a mild disease in some patients and progresses to a severe multi-organ and often fatal disease with respiratory failure are not known. Biomarkers that predict the course of disease are urgently needed. The aim of this study was to evaluate a large spectrum of established laboratory measurements. Patients and methods: Patients from the prospective PULMPOHOM and CORSAAR studies were recruited and comprised 35 patients with COVID-19, 23 with conventional pneumonia, and 28 control patients undergoing elective non-pulmonary surgery. Venous blood was used to measure the serum concentrations of 79 proteins by Luminex multiplex immunoassay technology. Distribution of biomarkers between groups and association with disease severity and outcomes were analyzed. Results: The biomarker profiles between the three groups differed significantly with elevation of specific proteins specific for the respective conditions. Several biomarkers correlated significantly with disease severity and death. Uniform manifold approximation and projection (UMAP) analysis revealed a significant separation of the three disease groups and separated between survivors and deceased patients. Different models were developed to predict mortality based on the baseline measurements of several protein markers. A score combining IL-1ra, IL-8, IL-10, MCP-1, SCF and CA-9 was associated with significantly higher mortality (AUC 0.929). Discussion: Several newly identified blood markers were significantly increased in patients with severe COVID-19 (AAT, EN-RAGE, myoglobin, SAP, TIMP-1, vWF, decorin) or in patients that died (IL-1ra, IL-8, IL-10, MCP-1, SCF, CA-9). The use of established assay technologies allows for rapid translation into clinical practice.},
    title = {Distinct Patterns of Blood Cytokines Beyond a Cytokine Storm Predict Mortality in COVID-19},
    volume = {Volume 14},
    journal = {Journal of Inflammation Research},
    doi = {10.2147/JIR.S320685}
}

Background: COVID-19 comprises several severity stages ranging from oligosymptomatic disease to multi-organ failure and fatal outcomes. The mechanisms why COVID-19 is a mild disease in some patients and progresses to a severe multi-organ and often fatal disease with respiratory failure are not known. Biomarkers that predict the course of disease are urgently needed. The aim of this study was to evaluate a large spectrum of established laboratory measurements. Patients and methods: Patients from the prospective PULMPOHOM and CORSAAR studies were recruited and comprised 35 patients with COVID-19, 23 with conventional pneumonia, and 28 control patients undergoing elective non-pulmonary surgery. Venous blood was used to measure the serum concentrations of 79 proteins by Luminex multiplex immunoassay technology. Distribution of biomarkers between groups and association with disease severity and outcomes were analyzed. Results: The biomarker profiles between the three groups differed significantly with elevation of specific proteins specific for the respective conditions. Several biomarkers correlated significantly with disease severity and death. Uniform manifold approximation and projection (UMAP) analysis revealed a significant separation of the three disease groups and separated between survivors and deceased patients. Different models were developed to predict mortality based on the baseline measurements of several protein markers. A score combining IL-1ra, IL-8, IL-10, MCP-1, SCF and CA-9 was associated with significantly higher mortality (AUC 0.929). Discussion: Several newly identified blood markers were significantly increased in patients with severe COVID-19 (AAT, EN-RAGE, myoglobin, SAP, TIMP-1, vWF, decorin) or in patients that died (IL-1ra, IL-8, IL-10, MCP-1, SCF, CA-9). The use of established assay technologies allows for rapid translation into clinical practice.

@article{chens4146702125410z,
    author = {Chen, Kellen and Kwon, Sun and Henn, Dominic and Kuehlmann, Britta and Tevlin, Ruth and Bonham, Clark and Griffin, Michelle and Trotsyuk, Artem and Borrelli, Mimi and Noishiki, Chikage and Padmanabhan, Jagannath and Barrera, Janos and Maan, Zeshaan and Dohi, Teruyuki and Mays, Chyna and Greco, Autumn and Sivaraj, Dharshan and Lin, John and Fehlmann, Tobias and Mermin-Bunnell, Alana M. and Mittal, Smiti and Hu, Michael S. and Zamaleeva, Alsu I. and Keller, Andreas and Rajadas, Jayakumar and Longaker, Michael T. and Januszyk, Michael and Gurtner, Geoffrey},
    year = {2021},
    month = {09},
    pages = {},
    abstract = {Tissue repair and healing remain among the most complicated processes that occur during postnatal life. Humans and other large organisms heal by forming fibrotic scar tissue with diminished function, while smaller organisms respond with scarless tissue regeneration and functional restoration. Well-established scaling principles reveal that organism size exponentially correlates with peak tissue forces during movement, and evolutionary responses have compensated by strengthening organ-level mechanical properties. How these adaptations may affect tissue injury has not been previously examined in large animals and humans. Here, we show that blocking mechanotransduction signaling through the focal adhesion kinase pathway in large animals significantly accelerates wound healing and enhances regeneration of skin with secondary structures such as hair follicles. In human cells, we demonstrate that mechanical forces shift fibroblasts toward pro-fibrotic phenotypes driven by ERK-YAP activation, leading to myofibroblast differentiation and excessive collagen production. Disruption of mechanical signaling specifically abrogates these responses and instead promotes regenerative fibroblast clusters characterized by AKT-EGR1.},
    title = {Disrupting biological sensors of force promotes tissue regeneration in large organisms},
    volume = {12},
    journal = {Nature Communications},
    doi = {10.1038/s41467-021-25410-z}
}

Tissue repair and healing remain among the most complicated processes that occur during postnatal life. Humans and other large organisms heal by forming fibrotic scar tissue with diminished function, while smaller organisms respond with scarless tissue regeneration and functional restoration. Well-established scaling principles reveal that organism size exponentially correlates with peak tissue forces during movement, and evolutionary responses have compensated by strengthening organ-level mechanical properties. How these adaptations may affect tissue injury has not been previously examined in large animals and humans. Here, we show that blocking mechanotransduction signaling through the focal adhesion kinase pathway in large animals significantly accelerates wound healing and enhances regeneration of skin with secondary structures such as hair follicles. In human cells, we demonstrate that mechanical forces shift fibroblasts toward pro-fibrotic phenotypes driven by ERK-YAP activation, leading to myofibroblast differentiation and excessive collagen production. Disruption of mechanical signaling specifically abrogates these responses and instead promotes regenerative fibroblast clusters characterized by AKT-EGR1.

@article{miethkes41570021003131,
    author = {Miethke, Marcus and Pieroni, Marco and Weber, Tilmann and Brönstrup, Mark and Hammann, Peter and Halby, Ludovic and Arimondo, Paola and Glaser, Philippe and Aigle, Bertrand and Bode, Helge and Moreira, Rui and Li, Yanyan and Luzhetskyy, Andriy and Medema, Marnix and Pernodet, Jean-Luc and Stadler, Marc and Tormo, Jose and Genilloud, Olga and Truman, Andrew and Weissman, Kira J. and Takano, Eriko and Sabatini, Stefano and Stegmann, Evi and Brötz-Oesterhelt, Heike and Wohlleben, Wolfgang and Seemann, Myriam and Empting, Martin and Hirsch, Anna K. H. and Loretz, Brigitta and Lehr, Claus-Michael and Titz, Alexander and Herrmann, Jennifer and Jaeger, Timo and Alt, Silke and Hesterkamp, Thomas and Winterhalter, Mathias and Schiefer, Andrea and Pfarr, Kenneth and Hoerauf, Achim and Graz, Heather and Graz, Michael and Lindvall, Mika and Ramurthy, Savithri and Karlén, Anders and Dongen, Maarten van and Petkovic, Hrvoje and Keller, Andreas and Peyrane, Frédéric and Donadio, Stefano and Fraisse, Laurent and Piddock, Laura J. V. and Gilbert, Ian H. and Moser, Heinz E. and Müller, Rolf},
    year = {2021},
    month = {08},
    pages = {1-24},
    abstract = {An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.},
    title = {Towards the sustainable discovery and development of new antibiotics},
    journal = {Nature Reviews Chemistry},
    doi = {10.1038/s41570-021-00313-1}
}

An ever-increasing demand for novel antimicrobials to treat life-threatening infections caused by the global spread of multidrug-resistant bacterial pathogens stands in stark contrast to the current level of investment in their development, particularly in the fields of natural-product-derived and synthetic small molecules. New agents displaying innovative chemistry and modes of action are desperately needed worldwide to tackle the public health menace posed by antimicrobial resistance. Here, our consortium presents a strategic blueprint to substantially improve our ability to discover and develop new antibiotics. We propose both short-term and long-term solutions to overcome the most urgent limitations in the various sectors of research and funding, aiming to bridge the gap between academic, industrial and political stakeholders, and to unite interdisciplinary expertise in order to efficiently fuel the translational pipeline for the benefit of future generations.

@article{huecker2021,
    author = {Hücker, Sarah M. and Fehlmann, Tobias and Werno, Christian and Weidele, Kathrin and Lüke, Florian and Schlenska-Lange, Anke and Klein, Christoph A. and Keller, Andreas and Kirsch, Stefan},
    year = {2021},
    month = {07},
    pages = {},
    abstract = {"Molecular single cell analyses provide insights into physiological and pathological processes. Here, in a stepwise approach, we first evaluate 19 protocols for single cell small RNA sequencing on MCF7 cells spiked with 1 pg of 1,006 miRNAs. Second, we analyze MCF7 single cell equivalents of the eight best protocols. Third, we sequence single cells from eight different cell lines and 67 circulating tumor cells (CTCs) from seven SCLC patients. Altogether, we analyze 244 different samples. We observe high reproducibility within protocols and reads covered a broad spectrum of RNAs. For the 67 CTCs, we detect a median of 68 miRNAs, with 10 miRNAs being expressed in 90% of tested cells. Enrichment analysis suggested the lung as the most likely organ of origin and enrichment of cancer-related categories. Even the identification of non-annotated candidate miRNAs was feasible, underlining the potential of single cell small RNA sequencing."},
    title = {Single-cell microRNA sequencing method comparison and application to cell lines and circulating lung tumor cells},
    journal = {Nature Communications},
    doi = {10.1038/s41467-021-24611-w},
    URL = {https://www.nature.com/articles/s41467-021-24611-w}
}

"Molecular single cell analyses provide insights into physiological and pathological processes. Here, in a stepwise approach, we first evaluate 19 protocols for single cell small RNA sequencing on MCF7 cells spiked with 1 pg of 1,006 miRNAs. Second, we analyze MCF7 single cell equivalents of the eight best protocols. Third, we sequence single cells from eight different cell lines and 67 circulating tumor cells (CTCs) from seven SCLC patients. Altogether, we analyze 244 different samples. We observe high reproducibility within protocols and reads covered a broad spectrum of RNAs. For the 67 CTCs, we detect a median of 68 miRNAs, with 10 miRNAs being expressed in 90% of tested cells. Enrichment analysis suggested the lung as the most likely organ of origin and enrichment of cancer-related categories. Even the identification of non-annotated candidate miRNAs was feasible, underlining the potential of single cell small RNA sequencing."

@article{erab321,
    author = {Hickl, Daniel and Drews, Franziska and Girke, Christopher and Zimmer, David and Mühlhaus, Timo and Hauth, Jan and Nordström, Karl and Trentmann, Oliver and Neuhaus, Ekkehard and Scheuring, David and Fehlmann, Tobias and Keller, Andreas and Martin, Simon and Möhlmann, Torsten},
    year = {2021},
    month = {07},
    pages = {},
    abstract = {The plant vacuole recycles proteins and RNA delivered to it by autophagy. Here, we provide a comprehensive characterization of the plant vacuolar RNAome by isolating intact vacuoles from Arabidopsis plants, subsequent RNA purification and deep sequencing. In the vacuolar RNAomes, we detected ribosomal RNAs, and transfer RNAs, including those of chloroplast origin and small RNA types in addition. As autophagy is a main mechanism for the transport of RNA to the vacuole, atg5-1 mutants deficient in autophagy were included in our analysis. We observed severely reduced amounts of most chloroplast-derived RNA species in these mutants. By comparison with the cellular RNA composition, indications for the upregulation of alternative RNA breakdown pathways were obtained. By contrast, vacuolar RNA processing and composition in plants lacking vacuolar ribonuclease 2, involved in cellular RNA homeostasis, only showed minor alterations, possibly because of the presence of further so far unknown vacuolar RNase species. Among the small RNA types, we detected mature miRNAs in all vacuolar preparations but at much lower frequency in atg5-1, raising the possibility of a biological role for vacuolar miRNAs.},
    title = {Differential degradation of RNA species by autophagy related pathways in Arabidopsis},
    journal = {Journal of experimental botany},
    doi = {10.1093/jxb/erab321},
    URL = {https://academic.oup.com/jxb/advance-article/doi/10.1093/jxb/erab321/6318437}
}

The plant vacuole recycles proteins and RNA delivered to it by autophagy. Here, we provide a comprehensive characterization of the plant vacuolar RNAome by isolating intact vacuoles from Arabidopsis plants, subsequent RNA purification and deep sequencing. In the vacuolar RNAomes, we detected ribosomal RNAs, and transfer RNAs, including those of chloroplast origin and small RNA types in addition. As autophagy is a main mechanism for the transport of RNA to the vacuole, atg5-1 mutants deficient in autophagy were included in our analysis. We observed severely reduced amounts of most chloroplast-derived RNA species in these mutants. By comparison with the cellular RNA composition, indications for the upregulation of alternative RNA breakdown pathways were obtained. By contrast, vacuolar RNA processing and composition in plants lacking vacuolar ribonuclease 2, involved in cellular RNA homeostasis, only showed minor alterations, possibly because of the presence of further so far unknown vacuolar RNase species. Among the small RNA types, we detected mature miRNAs in all vacuolar preparations but at much lower frequency in atg5-1, raising the possibility of a biological role for vacuolar miRNAs.

@article{ah13351,
    author = {Abu-Halima, Masood and Becker, Lea and Ayesh, Basim and Baus, Simona and Hamza, Amer and Fischer, Ulrike and Hammadeh, Mohamad Eid and Keller, Andreas and Meese, Eckart},
    year = {2021},
    month = {06},
    pages = {13351},
    abstract = {Women undergoing infertility treatment are routinely subjected to one or more tests of ovarian reserve. Therefore, an adequate assessment of the ovarian reserve is necessary for the treatment. In this study, we aimed to characterize the potential role of microRNAs (miRNAs) as biomarkers for women with different ovarian reserves. A total of 159 women were recruited in the study and classified according to their anti-Müllerian hormone (AMH) level into three groups: (1) low ovarian reserve (LAMH, n = 39), (2) normal ovarian reserve (NAMH, n = 80), and (3) high ovarian reserve (HAMH, n = 40). SurePrint Human miRNA array screening and reverse transcription-quantitative PCR (RT-qPCR) were respectively employed to screen and validate the miRNA abundance level in the three tested groups. Compared with NAMH, the abundance level of 34 and 98 miRNAs was found to be significantly altered in LAMH and HAMH, respectively. The abundance level of miRNAs was further validated by RT-qPCR in both, the screening samples as well as in an independent set of validation samples. The abundance levels of the validated miRNAs were significantly correlated with the AMH level. The best AUC value for the prediction of the increase and decrease in the AMH level was obtained for the miR-100-5p and miR-21-5p, respectively. The level of miRNAs abundance correlates with the level of AMH, which may serve as a tool for identifying women with a different ovarian reserve and may help to lay the ground for the development of novel diagnostic approaches.},
    title = {Characterization of micro-RNA in women with different ovarian reserve},
    journal = {Scientific Reports},
    doi = {10.1038/s41598-021-92901-w},
    URL = {https://www.nature.com/articles/s41598-021-92901-w}
}

Women undergoing infertility treatment are routinely subjected to one or more tests of ovarian reserve. Therefore, an adequate assessment of the ovarian reserve is necessary for the treatment. In this study, we aimed to characterize the potential role of microRNAs (miRNAs) as biomarkers for women with different ovarian reserves. A total of 159 women were recruited in the study and classified according to their anti-Müllerian hormone (AMH) level into three groups: (1) low ovarian reserve (LAMH, n = 39), (2) normal ovarian reserve (NAMH, n = 80), and (3) high ovarian reserve (HAMH, n = 40). SurePrint Human miRNA array screening and reverse transcription-quantitative PCR (RT-qPCR) were respectively employed to screen and validate the miRNA abundance level in the three tested groups. Compared with NAMH, the abundance level of 34 and 98 miRNAs was found to be significantly altered in LAMH and HAMH, respectively. The abundance level of miRNAs was further validated by RT-qPCR in both, the screening samples as well as in an independent set of validation samples. The abundance levels of the validated miRNAs were significantly correlated with the AMH level. The best AUC value for the prediction of the increase and decrease in the AMH level was obtained for the miR-100-5p and miR-21-5p, respectively. The level of miRNAs abundance correlates with the level of AMH, which may serve as a tool for identifying women with a different ovarian reserve and may help to lay the ground for the development of novel diagnostic approaches.

@article{mr2106,
    author = {Mueller, Ricarda and Bajric, Denis and Keceli, Gencay and Keller, Andreas and Dommisch, Henrik and Sharawy, Abdou and Schaefer, Arne},
    year = {2021},
    month = {06},
    pages = {},
    abstract = {We aimed to identify a microRNA (miRNA) that is significantly upregulated in blood and in cells of the oral mucosa upon exposure to the periodontitis main risk factors oral inflammation and tobacco smoke, to subsequently identify its target gene and to describe the molecular mechanism of gene regulation. Background: miRNAs are associated with many disorders. Array-based miRNA expression studies indicated a number of differentially expressed miRNAs in the pathology of oral diseases. However, these miRNAs mostly lacked replication, and their target genes have remained unknown. Methods: 863 miRNAs were analyzed in blood from 18 PD cases and 70 controls (Geniom Biochip). Selected miRNAs were analyzed for upregulation in the inflamed oral mucosa of PD patients using published miRNA expression profiling studies from gingival cells. hsa-miR-374b-5p mimic was overexpressed in primary gingival fibroblasts (pGFs) from 3 donors, and genome-wide mRNA expression was quantified (Clarion Array). Gene-specific regulation was validated by qRT-PCR and Luciferase activity in HeLa cells. Results: hsa-miR-374b-5p showed >twofold change (FC) in 3 independent studies performed in blood, gingival tissues, and cells. After hsa-miR-374b-5p overexpression, genome-wide expression analysis showed UHMK1 as top 1 downregulated gene in pGFs (p = 2.5 × 10⁻⁰⁴, fold change = −1.8). Reporter genes demonstrated that hsa-miR-374b-5p downregulates mRNA levels (p = .02; FC = −1.5), leading to reduction in protein activity (p = .013, FC = −1.3). Conclusions: hsa-miR-374b-5p is upregulated in blood and ginvial cells exposed to oral inflammation and tobacco smoke and regulates UHMK1, which has a role in osteoclast differentiation.},
    title = {hsa-miR-374b-5p regulates expression of the gene U2AF homology motif (UHM) kinase 1},
    journal = {Journal of Periodontal Research},
    doi = {10.1111/jre.12913},
    URL = {https://onlinelibrary.wiley.com/doi/10.1111/jre.12913}
}

We aimed to identify a microRNA (miRNA) that is significantly upregulated in blood and in cells of the oral mucosa upon exposure to the periodontitis main risk factors oral inflammation and tobacco smoke, to subsequently identify its target gene and to describe the molecular mechanism of gene regulation. Background: miRNAs are associated with many disorders. Array-based miRNA expression studies indicated a number of differentially expressed miRNAs in the pathology of oral diseases. However, these miRNAs mostly lacked replication, and their target genes have remained unknown. Methods: 863 miRNAs were analyzed in blood from 18 PD cases and 70 controls (Geniom Biochip). Selected miRNAs were analyzed for upregulation in the inflamed oral mucosa of PD patients using published miRNA expression profiling studies from gingival cells. hsa-miR-374b-5p mimic was overexpressed in primary gingival fibroblasts (pGFs) from 3 donors, and genome-wide mRNA expression was quantified (Clarion Array). Gene-specific regulation was validated by qRT-PCR and Luciferase activity in HeLa cells. Results: hsa-miR-374b-5p showed >twofold change (FC) in 3 independent studies performed in blood, gingival tissues, and cells. After hsa-miR-374b-5p overexpression, genome-wide expression analysis showed UHMK1 as top 1 downregulated gene in pGFs (p = 2.5 × 10⁻⁰⁴, fold change = −1.8). Reporter genes demonstrated that hsa-miR-374b-5p downregulates mRNA levels (p = .02; FC = −1.5), leading to reduction in protein activity (p = .013, FC = −1.3). Conclusions: hsa-miR-374b-5p is upregulated in blood and ginvial cells exposed to oral inflammation and tobacco smoke and regulates UHMK1, which has a role in osteoclast differentiation.

@article{yakf21,
    author = {Yang, Andrew and Kern, Fabian and Moran Losada, Patricia and Agam, Maayan and Maat, Christina and Schmartz, Georges and Fehlmann, Tobias and Stein, Julian and Schaum, Nick and Lee, Davis and Calcuttawala, Kruti and Vest, Ryan and Berdnik, Daniela and Lu, Nannan and Hahn, Oliver and Gate, David and McNerney, M. and Channappa, Divya and Cobos, Inma and Ludwig, Nicole and Schulz-Schaeffer, Walter J. and Keller, Andreas and Wyss-Coray, Tony},
    year = {2021},
    month = {06},
    pages = {},
    abstract = {},
    title = {Dysregulation of brain and choroid plexus cell types in severe COVID-19},
    journal = {Nature},
    doi = {10.1038/s41586-021-03710-0},
    URL = {https://www.nature.com/articles/s41586-021-03710-0}
}

@article{gp0521a,
    author = {Guimarães, Pedro and Keller, Andreas and Fehlmann, Tobias and Lammert, Frank and Casper, Mary},
    year = {2021},
    month = {05},
    pages = {},
    abstract = {Background and aims: For eosinophilic esophagitis (EoE) a substantial diagnostic delay is still a clinically relevant phenomenon. Deep learning-based algorithms have demonstrated potential in medical image analysis. Here we establish a convolutional neuronal network (CNN)-based approach that can distinguish EoE from normal findings and candida esophagitis. Methods: We trained and tested a CNN using 484 real-world endoscopic images from 134 subjects consisting of three classes (normal, EoE, and candidiasis). Images were split into two completely independent datasets. The proposed approach was evaluated against three trainee endoscopists on the test set. Model-explainability was enhanced by deep Taylor decomposition. Results: Global accuracy (0.915 [0.880-0.940]), sensitivity (0.871 [0.819-0.910]) and specificity (0.936 [0.910-0.955]) were significantly higher than for endoscopists on the test set. Global area under the ROC curve was 0.966 [0.954-0.975]. Results were highly reproducible. Explainability analysis found that the algorithm identified characteristic signs also used by endoscopists. Conclusions: Complex endoscopic classification tasks including more than two classes can be solved by CNN-based algorithms. Thus, our algorithm (https://ccb-test.cs.uni-saarland.de/EoE/) may assist clinicians in making the diagnosis of EoE. },
    title = {Deep-learning based detection of eosinophilic esophagitis},
    journal = {Endoscopy},
    doi = {10.1055/a-1520-8116},
    URL = {https://www.thieme-connect.de/products/ejournals/abstract/10.1055/a-1520-8116}
}

Background and aims: For eosinophilic esophagitis (EoE) a substantial diagnostic delay is still a clinically relevant phenomenon. Deep learning-based algorithms have demonstrated potential in medical image analysis. Here we establish a convolutional neuronal network (CNN)-based approach that can distinguish EoE from normal findings and candida esophagitis. Methods: We trained and tested a CNN using 484 real-world endoscopic images from 134 subjects consisting of three classes (normal, EoE, and candidiasis). Images were split into two completely independent datasets. The proposed approach was evaluated against three trainee endoscopists on the test set. Model-explainability was enhanced by deep Taylor decomposition. Results: Global accuracy (0.915 [0.880-0.940]), sensitivity (0.871 [0.819-0.910]) and specificity (0.936 [0.910-0.955]) were significantly higher than for endoscopists on the test set. Global area under the ROC curve was 0.966 [0.954-0.975]. Results were highly reproducible. Explainability analysis found that the algorithm identified characteristic signs also used by endoscopists. Conclusions: Complex endoscopic classification tasks including more than two classes can be solved by CNN-based algorithms. Thus, our algorithm (https://ccb-test.cs.uni-saarland.de/EoE/) may assist clinicians in making the diagnosis of EoE.

@article{gkab396,
    author = {Fehlmann, Tobias and Kern, Fabian and Hirsch, Pascal and Steinhaus, Robin and Seelow, Dominik and Keller, Andreas},
    year = {2021},
    month = {05},
    abstract = {With Aviator, we present a web service and repository that facilitates surveillance of online tools. Aviator consists of a user-friendly website and two modules, a literature-mining based general and a manually curated module. The general module currently checks 9417 websites twice a day with respect to their availability and stores many features (frontend and backend response time, required RAM and size of the web page, security certificates, analytic tools and trackers embedded in the webpage and others) in a data warehouse. Aviator is also equipped with an analysis functionality, for example authors can check and evaluate the availability of their own tools or those of their peers. Likewise, users can check the availability of a certain tool they intend to use in research or teaching to avoid including unstable tools. The curated section of Aviator offers additional services. We provide API snippets for common programming languages (Perl, PHP, Python, JavaScript) as well as an OpenAPI documentation for embedding in the backend of own web services for an automatic test of their function. We query the respective APIs twice a day and send automated notifications in case of an unexpected result. Naturally, the same analysis functionality as for the literature-based module is available for the curated section. Aviator can freely be used at https://www.ccb.uni-saarland.de/aviator.},
    title = {Aviator: a web service for monitoring the availability of web services},
    journal = {Nucleic Acids Research},
    doi = {10.1093/nar/gkab396},
    URL = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab396/6285262}
}

With Aviator, we present a web service and repository that facilitates surveillance of online tools. Aviator consists of a user-friendly website and two modules, a literature-mining based general and a manually curated module. The general module currently checks 9417 websites twice a day with respect to their availability and stores many features (frontend and backend response time, required RAM and size of the web page, security certificates, analytic tools and trackers embedded in the webpage and others) in a data warehouse. Aviator is also equipped with an analysis functionality, for example authors can check and evaluate the availability of their own tools or those of their peers. Likewise, users can check the availability of a certain tool they intend to use in research or teaching to avoid including unstable tools. The curated section of Aviator offers additional services. We provide API snippets for common programming languages (Perl, PHP, Python, JavaScript) as well as an OpenAPI documentation for embedding in the backend of own web services for an automatic test of their function. We query the respective APIs twice a day and send automated notifications in case of an unexpected result. Naturally, the same analysis functionality as for the literature-based module is available for the curated section. Aviator can freely be used at https://www.ccb.uni-saarland.de/aviator.

@article{he03583,
    author = {Warnat-Herresthal, Stefanie and Schultze, Hartmut and Shastry, Krishnaprasad and Manamohan, Sathyanarayanan and Mukherjee, Saikat and Garg, Vishesh and Sarveswara, Ravi and Händler, Kristian and Pickkers, Peter and Aziz, N. Ahmad and Ktena, Sofia and Tran, Florian and Bitzer, Michael and Ossowski, Stephan and Casadei, Nicolas and Herr, Christian and Petersheim, Daniel and Behrends, Uta and Kern, Fabian and Fehlmann, Tobias and Schommers, Philipp and Lehmann, Clara and Augustin, Max and Rybniker, Jan and Altmüller, Janine and Mishra, Neha and Bernardes, Joana P. and Krämer, Benjamin and Bonaguro, Lorenzo and Schulte-Schrepping, Jonas and Domenico, Elena De and Siever, Christian and Kraut, Michael and Desai, Milind and Monnet, Bruno and Saridaki, Maria and Siegel, Charles Martin and Drews, Anna and Nuesch-Germano, Melanie and Theis, Heidi and Heyckendorf, Jan and Schreiber, Stefan and Kim-Hellmuth, Sarah and COVID-19 Aachen Study (COVAS)and Nattermann, Jacob and Skowasch, Dirk and Kurth, Ingo and Keller, Andreas and Bals, Robert and Nürnberg, Peter and Rieß, Olaf and Rosenstiel, Philip and Netea, Mihai G. and Theis, Fabian and Mukherjee, Sach and Backes, Michael and Aschenbrenner, Anna C. and Ulas, Thomas and , Deutsche COVID-19 Omics Initiative (DeCOI)and Breteler, Monique M. B. and Giamarellos-Bourboulis, Evangelos J. and Kox, Matthijs and Becker, Matthias and Cheran, Sorin and Woodacre, Michael S. and Goh, Eng Lim and Schultze, Joachim},
    year = {2021},
    month = {05},
	pages = {},
    abstract = {Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine 1,2 . Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation 4,5 . Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning—a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine.},
    title = {Swarm Learning for decentralized and confidential clinical machine learning},
    journal = {Nature},
    doi = {10.1038/s41586-021-03583-3},
	URL = {https://www.nature.com/articles/s41586-021-03583-3}
}

Fast and reliable detection of patients with severe and heterogeneous illnesses is a major goal of precision medicine 1,2 . Patients with leukaemia can be identified using machine learning on the basis of their blood transcriptomes. However, there is an increasing divide between what is technically possible and what is allowed, because of privacy legislation 4,5 . Here, to facilitate the integration of any medical data from any data owner worldwide without violating privacy laws, we introduce Swarm Learning—a decentralized machine-learning approach that unites edge computing, blockchain-based peer-to-peer networking and coordination while maintaining confidentiality without the need for a central coordinator, thereby going beyond federated learning. To illustrate the feasibility of using Swarm Learning to develop disease classifiers using distributed data, we chose four use cases of heterogeneous diseases (COVID-19, tuberculosis, leukaemia and lung pathologies). With more than 16,400 blood transcriptomes derived from 127 clinical studies with non-uniform distributions of cases and controls and substantial study biases, as well as more than 95,000 chest X-ray images, we show that Swarm Learning classifiers outperform those developed at individual sites. In addition, Swarm Learning completely fulfils local confidentiality regulations by design. We believe that this approach will notably accelerate the introduction of precision medicine.

@article{gkab297,
    author = {Kern, Fabian and Aparicio-Puerta, Ernesto and Li, Yongping and Fehlmann, Tobias and Kehl, Tim and Wagner, Viktoria and Ray, Kamalika and Ludwig, Nicole and Lenhof, Hans-Peter and Meese, Eckart and Keller, Andreas},
    year = {2021},
    month = {05},
	pages = {},
    abstract = {Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.},
    title = {miRTargetLink 2.0—interactive miRNA target gene and target pathway networks},
    journal = {Nucleic Acids Research},
    doi = {10.1093/nar/gkab297},
	URL = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab297/6261786}
}

Which genes, gene sets or pathways are regulated by certain miRNAs? Which miRNAs regulate a particular target gene or target pathway in a certain physiological context? Answering such common research questions can be time consuming and labor intensive. Especially for researchers without computational experience, the integration of different data sources, selection of the right parameters and concise visualization can be demanding. A comprehensive analysis should be central to present adequate answers to complex biological questions. With miRTargetLink 2.0, we develop an all-in-one solution for human, mouse and rat miRNA networks. Users input in the unidirectional search mode either a single gene, gene set or gene pathway, alternatively a single miRNA, a set of miRNAs or an miRNA pathway. Moreover, genes and miRNAs can jointly be provided to the tool in the bidirectional search mode. For the selected entities, interaction graphs are generated from different data sources and dynamically presented. Connected application programming interfaces (APIs) to the tailored enrichment tools miEAA and GeneTrail facilitate downstream analysis of pathways and context-annotated categories of network nodes. MiRTargetLink 2.0 is freely accessible at https://www.ccb.uni-saarland.de/mirtargetlink2.

@article{gkab268,
    author = {Fehlmann, Tobias and Kern, Fabian and Laham, Omar and Backes, Christina and Solomon, Jeffrey and Hirsch, Pascal and Volz, Carsten and Müller, Rolf and Keller, Andreas},
    year = {2021},
    month = {04},
	pages = {},
    abstract = {Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.},
    title = {miRMaster 2.0: multi-species non-coding RNA sequencing analyses at scale},
    journal = {Nucleic acids research},
    doi = {10.1093/nar/gkab268},
	URL = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkab268/6238409}
}

Analyzing all features of small non-coding RNA sequencing data can be demanding and challenging. To facilitate this process, we developed miRMaster. After the analysis of over 125 000 human samples and 1.5 trillion human small RNA reads over 4 years, we present miRMaster 2 with a wide range of updates and new features. We extended our reference data sets so that miRMaster 2 now supports the analysis of eight species (e.g. human, mouse, chicken, dog, cow) and 10 non-coding RNA classes (e.g. microRNAs, piRNAs, tRNAs, rRNAs, circRNAs). We also incorporated new downstream analysis modules such as batch effect analysis or sample embeddings using UMAP, and updated annotation data bases included by default (miRBase, Ensembl, GtRNAdb). To accommodate the increasing popularity of single cell small-RNA sequencing data, we incorporated a module for unique molecular identifier (UMI) processing. Further, the output tables and graphics have been improved based on user feedback and new output formats that emerged in the community are now supported (e.g. miRGFF3). Finally, we integrated differential expression analysis with the miRNA enrichment analysis tool miEAA. miRMaster is freely available at https://www.ccb.uni-saarland.de/mirmaster2.

@article{andr13004,
    author = {Abu-Halima, Masood and Belkacemi, Anouar and Ayesh, Basim and Becker, Lea and Sindiani, Amer and Fischer, Ulrike and Hammadeh, Mohamad Eid and Keller, Andreas and Meese, Eckart},
    year = {2021},
    month = {03},
	pages = {},
    abstract = {Background Male infertility is a multifactorial syndrome with diverse phenotypic representations. MicroRNAs (miRNAs) are small, non‐coding RNAs that are involved in the post‐transcriptional regulation of gene expression. Altered abundance levels of ODF2 and UBQLN3 have been reported in patients with different spermatogenic impairments. However, the transcriptional regulation of these two genes by miR‐23a/b‐3p is still unclear. Objectives To investigate experimentally whether miR‐23a/b‐3p targets the genes ODF2 and UBQLN3 and whether this targeting impacts abundance levels of ODF2 and UBQLN3 in patients with oligoasthenozoospermia. Materials and methods A total of 92 men attending a fertility clinic were included in the study, including 46 oligoasthenozoospermic men and 46 age‐matched normozoospermic volunteers who served as controls. Reverse transcription‐quantitative PCR (RT‐qPCR), Western blot, and dual‐luciferase (Firefly‐Renilla) assays were used to validate the miRNAs and their target genes. Results RT‐qPCR revealed that miR‐23a/b‐3p was more abundant and ODF2 and UBQLN3 targets were less abundant in men with impaired spermatogenesis. Besides, Western blot shows that ODF2 and UBQLN3 protein levels were reduced in men with impaired spermatogenesis. In silico prediction and dual‐luciferase assays revealed that potential links exist between the higher abundance level of miR‐23a/b‐3p and the lower abundance level of ODF2 and UBQLN3 targets. Mutations in the miR‐23a/b‐3p‐binding site within the 3ˊUTRs (3ˊuntranslated regions) of ODF2 and UBQLN3 genes resulted in abrogated responsiveness to miR‐23a/b‐3p. Correlation analysis showed that sperm count, motility, and morphology were negatively correlated with miR‐23a/b‐3p and positively correlated with the lower abundance level of UBQLN3, while ODF lower abundance level was positively correlated with sperm motility. Conclusion Findings indicate that the higher abundance level of miR‐23a/b‐3p and the lower abundance level of ODF2 and UBQLN3 targets are associated with oligoasthenozoospermia and male subfertility.},
    title = {MicroRNA‐targeting in spermatogenesis: Over‐expressions of microRNA‐23a/b‐3p and its affected targeting of the genes ODF2 and UBQLN3 in spermatozoa of patients with oligoasthenozoospermia},
    journal = {Andrology},
    doi = {10.1111/andr.13004},
	URL = {https://onlinelibrary.wiley.com/doi/10.1111/andr.13004}
}

Background Male infertility is a multifactorial syndrome with diverse phenotypic representations. MicroRNAs (miRNAs) are small, non‐coding RNAs that are involved in the post‐transcriptional regulation of gene expression. Altered abundance levels of ODF2 and UBQLN3 have been reported in patients with different spermatogenic impairments. However, the transcriptional regulation of these two genes by miR‐23a/b‐3p is still unclear. Objectives To investigate experimentally whether miR‐23a/b‐3p targets the genes ODF2 and UBQLN3 and whether this targeting impacts abundance levels of ODF2 and UBQLN3 in patients with oligoasthenozoospermia. Materials and methods A total of 92 men attending a fertility clinic were included in the study, including 46 oligoasthenozoospermic men and 46 age‐matched normozoospermic volunteers who served as controls. Reverse transcription‐quantitative PCR (RT‐qPCR), Western blot, and dual‐luciferase (Firefly‐Renilla) assays were used to validate the miRNAs and their target genes. Results RT‐qPCR revealed that miR‐23a/b‐3p was more abundant and ODF2 and UBQLN3 targets were less abundant in men with impaired spermatogenesis. Besides, Western blot shows that ODF2 and UBQLN3 protein levels were reduced in men with impaired spermatogenesis. In silico prediction and dual‐luciferase assays revealed that potential links exist between the higher abundance level of miR‐23a/b‐3p and the lower abundance level of ODF2 and UBQLN3 targets. Mutations in the miR‐23a/b‐3p‐binding site within the 3ˊUTRs (3ˊuntranslated regions) of ODF2 and UBQLN3 genes resulted in abrogated responsiveness to miR‐23a/b‐3p. Correlation analysis showed that sperm count, motility, and morphology were negatively correlated with miR‐23a/b‐3p and positively correlated with the lower abundance level of UBQLN3, while ODF lower abundance level was positively correlated with sperm motility. Conclusion Findings indicate that the higher abundance level of miR‐23a/b‐3p and the lower abundance level of ODF2 and UBQLN3 targets are associated with oligoasthenozoospermia and male subfertility.

@article{kern2131,
	author = {Kern, Fabian and Fehlmann, Tobias and Violich, Ivo and Alsop, Eric and Hutchins, Elizabeth and Kahraman, Mustafa and Grammes, Nadja and Guimarães, Pedro and Backes, Christina and Poston, Kathleen and Casey, Bradford and Balling, Rudi and Geffers, Lars and Krüger, Rejko and Galasko, Douglas and Mollenhauer, Brit and Meese, Eckart and Wyss-Coray, Tony and Craig, David and Keuren-Jensen, Kendall Van  and Keller, Andreas},
	year = {2021},
	month = {03},
	pages = {309-322},
	title = {Deep sequencing of sncRNAs reveals hallmarks and regulatory modules of the transcriptome during Parkinson’s disease progression},
	abstract = {Noncoding RNAs have diagnostic and prognostic importance in Parkinson’s disease (PD). We studied circulating small noncoding RNAs (sncRNAs) in two large-scale longitudinal PD cohorts (Parkinson’s Progression Markers Initiative (PPMI) and Luxembourg Parkinson’s Study (NCER-PD)) and modeled their impact on the transcriptome. Sequencing of sncRNAs in 5,450 blood samples of 1,614 individuals in PPMI yielded 323 billion reads, most of which mapped to microRNAs but covered also other RNA classes such as piwi-interacting RNAs, ribosomal RNAs and small nucleolar RNAs. Dysregulated microRNAs associated with disease and disease progression occur in two distinct waves in the third and seventh decade of life. Originating predominantly from immune cells, they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. Profiling 1,553 samples from 1,024 individuals in the NCER-PD cohort validated biomarkers and main findings by an independent technology. Finally, network analysis of sncRNA and transcriptome sequencing from PPMI identified regulatory modules emerging in patients with progressing PD. The authors present a small noncoding RNA atlas characterizing two longitudinal Parkinson’s disease cohorts and reveal potential biomarkers for disease detection, their relation to molecular hallmarks of PD and regulatory disease-progression modules.},
	volume = {1},
	journal = {Nature Aging},
	doi = {10.1038/s43587-021-00042-6},
	URL = {https://www.nature.com/articles/s43587-021-00042-6}
}

Noncoding RNAs have diagnostic and prognostic importance in Parkinson’s disease (PD). We studied circulating small noncoding RNAs (sncRNAs) in two large-scale longitudinal PD cohorts (Parkinson’s Progression Markers Initiative (PPMI) and Luxembourg Parkinson’s Study (NCER-PD)) and modeled their impact on the transcriptome. Sequencing of sncRNAs in 5,450 blood samples of 1,614 individuals in PPMI yielded 323 billion reads, most of which mapped to microRNAs but covered also other RNA classes such as piwi-interacting RNAs, ribosomal RNAs and small nucleolar RNAs. Dysregulated microRNAs associated with disease and disease progression occur in two distinct waves in the third and seventh decade of life. Originating predominantly from immune cells, they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. Profiling 1,553 samples from 1,024 individuals in the NCER-PD cohort validated biomarkers and main findings by an independent technology. Finally, network analysis of sncRNA and transcriptome sequencing from PPMI identified regulatory modules emerging in patients with progressing PD. The authors present a small noncoding RNA atlas characterizing two longitudinal Parkinson’s disease cohorts and reveal potential biomarkers for disease detection, their relation to molecular hallmarks of PD and regulatory disease-progression modules.

@article{haas211,
    author = {Haas, Jan and Frese, Karen and Sedaghat-Hamedani, Farbod and Kayvanpour, Elham and Tappu, Rewati and Nietsch, Rouven and Tugrul, Oguz and Wisdom, Michael and Dietrich, Carsten and Amr, Ali and Weis, Tanja and Niederdränk, Torsten and Murphy, Michael and Krieg, Thomas and Dörr, Marcus and Völker, Uwe and Fielitz, Jens and Frey, Norbert and Felix, Stephan B. and Keller, Andreas and Katus, Hugo A. and Meder, Benjamin},
    year = {2021},
    month = {02},
    pages = {1999},
    title = {Energy Metabolites as Biomarkers in Ischemic and Dilated Cardiomyopathy},
    volume = {22},
    journal = {International Journal of Molecular Sciences},
    doi = {10.3390/ijms22041999},
	abstract = {With more than 25 million people affected, heart failure (HF) is a global threat. As energy production pathways are known to play a pivotal role in HF, we sought here to identify key metabolic changes in ischemic- and non-ischemic HF by using a multi-OMICS approach. Serum metabolites and mRNAseq and epigenetic DNA methylation profiles were analyzed from blood and left ventricular heart biopsy specimens of the same individuals. In total we collected serum from n = 82 patients with Dilated Cardiomyopathy (DCM) and n = 51 controls in the screening stage. We identified several metabolites involved in glycolysis and citric acid cycle to be elevated up to 5.7-fold in DCM (p = 1.7 × 10−6). Interestingly, cardiac mRNA and epigenetic changes of genes encoding rate-limiting enzymes of these pathways could also be found and validated in our second stage of metabolite assessment in n = 52 DCM, n = 39 ischemic HF and n = 57 controls. In conclusion, we identified a new set of metabolomic biomarkers for HF. We were able to identify underlying biological cascades that potentially represent suitable intervention targets.},
	URL = {https://www.mdpi.com/1422-0067/22/4/1999},
}

With more than 25 million people affected, heart failure (HF) is a global threat. As energy production pathways are known to play a pivotal role in HF, we sought here to identify key metabolic changes in ischemic- and non-ischemic HF by using a multi-OMICS approach. Serum metabolites and mRNAseq and epigenetic DNA methylation profiles were analyzed from blood and left ventricular heart biopsy specimens of the same individuals. In total we collected serum from n = 82 patients with Dilated Cardiomyopathy (DCM) and n = 51 controls in the screening stage. We identified several metabolites involved in glycolysis and citric acid cycle to be elevated up to 5.7-fold in DCM (p = 1.7 × 10−6). Interestingly, cardiac mRNA and epigenetic changes of genes encoding rate-limiting enzymes of these pathways could also be found and validated in our second stage of metabolite assessment in n = 52 DCM, n = 39 ischemic HF and n = 57 controls. In conclusion, we identified a new set of metabolomic biomarkers for HF. We were able to identify underlying biological cascades that potentially represent suitable intervention targets.

@article {mah211,
	author = {Abu-Halima, Masood and Meese, Eckart and Saleh, Mohamad and Keller, Andreas and Abdul-Khaliq, Hashim and Raedle-Hurst, Tanja},
	year = {2021},
	month = {01},
	pages = {619083},
	title = {MicroRNA-29b/c-3p Indicate Advanced Liver Fibrosis/Cirrhosis in Univentricular Heart Patients With and Without Fontan Palliation},
	volume = {7},
	journal = {Frontiers in Cardiovascular Medicine},
	doi = {10.3389/fcvm.2020.619083},
	abstract = {Aim: The present study aims to identify those microRNAs (miRNAs) in patients with univentricular heart (UVH) disease with and without Fontan palliation that may be associated with advanced liver fibrosis/cirrhosis. Materials and Methods: SurePrint™ 8 × 60K Human v21 miRNA arrays were used to determine the miRNA abundance profiles in the blood of 48 UVH patients with and without Fontan palliation and 32 matched healthy controls. The abundance levels of selected miRNAs have been validated by quantitative reverse transcription-polymerase chain reaction (RT-qPCR). Results: According to microarray analysis, 50 miRNAs were found to be significantly abundant in UVH patients of which miR-29b-3p and miR-29c-3p were significantly related to the model of end-stage liver disease (MELD)-Albumin and albumin-bilirubin (ALBI) score representing advanced liver fibrosis/cirrhosis. Relative expression levels of both miRNAs were significantly higher in patients with a higher collapsibility index representing venous hepatic congestion, a higher MELD-Albumin or ALBI score and incomplete or no Fontan palliation. In the logistic regression analysis, a MELD-Albumin score ≥ 11 or ALBI score > −2.6 were best predicted by total bilirubin (OR 6.630, P = 0.016), albumin (OR 0.424, P = 0.026), and miR-29c-3p (OR 33.060, P = 0.047). After adjustment to the status of Fontan palliation, however, no statistical significance of these parameters was found thus underlining the importance of palliation status on progression of liver fibrosis/ cirrhosis in UVH patients. Conclusions: In UVH patients with and without Fontan palliation, miR-29b-3p and miR-29c-3p seem to be markers of advanced liver fibrosis/cirrhosis and thus may be used in the risk assessment of these patients.},
	URL = {https://www.frontiersin.org/articles/10.3389/fcvm.2020.619083/full},
}

Aim: The present study aims to identify those microRNAs (miRNAs) in patients with univentricular heart (UVH) disease with and without Fontan palliation that may be associated with advanced liver fibrosis/cirrhosis. Materials and Methods: SurePrint™ 8 × 60K Human v21 miRNA arrays were used to determine the miRNA abundance profiles in the blood of 48 UVH patients with and without Fontan palliation and 32 matched healthy controls. The abundance levels of selected miRNAs have been validated by quantitative reverse transcription-polymerase chain reaction (RT-qPCR). Results: According to microarray analysis, 50 miRNAs were found to be significantly abundant in UVH patients of which miR-29b-3p and miR-29c-3p were significantly related to the model of end-stage liver disease (MELD)-Albumin and albumin-bilirubin (ALBI) score representing advanced liver fibrosis/cirrhosis. Relative expression levels of both miRNAs were significantly higher in patients with a higher collapsibility index representing venous hepatic congestion, a higher MELD-Albumin or ALBI score and incomplete or no Fontan palliation. In the logistic regression analysis, a MELD-Albumin score ≥ 11 or ALBI score > −2.6 were best predicted by total bilirubin (OR 6.630, P = 0.016), albumin (OR 0.424, P = 0.026), and miR-29c-3p (OR 33.060, P = 0.047). After adjustment to the status of Fontan palliation, however, no statistical significance of these parameters was found thus underlining the importance of palliation status on progression of liver fibrosis/ cirrhosis in UVH patients. Conclusions: In UVH patients with and without Fontan palliation, miR-29b-3p and miR-29c-3p seem to be markers of advanced liver fibrosis/cirrhosis and thus may be used in the risk assessment of these patients.

@article{10.1093/bib/bbaa346,
    author = {Schmartz, Georges Pierre and Kern, Fabian and Fehlmann, Tobias and Wagner, Viktoria and Fromm, Bastian and Keller, Andreas},
    title = {Encyclopedia of tools for the analysis of miRNA isoforms},
    journal = {Briefings in Bioinformatics},
    year = {2020},
    month = {12},
    abstract = {RNA sequencing data sets rapidly increase in quantity. For microRNAs (miRNAs), frequently dozens to hundreds of billion reads are generated per study. The quantification of annotated miRNAs and the prediction of new miRNAs are leading computational tasks. Now, the increased depth of coverage allows to gain deeper insights into the variability of miRNAs. The analysis of isoforms of miRNAs (isomiRs) is a trending topic, and a range of computational tools for the analysis of isomiRs has been developed. We provide an overview on 27 available computational solutions for the analysis of isomiRs. These include both stand-alone programs (17 tools) and web-based solutions (10 tools) and span a publication time range from 2010 to 2020. Seven of the tools were published in 2019 and 2020, confirming the rising importance of the topic. While most of the analyzed tools work for a broad range of organisms or are completely independent of a reference organism, several tools have been tailored for the analysis of human miRNA data or for plants. While 14 of the tools are general analysis tools of miRNAs, and isomiR analysis is one of their features, the remaining 13 tools have specifically been developed for isomiR analysis. A direct comparison on 20 deep sequencing data sets for selected tools provides insights into the heterogeneity of results. With our work, we provide users a comprehensive overview on the landscape of isomiR analysis tools and in that support the selection of the most appropriate tool for their respective research task.},
    issn = {1477-4054},
    doi = {10.1093/bib/bbaa346},
    url = {https://doi.org/10.1093/bib/bbaa346},
}

RNA sequencing data sets rapidly increase in quantity. For microRNAs (miRNAs), frequently dozens to hundreds of billion reads are generated per study. The quantification of annotated miRNAs and the prediction of new miRNAs are leading computational tasks. Now, the increased depth of coverage allows to gain deeper insights into the variability of miRNAs. The analysis of isoforms of miRNAs (isomiRs) is a trending topic, and a range of computational tools for the analysis of isomiRs has been developed. We provide an overview on 27 available computational solutions for the analysis of isomiRs. These include both stand-alone programs (17 tools) and web-based solutions (10 tools) and span a publication time range from 2010 to 2020. Seven of the tools were published in 2019 and 2020, confirming the rising importance of the topic. While most of the analyzed tools work for a broad range of organisms or are completely independent of a reference organism, several tools have been tailored for the analysis of human miRNA data or for plants. While 14 of the tools are general analysis tools of miRNAs, and isomiR analysis is one of their features, the remaining 13 tools have specifically been developed for isomiR analysis. A direct comparison on 20 deep sequencing data sets for selected tools provides insights into the heterogeneity of results. With our work, we provide users a comprehensive overview on the landscape of isomiR analysis tools and in that support the selection of the most appropriate tool for their respective research task.

@article{article2020x,
    author = {Henn, Dominic and Abu-Halima, Masood and Kahraman, Mustafa and Falkner, Florian and Fischer, Katharina and Barrera, Janos and Chen, Kellen and Gurtner, Geoffrey and Keller, Andreas and Kneser, Ulrich and Meese, Eckart and Schmidt, Volker},
    year = {2020},
    month = {12},
    abstract = {Arteriovenous (AV) fistulas for hemodialysis can lead to cardiac volume loading and increased serum brain natriuretic peptide (BNP) levels. Whether short-term AV loop placement in patients undergoing microsurgery has an impact on cardiac biomarkers and circulating microRNAs (miRNAs), potentially indicating an increased hemodynamic risk, remains elusive. Fifteen patients underwent AV loop placement with delayed free flap anastomosis for microsurgical reconstructions of lower extremity soft-tissue defects. N-terminal pro-BNP (NT-proBNP), copeptin (CT-proAVP), and miRNA expression profiles were determined in the peripheral blood before and after AV loop placement. MiRNA expression in the blood was correlated with miRNA expression from AV loop vascular tissue. Serum NT-proBNP and copeptin levels exceeded the upper reference limit after AV loop placement, with an especially strong NT-proBNP increase in patients with preexistent cardiac diseases. A miRNA signature of 4 up-regulated (miR-3198, miR-3127-5p, miR-1305, miR-1288-3p) and 2 down-regulated miRNAs (miR30a-5p, miR-145-5p) which are related to cardiovascular physiology, showed a significant systemic deregulation in blood and venous tissue after AV loop placement. AV loop placement causes serum elevations of NT-proBNP, copeptin as well as specific circulating miRNAs, indicating a potentially increased hemodynamic risk for patients with cardiovascular comorbidities, if free flap anastomosis is delayed.},
    title = {A multivariable miRNA signature delineates the systemic hemodynamic impact of arteriovenous shunt placement in a pilot study},
    volume = {10},
    journal = {Scientific Reports},
    doi = {10.1038/s41598-020-78905-y},
}

Arteriovenous (AV) fistulas for hemodialysis can lead to cardiac volume loading and increased serum brain natriuretic peptide (BNP) levels. Whether short-term AV loop placement in patients undergoing microsurgery has an impact on cardiac biomarkers and circulating microRNAs (miRNAs), potentially indicating an increased hemodynamic risk, remains elusive. Fifteen patients underwent AV loop placement with delayed free flap anastomosis for microsurgical reconstructions of lower extremity soft-tissue defects. N-terminal pro-BNP (NT-proBNP), copeptin (CT-proAVP), and miRNA expression profiles were determined in the peripheral blood before and after AV loop placement. MiRNA expression in the blood was correlated with miRNA expression from AV loop vascular tissue. Serum NT-proBNP and copeptin levels exceeded the upper reference limit after AV loop placement, with an especially strong NT-proBNP increase in patients with preexistent cardiac diseases. A miRNA signature of 4 up-regulated (miR-3198, miR-3127-5p, miR-1305, miR-1288-3p) and 2 down-regulated miRNAs (miR30a-5p, miR-145-5p) which are related to cardiovascular physiology, showed a significant systemic deregulation in blood and venous tissue after AV loop placement. AV loop placement causes serum elevations of NT-proBNP, copeptin as well as specific circulating miRNAs, indicating a potentially increased hemodynamic risk for patients with cardiovascular comorbidities, if free flap anastomosis is delayed.

@article{info:doi/10.2196/24514,
    author = {Grammes, Nadja and Millenaar, Dominic and Fehlmann, Tobias and Kern, Fabian and Böhm, Michael and Mahfoud, Felix and Keller, Andreas},
    title = "{Research Output and International Cooperation Among Countries During the COVID-19 Pandemic: Scientometric Analysis}",
    journal = {J Med Internet Res},
    year = {2020},
    month = {12},
    abstract = {Background: The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has instigated immediate and massive worldwide research efforts. Rapid publication of research data may be desirable but also carries the risk of quality loss. Objective: This analysis aimed to correlate the severity of the COVID-19 outbreak with its related scientific output per country. Methods: All articles related to the COVID-19 pandemic were retrieved from Web of Science and analyzed using the web application SciPE (science performance evaluation), allowing for large data scientometric analyses of the global geographical distribution of scientific output. Results: A total of 7185 publications, including 2592 articles, 2091 editorial materials, 2528 early access papers, 1479 letters, 633 reviews, and other contributions were extracted. The top 3 countries involved in COVID-19 research were the United States, China, and Italy. The confirmed COVID-19 cases or deaths per region correlated with scientific research output. The United States was most active in terms of collaborative efforts, sharing a significant amount of manuscript authorships with the United Kingdom, China, and Italy. The United States was China's most frequent collaborative partner, followed by the United Kingdom. Conclusions: The COVID-19 research landscape is rapidly developing and is driven by countries with a generally strong prepandemic research output but is also significantly affected by countries with a high prevalence of COVID-19 cases. Our findings indicate that the United States is leading international collaborative efforts.},
    issn = {1438-8871},
    doi = {10.2196/24514},
    url = {https://doi.org/10.2196/24514},
}

Background: The COVID-19 pandemic, caused by the novel coronavirus SARS-CoV-2, has instigated immediate and massive worldwide research efforts. Rapid publication of research data may be desirable but also carries the risk of quality loss. Objective: This analysis aimed to correlate the severity of the COVID-19 outbreak with its related scientific output per country. Methods: All articles related to the COVID-19 pandemic were retrieved from Web of Science and analyzed using the web application SciPE (science performance evaluation), allowing for large data scientometric analyses of the global geographical distribution of scientific output. Results: A total of 7185 publications, including 2592 articles, 2091 editorial materials, 2528 early access papers, 1479 letters, 633 reviews, and other contributions were extracted. The top 3 countries involved in COVID-19 research were the United States, China, and Italy. The confirmed COVID-19 cases or deaths per region correlated with scientific research output. The United States was most active in terms of collaborative efforts, sharing a significant amount of manuscript authorships with the United Kingdom, China, and Italy. The United States was China's most frequent collaborative partner, followed by the United Kingdom. Conclusions: The COVID-19 research landscape is rapidly developing and is driven by countries with a generally strong prepandemic research output but is also significantly affected by countries with a high prevalence of COVID-19 cases. Our findings indicate that the United States is leading international collaborative efforts.

@article{10.1093/nar/gkaa1161,
    author = {Kern, Fabian and Krammes, Lena and Danz, Karin and Diener, Caroline and Kehl, Tim and Küchler, Oliver and Fehlmann, Tobias and Kahraman, Mustafa and Rheinheimer, Stefanie and Aparicio-Puerta, Ernesto and Wagner, Sylvia and Ludwig, Nicole and Backes, Christina and Lenhof, Hans-Peter and von Briesen, Hagen and Hart, Martin and Keller, Andreas and Meese, Eckart},
    title = "{Validation of human microRNA target pathways enables evaluation of target prediction tools}",
    journal = {Nucleic Acids Research},
    year = {2020},
    month = {12},
    abstract = "{MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9\\% of the target genes for miR-34a-5p and 46.7\\% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkaa1161},
    url = {https://doi.org/10.1093/nar/gkaa1161},
}

MicroRNAs are regulators of gene expression. A wide-spread, yet not validated, assumption is that the targetome of miRNAs is non-randomly distributed across the transcriptome and that targets share functional pathways. We developed a computational and experimental strategy termed high-throughput miRNA interaction reporter assay (HiTmIR) to facilitate the validation of target pathways. First, targets and target pathways are predicted and prioritized by computational means to increase the specificity and positive predictive value. Second, the novel webtool miRTaH facilitates guided designs of reporter assay constructs at scale. Third, automated and standardized reporter assays are performed. We evaluated HiTmIR using miR-34a-5p, for which TNF- and TGFB-signaling, and Parkinson's Disease (PD)-related categories were identified and repeated the pipeline for miR-7-5p. HiTmIR validated 58.9\% of the target genes for miR-34a-5p and 46.7\% for miR-7-5p. We confirmed the targeting by measuring the endogenous protein levels of targets in a neuronal cell model. The standardized positive and negative targets are collected in the new miRATBase database, representing a resource for training, or benchmarking new target predictors. Applied to 88 target predictors with different confidence scores, TargetScan 7.2 and miRanda outperformed other tools. Our experiments demonstrate the efficiency of HiTmIR and provide evidence for an orchestrated miRNA-gene targeting.

@article{10.1093/nar/gkaa1122,
    author = {Li, Yongping and Fehlmann, Tobias and Borcherding, Adam and Drmanac, Snezana and Liu, Sophie and Groeger, Laura and Xu, Chongjun and Callow, Matthew and Villarosa, Christian and Jorjorian, Alexander and Kern, Fabian and Grammes, Nadja and Meese, Eckart and Jiang, Hui and Drmanac, Radoje and Ludwig, Nicole and Keller, Andreas},
    title = "{CoolMPS: evaluation of antibody labeling based massively parallel non-coding RNA sequencing}",
    journal = {Nucleic Acids Research},
    year = {2020},
    month = {12},
    abstract = "{Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94\\%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2\\%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkaa1122},
    url = {https://doi.org/10.1093/nar/gkaa1122},
}

Results of massive parallel sequencing-by-synthesis vary depending on the sequencing approach. CoolMPS™ is a new sequencing chemistry that incorporates bases by labeled antibodies. To evaluate the performance, we sequenced 240 human non-coding RNA samples (dementia patients and controls) with and without CoolMPS. The Q30 value as indicator of the per base sequencing quality increased from 91.8 to 94\%. The higher quality was reached across the whole read length. Likewise, the percentage of reads mapping to the human genome increased from 84.9 to 86.2\%. For both technologies, we computed similar distributions between different RNA classes (miRNA, piRNA, tRNA, snoRNA and yRNA) and within the classes. While standard sequencing-by-synthesis allowed to recover more annotated miRNAs, CoolMPS yielded more novel miRNAs. The correlation between the two methods was 0.97. Evaluating the diagnostic performance, we observed lower minimal P-values for CoolMPS (adjusted P-value of 0.0006 versus 0.0004) and larger effect sizes (Cohen's d of 0.878 versus 0.9). Validating 19 miRNAs resulted in a correlation of 0.852 between CoolMPS and reverse transcriptase-quantitative polymerase chain reaction. Comparison to data generated with Illumina technology confirmed a known shift in the overall RNA composition. With CoolMPS we evaluated a novel sequencing-by-synthesis technology showing high performance for the analysis of non-coding RNAs.

@article{10.1093/nar/gkaa1125,
    author = {Kern, Fabian and Fehlmann, Tobias and Keller, Andreas},
    title = "{On the lifetime of bioinformatics web services}",
    journal = {Nucleic Acids Research},
    volume = {48},
    number = {22},
    pages = {12523-12533},
    year = {2020},
    month = {12},
    abstract = "{Web services are used through all disciplines in life sciences and the online landscape is growing by hundreds of novel servers annually. However, availability varies, and maintenance practices are largely inconsistent. We screened the availability of 2396 web tools published during the past 10 years. All servers were accessed over 133 days and 318 668 index files were stored in a local database. The number of accessible tools almost linearly increases in time with highest availability for 2019 and 2020 (∼90\\%) and lowest for tools published in 2010 (∼50\\%). In a 133-day test frame, 31\\% of tools were always working, 48.4\\% occasionally and 20.6\\% never. Consecutive downtimes were typically below 5 days with a median of 1 day, and unevenly distributed over the weekdays. A rescue experiment on 47 tools that were published from 2019 onwards but never accessible showed that 51.1\\% of the tools could be restored in due time. We found a positive association between the number of citations and the probability of a web server being reachable. We then determined common challenges and formulated categorical recommendations for researchers planning to develop web-based resources. As implication of our study, we propose to develop a repository for automatic API testing and sustainability indexing.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkaa1125},
    url = {https://doi.org/10.1093/nar/gkaa1125},
}

Web services are used through all disciplines in life sciences and the online landscape is growing by hundreds of novel servers annually. However, availability varies, and maintenance practices are largely inconsistent. We screened the availability of 2396 web tools published during the past 10 years. All servers were accessed over 133 days and 318 668 index files were stored in a local database. The number of accessible tools almost linearly increases in time with highest availability for 2019 and 2020 (∼90\%) and lowest for tools published in 2010 (∼50\%). In a 133-day test frame, 31\% of tools were always working, 48.4\% occasionally and 20.6\% never. Consecutive downtimes were typically below 5 days with a median of 1 day, and unevenly distributed over the weekdays. A rescue experiment on 47 tools that were published from 2019 onwards but never accessible showed that 51.1\% of the tools could be restored in due time. We found a positive association between the number of citations and the probability of a web server being reachable. We then determined common challenges and formulated categorical recommendations for researchers planning to develop web-based resources. As implication of our study, we propose to develop a repository for automatic API testing and sustainability indexing.

@article{10.1093/nar/gkaa1127,
    author = {Hahn, Oliver and Fehlmann, Tobias and Zhang, Hui and Munson, Christy N and Vest, Ryan T and Borcherding, Adam and Liu, Sophie and Villarosa, Christian and Drmanac, Snezana and Drmanac, Rade and Keller, Andreas and Wyss-Coray, Tony},
    title = "{CoolMPS for robust sequencing of single-nuclear RNAs captured by droplet-based method}",
    journal = {Nucleic Acids Research},
    year = {2020},
    month = {12},
    abstract = "{Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.}",
    issn = {0305-1048},
    doi = {10.1093/nar/gkaa1127},
    url = {https://doi.org/10.1093/nar/gkaa1127},
}

Massively-parallel single-cell and single-nucleus RNA sequencing (scRNA-seq, snRNA-seq) requires extensive sequencing to achieve proper per-cell coverage, making sequencing resources and availability of sequencers critical factors for conducting deep transcriptional profiling. CoolMPS is a novel sequencing-by-synthesis approach that relies on nucleotide labeling by re-usable antibodies, but whether it is applicable to snRNA-seq has not been tested. Here, we use a low-cost and off-the-shelf protocol to chemically convert libraries generated with the widely-used Chromium 10X technology to be sequenceable with CoolMPS technology. To assess the quality and performance of converted libraries sequenced with CoolMPS, we generated a snRNA-seq dataset from the hippocampus of young and old mice. Native libraries were sequenced on an Illumina Novaseq and libraries that were converted to be compatible with CoolMPS were sequenced on a DNBSEQ-400RS. CoolMPS-derived data faithfully replicated key characteristics of the native library dataset, including correct estimation of ambient RNA-contamination, detection of captured cells, cell clustering results, spatial marker gene expression, inter- and intra-replicate differences and gene expression changes during aging. In conclusion, our results show that CoolMPS provides a viable alternative to standard sequencing of RNA from droplet-based libraries.

@article{SolomonKernFehlmannMeeseKeller_2020, 
    title={HumiR: Web Services, Tools and Databases for Exploring Human microRNA Data}, 
    author={Solomon, Jeffrey and Kern, Fabian and Fehlmann, Tobias and Meese, Eckart and Keller, Andreas}, 
    issn={2218-273X}, 
    series={11}, 
    volume={10}, 
    publisher={MDPI}, 
    journal={Biomolecules}, 
    year={2020},
    month = {12},
    doi={10.22028/D291-32734}, 
    abstract = "{For many research aspects on small non-coding RNAs, especially microRNAs, computational tools and databases are developed. This includes quantification of miRNAs, piRNAs, tRNAs and tRNA fragments, circRNAs and others. Furthermore, the prediction of new miRNAs, isomiRs, arm switch events, target and target pathway prediction and miRNA pathway enrichment are common tasks. Additionally, databases and resources containing expression profiles, e.g., from different tissues, organs or cell types, are generated. This information in turn leads to improved miRNA repositories. While most of the respective tools are implemented in a species-independent manner, we focused on tools for human small non-coding RNAs. This includes four aspects: (1) miRNA analysis tools (2) databases on miRNAs and variations thereof (3) databases on expression profiles (4) miRNA helper tools facilitating frequent tasks such as naming conversion or reporter assay design. Although dependencies between the tools exist and several tools are jointly used in studies, the interoperability is limited. We present HumiR, a joint web presence for our tools. HumiR facilitates an entry in the world of miRNA research, supports the selection of the right tool for a research task and represents the very first step towards a fully integrated knowledge-base for human small non-coding RNA research. We demonstrate the utility of HumiR by performing a very comprehensive analysis of Alzheimer’s miRNAs.}",
}

For many research aspects on small non-coding RNAs, especially microRNAs, computational tools and databases are developed. This includes quantification of miRNAs, piRNAs, tRNAs and tRNA fragments, circRNAs and others. Furthermore, the prediction of new miRNAs, isomiRs, arm switch events, target and target pathway prediction and miRNA pathway enrichment are common tasks. Additionally, databases and resources containing expression profiles, e.g., from different tissues, organs or cell types, are generated. This information in turn leads to improved miRNA repositories. While most of the respective tools are implemented in a species-independent manner, we focused on tools for human small non-coding RNAs. This includes four aspects: (1) miRNA analysis tools (2) databases on miRNAs and variations thereof (3) databases on expression profiles (4) miRNA helper tools facilitating frequent tasks such as naming conversion or reporter assay design. Although dependencies between the tools exist and several tools are jointly used in studies, the interoperability is limited. We present HumiR, a joint web presence for our tools. HumiR facilitates an entry in the world of miRNA research, supports the selection of the right tool for a research task and represents the very first step towards a fully integrated knowledge-base for human small non-coding RNA research. We demonstrate the utility of HumiR by performing a very comprehensive analysis of Alzheimer’s miRNAs.

@article{article2020y,
    author = {Fehlmann, Tobias and Lehallier, Benoit and Schaum, Nicholas and Hahn, Oliver and Kahraman, Mustafa and Li, Yongping and Grammes, Nadja and Geffers, Lars and Backes, Christina and Balling, Rudi and Kern, Fabian and Krüger, Rejko and Lammert, Frank and Ludwig, Nicole and Meder, Benjamin and Fromm, Bastian and Maetzler, Walter and Berg, Daniela and Brockmann, Kathrin and Deuschle, Christian and von Thaler, Anna-Katharina and Eschweiler, Gerhard W. and Milman, Sofiya and Barziliai, Nir and Reichert, Matthias and Wyss-Coray, Tony and Meese, Eckart and Keller, Andreas},
    year = {2020},
    month = {11},
    abstract = "{Aging is a key risk factor for chronic diseases of the elderly. MicroRNAs regulate post-transcriptional gene silencing through base-pair binding on their target mRNAs. We identified nonlinear changes in age-related microRNAs by analyzing whole blood from 1334 healthy individuals. We observed a larger influence of the age as compared to the sex and provide evidence for a shift to the 5’ mature form of miRNAs in healthy aging. The addition of 3059 diseased patients uncovered pan-disease and disease-specific alterations in aging profiles. Disease biomarker sets for all diseases were different between young and old patients. Computational deconvolution of whole-blood miRNAs into blood cell types suggests that cell intrinsic gene expression changes may impart greater significance than cell abundance changes to the whole blood miRNA profile. Altogether, these data provide a foundation for understanding the relationship between healthy aging and disease, and for the development of age-specific disease biomarkers.}",
    title = {Common diseases alter the physiological age-related blood microRNA profile},
    volume = {11},
    journal = {Nature Communications},
    doi = {10.1038/s41467-020-19665-1}
}

Aging is a key risk factor for chronic diseases of the elderly. MicroRNAs regulate post-transcriptional gene silencing through base-pair binding on their target mRNAs. We identified nonlinear changes in age-related microRNAs by analyzing whole blood from 1334 healthy individuals. We observed a larger influence of the age as compared to the sex and provide evidence for a shift to the 5’ mature form of miRNAs in healthy aging. The addition of 3059 diseased patients uncovered pan-disease and disease-specific alterations in aging profiles. Disease biomarker sets for all diseases were different between young and old patients. Computational deconvolution of whole-blood miRNAs into blood cell types suggests that cell intrinsic gene expression changes may impart greater significance than cell abundance changes to the whole blood miRNA profile. Altogether, these data provide a foundation for understanding the relationship between healthy aging and disease, and for the development of age-specific disease biomarkers.

@article {Harte001617,
	author = {Hart, Martin and Nickl, Laura and Walch-Rueckheim, Barbara and Krammes, Lena and Rheinheimer, Stefanie and Diener, Caroline and Taenzer, Tanja and Kehl, Tim and Sester, Martina and Lenhof, Hans-Peter and Keller, Andreas and Meese, Eckart},
	title = {Wrinkle in the plan: miR-34a-5p impacts chemokine signaling by modulating CXCL10/CXCL11/CXCR3-axis in CD4+, CD8+ T cells, and M1 macrophages},
	volume = {8},
	number = {2},
	year = {2020},
    month = {11},
	doi = {10.1136/jitc-2020-001617},
	publisher = {BMJ Specialist Journals},
	abstract = {Background In 2016 the first-in-human phase I study of a miRNA-based cancer therapy with a liposomal mimic of microRNA-34a-5p (miR-34a-5p) was closed due to five immune related serious adverse events (SAEs) resulting in four patient deaths. For future applications of miRNA mimics in cancer therapy it is mandatory to unravel the miRNA effects both on the tumor tissue and on immune cells. Here, we set out to analyze the impact of miR-34a-5p over-expression on the CXCL10/CXCL11/CXCR3 axis, which is central for the development of an effective cancer control.Methods We performed a whole genome expression analysis of miR-34a-5p transfected M1 macrophages followed by an over-representation and a protein{\textendash}protein network analysis. In-silico miRNA target prediction and dual luciferase assays were used for target identification and verification. Target genes involved in chemokine signaling were functionally analyzed in M1 macrophages, CD4+ and CD8+ T cells.Results A whole genome expression analysis of M1 macrophages with induced miR-34a-5p over-expression revealed an interaction network of downregulated target mRNAs including CXCL10 and CXCL11. In-silico target prediction in combination with dual luciferase assays identified direct binding of miR-34a-5p to the 3'UTRs of CXCL10 and CXCL11. Decreased CXCL10 and CXCL11 secretion was shown on the endogenous protein level and in the supernatant of miR-34a-5p transfected and activated M1 macrophages. To complete the analysis of the CXCL10/CXCL11/CXCR3 axis, we activated miR-34a-5p transfected CD4+ and CD8+ T cells by PMA/Ionomycin and found reduced levels of endogenous CXCR3 and CXCR3 on the cell surface.Conclusions MiR-34a-5p mimic administered by intravenous administration will likely not only be up-taken by the tumor cells but also by the immune cells. Our results indicate that miR-34a-5p over-expression leads in M1 macrophages to a reduced secretion of CXCL10 and CXCL11 chemokines and in CD4+ and CD8+ T cells to a reduced expression of CXCR3. As a result, less immune cells will be attracted to the tumor site. Furthermore, high levels of miR-34a-5p in naive CD4+ T cells can in turn hinder Th1 cell polarization through the downregulation of CXCR3 leading to a less pronounced activation of cytotoxic T lymphocytes, natural killer, and natural killer T cells and possibly contributing to lymphocytopenia.},
	URL = {https://jitc.bmj.com/content/8/2/e001617},
	journal = {Journal for ImmunoTherapy of Cancer},
}

Background In 2016 the first-in-human phase I study of a miRNA-based cancer therapy with a liposomal mimic of microRNA-34a-5p (miR-34a-5p) was closed due to five immune related serious adverse events (SAEs) resulting in four patient deaths. For future applications of miRNA mimics in cancer therapy it is mandatory to unravel the miRNA effects both on the tumor tissue and on immune cells. Here, we set out to analyze the impact of miR-34a-5p over-expression on the CXCL10/CXCL11/CXCR3 axis, which is central for the development of an effective cancer control.Methods We performed a whole genome expression analysis of miR-34a-5p transfected M1 macrophages followed by an over-representation and a protein–protein network analysis. In-silico miRNA target prediction and dual luciferase assays were used for target identification and verification. Target genes involved in chemokine signaling were functionally analyzed in M1 macrophages, CD4+ and CD8+ T cells.Results A whole genome expression analysis of M1 macrophages with induced miR-34a-5p over-expression revealed an interaction network of downregulated target mRNAs including CXCL10 and CXCL11. In-silico target prediction in combination with dual luciferase assays identified direct binding of miR-34a-5p to the 3'UTRs of CXCL10 and CXCL11. Decreased CXCL10 and CXCL11 secretion was shown on the endogenous protein level and in the supernatant of miR-34a-5p transfected and activated M1 macrophages. To complete the analysis of the CXCL10/CXCL11/CXCR3 axis, we activated miR-34a-5p transfected CD4+ and CD8+ T cells by PMA/Ionomycin and found reduced levels of endogenous CXCR3 and CXCR3 on the cell surface.Conclusions MiR-34a-5p mimic administered by intravenous administration will likely not only be up-taken by the tumor cells but also by the immune cells. Our results indicate that miR-34a-5p over-expression leads in M1 macrophages to a reduced secretion of CXCL10 and CXCL11 chemokines and in CD4+ and CD8+ T cells to a reduced expression of CXCR3. As a result, less immune cells will be attracted to the tumor site. Furthermore, high levels of miR-34a-5p in naive CD4+ T cells can in turn hinder Th1 cell polarization through the downregulation of CXCR3 leading to a less pronounced activation of cytotoxic T lymphocytes, natural killer, and natural killer T cells and possibly contributing to lymphocytopenia.

@article{10.1093/nar/gkaa788,
    author = {Diener, Caroline and Hart, Martin and Kehl, Tim and Rheinheimer, Stefanie and Ludwig, Nicole and Krammes, Lena and Pawusch, Sarah and Lenhof, Kerstin and Tänzer, Tanja and Schub, David and Sester, Martina and Walch-Rückheim, Barbara and Keller, Andreas and Lenhof, Hans-Peter and Meese, Eckart},
    title = {Quantitative and time-resolved miRNA pattern of early human T cell activation},
    journal = {Nucleic Acids Research},
    volume = {48},
    number = {18},
    pages = {10164-10183},
    year = {2020},
    month = {09},
    abstract = {T cells are central to the immune response against various pathogens and cancer cells. Complex networks of transcriptional and post-transcriptional regulators, including microRNAs (miRNAs), coordinate the T cell activation process. Available miRNA datasets, however, do not sufficiently dissolve the dynamic changes of miRNA controlled networks upon T cell activation. Here, we established a quantitative and time-resolved expression pattern for the entire miRNome over a period of 24 h upon human T-cell activation. Based on our time-resolved datasets, we identified central miRNAs and specified common miRNA expression profiles. We found the most prominent quantitative expression changes for miR-155-5p with a range from initially 40 molecules/cell to 1600 molecules/cell upon T-cell activation. We established a comprehensive dynamic regulatory network of both the up- and downstream regulation of miR-155. Upstream, we highlight IRF4 and its complexes with SPI1 and BATF as central for the transcriptional regulation of miR-155. Downstream of miR-155-5p, we verified 17 of its target genes by the time-resolved data recorded after T cell activation. Our data provide comprehensive insights into the range of stimulus induced miRNA abundance changes and lay the ground to identify efficient points of intervention for modifying the T cell response.},
    issn = {0305-1048},
    doi = {10.1093/nar/gkaa788},
    URL = {https://academic.oup.com/nar/article-pdf/48/18/10164/33856637/gkaa788.pdf},
}

T cells are central to the immune response against various pathogens and cancer cells. Complex networks of transcriptional and post-transcriptional regulators, including microRNAs (miRNAs), coordinate the T cell activation process. Available miRNA datasets, however, do not sufficiently dissolve the dynamic changes of miRNA controlled networks upon T cell activation. Here, we established a quantitative and time-resolved expression pattern for the entire miRNome over a period of 24 h upon human T-cell activation. Based on our time-resolved datasets, we identified central miRNAs and specified common miRNA expression profiles. We found the most prominent quantitative expression changes for miR-155-5p with a range from initially 40 molecules/cell to 1600 molecules/cell upon T-cell activation. We established a comprehensive dynamic regulatory network of both the up- and downstream regulation of miR-155. Upstream, we highlight IRF4 and its complexes with SPI1 and BATF as central for the transcriptional regulation of miR-155. Downstream of miR-155-5p, we verified 17 of its target genes by the time-resolved data recorded after T cell activation. Our data provide comprehensive insights into the range of stimulus induced miRNA abundance changes and lay the ground to identify efficient points of intervention for modifying the T cell response.

@article {Isakova25634,
    author = {Isakova, Alina and Fehlmann, Tobias and Keller, Andreas and Quake, Stephen R.},
    title = {A mouse tissue atlas of small noncoding RNA},
    volume = {117},
    number = {41},
    pages = {25634--25645},
    year = {2020},
    month = {09},
    doi = {10.1073/pnas.2002277117},
    publisher = {National Academy of Sciences},
    abstract = {We report a systematic unbiased analysis of small RNA molecule expression in 11 different tissues of the model organism mouse. We discovered uncharacterized noncoding RNA molecules and identified that \~{}30\% of total noncoding small RNA transcriptome are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. Distinct distribution patterns of small RNA across the body suggest the existence of tissue-specific mechanisms involved in noncoding RNA processing.Small noncoding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (microRNA [miRNA], small nucleolar RNA [snoRNA], small nuclear RNA [snRNA], small Cajal body-specific RNA [scaRNA], and transfer RNA [tRNA] fragments) across 11 mouse tissues by deep sequencing. Using 14 biological replicates spanning both sexes, we identified that \~{}30\% of small ncRNAs are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. We found that some miRNAs are subject to {\textquotedblleft}arm switching{\textquotedblright} between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of 11 profiled tissues, we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified in this study. Furthermore, by combining these findings with single-cell chromatin accessibility (scATAC-seq) data, we were able to connect identified brain-specific ncRNAs with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that these data will be a resource for the further identification of ncRNAs involved in tissue function in health and dysfunction in disease.The datasets generated and analyzed in the study have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) repository (GSE119661) (88). All study data are included in the article and SI Appendix.},
    issn = {0027-8424},
    URL = {https://www.pnas.org/content/117/41/25634},
    eprint = {https://www.pnas.org/content/117/41/25634.full.pdf},
    journal = {Proceedings of the National Academy of Sciences}
}

We report a systematic unbiased analysis of small RNA molecule expression in 11 different tissues of the model organism mouse. We discovered uncharacterized noncoding RNA molecules and identified that \ 30% of total noncoding small RNA transcriptome are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. Distinct distribution patterns of small RNA across the body suggest the existence of tissue-specific mechanisms involved in noncoding RNA processing.Small noncoding RNAs (ncRNAs) play a vital role in a broad range of biological processes both in health and disease. A comprehensive quantitative reference of small ncRNA expression would significantly advance our understanding of ncRNA roles in shaping tissue functions. Here, we systematically profiled the levels of five ncRNA classes (microRNA [miRNA], small nucleolar RNA [snoRNA], small nuclear RNA [snRNA], small Cajal body-specific RNA [scaRNA], and transfer RNA [tRNA] fragments) across 11 mouse tissues by deep sequencing. Using 14 biological replicates spanning both sexes, we identified that \ 30% of small ncRNAs are distributed across the body in a tissue-specific manner with some also being sexually dimorphic. We found that some miRNAs are subject to “arm switching” between healthy tissues and that tRNA fragments are retained within tissues in both a gene- and a tissue-specific manner. Out of 11 profiled tissues, we confirmed that brain contains the largest number of unique small ncRNA transcripts, some of which were previously annotated while others are identified in this study. Furthermore, by combining these findings with single-cell chromatin accessibility (scATAC-seq) data, we were able to connect identified brain-specific ncRNAs with their cell types of origin. These results yield the most comprehensive characterization of specific and ubiquitous small RNAs in individual murine tissues to date, and we expect that these data will be a resource for the further identification of ncRNAs involved in tissue function in health and dysfunction in disease.The datasets generated and analyzed in the study have been deposited in the National Center for Biotechnology Information Gene Expression Omnibus (GEO) repository (GSE119661) (88). All study data are included in the article and SI Appendix.

@article{MILLENAAR20201008,
    title = {Research in Atrial Fibrillation: A Scientometric Analysis Using the Novel Web Application SciPE},
    journal = {JACC: Clinical Electrophysiology},
    volume = {6},
    number = {8},
    pages = {1008 - 1018},
    year = {2020},
    month = {07},
    issn = {2405-500X},
    doi = {10.1016/j.jacep.2020.05.010},
    url = {http://www.sciencedirect.com/science/article/pii/S2405500X20303819},
    author = {Dominic Millenaar and Tobias Fehlmann and Sean Scholz and Valérie Pavlicek and Alexander Flohr and Markus Dillmann and Michael Böhm and Andreas Keller and Felix Mahfoud and Christian Ukena},
    abstract = {Objectives This study sought to determine the quantity and quality of publications in AF research using large-scale scientometric data analyses. Background Research in atrial fibrillation (AF) has increased over time. The increasing number of research papers makes it harder to identify relevant research work. Methods All 21,603 publications from 1945 to 2018 were retrieved from Web of Science and analyzed regarding geographical distribution of scientific output and international research cooperation. Results The total number of AF publications has significantly increased since the millennium change, from 3,063 (14.2%) in 1945 to 1999 to 18,540 (85.8%) publications in 2000 to 2018. AF research grew 10-fold compared with overall medical research since 1990 (ratio of AF publications to all publications: 0.02% (n = 99 of 410,701) in 1990 vs. 0.2% (n = 1,967 of 1,172,649) in 2018; p < 0.05). Quantitatively, the United States contributed 25.9% of AF research, followed by Japan (8.0%), Germany (7.8%), China (7.3%), and the United Kingdom (5.9%). In the all-time modified h-index, the United States ranked first (13.3% of all nations), followed by Canada (8.5%) and the United Kingdom (6.3%). In relation to population, Denmark was the best-rated nation, with the lowest number of inhabitants per publication (11,457), followed by Sweden (18,426) and the Netherlands (25,749), and per modified h-index (90,746), followed by Sweden (170,602) and the Netherlands (218,203). Measuring publications per research institute, Denmark again ranked first, with 19.2 publications per institute, followed by Italy (14.9) and Sweden (13.8). An intensive cooperation between nations was apparent. Conclusions This study showed an increase in publication activity in AF research. The United States was the leading country in quantity of research efforts. Related to population and research institutes, Denmark ranked first.}
}

Objectives This study sought to determine the quantity and quality of publications in AF research using large-scale scientometric data analyses. Background Research in atrial fibrillation (AF) has increased over time. The increasing number of research papers makes it harder to identify relevant research work. Methods All 21,603 publications from 1945 to 2018 were retrieved from Web of Science and analyzed regarding geographical distribution of scientific output and international research cooperation. Results The total number of AF publications has significantly increased since the millennium change, from 3,063 (14.2%) in 1945 to 1999 to 18,540 (85.8%) publications in 2000 to 2018. AF research grew 10-fold compared with overall medical research since 1990 (ratio of AF publications to all publications: 0.02% (n = 99 of 410,701) in 1990 vs. 0.2% (n = 1,967 of 1,172,649) in 2018; p < 0.05). Quantitatively, the United States contributed 25.9% of AF research, followed by Japan (8.0%), Germany (7.8%), China (7.3%), and the United Kingdom (5.9%). In the all-time modified h-index, the United States ranked first (13.3% of all nations), followed by Canada (8.5%) and the United Kingdom (6.3%). In relation to population, Denmark was the best-rated nation, with the lowest number of inhabitants per publication (11,457), followed by Sweden (18,426) and the Netherlands (25,749), and per modified h-index (90,746), followed by Sweden (170,602) and the Netherlands (218,203). Measuring publications per research institute, Denmark again ranked first, with 19.2 publications per institute, followed by Italy (14.9) and Sweden (13.8). An intensive cooperation between nations was apparent. Conclusions This study showed an increase in publication activity in AF research. The United States was the leading country in quantity of research efforts. Related to population and research institutes, Denmark ranked first.

@Article{Almanzar2020,
    author       = {The Tabula Muris Consortium},
    title        = {A single-cell transcriptomic atlas characterizes ageing tissues in the mouse},
    journal      = {Nature},
    year         = {2020},
    month        = {07},
    abstract     = {Ageing is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death1. Despite rapid advances over recent years, many of the molecular and cellular processes that underlie the progressive loss of healthy physiology are poorly understood2. To gain a better insight into these processes, here we generate a single-cell transcriptomic atlas across the lifespan of Mus musculus that includes data from 23 tissues and organs. We found cell-specific changes occurring across multiple cell types and organs, as well as age-related changes in the cellular composition of different organs. Using single-cell transcriptomic data, we assessed cell-type-specific manifestations of different hallmarks of ageing—such as senescence3, genomic instability4 and changes in the immune system2. This transcriptomic atlas—which we denote Tabula Muris Senis, or ‘Mouse Ageing Cell Atlas’—provides molecular information about how the most important hallmarks of ageing are reflected in a broad range of tissues and cell types.},
    doi          = {10.1038/s41586-020-2496-1},
    pii          = {10.1038/s41586-020-2496-1},
}

Ageing is characterized by a progressive loss of physiological integrity, leading to impaired function and increased vulnerability to death1. Despite rapid advances over recent years, many of the molecular and cellular processes that underlie the progressive loss of healthy physiology are poorly understood2. To gain a better insight into these processes, here we generate a single-cell transcriptomic atlas across the lifespan of Mus musculus that includes data from 23 tissues and organs. We found cell-specific changes occurring across multiple cell types and organs, as well as age-related changes in the cellular composition of different organs. Using single-cell transcriptomic data, we assessed cell-type-specific manifestations of different hallmarks of ageing—such as senescence3, genomic instability4 and changes in the immune system2. This transcriptomic atlas—which we denote Tabula Muris Senis, or ‘Mouse Ageing Cell Atlas’—provides molecular information about how the most important hallmarks of ageing are reflected in a broad range of tissues and cell types.

@Article{Schaum2020,
    author       = {Schaum, Nicholas and Lehallier, Benoit and Hahn, Oliver and Pálovics, Róbert and Hosseinzadeh, Shayan and Lee, Song E. and Sit, Rene and Lee, Davis P. and Losada, Patricia Morán and Zardeneta, Macy E. and Fehlmann, Tobias and Webber, James T. and McGeever, Aaron and Calcuttawala, Kruti and Zhang, Hui and Berdnik, Daniela and Mathur, Vidhu and Tan, Weilun and Zee, Alexander and Tan, Michelle and The Tabula Muris Consortium and Pisco, Angela Oliveira and Karkanias, Jim and Neff, Norma F. and Keller, Andreas and Darmanis, Spyros and Quake, Stephen R. and Wyss-Coray, Tony},
    title        = {Ageing hallmarks exhibit organ-specific temporal signatures},
    journal      = {Nature},
    year         = {2020},
    month        = {07},
    abstract     = {Ageing is the single greatest cause of disease and death worldwide, and understanding the associated processes could vastly improve quality of life. Although major categories of ageing damage have been identified—such as altered intercellular communication, loss of proteostasis and eroded mitochondrial function1—these deleterious processes interact with extraordinary complexity within and between organs, and a comprehensive, whole-organism analysis of ageing dynamics has been lacking. Here we performed bulk RNA sequencing of 17 organs and plasma proteomics at 10 ages across the lifespan of Mus musculus, and integrated these findings with data from the accompanying Tabula Muris Senis2—or ‘Mouse Ageing Cell Atlas’—which follows on from the original Tabula Muris3. We reveal linear and nonlinear shifts in gene expression during ageing, with the associated genes clustered in consistent trajectory groups with coherent biological functions—including extracellular matrix regulation, unfolded protein binding, mitochondrial function, and inflammatory and immune response. Notably, these gene sets show similar expression across tissues, differing only in the amplitude and the age of onset of expression. Widespread activation of immune cells is especially pronounced, and is first detectable in white adipose depots during middle age. Single-cell RNA sequencing confirms the accumulation of T cells and B cells in adipose tissue—including plasma cells that express immunoglobulin J—which also accrue concurrently across diverse organs. Finally, we show how gene expression shifts in distinct tissues are highly correlated with corresponding protein levels in plasma, thus potentially contributing to the ageing of the systemic circulation. Together, these data demonstrate a similar yet asynchronous inter- and intra-organ progression of ageing, providing a foundation from which to track systemic sources of declining health at old age.},
    doi          = {10.1038/s41586-020-2499-y},
    pii          = {10.1038/s41586-020-2499-y},
}

Ageing is the single greatest cause of disease and death worldwide, and understanding the associated processes could vastly improve quality of life. Although major categories of ageing damage have been identified—such as altered intercellular communication, loss of proteostasis and eroded mitochondrial function1—these deleterious processes interact with extraordinary complexity within and between organs, and a comprehensive, whole-organism analysis of ageing dynamics has been lacking. Here we performed bulk RNA sequencing of 17 organs and plasma proteomics at 10 ages across the lifespan of Mus musculus, and integrated these findings with data from the accompanying Tabula Muris Senis2—or ‘Mouse Ageing Cell Atlas’—which follows on from the original Tabula Muris3. We reveal linear and nonlinear shifts in gene expression during ageing, with the associated genes clustered in consistent trajectory groups with coherent biological functions—including extracellular matrix regulation, unfolded protein binding, mitochondrial function, and inflammatory and immune response. Notably, these gene sets show similar expression across tissues, differing only in the amplitude and the age of onset of expression. Widespread activation of immune cells is especially pronounced, and is first detectable in white adipose depots during middle age. Single-cell RNA sequencing confirms the accumulation of T cells and B cells in adipose tissue—including plasma cells that express immunoglobulin J—which also accrue concurrently across diverse organs. Finally, we show how gene expression shifts in distinct tissues are highly correlated with corresponding protein levels in plasma, thus potentially contributing to the ageing of the systemic circulation. Together, these data demonstrate a similar yet asynchronous inter- and intra-organ progression of ageing, providing a foundation from which to track systemic sources of declining health at old age.

@Article{10.1080/15476286.2020.1771945,
    author       = {Andreas Keller and Tobias Fehlmann and Christina Backes and Fabian Kern and Randi Gislefoss and Hilde Langseth and Trine B. Rounge and Nicole Ludwig and Eckart Meese},
    title        = {Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis},
    journal      = {RNA Biology},
    year         = {2020},
    month        = {06},
    abstract     = {MicroRNAs are regulators of gene expressionand may be key markers in liquid biopsy.Early diagnosis is an effective means to increase patients’ overall survival. We generated genome-wide miRNA profiles from serum of patients and controls from the population-based Janus Serum Bank (JSB) and analysed them by bioinformatics and artificial intelligence approaches. JSB contains sera from 318,628 originally healthy persons, more than 96,000 of whom developed cancer. We selected 210 serum samples from patients with lung, colon or breast cancer at three time points prior to diagnosis (up to 32 years prior to diagnosis with median 5 years interval between TPs), one time-point after diagnosis and from individually matched controls. The controls were matched on age and year of all pre-diagnostic sampling time-points for the corresponding case. Using ANOVA we report 70 significantly deregulated markers (adjusted p-value<0.05). The driver for the significance was the diagnostic time point (miR-575, miR-6821-5p, miR-630 with adjusted p-values<10−10). Further, 91miRNAs were differently expressed in pre-diagnostic samples as compared to controls (nominal p < 0.05). Self-organized maps (SOMs)indicated larges effects in lung cancer samples while breast cancer samples showed the least pronounced changes. SOMsalsohighlighted cancer and time point specific miRNA dys-regulation. Intriguingly, a detailed breakdown of the results highlighted that 51\% of all miRNAs were highly specific, either for a time-point or a cancer entity. Pathway analysis highlighted 12 pathways including Hipo signalling and ABC transporters.Our results indicate that tumours may be indicated by serum miRNAs decades prior the clinical manifestation.},
    doi          = {10.1080/15476286.2020.1771945},
    pii          = {10.1080/15476286.2020.1771945},
}

MicroRNAs are regulators of gene expressionand may be key markers in liquid biopsy.Early diagnosis is an effective means to increase patients’ overall survival. We generated genome-wide miRNA profiles from serum of patients and controls from the population-based Janus Serum Bank (JSB) and analysed them by bioinformatics and artificial intelligence approaches. JSB contains sera from 318,628 originally healthy persons, more than 96,000 of whom developed cancer. We selected 210 serum samples from patients with lung, colon or breast cancer at three time points prior to diagnosis (up to 32 years prior to diagnosis with median 5 years interval between TPs), one time-point after diagnosis and from individually matched controls. The controls were matched on age and year of all pre-diagnostic sampling time-points for the corresponding case. Using ANOVA we report 70 significantly deregulated markers (adjusted p-value<0.05). The driver for the significance was the diagnostic time point (miR-575, miR-6821-5p, miR-630 with adjusted p-values<10−10). Further, 91miRNAs were differently expressed in pre-diagnostic samples as compared to controls (nominal p < 0.05). Self-organized maps (SOMs)indicated larges effects in lung cancer samples while breast cancer samples showed the least pronounced changes. SOMsalsohighlighted cancer and time point specific miRNA dys-regulation. Intriguingly, a detailed breakdown of the results highlighted that 51% of all miRNAs were highly specific, either for a time-point or a cancer entity. Pathway analysis highlighted 12 pathways including Hipo signalling and ABC transporters.Our results indicate that tumours may be indicated by serum miRNAs decades prior the clinical manifestation.

@Article{cells9061442,
    author       = {Krammes, Lena and Hart, Martin and Rheinheimer, Stefanie and Diener, Caroline and Menegatti, Jennifer and Grässer, Friedrich and Keller, Andreas and Meese, Eckart},
    title        = {Induction of the Endoplasmic-Reticulum-Stress Response: MicroRNA-34a Targeting of the IRE1α-Branch},
    journal      = {Cells},
    year         = {2020},
    month        = {06},
    abstract     = {Neurodegenerative disorders such as Alzheimer’s disease (AD) and Parkinson’s disease (PD) are characterized by the accumulation of misfolded proteins in the endoplasmic reticulum (ER) and the unfolded protein response (UPR). Modulating the UPR is one of the major challenges to counteract the development of neurodegenerative disorders and other diseases with affected UPR. Here, we show that miR-34a-5p directly targets the IRE1α branch of the UPR, including the genes BIP, IRE1α, and XBP1. Upon induction of ER stress in neuronal cells, miR-34a-5p overexpression impacts the resulting UPR via a significant reduction in IRE1α and XBP1s that in turn leads to decreased viability, increased cytotoxicity and caspase activity. The possibility to modify the UPR signaling pathway by a single miRNA that targets central genes of the IRE1α branch offers new perspectives for future therapeutic approaches against neurodegeneration.},
    doi          = {10.3390/cells9061442},
    pii          = {10.3390/cells9061442},
}

Neurodegenerative disorders such as Alzheimer’s disease (AD) and Parkinson’s disease (PD) are characterized by the accumulation of misfolded proteins in the endoplasmic reticulum (ER) and the unfolded protein response (UPR). Modulating the UPR is one of the major challenges to counteract the development of neurodegenerative disorders and other diseases with affected UPR. Here, we show that miR-34a-5p directly targets the IRE1α branch of the UPR, including the genes BIP, IRE1α, and XBP1. Upon induction of ER stress in neuronal cells, miR-34a-5p overexpression impacts the resulting UPR via a significant reduction in IRE1α and XBP1s that in turn leads to decreased viability, increased cytotoxicity and caspase activity. The possibility to modify the UPR signaling pathway by a single miRNA that targets central genes of the IRE1α branch offers new perspectives for future therapeutic approaches against neurodegeneration.

@Article{jcm9051499,
    author       = {Gi, Weng-Tein and Haas, Jan and Sedaghat-Hamedani, Farbod and Kayvanpour, Elham and Tappu, Rewati and Lehmann, David Hermann and Shirvani Samani, Omid and Wisdom, Michael and Keller, Andreas and Katus, Hugo A. and Meder, Benjamin},
    title        = {Epigenetic Regulation of Alternative mRNA Splicing in Dilated Cardiomyopathy},
    journal      = {Journal of Clinical Medicine},
    year         = {2020},
    month        = {05},
    abstract     = {In recent years, the genetic architecture of dilated cardiomyopathy (DCM) has been more thoroughly elucidated. However, there is still insufficient knowledge on the modifiers and regulatory principles that lead to the failure of myocardial function. The current study investigates the association of epigenome-wide DNA methylation and alternative splicing, both of which are important regulatory principles in DCM. We analyzed screening and replication cohorts of cases and controls and identified distinct transcriptomic patterns in the myocardium that differ significantly, and we identified a strong association of intronic DNA methylation and flanking exons usage (p < 2 × 10−16). By combining differential exon usage (DEU) and differential methylation regions (DMR), we found a significant change of regulation in important sarcomeric and other DCM-associated pathways. Interestingly, inverse regulation of Titin antisense non-coding RNA transcript splicing and DNA methylation of a locus reciprocal to TTN substantiate these findings and indicate an additional role for non-protein-coding transcripts. In summary, this study highlights for the first time the close interrelationship between genetic imprinting by DNA methylation and the transport of this epigenetic information towards the dynamic mRNA splicing landscape. This expands our knowledge of the genome–environment interaction in DCM besides simple gene expression regulation.},
    doi          = {10.3390/jcm9051499},
    pii          = {10.3390/jcm9051499},
}

In recent years, the genetic architecture of dilated cardiomyopathy (DCM) has been more thoroughly elucidated. However, there is still insufficient knowledge on the modifiers and regulatory principles that lead to the failure of myocardial function. The current study investigates the association of epigenome-wide DNA methylation and alternative splicing, both of which are important regulatory principles in DCM. We analyzed screening and replication cohorts of cases and controls and identified distinct transcriptomic patterns in the myocardium that differ significantly, and we identified a strong association of intronic DNA methylation and flanking exons usage (p < 2 × 10−16). By combining differential exon usage (DEU) and differential methylation regions (DMR), we found a significant change of regulation in important sarcomeric and other DCM-associated pathways. Interestingly, inverse regulation of Titin antisense non-coding RNA transcript splicing and DNA methylation of a locus reciprocal to TTN substantiate these findings and indicate an additional role for non-protein-coding transcripts. In summary, this study highlights for the first time the close interrelationship between genetic imprinting by DNA methylation and the transport of this epigenetic information towards the dynamic mRNA splicing landscape. This expands our knowledge of the genome–environment interaction in DCM besides simple gene expression regulation.

@Article{10.1093/nar/gkaa306,
    author       = {Gerstner, Nico and Kehl, Tim and Lenhof, Kerstin and Müller, Anne and Mayer, Carolin and Eckhart, Lea and Grammes, Nadja Liddy and Diener, Caroline and Hart, Martin and Hahn, Oliver and Walter, Jörn and Wyss-Coray, Tony and Meese, Eckart and Keller, Andreas and Lenhof, Hans-Peter},
    title        = {GeneTrail 3: advanced high-throughput enrichment analysis},
    journal      = {Nucleic Acids Research},
    year         = {2020},
    month        = {05},
    abstract     = {We present GeneTrail 3, a major extension of our web service GeneTrail that offers rich functionality for the identification, analysis, and visualization of deregulated biological processes. Our web service provides a comprehensive collection of biological processes and signaling pathways for 12 model organisms that can be analyzed with a powerful framework for enrichment and network analysis of transcriptomic, miRNomic, proteomic, and genomic data sets. Moreover, GeneTrail offers novel workflows for the analysis of epigenetic marks, time series experiments, and single cell data. We demonstrate the capabilities of our web service in two case-studies, which highlight that GeneTrail is well equipped for uncovering complex molecular mechanisms. GeneTrail is freely accessible at: http://genetrail.bioinf.uni-sb.de.},
    doi          = {10.1093/nar/gkaa306},
    pii          = {10.1093/nar/gkaa306},
}

We present GeneTrail 3, a major extension of our web service GeneTrail that offers rich functionality for the identification, analysis, and visualization of deregulated biological processes. Our web service provides a comprehensive collection of biological processes and signaling pathways for 12 model organisms that can be analyzed with a powerful framework for enrichment and network analysis of transcriptomic, miRNomic, proteomic, and genomic data sets. Moreover, GeneTrail offers novel workflows for the analysis of epigenetic marks, time series experiments, and single cell data. We demonstrate the capabilities of our web service in two case-studies, which highlight that GeneTrail is well equipped for uncovering complex molecular mechanisms. GeneTrail is freely accessible at: http://genetrail.bioinf.uni-sb.de.

@Article{10.1093/nar/gkaa309,
    author       = {Kern, Fabian and Fehlmann, Tobias and Solomon, Jeffrey and Schwed, Louisa and Grammes, Nadja and Backes, Christina and Van Keuren-Jensen, Kendall and Craig, David Wesley and Meese, Eckart and Keller, Andreas},
    title        = {miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems},
    journal      = {Nucleic Acids Research},
    year         = {2020},
    month        = {05},
    abstract     = {Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from ten frequently investigated organisms. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miRBase miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualizations such as heatmaps and running sum curves with background distributions. We demonstrate the new features with case studies for human kidney cancer, a biomarker study on Parkinson’s disease from the PPMI cohort, and a mouse model for breast cancer. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.},
    doi          = {10.1093/nar/gkaa309},
    pii          = {10.1093/nar/gkaa309},
}

Gene set enrichment analysis has become one of the most frequently used applications in molecular biology research. Originally developed for gene sets, the same statistical principles are now available for all omics types. In 2016, we published the miRNA enrichment analysis and annotation tool (miEAA) for human precursor and mature miRNAs. Here, we present miEAA 2.0, supporting miRNA input from ten frequently investigated organisms. To facilitate inclusion of miEAA in workflow systems, we implemented an Application Programming Interface (API). Users can perform miRNA set enrichment analysis using either the web-interface, a dedicated Python package, or custom remote clients. Moreover, the number of category sets was raised by an order of magnitude. We implemented novel categories like annotation confidence level or localisation in biological compartments. In combination with the miRBase miRNA-version and miRNA-to-precursor converters, miEAA supports research settings where older releases of miRBase are in use. The web server also offers novel comprehensive visualizations such as heatmaps and running sum curves with background distributions. We demonstrate the new features with case studies for human kidney cancer, a biomarker study on Parkinson’s disease from the PPMI cohort, and a mouse model for breast cancer. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.

@Article{10.1093/nar/gkaa323,
    author       = {Kern, Fabian and Amand, Jeremy and Senatorov, Ilya and Isakova, Alina and Backes, Christina and Meese, Eckart and Keller, Andreas and Fehlmann, Tobias},
    title        = {miRSwitch: detecting microRNA arm shift and switch events},
    journal      = {Nucleic Acids Research},
    year         = {2020},
    month        = {05},
    abstract     = {Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30 521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customized arm switch analyses along with comprehensive visualizations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.},
    doi          = {10.1093/nar/gkaa323},
    pii          = {10.1093/nar/gkaa323},
}

Arm selection, the preferential expression of a 3′ or 5′ mature microRNA (miRNA), is a highly dynamic and tissue-specific process. Time-dependent expression shifts or switches between the arms are also relevant for human diseases. We present miRSwitch, a web server to facilitate the analysis and interpretation of arm selection events. Our species-independent tool evaluates pre-processed small non-coding RNA sequencing (sncRNA-seq) data, i.e. expression matrices or output files from miRNA quantification tools (miRDeep2, miRMaster, sRNAbench). miRSwitch highlights potential changes in the distribution of mature miRNAs from the same precursor. Group comparisons from one or several user-provided annotations (e.g. disease states) are possible. Results can be dynamically adjusted by choosing from a continuous range of highly specific to very sensitive parameters. Users can compare potential arm shifts in the provided data to a human reference map of pre-computed arm shift frequencies. We created this map from 46 tissues and 30 521 samples. As case studies we present novel arm shift information in a Alzheimer’s disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customized arm switch analyses along with comprehensive visualizations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.

@Article{KAYVANPOUR2020,
  author       = {Elham Kayvanpour and Weng-Tein Gi and Farbod Sedaghat-Hamedani and David H. Lehmann and Karen S. Frese and Jan Haas and Rewati Tappu and Omid Shirvani Samani and Rouven Nietsch and Mustafa Kahraman and Tobias Fehlmann and Matthias Müller-Hennessen and Tanja Weis and Evangelos Giannitsis and Torsten Niederdränk and Andreas Keller and Hugo A. Katus and Benjamin Meder},
  title        = {microRNA neural networks improve diagnosis of acute coronary syndrome (ACS)},
  journal      = {Journal of Molecular and Cellular Cardiology},
  year         = {2020},
  month        = {04},
  abstract     = {Background Cardiac troponins are the preferred biomarkers of acute myocardial infarction. Despite superior sensitivity, serial testing of Troponins to identify patients suffering acute coronary syndromes is still required in many cases to overcome limited specificity. Moreover, unstable angina pectoris relies on reported symptoms in the troponin-negative group. In this study, we investigated genome-wide miRNA levels in a prospective cohort of patients with clinically suspected ACS and determined their diagnostic value by applying an in silico neural network. Methods PAXgene blood and serum samples were drawn and hsTnT was measured in patients at initial presentation to our Chest-Pain Unit. After clinical and diagnostic workup, patients were adjudicated by senior cardiologists in duty to their final diagnosis: STEMI, NSTEMI, unstable angina pectoris and non-ACS patients. ACS patients and a cohort of healthy controls underwent deep transcriptome sequencing. Machine learning was implemented to construct diagnostic miRNA classifiers. Results We developed a neural network model which incorporates 34 validated ACS miRNAs, showing excellent classification results. By further developing additional machine learning models and selecting the best miRNAs, we achieved an accuracy of 0.96 (95% CI 0.96–0.97), sensitivity of 0.95, specificity of 0.96 and AUC of 0.99. The one-point hsTnT value reached an accuracy of 0.89, sensitivity of 0.82, specificity of 0.96, and AUC of 0.96. Conclusions Here we show the concept of neural network based biomarkers for ACS. This approach also opens the possibility to include multi-modal data points to further increase precision and perform classification of other ACS differential diagnoses.},
  doi          = {10.1016/j.yjmcc.2020.04.014},
  pii          = {10.1016/j.yjmcc.2020.04.014},
}

Background Cardiac troponins are the preferred biomarkers of acute myocardial infarction. Despite superior sensitivity, serial testing of Troponins to identify patients suffering acute coronary syndromes is still required in many cases to overcome limited specificity. Moreover, unstable angina pectoris relies on reported symptoms in the troponin-negative group. In this study, we investigated genome-wide miRNA levels in a prospective cohort of patients with clinically suspected ACS and determined their diagnostic value by applying an in silico neural network. Methods PAXgene blood and serum samples were drawn and hsTnT was measured in patients at initial presentation to our Chest-Pain Unit. After clinical and diagnostic workup, patients were adjudicated by senior cardiologists in duty to their final diagnosis: STEMI, NSTEMI, unstable angina pectoris and non-ACS patients. ACS patients and a cohort of healthy controls underwent deep transcriptome sequencing. Machine learning was implemented to construct diagnostic miRNA classifiers. Results We developed a neural network model which incorporates 34 validated ACS miRNAs, showing excellent classification results. By further developing additional machine learning models and selecting the best miRNAs, we achieved an accuracy of 0.96 (95% CI 0.96–0.97), sensitivity of 0.95, specificity of 0.96 and AUC of 0.99. The one-point hsTnT value reached an accuracy of 0.89, sensitivity of 0.82, specificity of 0.96, and AUC of 0.96. Conclusions Here we show the concept of neural network based biomarkers for ACS. This approach also opens the possibility to include multi-modal data points to further increase precision and perform classification of other ACS differential diagnoses.

@Article{10.1016/j.tig.2020.03.007,
    author       = {Fromm, Bastian and Keller, Andreas and Yang, Xiaozeng and Friedlander, Marc R. and Peterson, Kevin J. and Griffiths-Jones, Sam},
    title        = {Quo vadis microRNAs?},
    journal      = {Trends in Genetics},
    year         = {2020},
    month        = {04},
    abstract     = {Since 2002, published miRNAs have been collected and named by the online repository miRBase. However, with 11 000 annual publications this has become challenging. Recently, four specialized miRNA databases were published, addressing particular needs for diverse scientific communities. This development provides major opportunities for the future of miRNA annotation and nomenclature.},
    doi          = {10.1016/j.tig.2020.03.007},
    pii          = {10.1016/j.tig.2020.03.007},
}

Since 2002, published miRNAs have been collected and named by the online repository miRBase. However, with 11 000 annual publications this has become challenging. Recently, four specialized miRNA databases were published, addressing particular needs for diverse scientific communities. This development provides major opportunities for the future of miRNA annotation and nomenclature.

@Article{10.1371/journal.pone.0231402,
  author       = {Abu-Halima, Masood and Oberhoffer, Felix and Abd el Rahman, M. and Jung, Anna-Maria and Zemlin, Michael and Rohrer, Tilman and Kahraman, Mustafa and Keller, Andreas and Meese, Eckart and Abdul-Khaliq, Hashim},
  title        = {Insights from circulating microRNAs in cardiovascular entities in turner syndrome patients},
  journal      = {PLOS ONE},
  year         = {2020},
  month        = {04},
  abstract     = {Background Turner syndrome (TS) is a chromosomal disorder, in which a female is partially or entirely missing one of the two X chromosomes, with a prevalence of 1:2500 live female births. The present study aims to identify a circulating microRNA (miRNA) signature for TS patients with and without congenital heart disease (CHD). Methods Microarray platform interrogating 2549 miRNAs were used to detect the miRNA abundance levels in the blood of 33 TS patients and 14 age-matched healthy volunteer controls (HVs). The differentially abundant miRNAs between the two groups were further validated by RT-qPCR. Results We identified 60 differentially abundant miRNA in the blood of TS patients compared to HVs, from which, 41 and 19 miRNAs showed a higher and a lower abundance levels in TS patients compared to HVs, respectively. RT-qPCR confirmed the significantly higher abundance levels of eight miRNAs namely miR-374b-5p, miR-199a-5p, miR-340-3p, miR-125b-5p, miR-30e-3p, miR-126-3p, miR-5695, and miR-26b-5p in TS patients as compared with the HVs. The abundance level of miR-5695 was higher in TS patients displaying CHD as compared to TS patients without CHD (p = 0.0265; log2-fold change 1.99); whereas, the abundance level of miR-126-3p was lower in TS patients with congenital aortic valve disease (AVD) compared to TS patients without BAV (p = 0.0139, log2-fold change 1.52). The clinical feature statistics revealed that miR-126-3p had a significant correlation with sinotubular junction Z-score (r = 0.42; p = 0.0154). Conclusion The identified circulating miRNAs signature for TS patients with manifestations associated with cardiovascular diseases provide new insights into the molecular mechanism of TS that may guide the development of novel diagnostic approaches.},
  doi          = {10.1371/journal.pone.0231402},
  pii          = {10.1371/journal.pone.0231402},
}

Background Turner syndrome (TS) is a chromosomal disorder, in which a female is partially or entirely missing one of the two X chromosomes, with a prevalence of 1:2500 live female births. The present study aims to identify a circulating microRNA (miRNA) signature for TS patients with and without congenital heart disease (CHD). Methods Microarray platform interrogating 2549 miRNAs were used to detect the miRNA abundance levels in the blood of 33 TS patients and 14 age-matched healthy volunteer controls (HVs). The differentially abundant miRNAs between the two groups were further validated by RT-qPCR. Results We identified 60 differentially abundant miRNA in the blood of TS patients compared to HVs, from which, 41 and 19 miRNAs showed a higher and a lower abundance levels in TS patients compared to HVs, respectively. RT-qPCR confirmed the significantly higher abundance levels of eight miRNAs namely miR-374b-5p, miR-199a-5p, miR-340-3p, miR-125b-5p, miR-30e-3p, miR-126-3p, miR-5695, and miR-26b-5p in TS patients as compared with the HVs. The abundance level of miR-5695 was higher in TS patients displaying CHD as compared to TS patients without CHD (p = 0.0265; log2-fold change 1.99); whereas, the abundance level of miR-126-3p was lower in TS patients with congenital aortic valve disease (AVD) compared to TS patients without BAV (p = 0.0139, log2-fold change 1.52). The clinical feature statistics revealed that miR-126-3p had a significant correlation with sinotubular junction Z-score (r = 0.42; p = 0.0154). Conclusion The identified circulating miRNAs signature for TS patients with manifestations associated with cardiovascular diseases provide new insights into the molecular mechanism of TS that may guide the development of novel diagnostic approaches.

@Article{Diener2020,
    author       = {Diener, Caroline and Keller, Andreas and Meese, Eckart},
    title        = {Untersuchung von miRNAs mithilfe getrockneter Blutstropfen},
    journal      = {BIOspektrum},
    year         = {2020},
    month        = {03},
    pages        = {174-176},
    abstract     = {Due to their connection to a great diversity of diseases and their prevalence in blood, microRNAs (miRNAs) are envisaged as biomarkers in liquid biopsy diagnostics. Utilizing dried blood spots (DBS) for the isolation of miRNAs greatly facilitates both the sample collection and the storage in comparison to liquid blood. MiRNAs isolated from DBS can be used for the analysis of individual miRNAs and for high-throughput analyses of the entire miRNome.},
    doi          = {10.1007/s12268-020-1356-8},
    pii          = {10.1007/s12268-020-1356-8},
}

Due to their connection to a great diversity of diseases and their prevalence in blood, microRNAs (miRNAs) are envisaged as biomarkers in liquid biopsy diagnostics. Utilizing dried blood spots (DBS) for the isolation of miRNAs greatly facilitates both the sample collection and the storage in comparison to liquid blood. MiRNAs isolated from DBS can be used for the analysis of individual miRNAs and for high-throughput analyses of the entire miRNome.

@Article{ABUHALIMA2020970,
  author       = {Masood Abu-Halima and Zyiad Abu Khaizaran and Basim M. Ayesh and Ulrike Fischer and Salem Abu Khaizaran and Feras Al-Battah and Mohamad Hammadeh and Andreas Keller and Eckart Meese},
  title        = {MicroRNAs in combined spent culture media and sperm are associated with embryo quality and pregnancy outcome},
  journal      = {Fertility and Sterility},
  year         = {2020},
  month        = {03},
  abstract     = {Objective: To identify differentially abundant miRNAs in sperm samples and spent culture media (SCM) of embryos of different grade toward a prediction of pregnancy outcome. Design: Array-based reverse-transcription quantitative polymerase chain reaction profiling and validation. Setting: University research institute and in vitro fertilization center. Patient(s): Couples (n = 61) undergoing infertility treatment with the use of intracytoplasmic sperm injection. Interventions(s): None. Main outcome measure(s): Abundance levels of miRNAs in combined SCM of embryos of different quality and in sperm samples associated with pregnancy outcome. Result(s): Out of 372 screened miRNAs, miR-19b-3p and let-7a-5p were detected consistently in all SCM and sperm samples. The abundance levels of miRNAs were significantly altered between SCM of embryos with different quality (G1, G2, and G3 grades). Specifically, miR-320a and miR-15a-5p were differentially abundant in G1 vs. G2, miR-21-5p in G1 vs. G3, and miR-20a-5p in G2 vs. G3. The abundance levels of combined SCM and sperm derived miRNAs were also significantly altered between different pregnancy outcomes. MiR-19b-3p showed the highest area under the receiver operating characteristic curve values between positive and negative outcomes, with lower abundance levels in both combined SCM and sperm samples associated with a positive pregnancy outcome. MiR-320a, miR-15a-5p, miR-21-5p, and miR-20a-5p showed similar results in combined SCM samples. Conclusion(s): miRNA abundance levels in combined SCM and sperm differed significantly depending on embryo quality and pregnancy outcome. MiR-19b-3p may serve as a potential biomarker to predict pregnancy outcome. Keywords: IVF; MicroRNA; embryogenesis; embryonic culture media; spermatogenesis.},
  doi          = {10.1016/j.fertnstert.2019.12.028},
  pii          = {10.1016/j.fertnstert.2019.12.028},
}

Objective: To identify differentially abundant miRNAs in sperm samples and spent culture media (SCM) of embryos of different grade toward a prediction of pregnancy outcome. Design: Array-based reverse-transcription quantitative polymerase chain reaction profiling and validation. Setting: University research institute and in vitro fertilization center. Patient(s): Couples (n = 61) undergoing infertility treatment with the use of intracytoplasmic sperm injection. Interventions(s): None. Main outcome measure(s): Abundance levels of miRNAs in combined SCM of embryos of different quality and in sperm samples associated with pregnancy outcome. Result(s): Out of 372 screened miRNAs, miR-19b-3p and let-7a-5p were detected consistently in all SCM and sperm samples. The abundance levels of miRNAs were significantly altered between SCM of embryos with different quality (G1, G2, and G3 grades). Specifically, miR-320a and miR-15a-5p were differentially abundant in G1 vs. G2, miR-21-5p in G1 vs. G3, and miR-20a-5p in G2 vs. G3. The abundance levels of combined SCM and sperm derived miRNAs were also significantly altered between different pregnancy outcomes. MiR-19b-3p showed the highest area under the receiver operating characteristic curve values between positive and negative outcomes, with lower abundance levels in both combined SCM and sperm samples associated with a positive pregnancy outcome. MiR-320a, miR-15a-5p, miR-21-5p, and miR-20a-5p showed similar results in combined SCM samples. Conclusion(s): miRNA abundance levels in combined SCM and sperm differed significantly depending on embryo quality and pregnancy outcome. MiR-19b-3p may serve as a potential biomarker to predict pregnancy outcome. Keywords: IVF; MicroRNA; embryogenesis; embryonic culture media; spermatogenesis.

@Article{10.1186/s12931-020-1317-2,
  author       = {Herr, Christian and Tsitouras, Konstantinos and Niederstraßer, Julia and Backes, Christina and Beisswenger, Christoph and Dong, Li and Guillot, Loïc and Keller, Andreas and Bals, Robert},
  title        = {Cigarette smoke and electronic cigarettes differentially activate bronchial epithelial cells},
  journal      = {BioMed Central},
  year         = {2020},
  pages        = {67},
  month        = {03},
  abstract     = {Abstract MicroRNAs (miRNAs) have recently received a significant amount of attention due to their remarkable influence on post-transcriptional gene regulation. In this study, we aim to provide a catalogue of miRNAs present in spermatozoa, seminal plasma and testicular tissue. Expression profiles of miRNA in spermatozoa and seminal plasma of 16 proven fertile men and testicular tissue of eight men with morphologically and/or histologically confirmed obstructive azoospermia were determined by microarray and RT-qPCR in combination with bioinformatics analyses. A total of 123, 156 and 133 miRNAs were consistently detected in spermatozoa, seminal plasma and testicular tissue respectively. Sixty-four miRNAs were shared across all sample types. Based on miRNAs expression level present in each group, correlation analysis showed moderate-to-strong correlations within the spermatozoa and seminal plasma samples and a wider range of correlations within the testicular tissue samples. The target genes of known miRNAs appeared to be involved in a wide range of biological processes related to reproduction, development and differentiation of germ cells. Our results suggest that there is a certain similarity between spermatozoa and seminal plasma for the relative miRNA expression changes with respect to testicular tissue and provide an overview of the miRNAs present in each sample type.},
  doi          = {10.1186/s12931-020-1317-2},
  pii          = {10.1186/s12931-020-1317-2},
}

Abstract MicroRNAs (miRNAs) have recently received a significant amount of attention due to their remarkable influence on post-transcriptional gene regulation. In this study, we aim to provide a catalogue of miRNAs present in spermatozoa, seminal plasma and testicular tissue. Expression profiles of miRNA in spermatozoa and seminal plasma of 16 proven fertile men and testicular tissue of eight men with morphologically and/or histologically confirmed obstructive azoospermia were determined by microarray and RT-qPCR in combination with bioinformatics analyses. A total of 123, 156 and 133 miRNAs were consistently detected in spermatozoa, seminal plasma and testicular tissue respectively. Sixty-four miRNAs were shared across all sample types. Based on miRNAs expression level present in each group, correlation analysis showed moderate-to-strong correlations within the spermatozoa and seminal plasma samples and a wider range of correlations within the testicular tissue samples. The target genes of known miRNAs appeared to be involved in a wide range of biological processes related to reproduction, development and differentiation of germ cells. Our results suggest that there is a certain similarity between spermatozoa and seminal plasma for the relative miRNA expression changes with respect to testicular tissue and provide an overview of the miRNAs present in each sample type.

@Article{10.1001/jamaoncol.2020.0001,
  author       = {Fehlmann, Tobias and Kahraman, Mustafa and Ludwig, Nicole and Backes, Christina and Galata, Valentina and Keller, Verena and Geffers, Lars and Mercaldo, Nathaniel and Hornung, Daniela and Weis, Tanja and Kayvanpour, Elham and Abu-Halima, Masood and Deuschle, Christian and Schulte, Claudia and Suenkel, Ulrike and von Thaler, Anna-Katharina and Maetzler, Walter and Herr, Christian and Fähndrich, Sebastian and Vogelmeier, Claus and Guimaraes, Pedro and Hecksteden, Anne and Meyer, Tim and Metzger, Florian and Diener, Caroline and Deutscher, Stephanie and Abdul-Khaliq, Hashim and Stehle, Ingo and Haeusler, Sebastian and Meiser, Andreas and Groesdonk, Heinrich V and Volk, Thomas and Lenhof, Hans-Peter and Katus, Hugo and Balling, Rudi and Meder, Benjamin and Kruger, Rejko and Huwer, Hanno and Bals, Robert and Meese, Eckart and Keller, Andreas},
  title        = {Evaluating the Use of Circulating MicroRNA Profiles for Lung Cancer Detection in Symptomatic Patients},
  journal      = {JAMA Oncology},
  year         = {2020},
  month        = {03},
  abstract     = {The overall low survival rate of patients with lung cancer calls for improved detection tools to enable better treatment options and improved patient outcomes. Multivariable molecular signatures, such as blood-borne microRNA (miRNA) signatures, may have high rates of sensitivity and specificity but require additional studies with large cohorts and standardized measurements to confirm the generalizability of miRNA signatures.To investigate the use of blood-borne miRNAs as potential circulating markers for detecting lung cancer in an extended cohort of symptomatic patients and control participants.This multicenter, cohort study included patients from case-control and cohort studies (TREND and COSYCONET) with 3102 patients being enrolled by convenience sampling between March 3, 2009, and March 19, 2018. For the cohort study TREND, population sampling was performed. Clinical diagnoses were obtained for 3046 patients (606 patients with non–small cell and small cell lung cancer, 593 patients with nontumor lung diseases, 883 patients with diseases not affecting the lung, and 964 unaffected control participants). No samples were removed because of experimental issues. The collected data were analyzed between April 2018 and November 2019.Sensitivity and specificity of liquid biopsy using miRNA signatures for detection of lung cancer.A total of 3102 patients with a mean (SD) age of 61.1 (16.2) years were enrolled. Data on the sex of the participants were available for 2856 participants; 1727 (60.5\\%) were men. Genome-wide miRNA profiles of blood samples from 3046 individuals were evaluated by machine-learning methods. Three classification scenarios were investigated by splitting the samples equally into training and validation sets. First, a 15-miRNA signature from the training set was used to distinguish patients diagnosed with lung cancer from all other individuals in the validation set with an accuracy of 91.4\\% (95\\% CI, 91.0\\%-91.9\\%), a sensitivity of 82.8\\% (95\\% CI, 81.5\\%-84.1\\%), and a specificity of 93.5\\% (95\\% CI, 93.2\\%-93.8\\%). Second, a 14-miRNA signature from the training set was used to distinguish patients with lung cancer from patients with nontumor lung diseases in the validation set with an accuracy of 92.5\\% (95\\% CI, 92.1\\%-92.9\\%), sensitivity of 96.4\\% (95\\% CI, 95.9\\%-96.9\\%), and specificity of 88.6\\% (95\\% CI, 88.1\\%-89.2\\%). Third, a 14-miRNA signature from the training set was used to distinguish patients with early-stage lung cancer from all individuals without lung cancer in the validation set with an accuracy of 95.9\\% (95\\% CI, 95.7\\%-96.2\\%), sensitivity of 76.3\\% (95\\% CI, 74.5\\%-78.0\\%), and specificity of 97.5\\% (95\\% CI, 97.2\\%-97.7\\%).The findings of the study suggest that the identified patterns of miRNAs may be used as a component of a minimally invasive lung cancer test, complementing imaging, sputum cytology, and biopsy tests.},
  doi          = {10.1001/jamaoncol.2020.0001},
  pii          = {10.1001/jamaoncol.2020.0001},
}

The overall low survival rate of patients with lung cancer calls for improved detection tools to enable better treatment options and improved patient outcomes. Multivariable molecular signatures, such as blood-borne microRNA (miRNA) signatures, may have high rates of sensitivity and specificity but require additional studies with large cohorts and standardized measurements to confirm the generalizability of miRNA signatures.To investigate the use of blood-borne miRNAs as potential circulating markers for detecting lung cancer in an extended cohort of symptomatic patients and control participants.This multicenter, cohort study included patients from case-control and cohort studies (TREND and COSYCONET) with 3102 patients being enrolled by convenience sampling between March 3, 2009, and March 19, 2018. For the cohort study TREND, population sampling was performed. Clinical diagnoses were obtained for 3046 patients (606 patients with non–small cell and small cell lung cancer, 593 patients with nontumor lung diseases, 883 patients with diseases not affecting the lung, and 964 unaffected control participants). No samples were removed because of experimental issues. The collected data were analyzed between April 2018 and November 2019.Sensitivity and specificity of liquid biopsy using miRNA signatures for detection of lung cancer.A total of 3102 patients with a mean (SD) age of 61.1 (16.2) years were enrolled. Data on the sex of the participants were available for 2856 participants; 1727 (60.5\%) were men. Genome-wide miRNA profiles of blood samples from 3046 individuals were evaluated by machine-learning methods. Three classification scenarios were investigated by splitting the samples equally into training and validation sets. First, a 15-miRNA signature from the training set was used to distinguish patients diagnosed with lung cancer from all other individuals in the validation set with an accuracy of 91.4\% (95\% CI, 91.0\%-91.9\%), a sensitivity of 82.8\% (95\% CI, 81.5\%-84.1\%), and a specificity of 93.5\% (95\% CI, 93.2\%-93.8\%). Second, a 14-miRNA signature from the training set was used to distinguish patients with lung cancer from patients with nontumor lung diseases in the validation set with an accuracy of 92.5\% (95\% CI, 92.1\%-92.9\%), sensitivity of 96.4\% (95\% CI, 95.9\%-96.9\%), and specificity of 88.6\% (95\% CI, 88.1\%-89.2\%). Third, a 14-miRNA signature from the training set was used to distinguish patients with early-stage lung cancer from all individuals without lung cancer in the validation set with an accuracy of 95.9\% (95\% CI, 95.7\%-96.2\%), sensitivity of 76.3\% (95\% CI, 74.5\%-78.0\%), and specificity of 97.5\% (95\% CI, 97.2\%-97.7\%).The findings of the study suggest that the identified patterns of miRNAs may be used as a component of a minimally invasive lung cancer test, complementing imaging, sputum cytology, and biopsy tests.

@Article{e2020,
  author       = {Warmerdam, Elke and Hausdorff, Jeffrey M and Atrsaei, Arash and Zhou, Yuhan and Mirelman, Anat and Aminian, Kamiar and Espay, Alberto J and Hansen, Clint and Evers, Luc J W and Keller, Andreas and Lamoth, Claudine and Pilotto, Andrea and Rochester, Lynn and Schmidt, Gerhard and Bloem, Bastiaan R and Maetzler, Walter },
  title        = {Long-term unsupervised mobility assessment in movement disorders},
  journal      = {The Lancet Neurology},
  year         = {2020},
  month        = {02},
  pages        = {1474-4422},
  abstract     = {Mobile health technologies (wearable, portable, body-fixed sensors, or domestic-integrated devices) that quantify mobility in unsupervised, daily living environments are emerging as complementary clinical assessments. Data collected in these ecologically valid, patient-relevant settings can overcome limitations of conventional clinical assessments, as they capture fluctuating and rare events. These data could support clinical decision making and could also serve as outcomes in clinical trials. However, studies that directly compared assessments made in unsupervised and supervised (eg, in the laboratory or hospital) settings point to large disparities, even in the same parameters of mobility. These differences appear to be affected by psychological, physiological, cognitive, environmental, and technical factors, and by the types of mobilities and diagnoses assessed. To facilitate the successful adaptation of the unsupervised assessment of mobility into clinical practice and clinical trials, clinicians and researchers should consider these disparities and the multiple factors that contribute to them.},
  doi          = {10.1016/S1474-4422(19)30397-7},
  pii          = {10.1016/S1474-4422(19)30397-7},
}

Mobile health technologies (wearable, portable, body-fixed sensors, or domestic-integrated devices) that quantify mobility in unsupervised, daily living environments are emerging as complementary clinical assessments. Data collected in these ecologically valid, patient-relevant settings can overcome limitations of conventional clinical assessments, as they capture fluctuating and rare events. These data could support clinical decision making and could also serve as outcomes in clinical trials. However, studies that directly compared assessments made in unsupervised and supervised (eg, in the laboratory or hospital) settings point to large disparities, even in the same parameters of mobility. These differences appear to be affected by psychological, physiological, cognitive, environmental, and technical factors, and by the types of mobilities and diagnoses assessed. To facilitate the successful adaptation of the unsupervised assessment of mobility into clinical practice and clinical trials, clinicians and researchers should consider these disparities and the multiple factors that contribute to them.

@Article{doi:10.1111/and.13503,
  author       = {Abu-Halima, Masood and Galata, Valentina and Backes, Christina and Keller, Andreas and Hammadeh, Mohamad and Meese, Eckart},
  title        = {MicroRNA signature in spermatozoa and seminal plasma of proven fertile men and in testicular tissue of men with obstructive azoospermia},
  journal      = {Andrologia},
  year         = {2019},
  pages        = {e13503},
  abstract     = {Abstract MicroRNAs (miRNAs) have recently received a significant amount of attention due to their remarkable influence on post-transcriptional gene regulation. In this study, we aim to provide a catalogue of miRNAs present in spermatozoa, seminal plasma and testicular tissue. Expression profiles of miRNA in spermatozoa and seminal plasma of 16 proven fertile men and testicular tissue of eight men with morphologically and/or histologically confirmed obstructive azoospermia were determined by microarray and RT-qPCR in combination with bioinformatics analyses. A total of 123, 156 and 133 miRNAs were consistently detected in spermatozoa, seminal plasma and testicular tissue respectively. Sixty-four miRNAs were shared across all sample types. Based on miRNAs expression level present in each group, correlation analysis showed moderate-to-strong correlations within the spermatozoa and seminal plasma samples and a wider range of correlations within the testicular tissue samples. The target genes of known miRNAs appeared to be involved in a wide range of biological processes related to reproduction, development and differentiation of germ cells. Our results suggest that there is a certain similarity between spermatozoa and seminal plasma for the relative miRNA expression changes with respect to testicular tissue and provide an overview of the miRNAs present in each sample type.},
  doi          = {10.1111/and.13503},
  pii          = {10.1111/and.13503},
}

Abstract MicroRNAs (miRNAs) have recently received a significant amount of attention due to their remarkable influence on post-transcriptional gene regulation. In this study, we aim to provide a catalogue of miRNAs present in spermatozoa, seminal plasma and testicular tissue. Expression profiles of miRNA in spermatozoa and seminal plasma of 16 proven fertile men and testicular tissue of eight men with morphologically and/or histologically confirmed obstructive azoospermia were determined by microarray and RT-qPCR in combination with bioinformatics analyses. A total of 123, 156 and 133 miRNAs were consistently detected in spermatozoa, seminal plasma and testicular tissue respectively. Sixty-four miRNAs were shared across all sample types. Based on miRNAs expression level present in each group, correlation analysis showed moderate-to-strong correlations within the spermatozoa and seminal plasma samples and a wider range of correlations within the testicular tissue samples. The target genes of known miRNAs appeared to be involved in a wide range of biological processes related to reproduction, development and differentiation of germ cells. Our results suggest that there is a certain similarity between spermatozoa and seminal plasma for the relative miRNA expression changes with respect to testicular tissue and provide an overview of the miRNAs present in each sample type.

@Article{10.1002/1878-0261.12620,
  author       = {Umu, Sinan Ugur and Langseth, Hilde and Keller, Andreas and Meese, Eckart and Helland, Aslaug and Lyle, Robert and Rounge, Trine B},
  title        = {A 10-year prediagnostic follow-up study shows that serum RNA signals are highly dynamic in lung carcinogenesis},
  journal      = {Molecular oncology},
  year         = {2019},
  pages        = {235-247},
  abstract     = {The majority of lung cancer (LC) patients are diagnosed at a late stage, and survival is poor. Circulating RNA molecules are known to have a role in cancer; however, their involvement before diagnosis remains an open question. In this study, we investigated circulating RNA dynamics in prediagnostic LC samples, focusing on smokers, to identify if and when disease-related signals can be detected in serum. We sequenced small RNAs in 542 serum LC samples donated up to 10 years before diagnosis and 519 matched cancer-free controls coming from 905 individuals in the Janus Serum Bank. This sample size provided sufficient statistical power to independently analyze time to diagnosis, stage, and histology. The results showed dynamic changes in differentially expressed circulating RNAs specific to LC histology and stage. The greatest number of differentially expressed RNAs was identified around 7 years before diagnosis for early-stage LC and 1-4 years prior to diagnosis for locally advanced and advanced-stage LC, regardless of LC histology. Furthermore, NSCLC and SCLC histologies have distinct prediagnostic signals. The majority of differentially expressed RNAs were associated with cancer-related pathways. The dynamic RNA signals pinpointed different phases of tumor development over time. Stage-specific RNA profiles may be associated with tumor aggressiveness. Our results improve the molecular understanding of carcinogenesis. They indicate substantial opportunity for screening and improved treatment and will guide further research on early detection of LC. However, the dynamic nature of the RNA signals also suggests challenges for prediagnostic biomarker discovery.},
  doi          = {10.1002/1878-0261.12620},
  pii          = {10.1002/1878-0261.12620},
}

The majority of lung cancer (LC) patients are diagnosed at a late stage, and survival is poor. Circulating RNA molecules are known to have a role in cancer; however, their involvement before diagnosis remains an open question. In this study, we investigated circulating RNA dynamics in prediagnostic LC samples, focusing on smokers, to identify if and when disease-related signals can be detected in serum. We sequenced small RNAs in 542 serum LC samples donated up to 10 years before diagnosis and 519 matched cancer-free controls coming from 905 individuals in the Janus Serum Bank. This sample size provided sufficient statistical power to independently analyze time to diagnosis, stage, and histology. The results showed dynamic changes in differentially expressed circulating RNAs specific to LC histology and stage. The greatest number of differentially expressed RNAs was identified around 7 years before diagnosis for early-stage LC and 1-4 years prior to diagnosis for locally advanced and advanced-stage LC, regardless of LC histology. Furthermore, NSCLC and SCLC histologies have distinct prediagnostic signals. The majority of differentially expressed RNAs were associated with cancer-related pathways. The dynamic RNA signals pinpointed different phases of tumor development over time. Stage-specific RNA profiles may be associated with tumor aggressiveness. Our results improve the molecular understanding of carcinogenesis. They indicate substantial opportunity for screening and improved treatment and will guide further research on early detection of LC. However, the dynamic nature of the RNA signals also suggests challenges for prediagnostic biomarker discovery.

@Article{Hochfeld2019,
  author       = {Lara M Hochfeld and Andreas Keller and Thomas Anhalt and Nadine Fricker and Markus M Nöthen and Stefanie Heilmann-Heimbach},
  title        = {Insights into Male Androgenetic Alopecia: Differential Gene Expression Profiling of Plucked Hair Follicles and Integration with Genetic Data},
  journal      = {Journal of Investigative Dermatology},
  publisher    = {Elsevier},
  year         = {2019},
  volume       = {139},
  issue        = {1},
  pages        = {235-238},
  issn         = {235-238},
  issn-linking = {235-238},
  month        = jan,
  doi          = {10.1016/j.jid.2018.06.182},
  pii          = {10.1016/j.jid.2018.06.182},
}

@Article{Juzenas2019,
  author       = {S Juzenas and M Hübenthal and S Zeissig and N Strüning and A Keller and D Schulte and M D'Amato and Carl Mårten Lindqvist and J Kupcinskas and S Schreiber and Jonas Halfvarson and G Hemmrich-Stanisak and A Franke},
  title        = {Sequencing-based hematopoietic miRNA landscape reveals common and distinct features of autoimmune inflammatory phenotypes},
  journal      = {Journal of Crohn's & Colitis},
  publisher    = {Oxford University Press},
  year         = {2019},
  volume       = {13},
  issue        = {Suppl. 1},
  pages        = {S614-S614},
  issn         = {S614-S614},
  issn-linking = {S614-S614},
  abstract     = {Background: MiRNAs represent a class of small non-coding RNAs which are involved in regulation of protein-coding gene expression. Being implicated in various processes such as development and regu-latory circuits of cells, miRNAs also play an important role in the etiology of a variety of diseases. Imbalance of the regulatory pro-cesses within immune system development and response may lead to disturbed production of pro-inflammatory cytokines and over-reactivity of the immune cells, thus causing relapsing inflamma-tion, a characteristic feature of inflammatory bowel disease (IBD). Recent studies of colonic miRNAs employed NGS for the distinction between CD, UC and healthy controls, or among different CD sub-types. However, NGS-based profiles of blood-circulating miRNAs have thus far not been investigated in the context of IBD together with other immune-mediated diseases, including ankylosing spon-dylitis, psoriasis, systemic lupus erythematosus, rheumatoid arthritis and sarcoidosis, as well as non-immune hemolytic-uremic syndrome. Methods: Study participants were recruited in Germany and Sweden, where peripheral blood samples (PAXgene) as well as phenotypical and clinical information (such as treatment status, dis-ease activity and location) was collected. Small RNA transcriptomes of 680 individuals (Figure 1) were sequenced using Illumina NGS platform. Small RNA-seq data preprocessing and quantification were performed using cutadapt and miraligner (ref. miRBase v22), respectively. Differential expression analysis (DESeq2) and correla-tion (Spearman) analysis have been performed to identify disease activity-, trait- and treatment-specific miRNA signatures. These sig-natures were then utilized in a machine-learning approach to build classification models for IBD diagnostics. Results: The results of multiple pairwise differential expression anal-yses among different immune-mediated inflammatory conditions and healthy controls revealed inflammation-specific as well and dis-ease-specific deregulation of miRNAs. Correlation analysis identified miRNAs positively and negatively correlated with IBD activity. The preliminary results of machine learning classifiers based on miRNA profiles showed that median Matthews correlation coefficient for all model types showed remarkable predictive performance estimated as being 1.00 (median over main diagnoses), as well as ranging from 0.68 to 0.76 (median over CD location) and from 0.69 to 0.77 (median over UC extent). Conclusions: Immune-mediated inflammatory diseases share com-mon and distinct differentially expressed miRNAs, which have a potential to be used in the diagnostics of IBD, including the evalua-tion of the disease activity.},
  doi          = {10.1093/ecco-jcc/jjz046.002},
  pii          = {10.1093/ecco-jcc/jjz046.002},
}

Background: MiRNAs represent a class of small non-coding RNAs which are involved in regulation of protein-coding gene expression. Being implicated in various processes such as development and regu-latory circuits of cells, miRNAs also play an important role in the etiology of a variety of diseases. Imbalance of the regulatory pro-cesses within immune system development and response may lead to disturbed production of pro-inflammatory cytokines and over-reactivity of the immune cells, thus causing relapsing inflamma-tion, a characteristic feature of inflammatory bowel disease (IBD). Recent studies of colonic miRNAs employed NGS for the distinction between CD, UC and healthy controls, or among different CD sub-types. However, NGS-based profiles of blood-circulating miRNAs have thus far not been investigated in the context of IBD together with other immune-mediated diseases, including ankylosing spon-dylitis, psoriasis, systemic lupus erythematosus, rheumatoid arthritis and sarcoidosis, as well as non-immune hemolytic-uremic syndrome. Methods: Study participants were recruited in Germany and Sweden, where peripheral blood samples (PAXgene) as well as phenotypical and clinical information (such as treatment status, dis-ease activity and location) was collected. Small RNA transcriptomes of 680 individuals (Figure 1) were sequenced using Illumina NGS platform. Small RNA-seq data preprocessing and quantification were performed using cutadapt and miraligner (ref. miRBase v22), respectively. Differential expression analysis (DESeq2) and correla-tion (Spearman) analysis have been performed to identify disease activity-, trait- and treatment-specific miRNA signatures. These sig-natures were then utilized in a machine-learning approach to build classification models for IBD diagnostics. Results: The results of multiple pairwise differential expression anal-yses among different immune-mediated inflammatory conditions and healthy controls revealed inflammation-specific as well and dis-ease-specific deregulation of miRNAs. Correlation analysis identified miRNAs positively and negatively correlated with IBD activity. The preliminary results of machine learning classifiers based on miRNA profiles showed that median Matthews correlation coefficient for all model types showed remarkable predictive performance estimated as being 1.00 (median over main diagnoses), as well as ranging from 0.68 to 0.76 (median over CD location) and from 0.69 to 0.77 (median over UC extent). Conclusions: Immune-mediated inflammatory diseases share com-mon and distinct differentially expressed miRNAs, which have a potential to be used in the diagnostics of IBD, including the evalua-tion of the disease activity.

@Article{Volz2019,
  author       = {Carsten Volz and Jonas Ramoni and Stephan Beisken and Valentina Galata and Andreas Keller and Achim Plum and Andreas E Posch and Rolf Müller},
  title        = {Clinical Resistome Screening of 1,110 Escherichia coli Isolates Efficiently Recovers Diagnostically Relevant Antibiotic Resistance Biomarkers and Potential Novel Resistance Mechanisms},
  journal      = {Frontiers in microbiology},
  publisher    = {Frontiers},
  year         = {2019},
  volume       = {10},
  pages        = {1671},
  issn         = {1671},
  issn-linking = {1671},
  abstract     = {Multidrug-resistant pathogens represent one of the biggest global healthcare challenges. Molecular diagnostics can guide effective antibiotics therapy but relies on validated, predictive biomarkers. Here we present a novel, universally applicable workflow for rapid identification of antimicrobial resistance (AMR) biomarkers from clinical Escherichia coli isolates and quantitatively evaluate the potential to recover causal biomarkers for observed resistance phenotypes. For this, a metagenomic plasmid library from 1,110 clinical E. coli isolates was created and used for high-throughput screening to identify biomarker candidates against Tobramycin (TOB), Ciprofloxacin (CIP), and Trimethoprim-Sulfamethoxazole (TMP-SMX). Identified candidates were further validated in vitro and also evaluated in silico for their diagnostic performance based on matched genotype-phenotype data. AMR biomarkers recovered by the metagenomics screening approach mechanistically explained 77% of observed resistance phenotypes for Tobramycin, 76% for Trimethoprim-Sulfamethoxazole, and 20% Ciprofloxacin. Sensitivity for Ciprofloxacin resistance detection could be improved to 97% by complementing results with AMR biomarkers that are undiscoverable due to intrinsic limitations of the workflow. Additionally, when combined in a multiplex diagnostic in silico panel, the identified AMR biomarkers reached promising positive and negative predictive values of up to 97 and 99%, respectively. Finally, we demonstrate that the developed workflow can be used to identify potential novel resistance mechanisms.},
  doi          = {10.3389/fmicb.2019.01671},
  pii          = {10.3389/fmicb.2019.01671},
}

Multidrug-resistant pathogens represent one of the biggest global healthcare challenges. Molecular diagnostics can guide effective antibiotics therapy but relies on validated, predictive biomarkers. Here we present a novel, universally applicable workflow for rapid identification of antimicrobial resistance (AMR) biomarkers from clinical Escherichia coli isolates and quantitatively evaluate the potential to recover causal biomarkers for observed resistance phenotypes. For this, a metagenomic plasmid library from 1,110 clinical E. coli isolates was created and used for high-throughput screening to identify biomarker candidates against Tobramycin (TOB), Ciprofloxacin (CIP), and Trimethoprim-Sulfamethoxazole (TMP-SMX). Identified candidates were further validated in vitro and also evaluated in silico for their diagnostic performance based on matched genotype-phenotype data. AMR biomarkers recovered by the metagenomics screening approach mechanistically explained 77% of observed resistance phenotypes for Tobramycin, 76% for Trimethoprim-Sulfamethoxazole, and 20% Ciprofloxacin. Sensitivity for Ciprofloxacin resistance detection could be improved to 97% by complementing results with AMR biomarkers that are undiscoverable due to intrinsic limitations of the workflow. Additionally, when combined in a multiplex diagnostic in silico panel, the identified AMR biomarkers reached promising positive and negative predictive values of up to 97 and 99%, respectively. Finally, we demonstrate that the developed workflow can be used to identify potential novel resistance mechanisms.

@Article{Fehlmann2019,
  author       = {Tobias Fehlmann and Thomas Laufer and Christina Backes and Mustafa Kahramann and Julia Alles and Ulrike Fischer and Marie Minet and Nicole Ludwig and Fabian Kern and Tim Kehl and Valentina Galata and Aneta Düsterloh and Hannah Schrörs and Jochen Kohlhaas and Robert Bals and Hanno Huwer and Lars Geffers and Rejko Krüger and Rudi Balling and Hans-Peter Lenhof and Eckart Meese and Andreas Keller},
  title        = {Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity},
  journal      = {RNA biology},
  publisher    = {Taylor & Francis},
  year         = {2019},
  volume       = {16},
  issue        = {1},
  pages        = {93-103},
  issn         = {93-103},
  issn-linking = {93-103},
  month        = jan,
  abstract     = {The validation of microRNAs (miRNAs) identified by next generation sequencing involves amplification-free and hybridization-based detection of transcripts as criteria for confirming valid miRNAs. Since respective validation is frequently not performed, miRNA repositories likely still contain a substantial fraction of false positive candidates while true miRNAs are not stored in the repositories yet. Especially if downstream analyses are performed with these candidates (e.g. target or pathway prediction), the results may be misleading. In the present study, we evaluated 558 mature miRNAs from miRBase and 1,709 miRNA candidates from next generation sequencing experiments by amplification-free hybridization and investigated their distributions in patients with various disease conditions. Notably, the most significant miRNAs in diseases are often not contained in the miRBase. However, these candidates are evolutionary highly conserved. From the expression patterns, target gene and pathway analyses and evolutionary conservation analyses, we were able to shed light on the complexity of miRNAs in humans. Our data also highlight that a more thorough validation of miRNAs identified by next generation sequencing is required. The results are available in miRCarta (https://mircarta.cs.uni-saarland.de).},
  doi          = {10.1080/15476286.2018.1559689},
  pii          = {10.1080/15476286.2018.1559689},
}

The validation of microRNAs (miRNAs) identified by next generation sequencing involves amplification-free and hybridization-based detection of transcripts as criteria for confirming valid miRNAs. Since respective validation is frequently not performed, miRNA repositories likely still contain a substantial fraction of false positive candidates while true miRNAs are not stored in the repositories yet. Especially if downstream analyses are performed with these candidates (e.g. target or pathway prediction), the results may be misleading. In the present study, we evaluated 558 mature miRNAs from miRBase and 1,709 miRNA candidates from next generation sequencing experiments by amplification-free hybridization and investigated their distributions in patients with various disease conditions. Notably, the most significant miRNAs in diseases are often not contained in the miRBase. However, these candidates are evolutionary highly conserved. From the expression patterns, target gene and pathway analyses and evolutionary conservation analyses, we were able to shed light on the complexity of miRNAs in humans. Our data also highlight that a more thorough validation of miRNAs identified by next generation sequencing is required. The results are available in miRCarta (https://mircarta.cs.uni-saarland.de).

@Article{Hart2019,
  author       = {Martin Hart and Barbara Walch-Rückheim and Kim S Friedmann and Stefanie Rheinheimer and Tanja Tänzer and Birgit Glombitza and Martina Sester and Hans-Peter Lenhof and Markus Hoth and Eva C Schwarz and Andreas Keller and Eckart Meese},
  title        = {miR-34a: a new player in the regulation of T cell function by modulation of NF-κB signaling},
  journal      = {Cell death & disease},
  publisher    = {Nature Publishing Group},
  year         = {2019},
  volume       = {10},
  issue        = {2},
  pages        = {46},
  issn         = {46},
  issn-linking = {46},
  month        = jan,
  abstract     = {NF-κB functions as modulator of T cell receptor-mediated signaling and transcriptional regulator of miR-34a. Our in silico analysis revealed that miR-34a impacts the NF-κB signalosome with miR-34a binding sites in 14 key members of the NF-κB signaling pathway. Functional analysis identified five target genes of miR-34a including PLCG1, CD3E, PIK3CB, TAB2, and NFΚBIA. Overexpression of miR-34a in CD4+ and CD8+ T cells led to a significant decrease of NFΚBIA as the most downstream cytoplasmic NF-κB member, a reduced cell surface abundance of TCRA and CD3E, and to a reduction of T cell killing capacity. Inhibition of miR-34a caused an increase of NFΚBIA, TCRA, and CD3E. Notably, activation of CD4+ and CD8+ T cells entrails a gradual increase of miR-34a. Our results lend further support to a model with miR-34a as a central NF-κB regulator in T cells.},
  doi          = {10.1038/s41419-018-1295-1},
  pii          = {10.1038/s41419-018-1295-1},
}

NF-κB functions as modulator of T cell receptor-mediated signaling and transcriptional regulator of miR-34a. Our in silico analysis revealed that miR-34a impacts the NF-κB signalosome with miR-34a binding sites in 14 key members of the NF-κB signaling pathway. Functional analysis identified five target genes of miR-34a including PLCG1, CD3E, PIK3CB, TAB2, and NFΚBIA. Overexpression of miR-34a in CD4+ and CD8+ T cells led to a significant decrease of NFΚBIA as the most downstream cytoplasmic NF-κB member, a reduced cell surface abundance of TCRA and CD3E, and to a reduction of T cell killing capacity. Inhibition of miR-34a caused an increase of NFΚBIA, TCRA, and CD3E. Notably, activation of CD4+ and CD8+ T cells entrails a gradual increase of miR-34a. Our results lend further support to a model with miR-34a as a central NF-κB regulator in T cells.

@Article{Ayoubian2019,
  author       = {Hiresh Ayoubian and Nicole Ludwig and Tobias Fehlmann and Jennifer Menegatti and Laura Gröger and Eleni Anastasiadou and Pankaj Trivedi and Andreas Keller and Eckart Meese and Friedrich A Grässer},
  title        = {Epstein-Barr Virus Infection of Cell Lines Derived from Diffuse Large B-Cell Lymphomas Alters MicroRNA Loading of the Ago2 Complex},
  journal      = {Journal of virology},
  publisher    = {American Society for Microbiology Journals},
  year         = {2019},
  volume       = {93},
  issue        = {3},
  pages        = {e01297-18},
  issn         = {e01297-18},
  issn-linking = {e01297-18},
  month        = feb,
  abstract     = {Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoid tumor which is occasionally Epstein-Barr virus (EBV) positive and is further subtyped as activated B-cell DLBCL (ABC-DLBCL) and germinal center B-cell DLBCL (GCB-DLBCL), which has implications for prognosis and treatment. We performed Ago2 RNA immunoprecipitation followed by high-throughput RNA sequencing (Ago2-RIP-seq) to capture functionally active microRNAs (miRNAs) in EBV-negative ABC-DLBCL and GCB-DLBCL cell lines and their EBV-infected counterparts. In parallel, total miRNA profiles of these cells were determined to capture the cellular miRNA profile for comparison with the functionally active profile. Selected miRNAs with differential abundances were validated using real-time quantitative PCR (RT-qPCR) and Northern blotting. We found 6 miRNAs with differential abundances (2 upregulated and 4 downregulated miRNAs) between EBV-negative and -positive ABC-DLBCL cells and 12 miRNAs with differential abundances (3 upregulated and 9 downregulated miRNAs) between EBV-negative and -positive GCB-DLBCL cells. Eight and twelve miRNAs were confirmed using RT-qPCR in ABC-DLBCL and GCB-DLBCL cells, respectively. Selected miRNAs were analyzed in additional type I/II versus type III EBV latency DLBCL cell lines. Furthermore, upregulation of miR-221-3p and downregulation of let7c-5p in ABC-DLBCL cells and upregulation of miR-363-3p and downregulation of miR-423-5p in GCB-DLBCL cells were verified using RIP-Northern blotting. Our comprehensive sequence analysis of the DLBCL miRNA profiles identified sets of deregulated miRNAs by Ago2-RIP-seq. Our Ago2-IP-seq miRNA profile could be considered an important data set for the detection of deregulated functionally active miRNAs in DLBCLs and could possibly lead to the identification of miRNAs as biomarkers for the classification of DLBCLs or even as targets for personalized targeted treatment. IMPORTANCE Diffuse large B-cell lymphoma (DLBCL) is a highly aggressive tumor of lymphoid origin which is occasionally Epstein-Barr virus (EBV) positive. MicroRNAs are found in most multicellular organisms and even in viruses such as EBV. They regulate the synthesis of proteins by binding to their cognate mRNA. MicroRNAs are tethered to their target mRNAs by “Argonaute” proteins. Here we compared the overall miRNA content of the Ago2 complex by differential loading to the overall content of miRNAs in two DLBCL cell lines and their EBV-converted counterparts. In all cell lines, the Ago2 load was different from the overall expression of miRNAs. In addition, the loading of the Ago2 complex was changed upon infection with EBV. This indicates that the virus not only changes the overall content of miRNAs but also influences the expression of proteins by affecting the Ago complexes.},
  doi          = {10.1128/JVI.01297-18},
  pii          = {10.1128/JVI.01297-18},
}

Diffuse large B-cell lymphoma (DLBCL) is an aggressive lymphoid tumor which is occasionally Epstein-Barr virus (EBV) positive and is further subtyped as activated B-cell DLBCL (ABC-DLBCL) and germinal center B-cell DLBCL (GCB-DLBCL), which has implications for prognosis and treatment. We performed Ago2 RNA immunoprecipitation followed by high-throughput RNA sequencing (Ago2-RIP-seq) to capture functionally active microRNAs (miRNAs) in EBV-negative ABC-DLBCL and GCB-DLBCL cell lines and their EBV-infected counterparts. In parallel, total miRNA profiles of these cells were determined to capture the cellular miRNA profile for comparison with the functionally active profile. Selected miRNAs with differential abundances were validated using real-time quantitative PCR (RT-qPCR) and Northern blotting. We found 6 miRNAs with differential abundances (2 upregulated and 4 downregulated miRNAs) between EBV-negative and -positive ABC-DLBCL cells and 12 miRNAs with differential abundances (3 upregulated and 9 downregulated miRNAs) between EBV-negative and -positive GCB-DLBCL cells. Eight and twelve miRNAs were confirmed using RT-qPCR in ABC-DLBCL and GCB-DLBCL cells, respectively. Selected miRNAs were analyzed in additional type I/II versus type III EBV latency DLBCL cell lines. Furthermore, upregulation of miR-221-3p and downregulation of let7c-5p in ABC-DLBCL cells and upregulation of miR-363-3p and downregulation of miR-423-5p in GCB-DLBCL cells were verified using RIP-Northern blotting. Our comprehensive sequence analysis of the DLBCL miRNA profiles identified sets of deregulated miRNAs by Ago2-RIP-seq. Our Ago2-IP-seq miRNA profile could be considered an important data set for the detection of deregulated functionally active miRNAs in DLBCLs and could possibly lead to the identification of miRNAs as biomarkers for the classification of DLBCLs or even as targets for personalized targeted treatment. IMPORTANCE Diffuse large B-cell lymphoma (DLBCL) is a highly aggressive tumor of lymphoid origin which is occasionally Epstein-Barr virus (EBV) positive. MicroRNAs are found in most multicellular organisms and even in viruses such as EBV. They regulate the synthesis of proteins by binding to their cognate mRNA. MicroRNAs are tethered to their target mRNAs by “Argonaute” proteins. Here we compared the overall miRNA content of the Ago2 complex by differential loading to the overall content of miRNAs in two DLBCL cell lines and their EBV-converted counterparts. In all cell lines, the Ago2 load was different from the overall expression of miRNAs. In addition, the loading of the Ago2 complex was changed upon infection with EBV. This indicates that the virus not only changes the overall content of miRNAs but also influences the expression of proteins by affecting the Ago complexes.

@Article{Rocha2019,
  author       = {Sara Rocha and Joana Carvalho and Patrícia Oliveira and Maren Voglstaetter and Domitille Schvartz and Andreas R Thomsen and Nadia Walter and Richa Khanduri and Jean-Charles Sanchez and Andreas Keller and Carla Oliveira and Irina Nazarenko},
  title        = {3d cellular architecture affects microrna and protein cargo of extracellular vesicles},
  journal      = {Advanced Science},
  year         = {2019},
  volume       = {6},
  issue        = {4},
  pages        = {1800948},
  issn         = {1800948},
  issn-linking = {1800948},
  month        = feb,
  abstract     = {The success of malignant tumors is conditioned by the intercellular communication between tumor cells and their microenvironment, with extracellular vesicles (EVs) acting as main mediators. While the value of 3D conditions to study tumor cells is well established, the impact of cellular architecture on EV content and function is not investigated yet. Here, a recently developed 3D cell culture microwell array is adapted for EV production and a comprehensive comparative analysis of biochemical features, RNA and proteomic profiles of EVs secreted by 2D vs 3D cultures of gastric cancer cells, is performed. 3D cultures are significantly more efficient in producing EVs than 2D cultures. Global upregulation of microRNAs and downregulation of proteins in 3D are observed, indicating their dynamic coregulation in response to cellular architecture, with the ADP-ribosylation factor 6 signaling pathway significantly downregulated in 3D EVs. The data strengthen the biological relevance of cellular architecture for production and cargo of EVs.},
  doi          = {10.1002/advs.201800948},
  pii          = {10.1002/advs.201800948},
}

The success of malignant tumors is conditioned by the intercellular communication between tumor cells and their microenvironment, with extracellular vesicles (EVs) acting as main mediators. While the value of 3D conditions to study tumor cells is well established, the impact of cellular architecture on EV content and function is not investigated yet. Here, a recently developed 3D cell culture microwell array is adapted for EV production and a comprehensive comparative analysis of biochemical features, RNA and proteomic profiles of EVs secreted by 2D vs 3D cultures of gastric cancer cells, is performed. 3D cultures are significantly more efficient in producing EVs than 2D cultures. Global upregulation of microRNAs and downregulation of proteins in 3D are observed, indicating their dynamic coregulation in response to cellular architecture, with the ADP-ribosylation factor 6 signaling pathway significantly downregulated in 3D EVs. The data strengthen the biological relevance of cellular architecture for production and cargo of EVs.

@Article{Diener2019,
  author       = {Caroline Diener and Valentina Galata and Andreas Keller and Eckart Meese},
  title        = {MicroRNA profiling from dried blood samples},
  journal      = {Critical reviews in clinical laboratory sciences},
  publisher    = {Taylor & Francis},
  year         = {2019},
  volume       = {56},
  issue        = {2},
  pages        = {111-117},
  issn         = {111-117},
  issn-linking = {111-117},
  month        = feb,
  abstract     = {10.1080/10408363.2018.1561641},
  doi          = {10.1080/10408363.2018.1561641},
  pii          = {MicroRNAs (miRNAs) hold great promise as blood-borne and circulating biomarkers for numerous diseases. However, the reliability of such liquid biopsies is particularly impacted by problems associated with the handling of biological liquids in the pre-analytical stage of biomarker processing. Dried blood spots (DBS) and other capillary blood microsampling devices offer a way to circumvent many of these complications. DBS are supposed to be far less sensitive to collection protocols, storage conditions, and transport processes, while offering the possibility for a decentralized sample collection. In addition, DBS are minimally invasive and require very small amounts of blood, thereby facilitating blood collection from small children or patients at risk by blood drawing. Here, we summarize the current state of knowledge about DBS-derived miRNAs. Experimental studies on miRNA from DBS especially emphasize the influence of the adsorptive material and the importance of drying and rehydration protocols. The present studies are, however, difficult to compare as they use different readout-systems, ranging from PCR-based quantification of single miRNAs to next-generation sequencing (NGS) of the entire miRNome. The data underscore the need for procedure standardization and the development of general guidelines on handling and evaluating miRNA biomarkers derived from DBS.},
}

10.1080/10408363.2018.1561641

@Article{Manier2019,
  author       = {Sascha K Manier and Andreas Keller and Jan Schäper and Markus R Meyer},
  title        = {Untargeted metabolomics by high resolution mass spectrometry coupled to normal and reversed phase liquid chromatography as a tool to study the in vitro biotransformation of new psychoactive substances},
  journal      = {Scientific reports},
  publisher    = {Nature Publishing Group},
  year         = {2019},
  volume       = {9},
  issue        = {1},
  pages        = {2741},
  issn         = {2741},
  issn-linking = {2741},
  month        = feb,
  abstract     = {In 2016, several synthetic cathinones were seized by the State Bureau of Criminal Investigation Bavaria in Germany. Due to their previous appearances in other countries their metabolism was already investigated in human urine as well as different in vitro models. These investigations were conducted using ordinary metabolism studies for drugs of abuse by using general knowledge about drug metabolism and visual comparison of mass spectra. The present study aimed to use untargeted metabolomics to support and improve those methods that highly depend on the investigators experience. Incubations were conducted using pooled human liver microsomes (pHLM) and the two cathinones 1-phenyl-2-(1-pyrrolidinyl)-1-butanone and 1-phenyl-2-(1-pyrrolidinyl)-1-heptanone. Samples were analyzed by LC-HRMS/MS using a metabolomics workflow consisting of a reversed phase or normal phase separation followed by electrospray ionization and full scan in positive or negative mode. LC-MS data was afterwards statistically evaluated using principal component analysis, t-distributed stochastic neighborhood embedding, and hierarchical clustering. Significant features were then identified using MS/MS. The workflow revealed 24 significant features after 1-phenyl-2-(1-pyrrolidinyl)-1-butanone and 39 after 1-phenyl-2-(1-pyrrolidinyl)-1-heptanone incubation, consisting of adducts, artifacts, isomers, and metabolites. The applied untargeted metabolomics strategy was able to find almost all of the metabolites that were previously described for 1-phenyl-2-(1-pyrrolidinyl)-1-butanone in literature as well as three additional metabolites. Concerning 1-phenyl-2-(1-pyrrolidinyl)-1-heptanone biotransformation in pHLM, merely four metabolites described in primary human hepatocytes and human urine were not found. This study revealed that untargeted metabolomics workflows are well suited to support biotransformation studies at least of the investigated compounds in pHLM.},
  doi          = {10.1038/s41598-019-39235-w},
  pii          = {10.1038/s41598-019-39235-w},
}

In 2016, several synthetic cathinones were seized by the State Bureau of Criminal Investigation Bavaria in Germany. Due to their previous appearances in other countries their metabolism was already investigated in human urine as well as different in vitro models. These investigations were conducted using ordinary metabolism studies for drugs of abuse by using general knowledge about drug metabolism and visual comparison of mass spectra. The present study aimed to use untargeted metabolomics to support and improve those methods that highly depend on the investigators experience. Incubations were conducted using pooled human liver microsomes (pHLM) and the two cathinones 1-phenyl-2-(1-pyrrolidinyl)-1-butanone and 1-phenyl-2-(1-pyrrolidinyl)-1-heptanone. Samples were analyzed by LC-HRMS/MS using a metabolomics workflow consisting of a reversed phase or normal phase separation followed by electrospray ionization and full scan in positive or negative mode. LC-MS data was afterwards statistically evaluated using principal component analysis, t-distributed stochastic neighborhood embedding, and hierarchical clustering. Significant features were then identified using MS/MS. The workflow revealed 24 significant features after 1-phenyl-2-(1-pyrrolidinyl)-1-butanone and 39 after 1-phenyl-2-(1-pyrrolidinyl)-1-heptanone incubation, consisting of adducts, artifacts, isomers, and metabolites. The applied untargeted metabolomics strategy was able to find almost all of the metabolites that were previously described for 1-phenyl-2-(1-pyrrolidinyl)-1-butanone in literature as well as three additional metabolites. Concerning 1-phenyl-2-(1-pyrrolidinyl)-1-heptanone biotransformation in pHLM, merely four metabolites described in primary human hepatocytes and human urine were not found. This study revealed that untargeted metabolomics workflows are well suited to support biotransformation studies at least of the investigated compounds in pHLM.

@Article{Alles2019,
  author       = {Julia Alles and Tobias Fehlmann and Ulrike Fischer and Christina Backes and Valentina Galata and Marie Minet and Martin Hart and Masood Abu-Halima and Friedrich A Grässer and Hans-Peter Lenhof and Andreas Keller and Eckart Meese},
  title        = {An estimate of the total number of true human miRNAs},
  journal      = {Nucleic acids research},
  publisher    = {Oxford University Press},
  year         = {2019},
  volume       = {47},
  issue        = {7},
  pages        = {3353-3364},
  issn         = {3353-3364},
  issn-linking = {3353-3364},
  month        = mar,
  abstract     = {While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.7 billion sequencing reads and excluded falsely annotated and low quality data. Our high-throughput analysis identified 65% of 24 127 mature miRNA candidates as likely false-positives. Using northern blotting, we experimentally validated miRBase entries and novel miRNA candidates. By exogenous overexpression of 108 precursors that encode 205 mature miRNAs, we confirmed 68.5% of the miRBase entries with the confirmation rate going up to 94.4% for the high-confidence entries and 18.3% of the novel miRNA candidates. Analyzing endogenous miRNAs, we verified the expression of 8 miRNAs in 12 different human cell lines. In total, we extrapolated 2300 true human mature miRNAs, 1115 of which are currently annotated in miRBase V22. The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNAs.},
  doi          = {10.1093/nar/gkz097},
  pii          = {10.1093/nar/gkz097},
}

While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.7 billion sequencing reads and excluded falsely annotated and low quality data. Our high-throughput analysis identified 65% of 24 127 mature miRNA candidates as likely false-positives. Using northern blotting, we experimentally validated miRBase entries and novel miRNA candidates. By exogenous overexpression of 108 precursors that encode 205 mature miRNAs, we confirmed 68.5% of the miRBase entries with the confirmation rate going up to 94.4% for the high-confidence entries and 18.3% of the novel miRNA candidates. Analyzing endogenous miRNAs, we verified the expression of 8 miRNAs in 12 different human cell lines. In total, we extrapolated 2300 true human mature miRNAs, 1115 of which are currently annotated in miRBase V22. The experimentally validated miRNAs will contribute to revising targetomes hypothesized by utilizing falsely annotated miRNAs.

@Article{Kehl2019,
  author       = {Tim Kehl and Lara Schneider and Kathrin Kattler and Daniel Stöckel and Jenny Wegert and Nico Gerstner and Nicole Ludwig and Ute Distler and Stefan Tenzer and Manfred Gessler and Jörn Walter and Andreas Keller and Norbert Graf and Eckart Meese and Hans-Peter Lenhof},
  title        = {The role of TCF3 as potential master regulator in blastemal Wilms tumors},
  journal      = {International journal of cancer},
  publisher    = {John Wiley & Sons, Inc.},
  year         = {2019},
  volume       = {144},
  issue        = {6},
  pages        = {1432-1443},
  issn         = {1432-1443},
  issn-linking = {1432-1443},
  month        = mar,
  abstract     = {Wilms tumors are the most common type of pediatric kidney tumors. While the overall prognosis for patients is favorable, especially tumors that exhibit a blastemal subtype after preoperative chemotherapy have a poor prognosis. For an improved risk assessment and therapy stratification, it is essential to identify the driving factors that are distinctive for this aggressive subtype. In our study, we compared gene expression profiles of 33 tumor biopsies (17 blastemal and 16 other tumors) after neoadjuvant chemotherapy. The analysis of this dataset using the Regulator Gene Association Enrichment algorithm successfully identified several biomarkers and associated molecular mechanisms that distinguish between blastemal and nonblastemal Wilms tumors. Specifically, regulators involved in embryonic development and epigenetic processes like chromatin remodeling and histone modification play an essential role in blastemal tumors. In this context, we especially identified TCF3 as the central regulatory element. Furthermore, the comparison of ChIP-Seq data of Wilms tumor cell cultures from a blastemal mouse xenograft and a stromal tumor provided further evidence that the chromatin states of blastemal cells share characteristics with embryonic stem cells that are not present in the stromal tumor cell line. These stem-cell like characteristics could potentially add to the increased malignancy and chemoresistance of the blastemal subtype. Along with TCF3, we detected several additional biomarkers that are distinctive for blastemal Wilms tumors after neoadjuvant chemotherapy and that may provide leads for new therapeutic regimens.},
  doi          = {10.1002/ijc.31834},
  pii          = {10.1002/ijc.31834},
}

Wilms tumors are the most common type of pediatric kidney tumors. While the overall prognosis for patients is favorable, especially tumors that exhibit a blastemal subtype after preoperative chemotherapy have a poor prognosis. For an improved risk assessment and therapy stratification, it is essential to identify the driving factors that are distinctive for this aggressive subtype. In our study, we compared gene expression profiles of 33 tumor biopsies (17 blastemal and 16 other tumors) after neoadjuvant chemotherapy. The analysis of this dataset using the Regulator Gene Association Enrichment algorithm successfully identified several biomarkers and associated molecular mechanisms that distinguish between blastemal and nonblastemal Wilms tumors. Specifically, regulators involved in embryonic development and epigenetic processes like chromatin remodeling and histone modification play an essential role in blastemal tumors. In this context, we especially identified TCF3 as the central regulatory element. Furthermore, the comparison of ChIP-Seq data of Wilms tumor cell cultures from a blastemal mouse xenograft and a stromal tumor provided further evidence that the chromatin states of blastemal cells share characteristics with embryonic stem cells that are not present in the stromal tumor cell line. These stem-cell like characteristics could potentially add to the increased malignancy and chemoresistance of the blastemal subtype. Along with TCF3, we detected several additional biomarkers that are distinctive for blastemal Wilms tumors after neoadjuvant chemotherapy and that may provide leads for new therapeutic regimens.

@Article{Fehlmann2019,
  author       = {Tobias Fehlmann and Christina Backes and Marcello Pirritano and Thomas Laufer and Valentina Galata and Fabian Kern and Mustafa Kahraman and Gilles Gasparoni and Nicole Ludwig and Hans-Peter Lenhof and Henrike A Gregersen and Richard Francke and Eckart Meese and Martin Simon and Andreas Keller},
  title        = {The sncRNA Zoo: a repository for circulating small noncoding RNAs in animals},
  journal      = {Nucleic acids research},
  publisher    = {Oxford University Press},
  year         = {2019},
  volume       = {47},
  issue        = {9},
  pages        = {4431-4441},
  issn         = {4431-4441},
  issn-linking = {4431-4441},
  month        = apr,
  abstract     = {The repertoire of small noncoding RNAs (sncRNAs), particularly miRNAs, in animals is considered to be evolutionarily conserved. Studies on sncRNAs are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expression (including miRNAs, snoRNAs, YRNAs and tRNAs), we performed low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens. Notably, none of the species under investigation were previously annotated in any miRNA reference database. Sequencing was performed on blood cells as they are amongst the most accessible, stable and abundant sources of the different sncRNA classes. We evaluated and compared the composition and nature of sncRNAs across the different species by computational approaches. While the distribution of sncRNAs in the different RNA classes varied significantly, general evolutionary patterns were maintained. In particular, miRNA sequences and expression were found to be even more conserved than previously assumed. To make the results available for other researchers, all data, including expression profiles at the species and family levels, and different tools for viewing, filtering and searching the data are freely available in the online resource ASRA (Animal sncRNA Atlas) at https://www.ccb.uni-saarland.de/asra/.},
  doi          = {10.1093/nar/gkz227},
  pii          = {10.1093/nar/gkz227},
}

The repertoire of small noncoding RNAs (sncRNAs), particularly miRNAs, in animals is considered to be evolutionarily conserved. Studies on sncRNAs are often largely based on homology-based information, relying on genomic sequence similarity and excluding actual expression data. To obtain information on sncRNA expression (including miRNAs, snoRNAs, YRNAs and tRNAs), we performed low-input-volume next-generation sequencing of 500 pg of RNA from 21 animals at two German zoological gardens. Notably, none of the species under investigation were previously annotated in any miRNA reference database. Sequencing was performed on blood cells as they are amongst the most accessible, stable and abundant sources of the different sncRNA classes. We evaluated and compared the composition and nature of sncRNAs across the different species by computational approaches. While the distribution of sncRNAs in the different RNA classes varied significantly, general evolutionary patterns were maintained. In particular, miRNA sequences and expression were found to be even more conserved than previously assumed. To make the results available for other researchers, all data, including expression profiles at the species and family levels, and different tools for viewing, filtering and searching the data are freely available in the online resource ASRA (Animal sncRNA Atlas) at https://www.ccb.uni-saarland.de/asra/.

@Article{Schneider2019,
  author       = {Lara Schneider and Tim Kehl and Kristina Thedinga and Nadja Liddy Grammes and Christina Backes and Christopher Mohr and Benjamin Schubert and Kerstin Lenhof and Nico Gerstner and Andreas Daniel Hartkopf and Markus Wallwiener and Oliver Kohlbacher and Andreas Keller and Eckart Meese and Norbert Graf and Hans-Peter Lenhof},
  title        = {ClinOmicsTrailbc: a visual analytics tool for breast cancer treatment stratification},
  journal      = {Bioinformatics},
  year         = {2019},
  pages        = {1367-4803},
  issn         = {1367-4803},
  issn-linking = {1367-4803},
  month        = apr,
  abstract     = {Motivation: Breast cancer is the second leading cause of cancer death among women. Tumors, even of the same histopathological subtype, exhibit a high genotypic diversity that impedes therapy stratification and that hence must be accounted for in the treatment decision-making process. Results: Here, we present ClinOmicsTrailbc, a comprehensive visual analytics tool for breast cancer decision support that provides a holistic assessment of standard-of-care targeted drugs, candidates for drug repositioning and immunotherapeutic approaches. To this end, our tool analyzes and visualizes clinical markers and (epi-)genomics and transcriptomics datasets to identify and evaluate the tumor’s main driver mutations, the tumor mutational burden, activity patterns of core cancer-relevant pathways, drug-specific biomarkers, the status of molecular drug targets and pharmacogenomic influences. In order to demonstrate ClinOmicsTrailbc’s rich functionality, we present three case studies highlighting various ways in which ClinOmicsTrailbc can support breast cancer precision medicine. ClinOmicsTrailbc is a powerful integrated visual analytics tool for breast cancer research in general and for therapy stratification in particular, assisting oncologists to find the best possible treatment options for their breast cancer patients based on actionable, evidence-based results. Availability and implementation: ClinOmicsTrailbc can be freely accessed at https://clinomicstrail.bioinf.uni-sb.de. Supplementary information: Supplementary data are available at Bioinformatics online.},
  doi          = {10.1093/bioinformatics/btz302},
  pii          = {10.1093/bioinformatics/btz302},
}

Motivation: Breast cancer is the second leading cause of cancer death among women. Tumors, even of the same histopathological subtype, exhibit a high genotypic diversity that impedes therapy stratification and that hence must be accounted for in the treatment decision-making process. Results: Here, we present ClinOmicsTrailbc, a comprehensive visual analytics tool for breast cancer decision support that provides a holistic assessment of standard-of-care targeted drugs, candidates for drug repositioning and immunotherapeutic approaches. To this end, our tool analyzes and visualizes clinical markers and (epi-)genomics and transcriptomics datasets to identify and evaluate the tumor’s main driver mutations, the tumor mutational burden, activity patterns of core cancer-relevant pathways, drug-specific biomarkers, the status of molecular drug targets and pharmacogenomic influences. In order to demonstrate ClinOmicsTrailbc’s rich functionality, we present three case studies highlighting various ways in which ClinOmicsTrailbc can support breast cancer precision medicine. ClinOmicsTrailbc is a powerful integrated visual analytics tool for breast cancer research in general and for therapy stratification in particular, assisting oncologists to find the best possible treatment options for their breast cancer patients based on actionable, evidence-based results. Availability and implementation: ClinOmicsTrailbc can be freely accessed at https://clinomicstrail.bioinf.uni-sb.de. Supplementary information: Supplementary data are available at Bioinformatics online.

@Article{Abu-Halima2019,
  author       = {Masood Abu-Halima and Basim M Ayesh and Martin Hart and Julia Alles and Ulrike Fischer and Mohamad Hammadeh and Andreas Keller and Mahmoud Huleihel and Eckart Meese},
  title        = {Differential expression of miR-23a/b-3p and its target genes in male patients with subfertility},
  journal      = {Fertility and sterility},
  publisher    = {Elsevier},
  year         = {2019},
  volume       = {112},
  issue        = {2},
  pages        = {241-242},
  issn         = {241-242},
  issn-linking = {241-242},
  month        = may,
  abstract     = {Objective: To elucidate the potential regulatory function of miR-23a/b-3p on spermatogenesis-specific genes. Design: Reverse transcription quantitative polymerase chain reaction (RT-qPCR) validation, Northern blot, dual luciferase assay, and Western blot confirmation. Setting: University research and clinical institutes. Patient(s): A total of 115 men presenting at an infertility clinic. Intervention(s): None. Main Outcome Measure(s): Significant higher abundance levels of miR-23a/b-3p and lower abundance levels of PFKFB4, HMMR, SPATA6, and TEX15 in oligoasthenozoospermic men compared with those in normozoospermic men. Result(s): In oligoasthenozoospermic men, the abundance levels of miR-23a/b-3p were significantly higher when compared with controls as determined by RT-qPCR. After in silico prediction of potential targets of miR-23a/b-3p, PFKFB4, HMMR, SPATA6, and TEX15 have been identified as direct targets by dual luciferase assays. Mutations in the miR-23a/b-3p binding site within the 3′UTRs resulted in abrogated responsiveness to miR-23a/b-3p. PFKFB4, HMMR, SPATA6, and TEX15 mRNA and HMMR and SPATA6 protein levels were significantly lower in oligoasthenozoospermic men compared with in normozoospermic men. Correlation analysis showed that the sperm count, motility, and morphology were negatively correlated with miR-23a/b-3p and positively correlated with PFKFB4, HMMR, SPATA6, and TEX15 abundance levels (lower ΔCt, the higher abundance levels). Conclusion(s): This study establishes a link between up-regulation of miR-23a/b-3p and the coincident down-regulation of four expressed genes in the sperm of men with oligoasthenozoospermia, compared with men with normozoospermia. This study provides a novel insight into some of the mechanisms leading to male subfertility, offering a possible therapeutic target for treatment, or even for male contraception.},
  doi          = {10.1016/j.fertnstert.2019.03.025},
  pii          = {10.1016/j.fertnstert.2019.03.025},
}

Objective: To elucidate the potential regulatory function of miR-23a/b-3p on spermatogenesis-specific genes. Design: Reverse transcription quantitative polymerase chain reaction (RT-qPCR) validation, Northern blot, dual luciferase assay, and Western blot confirmation. Setting: University research and clinical institutes. Patient(s): A total of 115 men presenting at an infertility clinic. Intervention(s): None. Main Outcome Measure(s): Significant higher abundance levels of miR-23a/b-3p and lower abundance levels of PFKFB4, HMMR, SPATA6, and TEX15 in oligoasthenozoospermic men compared with those in normozoospermic men. Result(s): In oligoasthenozoospermic men, the abundance levels of miR-23a/b-3p were significantly higher when compared with controls as determined by RT-qPCR. After in silico prediction of potential targets of miR-23a/b-3p, PFKFB4, HMMR, SPATA6, and TEX15 have been identified as direct targets by dual luciferase assays. Mutations in the miR-23a/b-3p binding site within the 3′UTRs resulted in abrogated responsiveness to miR-23a/b-3p. PFKFB4, HMMR, SPATA6, and TEX15 mRNA and HMMR and SPATA6 protein levels were significantly lower in oligoasthenozoospermic men compared with in normozoospermic men. Correlation analysis showed that the sperm count, motility, and morphology were negatively correlated with miR-23a/b-3p and positively correlated with PFKFB4, HMMR, SPATA6, and TEX15 abundance levels (lower ΔCt, the higher abundance levels). Conclusion(s): This study establishes a link between up-regulation of miR-23a/b-3p and the coincident down-regulation of four expressed genes in the sperm of men with oligoasthenozoospermia, compared with men with normozoospermia. This study provides a novel insight into some of the mechanisms leading to male subfertility, offering a possible therapeutic target for treatment, or even for male contraception.

@Article{Ludwig2019,
  author       = {Nicole Ludwig and Anne Hecksteden and Mustafa Kahraman and Tobias Fehlmann and Thomas Laufer and Fabian Kern and Tim Meyer and Eckart Meese and Andreas Keller and Christina Backes},
  title        = {Spring is in the air: seasonal profiles indicate vernal change of miRNA activity},
  journal      = {RNA biology},
  publisher    = {Taylor & Francis},
  year         = {2019},
  volume       = {16},
  issue        = {8},
  pages        = {1034-1043},
  issn         = {1-10},
  issn-linking = {1-10},
  month        = may,
  abstract     = {The envisioned application of miRNAs as diagnostic or prognostic biomarkers calls for an in-depth understanding of their distribution and variability in different physiological states. While effects with respect to ethnic origin, age, or gender are known, the inter-individual variability of miRNAs across the four seasons remained largely hidden. We sequentially profiled the complete repertoire of blood-borne miRNAs for 25 physiologically normal individuals in spring, summer, fall, and winter (altogether 95 samples) and validated the results on 292 individuals (919 samples collected with the Mitra home sampling device) by RT-qPCR. Principal variance component analysis suggests that the largest variability observed in miRNA expression is due to individual variability and the individuals’ gender. But the results also highlight a deviation of miRNA activity in samples collected during spring time. Following adjustment for multiple testing, remarkable differences are observed between spring and fall (77 miRNAs). The two most dys-regulated miRNAs were miR-181c-5p and miR-106b-5p (adjusted p-value of 0.007). Other significant miRNAs include miR-140-3p, miR-21-3p, and let-7c-5p. The dys-regulation was validated by RT-qPCR. Systems biology analysis further provides strong evidence for the immunological origin of the signals: dys-regulated miRNAs are enriched in CD56 cells and belong to various signalling and immune-system-related pathways. Our data suggest that besides known confounding factors such as age and sex, also the season in which a test is conducted might have a considerable influence on the expression of blood-borne miRNAs and subsequently might interfere with diagnosis based on such signatures.},
  doi          = {10.1080/15476286.2019.1612217},
  pii          = {10.1080/15476286.2019.1612217},
}

The envisioned application of miRNAs as diagnostic or prognostic biomarkers calls for an in-depth understanding of their distribution and variability in different physiological states. While effects with respect to ethnic origin, age, or gender are known, the inter-individual variability of miRNAs across the four seasons remained largely hidden. We sequentially profiled the complete repertoire of blood-borne miRNAs for 25 physiologically normal individuals in spring, summer, fall, and winter (altogether 95 samples) and validated the results on 292 individuals (919 samples collected with the Mitra home sampling device) by RT-qPCR. Principal variance component analysis suggests that the largest variability observed in miRNA expression is due to individual variability and the individuals’ gender. But the results also highlight a deviation of miRNA activity in samples collected during spring time. Following adjustment for multiple testing, remarkable differences are observed between spring and fall (77 miRNAs). The two most dys-regulated miRNAs were miR-181c-5p and miR-106b-5p (adjusted p-value of 0.007). Other significant miRNAs include miR-140-3p, miR-21-3p, and let-7c-5p. The dys-regulation was validated by RT-qPCR. Systems biology analysis further provides strong evidence for the immunological origin of the signals: dys-regulated miRNAs are enriched in CD56 cells and belong to various signalling and immune-system-related pathways. Our data suggest that besides known confounding factors such as age and sex, also the season in which a test is conducted might have a considerable influence on the expression of blood-borne miRNAs and subsequently might interfere with diagnosis based on such signatures.

@Article{Galata2019,
  author       = {Valentina Galata and Cedric C Laczny and Christina Backes and Georg Hemmrich-Stanisak and Susanne Schmolke and Andre Franke and Eckart Meese and Mathias Herrmann and Lutz von Mueller and Achim Plum and Rolf Mueller and Cord Stähler and Andreas E Posch and Andreas Keller},
  title        = {Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates},
  journal      = {Genomics, proteomics & bioinformatics},
  publisher    = {Elsevier},
  year         = {2019},
  volume       = {17},
  issue        = {2},
  pages        = {169-182},
  issn         = {169-182},
  issn-linking = {169-182},
  month        = may,
  abstract     = {Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene–drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com.},
  doi          = {10.1016/j.gpb.2018.11.002},
  pii          = {10.1016/j.gpb.2018.11.002},
}

Emerging antibiotic resistance is a major global health threat. The analysis of nucleic acid sequences linked to susceptibility phenotypes facilitates the study of genetic antibiotic resistance determinants to inform molecular diagnostics and drug development. We collected genetic data (11,087 newly-sequenced whole genomes) and culture-based resistance profiles (10,991 out of the 11,087 isolates comprehensively tested against 22 antibiotics in total) of clinical isolates including 18 main species spanning a time period of 30 years. Species and drug specific resistance patterns were observed including increased resistance rates for Acinetobacter baumannii to carbapenems and for Escherichia coli to fluoroquinolones. Species-level pan-genomes were constructed to reflect the genetic repertoire of the respective species, including conserved essential genes and known resistance factors. Integrating phenotypes and genotypes through species-level pan-genomes allowed to infer gene–drug resistance associations using statistical testing. The isolate collection and the analysis results have been integrated into GEAR-base, a resource available for academic research use free of charge at https://gear-base.com.

@Article{Fischer2019,
  author       = {Ulrike Fischer and Christina Backes and Tobias Fehlmann and Valentina Galata and Andreas Keller and Eckart Meese},
  title        = {Prospect and challenge of detecting dynamic gene copy number increases in stem cells by whole genome sequencing},
  journal      = {Journal of Molecular Medicine},
  publisher    = {Springer Berlin Heidelberg},
  year         = {2019},
  volume       = {97},
  issue        = {8},
  pages        = {1099–1111},
  issn         = {1432-1440},
  issn-linking = {1099–1111},
  month        = may,
  abstract     = {Gene amplification is an evolutionarily well-conserved and highly efficient mechanism to increase the amount of specific proteins. In humans, gene amplification is a hallmark of cancer and has recently been found during stem cell differentiation. Amplifications in stem cells are restricted to specific tissue areas and time windows, rendering their detection difficult. Here, we report on the performance of deep WGS sequencing (average 82-fold depth of coverage) on the BGISEQ with nanoball technology to detect amplifications in human mesenchymal and neural stem cells. As reference technology, we applied array-based comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH), and qPCR. Using different in silico strategies for amplification detection, we analyzed the potential of WGS for amplification detection. Our results provide evidence that WGS accurately identifies changes of the copy number profiles in human stem cell differentiation. However, the identified changes are not in all cases consistent between WGS and aCGH. The results between WGS and the validation by qPCR were concordant in 83.3% of all tested 36 cases. In sum, both genome-wide techniques, aCGH and WGS, have unique advantages and specific challenges, calling for locus-specific confirmation by the low-throughput approaches qPCR or FISH.},
  doi          = {10.1007/s00109-019-01792-y},
  pii          = {10.1007/s00109-019-01792-y},
}

Gene amplification is an evolutionarily well-conserved and highly efficient mechanism to increase the amount of specific proteins. In humans, gene amplification is a hallmark of cancer and has recently been found during stem cell differentiation. Amplifications in stem cells are restricted to specific tissue areas and time windows, rendering their detection difficult. Here, we report on the performance of deep WGS sequencing (average 82-fold depth of coverage) on the BGISEQ with nanoball technology to detect amplifications in human mesenchymal and neural stem cells. As reference technology, we applied array-based comparative genomic hybridization (aCGH), fluorescence in situ hybridization (FISH), and qPCR. Using different in silico strategies for amplification detection, we analyzed the potential of WGS for amplification detection. Our results provide evidence that WGS accurately identifies changes of the copy number profiles in human stem cell differentiation. However, the identified changes are not in all cases consistent between WGS and aCGH. The results between WGS and the validation by qPCR were concordant in 83.3% of all tested 36 cases. In sum, both genome-wide techniques, aCGH and WGS, have unique advantages and specific challenges, calling for locus-specific confirmation by the low-throughput approaches qPCR or FISH.

@Article{Manier2019,
  author       = {Sascha K Manier and Andreas Keller and Markus R Meyer},
  title        = {Automated optimization of XCMS parameters for improved peak picking of liquid chromatography–mass spectrometry data using the coefficient of variation and parameter sweeping for untargeted metabolomics},
  journal      = {Drug testing and analysis},
  publisher    = {},
  year         = {2019},
  volume       = {11},
  issue        = {6},
  pages        = {752-761},
  issn         = {752-761},
  issn-linking = {752-761},
  month        = jun,
  abstract     = {Accurate peak picking and further processing is a current challenge in the analysis of untargeted metabolomics using liquid chromatography–mass spectrometry (LC–MS) data. The optimization of these processes is crucial to obtain proper results. This study investigated and optimized the detection of peaks by XCMS, a widely used R package for peak picking and processing of high-resolution LC–MS metabolomics data by their coefficient of variation using neat standard solutions of drug like compounds. The obtained results were additionally verified by using fortified pooled plasma samples. Settings of the mass spectrometer were optimized by recommendations in literature to enable a reliable detection of the investigated analytes. XCMS parameters were evaluated using a comprehensive parameter sweeping approach. The optimization steps were statistically evaluated and further visualized after principal component analysis (PCA). Concerning the lower concentrated solution in methanol samples, the optimization of both mass spectrometer and XCMS parameters improved the median coefficient of variation from 24% to 7%, retention time fluctuation from 9.3 seconds to 0.54 seconds, and fluctuation of the mass to charge ratio (m/z) from m/z 0.00095 to m/z 0.00028. The number of parent compounds and their related species annotated by CAMERA increased from 88 to 113 while the total amount of features decreased from 3282 to 428. Optimized MS settings such as increased resolution led to a higher specificity of peak picking. PCA supported these findings by showing the best clustering of samples after optimization of both mass spectrometer and XCMS parameters. The results implied that peak picking needs to be individually adapted for the experimental set up. Reducing unwanted variation in the data set was most successful after combining high resolving power with strict peak picking settings.},
  doi          = {10.1002/dta.2552},
  pii          = {10.1002/dta.2552},
}

Accurate peak picking and further processing is a current challenge in the analysis of untargeted metabolomics using liquid chromatography–mass spectrometry (LC–MS) data. The optimization of these processes is crucial to obtain proper results. This study investigated and optimized the detection of peaks by XCMS, a widely used R package for peak picking and processing of high-resolution LC–MS metabolomics data by their coefficient of variation using neat standard solutions of drug like compounds. The obtained results were additionally verified by using fortified pooled plasma samples. Settings of the mass spectrometer were optimized by recommendations in literature to enable a reliable detection of the investigated analytes. XCMS parameters were evaluated using a comprehensive parameter sweeping approach. The optimization steps were statistically evaluated and further visualized after principal component analysis (PCA). Concerning the lower concentrated solution in methanol samples, the optimization of both mass spectrometer and XCMS parameters improved the median coefficient of variation from 24% to 7%, retention time fluctuation from 9.3 seconds to 0.54 seconds, and fluctuation of the mass to charge ratio (m/z) from m/z 0.00095 to m/z 0.00028. The number of parent compounds and their related species annotated by CAMERA increased from 88 to 113 while the total amount of features decreased from 3282 to 428. Optimized MS settings such as increased resolution led to a higher specificity of peak picking. PCA supported these findings by showing the best clustering of samples after optimization of both mass spectrometer and XCMS parameters. The results implied that peak picking needs to be individually adapted for the experimental set up. Reducing unwanted variation in the data set was most successful after combining high resolving power with strict peak picking settings.

@Article{Trautmann2019,
  author       = {Simone Trautmann and Ahmad Barghash and Claudia Fecher-Trost and Pascal Schalkowsky and Christian Hannig and Jasmin Kirsch and Stefan Rupf and Andreas Keller and Volkhard Helms and Matthias Hannig},
  title        = {Proteomic Analysis of the Initial Oral Pellicle in Caries-Active and Caries-Free Individuals},
  journal      = {PROTEOMICS–Clinical Applications},
  year         = {2019},
  volume       = {13},
  issue        = {4},
  pages        = {1800143},
  issn         = {1800143},
  issn-linking = {1800143},
  month        = jul,
  abstract     = {Purpose: To 1) elucidate individual proteomic profiles of the 3-min biofilm of caries-active and caries-free individuals and 2) compare these proteomic profiles against the background of caries. Experimental design: The initial oral pellicle of 12 caries-active and 12 caries-free individuals is generated in situ on ceramics specimens. The individual, host-specific proteomic profiles of this basic pellicle layer are analyzed by a chemical elution protocol combined with an elaborate mass spectrometry and evaluated bioinformatically. Results: A total of 1188 different proteins are identified. Additionally, 68 proteins are present in the profiles of all individuals, suggesting them as ubiquitously occurring base-proteins of the initial human pellicle. Thereof, the single profiles exhibit high inter-individual differences independent of their group affiliation, stating the initial pellicle to represent a rather “individual fingerprint”. Quantitative analyses imply slight indication for 23 proteins potentially capable of counting for caries-specific biomarkers. Conclusions and clinical relevance: The introduced protocol enables the individual analysis of minimal protein amounts and allows for highly precise characterizations and comparisons of individual proteomic profiles. The results contain a considerable higher extent of protein identifications and might serve as a base for future large scale analyzes to identify discrimination factors for the development of caries susceptibility tests.},
  doi          = {10.1002/prca.201800143},
  pii          = {10.1002/prca.201800143},
}

Purpose: To 1) elucidate individual proteomic profiles of the 3-min biofilm of caries-active and caries-free individuals and 2) compare these proteomic profiles against the background of caries. Experimental design: The initial oral pellicle of 12 caries-active and 12 caries-free individuals is generated in situ on ceramics specimens. The individual, host-specific proteomic profiles of this basic pellicle layer are analyzed by a chemical elution protocol combined with an elaborate mass spectrometry and evaluated bioinformatically. Results: A total of 1188 different proteins are identified. Additionally, 68 proteins are present in the profiles of all individuals, suggesting them as ubiquitously occurring base-proteins of the initial human pellicle. Thereof, the single profiles exhibit high inter-individual differences independent of their group affiliation, stating the initial pellicle to represent a rather “individual fingerprint”. Quantitative analyses imply slight indication for 23 proteins potentially capable of counting for caries-specific biomarkers. Conclusions and clinical relevance: The introduced protocol enables the individual analysis of minimal protein amounts and allows for highly precise characterizations and comparisons of individual proteomic profiles. The results contain a considerable higher extent of protein identifications and might serve as a base for future large scale analyzes to identify discrimination factors for the development of caries susceptibility tests.

@Article{Orth2019,
  author       = {Marcel Orth and Claudia Scheuer and Christina Backes and Andreas Keller and Mika F Rollmann and Benedikt J Braun and Nicole Ludwig and Eckart Meese and Tim Pohlemann and Matthias W Laschke and Michael D Menger and Tina Histing},
  title        = {Profiling microRNA expression in murine bone healing and non-union formation: Role of miR-140 during the early stage of bone healing},
  journal      = {PloS one},
  publisher    = {Public Library of Science},
  year         = {2019},
  volume       = {14},
  issue        = {7},
  pages        = {e0218395},
  issn         = {e0218395},
  issn-linking = {e0218395},
  month        = jul,
  abstract     = {Although cellular and molecular mechanisms during the course of bone healing have been thoroughly investigated, the regulation of gene expression by microRNA during bone regeneration is still poorly understood. We hypothesized that nonunion formation is associated with different microRNA expression patterns and that target proteins of these microRNAs are differently expressed in callus tissue of nonunions compared to physiologically healing bones. In a well-established femoral osteotomy model in CD-1 mice osteotomies were induced which result either in healing or in nonunion formation. MicroRNA and target protein expression was evaluated by microarray, quantitative real-time polymerase chain reaction (qrt-PCR) and Western blot. Microarray analyses demonstrated 44 microRNAs to be relevant for nonunion formation compared to physiological bone healing. In nonunions qrt-PCR could validate a higher expression of microRNA-140-3p and microRNA-140-5p. This was associated with a reduced expression of Dnpep and stromal cell-derived factor (SDF)-1α, which are both known to be target proteins of microRNA-140 and also to be involved in the process of bone healing. These data suggest that an increased expression of microRNA-140-3p and microRNA-140-5p markedly contributes to the development of nonunions, most probably by affecting bone morphogenetic protein (BMP)-2 function during the early stage of healing due to a reduced SDF-1α expression.},
  doi          = {10.1371/journal.pone.0218395},
  pii          = {10.1371/journal.pone.0218395},
}

Although cellular and molecular mechanisms during the course of bone healing have been thoroughly investigated, the regulation of gene expression by microRNA during bone regeneration is still poorly understood. We hypothesized that nonunion formation is associated with different microRNA expression patterns and that target proteins of these microRNAs are differently expressed in callus tissue of nonunions compared to physiologically healing bones. In a well-established femoral osteotomy model in CD-1 mice osteotomies were induced which result either in healing or in nonunion formation. MicroRNA and target protein expression was evaluated by microarray, quantitative real-time polymerase chain reaction (qrt-PCR) and Western blot. Microarray analyses demonstrated 44 microRNAs to be relevant for nonunion formation compared to physiological bone healing. In nonunions qrt-PCR could validate a higher expression of microRNA-140-3p and microRNA-140-5p. This was associated with a reduced expression of Dnpep and stromal cell-derived factor (SDF)-1α, which are both known to be target proteins of microRNA-140 and also to be involved in the process of bone healing. These data suggest that an increased expression of microRNA-140-3p and microRNA-140-5p markedly contributes to the development of nonunions, most probably by affecting bone morphogenetic protein (BMP)-2 function during the early stage of healing due to a reduced SDF-1α expression.

@Article{Guimaraes2019,
  author       = {Pedro Guimaraes and Andreas Keller and Tobias Fehlmann and Frank Lammert and Markus Casper},
  title        = {Deep-learning based detection of gastric precancerous conditions},
  journal      = {Gut},
  publisher    = {BMJ Publishing Group},
  year         = {2019},
  pages        = {0017-5749},
  issn         = {0017-5749},
  issn-linking = {0017-5749},
  month        = aug,
  abstract     = {Conventional white-light endoscopy has high interobserver variability for the diagnosis of gastric precancerous conditions. Here we present a deep-learning (DL) approach for the diagnosis of atrophic gastritis developed and trained using real-world endoscopic images from the proximal stomach. The model achieved an accuracy of 93% (area under the curve (AUC): 0.98; F-score 0.93) in an independent data set, outperforming expert endoscopists. DL may overcome conventional appraisal of white-light endoscopy and support human decision making. The algorithm is available free of charge via a web-based interface (https://www.ccb.uni-saarland.de/atrophy).},
  doi          = {10.1136/gutjnl-2019-319347},
  pii          = {10.1136/gutjnl-2019-319347},
}

Conventional white-light endoscopy has high interobserver variability for the diagnosis of gastric precancerous conditions. Here we present a deep-learning (DL) approach for the diagnosis of atrophic gastritis developed and trained using real-world endoscopic images from the proximal stomach. The model achieved an accuracy of 93% (area under the curve (AUC): 0.98; F-score 0.93) in an independent data set, outperforming expert endoscopists. DL may overcome conventional appraisal of white-light endoscopy and support human decision making. The algorithm is available free of charge via a web-based interface (https://www.ccb.uni-saarland.de/atrophy).

@Article{Kern2019,
  author       = {Fabian Kern and Nicole Ludwig and Christina Backes and Esther Maldener and Tobias Fehlmann and Artur Suleymanov and Eckart Meese and Anne Hecksteden and Andreas Keller and Tim Meyer},
  title        = {Systematic assessment of blood-borne microRNAs highlights molecular profiles of endurance sport and carbohydrate uptake},
  journal      = {Cells},
  publisher    = {Multidisciplinary Digital Publishing Institute},
  year         = {2019},
  volume       = {8},
  issue        = {9},
  pages        = {1045},
  issn         = {1045},
  issn-linking = {1045},
  month        = sep,
  abstract     = {Multiple studies endorsed the positive effect of regular exercise on mental and physical health. However, the molecular mechanisms underlying training-induced fitness in combination with personal life-style remain largely unexplored. Circulating biomarkers such as microRNAs (miRNAs) offer themselves for studying systemic and cellular changes since they can be collected from the bloodstream in a low-invasive manner. In Homo sapiens miRNAs are known to regulate a substantial number of protein-coding genes in a post-transcriptional manner and hence are of great interest to understand differential gene expression profiles, offering a cost-effective mechanism to study molecular training adaption, and connecting the dots from genomics to observed phenotypes. Here, we investigated molecular expression patterns of 2549 miRNAs in whole-blood samples from 23 healthy and untrained adult participants of a cross-over study, consisting of eight weeks of endurance training, with several sessions per week, followed by 8 weeks of washout and another 8 weeks of running, using microarrays. Participants were randomly assigned to one of the two study groups, one of which administered carbohydrates before each session in the first training period, and switching the treatment group for the second training period. During running sessions clinical parameters as heartbeat frequency were recorded. This information was extended with four measurements of maximum oxygen uptake (VO 2 max) for each participant. We observed that multiple circulating miRNAs show expression changes after endurance training, leveraging the capability to separate the blood samples by training status. To this end, we demonstrate that most of the variance in miRNA expression can be explained by both common and known biological and technical factors. Our findings highlight six distinct clusters of miRNAs, each exhibiting an oscillating expression profile across the four study timepoints, that can effectively be utilized to predict phenotypic VO 2 max levels. In addition, we identified miR-532-5p as a candidate marker to determine personal alterations in physical training performance on a case-by-case analysis taking the influence of a carbohydrate-rich nutrition into account. In literature, miR-532-5p is known as a common down-regulated miRNA in diabetes and obesity, possibly providing a molecular link between cellular homeostasis, personal fitness levels, and health in aging. We conclude that circulating miRNA expression can be altered due to regular endurance training, independent of the carbohydrate (CHO) availability in the training timeframe. Further validation studies are required to confirm the role of exercise-affected miRNAs and the extraordinary function of miR-532-5p in modulating the metabolic response to a high availability of glucose.},
  doi          = {10.3390/cells8091045},
  pii          = {10.3390/cells8091045},
}

Multiple studies endorsed the positive effect of regular exercise on mental and physical health. However, the molecular mechanisms underlying training-induced fitness in combination with personal life-style remain largely unexplored. Circulating biomarkers such as microRNAs (miRNAs) offer themselves for studying systemic and cellular changes since they can be collected from the bloodstream in a low-invasive manner. In Homo sapiens miRNAs are known to regulate a substantial number of protein-coding genes in a post-transcriptional manner and hence are of great interest to understand differential gene expression profiles, offering a cost-effective mechanism to study molecular training adaption, and connecting the dots from genomics to observed phenotypes. Here, we investigated molecular expression patterns of 2549 miRNAs in whole-blood samples from 23 healthy and untrained adult participants of a cross-over study, consisting of eight weeks of endurance training, with several sessions per week, followed by 8 weeks of washout and another 8 weeks of running, using microarrays. Participants were randomly assigned to one of the two study groups, one of which administered carbohydrates before each session in the first training period, and switching the treatment group for the second training period. During running sessions clinical parameters as heartbeat frequency were recorded. This information was extended with four measurements of maximum oxygen uptake (VO 2 max) for each participant. We observed that multiple circulating miRNAs show expression changes after endurance training, leveraging the capability to separate the blood samples by training status. To this end, we demonstrate that most of the variance in miRNA expression can be explained by both common and known biological and technical factors. Our findings highlight six distinct clusters of miRNAs, each exhibiting an oscillating expression profile across the four study timepoints, that can effectively be utilized to predict phenotypic VO 2 max levels. In addition, we identified miR-532-5p as a candidate marker to determine personal alterations in physical training performance on a case-by-case analysis taking the influence of a carbohydrate-rich nutrition into account. In literature, miR-532-5p is known as a common down-regulated miRNA in diabetes and obesity, possibly providing a molecular link between cellular homeostasis, personal fitness levels, and health in aging. We conclude that circulating miRNA expression can be altered due to regular endurance training, independent of the carbohydrate (CHO) availability in the training timeframe. Further validation studies are required to confirm the role of exercise-affected miRNAs and the extraordinary function of miR-532-5p in modulating the metabolic response to a high availability of glucose.

@Article{Casper2019,
  author       = {M Casper and P Guimarães and T Fehlmann and A Keller and F Lammert},
  title        = {Deep-Learning basierter Bildanalyse-Algorithmus zur Erkennung der atrophischen Gastritis},
  journal      = {Zeitschrift für Gastroenterologie},
  publisher    = {Georg Thieme Verlag KG},
  year         = {2019},
  volume       = {57},
  issue        = {09},
  pages        = {KV 406},
  issn         = {406},
  issn-linking = {406},
  month        = sep,
  abstract     = {Einleitung: Chronisch-entzündliche Prozesse der Magenschleimhaut initiieren die Entstehung präkanzeröser Bedingungen (chronisch atrophische Gastritis, intestinale Metaplasie), die dann über die Dysplasie in ein Magenkarzinom vom intestinalen Typ münden können. Die konventionelle Weißlichtendoskopie hat eine niedrig Sensitivitäten und Spezifität zur Identifizierung dieser präkanzerösen Veränderungen. Ziel war daher die Etablierung eines Computer-Algorithmus zur automatisierten Bildanalyse und Diagnose. Patienten und Methodik: Mithilfe von 200 Real-life-Endoskopiebildern (Magenfundus und -corpus) von Patienten mit histopathologisch gesicherter bzw. ausgeschlossener atrophischer Gastritis (jeweils 100) wurde unter Nutzung eines vortrainierten Modells ein Deep learning (DL)-basierter Algorithmus zur Bildanalyse etabliert. Ein zweiter unabhängiger Datensatz (70 Bilder; 30 mit und 40 ohne Atrophie) wurde zur Validierung des Diagnosealgorithmus genutzt. Diese Bilder wurden unabhängig durch Endoskopiker bewertet. Ergebnisse: Der DL-basierte Diagnosealgorithmus lieferte für alle Bilder ein Ergebnis. Die Diagnosegenauigkeit der automatisierten Bildanalyse lag bei 0,93und der F1-Score betrug 0,92 bei einer Sensitivität von 1,00 und einer Spezifität von 0,86. Der positive prädiktive Wert (PPV) war 0,88, der negativ prädiktive Wert (NPV) 1,00. Für die Bildauswertung durch Endoskopiker ergaben sich eine Genauigkeit von 0,80 ± 0,07), ein F1-Score von 0,76 ± 0,13), eine Sensitivität von 0,80 ± 0,26), eine Spezifität von 0,80 ± 0,17, ein PPV von 0,80 ± 0,15 und ein NPV von 0,88 ± 0,14). Damit konnte für die Parameter diagnostische Genauigkeit und F1-Score eine signifikante Überlegenheit der automatisierten Bildanalyse mittels DL gezeigt werden (p < 0,05). Schlussfolgerungen: Die automatisierte Diagnose unter Nutzung von DL kann für endoskopische Fragestellungen angewendet werden. Dabei lag der Fokus bislang auf der Detektion fokaler Schleimhautveränderungen (z.B. Polpyen). Hier konnten wir zeigen, dass auch visuell schwierig zu diagnostizierende diffuse Schleimhautveränderungen zuverlässig ohne Biopsie klassifiziert werden können. Unser Diagnosealgorithmus kann online unter https://ccb-test.cs.uni-saarland.de/atrophy/genutzt werden.},
  doi          = {10.1055/s-0039-1695506},
  pii          = {10.1055/s-0039-1695506},
}

Einleitung: Chronisch-entzündliche Prozesse der Magenschleimhaut initiieren die Entstehung präkanzeröser Bedingungen (chronisch atrophische Gastritis, intestinale Metaplasie), die dann über die Dysplasie in ein Magenkarzinom vom intestinalen Typ münden können. Die konventionelle Weißlichtendoskopie hat eine niedrig Sensitivitäten und Spezifität zur Identifizierung dieser präkanzerösen Veränderungen. Ziel war daher die Etablierung eines Computer-Algorithmus zur automatisierten Bildanalyse und Diagnose. Patienten und Methodik: Mithilfe von 200 Real-life-Endoskopiebildern (Magenfundus und -corpus) von Patienten mit histopathologisch gesicherter bzw. ausgeschlossener atrophischer Gastritis (jeweils 100) wurde unter Nutzung eines vortrainierten Modells ein Deep learning (DL)-basierter Algorithmus zur Bildanalyse etabliert. Ein zweiter unabhängiger Datensatz (70 Bilder; 30 mit und 40 ohne Atrophie) wurde zur Validierung des Diagnosealgorithmus genutzt. Diese Bilder wurden unabhängig durch Endoskopiker bewertet. Ergebnisse: Der DL-basierte Diagnosealgorithmus lieferte für alle Bilder ein Ergebnis. Die Diagnosegenauigkeit der automatisierten Bildanalyse lag bei 0,93und der F1-Score betrug 0,92 bei einer Sensitivität von 1,00 und einer Spezifität von 0,86. Der positive prädiktive Wert (PPV) war 0,88, der negativ prädiktive Wert (NPV) 1,00. Für die Bildauswertung durch Endoskopiker ergaben sich eine Genauigkeit von 0,80 ± 0,07), ein F1-Score von 0,76 ± 0,13), eine Sensitivität von 0,80 ± 0,26), eine Spezifität von 0,80 ± 0,17, ein PPV von 0,80 ± 0,15 und ein NPV von 0,88 ± 0,14). Damit konnte für die Parameter diagnostische Genauigkeit und F1-Score eine signifikante Überlegenheit der automatisierten Bildanalyse mittels DL gezeigt werden (p < 0,05). Schlussfolgerungen: Die automatisierte Diagnose unter Nutzung von DL kann für endoskopische Fragestellungen angewendet werden. Dabei lag der Fokus bislang auf der Detektion fokaler Schleimhautveränderungen (z.B. Polpyen). Hier konnten wir zeigen, dass auch visuell schwierig zu diagnostizierende diffuse Schleimhautveränderungen zuverlässig ohne Biopsie klassifiziert werden können. Unser Diagnosealgorithmus kann online unter https://ccb-test.cs.uni-saarland.de/atrophy/genutzt werden.

@Article{Keller2019,
  author       = {Andreas Keller and Nicole Ludwig and Tobias Fehlmann and Mustafa Kahraman and Christina Backes and Fabian Kern and Claus F Vogelmeier and Caroline Diener and Ulrike Fischer and Frank Biertz and Christian Herr and Rudolf A Jörres and Hans-Peter Lenhof and Robert Bals and Eckart Meese},
  title        = {Low miR-150-5p and miR-320b Expression Predicts Reduced Survival of COPD Patients},
  journal      = {Cells},
  publisher    = {Multidisciplinary Digital Publishing Institute},
  year         = {2019},
  volume       = {8},
  issue        = {10},
  pages        = {1162},
  issn         = {1162},
  issn-linking = {1162},
  month        = sep,
  abstract     = {Chronic obstructive pulmonary disease (COPD) is associated with an increased risk of death, reducing life expectancy on average between 5 and 7 years. The survival time after diagnosis, however, varies considerably as a result of the heterogeneity of COPD. Therefore, markers that predict individual survival of COPD patients are of great value. We analyzed baseline molecular profiles and collected 54 months of follow-up data of the cohort study “COPD and SYstemic consequences-COmorbidities NETwork”(COSYCONET). Genome-wide microRNA signatures from whole blood collected at time of the inclusion in the study were generated for 533 COPD patients including patients that deceased during the 54-month follow-up period (n= 53) and patients that survived this period (n= 480). We identified two blood-born microRNAs (miR-150-5p and miR-320b) that were highly predictive for survival of COPD patients. The expression change was then confirmed by RT-qPCR in 245 individuals. Ninety percent of patients with highest expression of miR-150-5p survived the 54-month period in contrast to only 50% of patients with lowest expression intensity. Moreover, the abundance of the oncogenic miR-150-5p in blood of COPD patients was predictive for the development of cancer. Thus, molecular profiles measured at the time of a COPD diagnosis have a high predictive power for the survival of patients.},
  doi          = {10.3390/cells8101162},
  pii          = {10.3390/cells8101162},
}

Chronic obstructive pulmonary disease (COPD) is associated with an increased risk of death, reducing life expectancy on average between 5 and 7 years. The survival time after diagnosis, however, varies considerably as a result of the heterogeneity of COPD. Therefore, markers that predict individual survival of COPD patients are of great value. We analyzed baseline molecular profiles and collected 54 months of follow-up data of the cohort study “COPD and SYstemic consequences-COmorbidities NETwork”(COSYCONET). Genome-wide microRNA signatures from whole blood collected at time of the inclusion in the study were generated for 533 COPD patients including patients that deceased during the 54-month follow-up period (n= 53) and patients that survived this period (n= 480). We identified two blood-born microRNAs (miR-150-5p and miR-320b) that were highly predictive for survival of COPD patients. The expression change was then confirmed by RT-qPCR in 245 individuals. Ninety percent of patients with highest expression of miR-150-5p survived the 54-month period in contrast to only 50% of patients with lowest expression intensity. Moreover, the abundance of the oncogenic miR-150-5p in blood of COPD patients was predictive for the development of cancer. Thus, molecular profiles measured at the time of a COPD diagnosis have a high predictive power for the survival of patients.

@Article{Henn2019,
  author       = {Dominic Henn and Masood Abu-Halima and Dominik Wermke and Florian Falkner and Benjamin Thomas and Christoph Köpple and Nicole Ludwig and Matthias Schulte and Marc A Brockmann and Yoo-Jin Kim and Justin M Sacks and Ulrich Kneser and Andreas Keller and Eckart Meese and Volker J Schmidt},
  title        = {MicroRNA-regulated pathways of flow-stimulated angiogenesis and vascular remodeling in vivo},
  journal      = {Journal of translational medicine},
  publisher    = {BioMed Central},
  year         = {2019},
  volume       = {17},
  issue        = {1},
  pages        = {22},
  issn         = {22},
  issn-linking = {22},
  abstract     = {Background: Vascular shear stress promotes endothelial cell sprouting in vitro. The impact of hemodynamic forces on microRNA (miRNA) and gene expression within growing vascular networks in vivo, however, remain poorly investigated. Arteriovenous (AV) shunts are an established model for induction of neoangiogenesis in vivo and can serve as a tool for analysis of hemodynamic effects on miRNA and gene expression profiles over time. Methods: AV shunts were microsurgically created in rats and explanted on postoperative days 5, 10 and 15. Neoangiogenesis was confirmed by histologic analysis and micro-computed tomography. MiRNA and gene expression profiles were determined in tissue specimens from AV shunts by microarray analysis and quantitative real-time polymerase chain reaction and compared with sham-operated veins by bioinformatics analysis. Changes in protein expression within AV shunt endothelial cells were determined by immunohistochemistry. Results: Samples from AV shunts exhibited a strong overexpression of proangiogenic cytokines, oxygenation-associated genes (HIF1A, HMOX1), and angiopoetic growth factors. Significant inverse correlations of the expressions of miR-223-3p, miR-130b-3p, miR-19b-3p, miR-449a-5p, and miR-511-3p which were up-regulated in AV shunts, and miR-27b-3p, miR-10b-5p, let-7b-5p, and let-7c-5p, which were down-regulated in AV shunts, with their predicted interacting targets C–X–C chemokine receptor 2 (CXCR2), interleukin-1 alpha (IL1A), ephrin receptor kinase 2 (EPHA2), synaptojanin-2 binding protein (SYNJ2BP), forkhead box C1 (FOXC1) were present. CXCL2 and IL1A overexpression in AV shunt endothelium was confirmed at the protein level by immunohistochemistry. Conclusions: Our data indicate that flow-stimulated angiogenesis is determined by an upregulation of cytokines, oxygenation associated genes and miRNA-dependent regulation of FOXC1, EPHA2 and SYNJ2BP},
  doi          = {10.1186/s12967-019-1767-9},
  pii          = {10.1186/s12967-019-1767-9},
}

Background: Vascular shear stress promotes endothelial cell sprouting in vitro. The impact of hemodynamic forces on microRNA (miRNA) and gene expression within growing vascular networks in vivo, however, remain poorly investigated. Arteriovenous (AV) shunts are an established model for induction of neoangiogenesis in vivo and can serve as a tool for analysis of hemodynamic effects on miRNA and gene expression profiles over time. Methods: AV shunts were microsurgically created in rats and explanted on postoperative days 5, 10 and 15. Neoangiogenesis was confirmed by histologic analysis and micro-computed tomography. MiRNA and gene expression profiles were determined in tissue specimens from AV shunts by microarray analysis and quantitative real-time polymerase chain reaction and compared with sham-operated veins by bioinformatics analysis. Changes in protein expression within AV shunt endothelial cells were determined by immunohistochemistry. Results: Samples from AV shunts exhibited a strong overexpression of proangiogenic cytokines, oxygenation-associated genes (HIF1A, HMOX1), and angiopoetic growth factors. Significant inverse correlations of the expressions of miR-223-3p, miR-130b-3p, miR-19b-3p, miR-449a-5p, and miR-511-3p which were up-regulated in AV shunts, and miR-27b-3p, miR-10b-5p, let-7b-5p, and let-7c-5p, which were down-regulated in AV shunts, with their predicted interacting targets C–X–C chemokine receptor 2 (CXCR2), interleukin-1 alpha (IL1A), ephrin receptor kinase 2 (EPHA2), synaptojanin-2 binding protein (SYNJ2BP), forkhead box C1 (FOXC1) were present. CXCL2 and IL1A overexpression in AV shunt endothelium was confirmed at the protein level by immunohistochemistry. Conclusions: Our data indicate that flow-stimulated angiogenesis is determined by an upregulation of cytokines, oxygenation associated genes and miRNA-dependent regulation of FOXC1, EPHA2 and SYNJ2BP

@Article{Becker2019,
  author       = {André Becker and Giovanna Vella and Valentina Galata and Katharina Rentz and Christoph Beisswenger and Christian Herr and Jörn Walter and Sascha Tierling and Hortense Slevogt and Andreas Keller and Robert Bals},
  title        = {The composition of the pulmonary microbiota in sarcoidosis–an observational study},
  journal      = {Respiratory research},
  publisher    = {BioMed Central},
  year         = {2019},
  volume       = {20},
  issue        = {1},
  pages        = {46},
  issn         = {46},
  issn-linking = {46},
  abstract     = {Sarcoidosis is a systemic disease of unknown etiology. The disease mechanisms are largely speculative and may include the role microbial patterns that initiate and drive an underlying immune process. The aim of this study was to characterize the microbiota of the lung of patients with sarcoidosis and compare its composition and diversity with the results from patients with other interstitial lung disease (ILD) and historic healthy controls. Patients (sarcoidosis, n = 31; interstitial lung disease, n = 19) were recruited within the PULMOHOM study, a prospective cohort study to characterize inflammatory processes in pulmonary diseases. Bronchoscopy of the middle lobe or the lingula was performed and the recovered fluid was immediately sent for analysis of the pulmonary microbiota by 16sRNA gene sequencing. Subsequent bioinformatic analysis was performed to compare the groups. There were no significant differences between patients with sarcoidosis or other ILDs with regard to microbiome composition and diversity. In addition, the abundance of the genera Atopobium, Fusobacterium, Mycobacterium or Propionibacterium were not different between the two groups. There were no gross differences to historical healthy controls. The analysis of the pulmonary microbiota based on 16sRNA gene sequencing did not show a significant dysbiosis in patients with sarcoidosis as compared to other ILD patients. These data do not exclude a microbiological component in the pathogenesis of sarcoidosis.},
  doi          = {10.1186/s12931-019-1013-2},
  pii          = {10.1186/s12931-019-1013-2},
}

Sarcoidosis is a systemic disease of unknown etiology. The disease mechanisms are largely speculative and may include the role microbial patterns that initiate and drive an underlying immune process. The aim of this study was to characterize the microbiota of the lung of patients with sarcoidosis and compare its composition and diversity with the results from patients with other interstitial lung disease (ILD) and historic healthy controls. Patients (sarcoidosis, n = 31; interstitial lung disease, n = 19) were recruited within the PULMOHOM study, a prospective cohort study to characterize inflammatory processes in pulmonary diseases. Bronchoscopy of the middle lobe or the lingula was performed and the recovered fluid was immediately sent for analysis of the pulmonary microbiota by 16sRNA gene sequencing. Subsequent bioinformatic analysis was performed to compare the groups. There were no significant differences between patients with sarcoidosis or other ILDs with regard to microbiome composition and diversity. In addition, the abundance of the genera Atopobium, Fusobacterium, Mycobacterium or Propionibacterium were not different between the two groups. There were no gross differences to historical healthy controls. The analysis of the pulmonary microbiota based on 16sRNA gene sequencing did not show a significant dysbiosis in patients with sarcoidosis as compared to other ILD patients. These data do not exclude a microbiological component in the pathogenesis of sarcoidosis.

@Article{Hart2019,
  author       = {Martin Hart and Barbara Walch-Rückheim and Lena Krammes and Tim Kehl and Stefanie Rheinheimer and Tanja Tänzer and Birgit Glombitza and Martina Sester and Hans-Peter Lenhof and Andreas Keller and Eckart Meese},
  title        = {miR-34a as hub of T cell regulation networks},
  journal      = {Journal for immunotherapy of cancer},
  publisher    = {BioMed Central},
  year         = {2019},
  volume       = {7},
  issue        = {1},
  pages        = {187},
  issn         = {187},
  issn-linking = {187},
  abstract     = {Micro(mi)RNAs are increasingly recognized as central regulators of immune cell function. While it has been predicted that miRNAs have multiple targets, the majority of these predictions still await experimental confirmation. Here, miR-34a, a well-known tumor suppressor, is analyzed for targeting genes involved in immune system processes of leucocytes. Using an in-silico approach, we combined miRNA target prediction with GeneTrail2, a web tool for Multi-omics enrichment analysis, to identify miR-34a target genes, which are involved in the immune system process subcategory of Gene Ontology. Out of the 193 predicted target genes in this subcategory we experimentally tested 22 target genes and confirmed binding of miR-34a to 14 target genes including VAMP2, IKBKE, MYH9, MARCH8, KLRK1, CD11A, TRAFD1, CCR1, PYDC1, PRF1, PIK3R2, PIK3CD, AP1B1, and ADAM10 by dual luciferase assays. By transfecting Jurkat, primary CD4+ and CD8+ T cells with miR-34a, we demonstrated that ectopic expression of miR-34a leads to reduced levels of endogenous VAMP2 and CD11A, which are central to the analyzed subcategories. Functional downstream analysis of miR-34a over-expression in activated CD8+ T cells exhibits a distinct decrease of PRF1 secretion. By simultaneous targeting of 14 mRNAs miR-34a acts as major hub of T cell regulatory networks suggesting to utilize miR-34a as target of intervention towards a modulation of the immune responsiveness of T-cells in a broad tumor context.},
  doi          = {10.1186/s40425-019-0670-5},
  pii          = {10.1186/s40425-019-0670-5},
}

Micro(mi)RNAs are increasingly recognized as central regulators of immune cell function. While it has been predicted that miRNAs have multiple targets, the majority of these predictions still await experimental confirmation. Here, miR-34a, a well-known tumor suppressor, is analyzed for targeting genes involved in immune system processes of leucocytes. Using an in-silico approach, we combined miRNA target prediction with GeneTrail2, a web tool for Multi-omics enrichment analysis, to identify miR-34a target genes, which are involved in the immune system process subcategory of Gene Ontology. Out of the 193 predicted target genes in this subcategory we experimentally tested 22 target genes and confirmed binding of miR-34a to 14 target genes including VAMP2, IKBKE, MYH9, MARCH8, KLRK1, CD11A, TRAFD1, CCR1, PYDC1, PRF1, PIK3R2, PIK3CD, AP1B1, and ADAM10 by dual luciferase assays. By transfecting Jurkat, primary CD4+ and CD8+ T cells with miR-34a, we demonstrated that ectopic expression of miR-34a leads to reduced levels of endogenous VAMP2 and CD11A, which are central to the analyzed subcategories. Functional downstream analysis of miR-34a over-expression in activated CD8+ T cells exhibits a distinct decrease of PRF1 secretion. By simultaneous targeting of 14 mRNAs miR-34a acts as major hub of T cell regulatory networks suggesting to utilize miR-34a as target of intervention towards a modulation of the immune responsiveness of T-cells in a broad tumor context.

@Article{Karpinski2019,
  author       = {Karpinski P. and Kahraman M. and Ludwig N. and Skiba P. and Kosinska M. and Rosiek-Biegus M. and Królewicz E. and Panaszek B. and Nittner-Marszalska M. and Blin N. and Keller A. and Meese E. and Sasiadek MM.},
  title        = {Limited Long-Term Impact of Insect Venom Immunotherapy on the Micro-RNA Landscape in Whole Blood.},
  journal      = {J Investig Allergol Clin Immunol.},
  publisher    = {JIACI},
  year         = {2019},
  volume       = {29},
  issue        = {3},
  pages        = {206-212},
  abstract     = {Objective: To perform a genome-wide characterization of changes in microRNA (miRNA) expression during the course of venom immunotherapy (VIT). Methods: miRNA was isolated from the whole-blood of 13 allergic patients and 14 controls, who experienced no allergic reaction upon stings by honeybees and wasps. We analyzed 2549 miRNAs from the whole blood of these patients prior to VIT and 12 months after the start of VIT. The results for differential expression obtained on a microarray platform were confirmed by quantitative real-time PCR. Out of the 13 patients, 8 had a negative allergic reaction with VIT, thus indicating that this approach was successful. Results: By comparing time points before and 12 months after ultrarush VIT, correlation analysis and principal component analysis both indicated a limited effect of VIT on the overall miRNA expression pattern. Volcano plot analysis based on raw P values revealed few deregulated miRNAs, most of which were increasingly expressed after VIT as compared with before VIT. Based on the 50 most altered miRNAs, no clear clustering was observed before or after VIT. Conclusions: Our results indicate an overall reduced effect of VIT on the miRNA expression pattern in whole blood. Key words: miRNA, Whole genome, Blood, Expression, Venom immunotherapy},
  doi          = {10.18176/jiaci.0303},
  pii          = {10.18176/jiaci.0303},
}

Objective: To perform a genome-wide characterization of changes in microRNA (miRNA) expression during the course of venom immunotherapy (VIT). Methods: miRNA was isolated from the whole-blood of 13 allergic patients and 14 controls, who experienced no allergic reaction upon stings by honeybees and wasps. We analyzed 2549 miRNAs from the whole blood of these patients prior to VIT and 12 months after the start of VIT. The results for differential expression obtained on a microarray platform were confirmed by quantitative real-time PCR. Out of the 13 patients, 8 had a negative allergic reaction with VIT, thus indicating that this approach was successful. Results: By comparing time points before and 12 months after ultrarush VIT, correlation analysis and principal component analysis both indicated a limited effect of VIT on the overall miRNA expression pattern. Volcano plot analysis based on raw P values revealed few deregulated miRNAs, most of which were increasingly expressed after VIT as compared with before VIT. Based on the 50 most altered miRNAs, no clear clustering was observed before or after VIT. Conclusions: Our results indicate an overall reduced effect of VIT on the miRNA expression pattern in whole blood. Key words: miRNA, Whole genome, Blood, Expression, Venom immunotherapy

@Article{Ludwig2019,
  author       = {Nicole Ludwig and Tobias Fehlmann and Fabian Kern and Manfred Gogol and Walter Maetzler and Stephanie Deutscher and Simone Gurlit and ClaudiaSchulte and Anna-Katharinavon Thaler and Christian Deuschle and Florian Metzger and Daniela Berg and Ulrike Suenkel and Verena Keller and Christina Backes and Hans-Peter Lenhof and Eckart Meese and Andreas Keller},
  title        = {Machine Learning to Detect Alzheimer's Disease from Circulating Non-coding RNAs.},
  journal      = {Genomics, Proteomics & Bioinformatics},
  publisher    = {ScienceDirect},
  year         = {2019},
  volume       = {17},
  issue        = {4},
  pages        = {430-440},
  abstract     = {Blood-borne small non-coding (sncRNAs) are among the prominent candidates for blood-based diagnostic tests. Often, high-throughput approaches are applied to discover biomarker signatures. These have to be validated in larger cohorts and evaluated by adequate statistical learning approaches. Previously, we published high-throughput sequencing based microRNA (miRNA) signatures in Alzheimer’s disease (AD) patients in the United States (US) and Germany. Here, we determined abundance levels of 21 known circulating miRNAs in 465 individuals encompassing AD patients and controls by RT-qPCR. We computed models to assess the relation between miRNA expression and phenotypes, gender, age, or disease severity (Mini-Mental State Examination; MMSE). Of the 21 miRNAs, expression levels of 20 miRNAs were consistently de-regulated in the US and German cohorts. 18 miRNAs were significantly correlated with neurodegeneration (Benjamini-Hochberg adjusted P < 0.05) with highest significance for miR-532-5p (Benjamini-Hochberg adjusted P = 4.8 × 10−30). Machine learning models reached an area under the curve (AUC) value of 87.6% in differentiating AD patients from controls. Further, ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted P = 0.0002). Interestingly, the miRNAs with lower abundance in AD were enriched in monocytes and T-helper cells, while those up-regulated in AD were enriched in serum, exosomes, cytotoxic t-cells, and B-cells. Our study represents the next important step in translational research for a miRNA-based AD test.},
  doi          = {10.1016/j.gpb.2019.09.004},
  pii          = {10.1016/j.gpb.2019.09.004},
}

Blood-borne small non-coding (sncRNAs) are among the prominent candidates for blood-based diagnostic tests. Often, high-throughput approaches are applied to discover biomarker signatures. These have to be validated in larger cohorts and evaluated by adequate statistical learning approaches. Previously, we published high-throughput sequencing based microRNA (miRNA) signatures in Alzheimer’s disease (AD) patients in the United States (US) and Germany. Here, we determined abundance levels of 21 known circulating miRNAs in 465 individuals encompassing AD patients and controls by RT-qPCR. We computed models to assess the relation between miRNA expression and phenotypes, gender, age, or disease severity (Mini-Mental State Examination; MMSE). Of the 21 miRNAs, expression levels of 20 miRNAs were consistently de-regulated in the US and German cohorts. 18 miRNAs were significantly correlated with neurodegeneration (Benjamini-Hochberg adjusted P < 0.05) with highest significance for miR-532-5p (Benjamini-Hochberg adjusted P = 4.8 × 10−30). Machine learning models reached an area under the curve (AUC) value of 87.6% in differentiating AD patients from controls. Further, ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted P = 0.0002). Interestingly, the miRNAs with lower abundance in AD were enriched in monocytes and T-helper cells, while those up-regulated in AD were enriched in serum, exosomes, cytotoxic t-cells, and B-cells. Our study represents the next important step in translational research for a miRNA-based AD test.

@Article{Iram2019,
  author       = {Tal Iram and Andreas Keller and Tony Wyss-Coray},
  title        = {An 80,000-Piece Puzzle of Alzheimer's Disease.},
  journal      = {Immunity},
  publisher    = {CellPress},
  year         = {2019},
  volume       = {50},
  issue        = {6},
  pages        = {1349-1351},
  abstract     = {To gain unfettered insight into one of the scourges of our aging societies, Mathys and colleagues in Nature (Mathys et al., 2019) illuminate the brain transcriptome of Alzheimer's disease at single-cell resolution. Their findings implicate oligodendrocytes, a cell type largely neglected in Alzheimer's disease research, and sex in the disease in intriguing ways.},
  doi          = {10.1016/j.immuni.2019.05.016},
  pii          = {10.1016/j.immuni.2019.05.016},
}

To gain unfettered insight into one of the scourges of our aging societies, Mathys and colleagues in Nature (Mathys et al., 2019) illuminate the brain transcriptome of Alzheimer's disease at single-cell resolution. Their findings implicate oligodendrocytes, a cell type largely neglected in Alzheimer's disease research, and sex in the disease in intriguing ways.

@Article{Abu-Halima2019,
  author       = {Abu-Halima Masood and Meese Eckart and Saleh Mohamad Ali and Keller Andreas and Abdul-Khaliq Hashim and Raedle-Hurst Tanja},
  title        = {Micro-RNA 150-5p predicts overt heart failure in patients with univentricular hearts.},
  journal      = {PLoS One},
  publisher    = {PubMed},
  year         = {2019},
  volume       = {14},
  issue        = {10},
  pages        = {e0223606},
  abstract     = {BACKGROUND: In patients with left heart failure, micro-RNAs (miRNAs) have been shown to be of diagnostic and prognostic value. The present study aims to identify those miRNAs in patients with univentricular heart (UVH) disease that may be associated with overt heart failure. METHODS: A large panel of human miRNA arrays were used to determine miRNA expression profiles in the blood of 48 UVH patients and 32 healthy controls. For further selection, the most abundantly expressed miRNA arrays were related to clinical measures of heart failure and selected miRNAs validated by polymerase chain reaction were used for the prediction of overt heart failure and all-cause mortality. RESULTS: According to microarray analysis, 50 miRNAs were found to be significantly abundant in UVH patients of which miR-150-5p was best related to heart failure parameters. According to ROC analysis, NT-proBNP levels (AUC 0.940, 95% CI 0.873-1.000; p = 0.001), miR-150-5p (AUC 0.905, 95% CI 0.779-1.000; p = 0.001) and a higher NYHA class ≥ III (AUC 0.893, 95% CI 0.713-1.000; p = 0.002) were the 3 most significant predictors of overt heart failure. Using a combined biomarker model, AUC increased to 0.980 indicating an additive value of miR-150-5p. Moreover, in the multivariate analysis, a higher NYHA class ≥ III (p = 0.005) and miR-150-5p (p = 0.006) turned out to be independent predictors of overt heart failure. CONCLUSION: In patients with UVH, miR-150-5p is an independent predictor of overt heart failure and thus may be used in the risk assessment of these patients.},
  doi          = {10.1371/journal.pone.0223606},
  pii          = {10.1371/journal.pone.0223606},
}

BACKGROUND: In patients with left heart failure, micro-RNAs (miRNAs) have been shown to be of diagnostic and prognostic value. The present study aims to identify those miRNAs in patients with univentricular heart (UVH) disease that may be associated with overt heart failure. METHODS: A large panel of human miRNA arrays were used to determine miRNA expression profiles in the blood of 48 UVH patients and 32 healthy controls. For further selection, the most abundantly expressed miRNA arrays were related to clinical measures of heart failure and selected miRNAs validated by polymerase chain reaction were used for the prediction of overt heart failure and all-cause mortality. RESULTS: According to microarray analysis, 50 miRNAs were found to be significantly abundant in UVH patients of which miR-150-5p was best related to heart failure parameters. According to ROC analysis, NT-proBNP levels (AUC 0.940, 95% CI 0.873-1.000; p = 0.001), miR-150-5p (AUC 0.905, 95% CI 0.779-1.000; p = 0.001) and a higher NYHA class ≥ III (AUC 0.893, 95% CI 0.713-1.000; p = 0.002) were the 3 most significant predictors of overt heart failure. Using a combined biomarker model, AUC increased to 0.980 indicating an additive value of miR-150-5p. Moreover, in the multivariate analysis, a higher NYHA class ≥ III (p = 0.005) and miR-150-5p (p = 0.006) turned out to be independent predictors of overt heart failure. CONCLUSION: In patients with UVH, miR-150-5p is an independent predictor of overt heart failure and thus may be used in the risk assessment of these patients.

@Article{Scholz2019,
  author       = {Sean S. Scholz and Markus Dillmann and Alexander Flohr and Christina Backes and Tobias Fehlmann and Dominic Millenaar and Christian Ukena and Michael Böhm and Andreas Keller and Felix Mahfoud},
  title        = {Contemporary scientometric analyses using a novel web application: the science performance evaluation (SciPE) approach},
  journal      = {Clin Res Cardiol},
  year         = {2019},
  pages        = {1–9},
  abstract     = {AIMS: We aimed at developing a structured study protocol utilizing the bibliographic web-application science performance evaluation (SciPE) to perform comprehensive scientometric analyses. METHODS AND RESULTS: Metadata related to publications derived from online databases were processed and visualized by transferring the information to an undirected multipartite graph and distinct partitioned sets of nodes. Also, institution-specific data were normalized and merged allowing precise geocoordinate positioning, to enable heatmapping and valid identification. As a result, verified, processed data regarding articles, institutions, journals, authors gender, nations and subject categories can be obtained. We recommend including the total number of publications, citations, the population, research institutions, gross domestic product, and the country-specific modified Hirsch Index and to form corresponding ratios (e.g., population/publication). Also, our approach includes implementation of bioinformatical methods such as heatmapping based on exact geocoordinates, simple chord diagrams, and the central implementation of specific ratios with plain visualization techniques. CONCLUSION: This protocol allows precise conduction of contemporaneous scientometric analyses based on bioinformatic and meta-analytical techniques, allowing to evaluate and contextualize scientific efforts. Data presentation with the depicted visualization techniques is mandatory for transparent and consistent analyses of research output across different nations and topics. Research performance can then be discussed in a synopsis of all findings. KEYWORDS: Bibliometrics; Bibliometry; Meta-analysis; Research assessment; Scientometry},
  doi          = {10.1007/s00392-019-01568-x},
  pii          = {10.1007/s00392-019-01568-x},
}

AIMS: We aimed at developing a structured study protocol utilizing the bibliographic web-application science performance evaluation (SciPE) to perform comprehensive scientometric analyses. METHODS AND RESULTS: Metadata related to publications derived from online databases were processed and visualized by transferring the information to an undirected multipartite graph and distinct partitioned sets of nodes. Also, institution-specific data were normalized and merged allowing precise geocoordinate positioning, to enable heatmapping and valid identification. As a result, verified, processed data regarding articles, institutions, journals, authors gender, nations and subject categories can be obtained. We recommend including the total number of publications, citations, the population, research institutions, gross domestic product, and the country-specific modified Hirsch Index and to form corresponding ratios (e.g., population/publication). Also, our approach includes implementation of bioinformatical methods such as heatmapping based on exact geocoordinates, simple chord diagrams, and the central implementation of specific ratios with plain visualization techniques. CONCLUSION: This protocol allows precise conduction of contemporaneous scientometric analyses based on bioinformatic and meta-analytical techniques, allowing to evaluate and contextualize scientific efforts. Data presentation with the depicted visualization techniques is mandatory for transparent and consistent analyses of research output across different nations and topics. Research performance can then be discussed in a synopsis of all findings. KEYWORDS: Bibliometrics; Bibliometry; Meta-analysis; Research assessment; Scientometry

@Article{Kehl2019,
  author       = {Tim Kehl and Fabian Kern and Christina Backes and Tobias Fehlmann and Daniel Stöckel and Eckart Meese and Hans-Peter Lenhof and Andreas Keller},
  title        = {miRPathDB 2.0: a novel release of the miRNA Pathway Dictionary Database.},
  journal      = {Nucleic Acids Research},
  year         = {2019},
  volume       = {48},
  issue        = {D1},
  pages        = {D142–D147},
  abstract     = {Since the initial release of miRPathDB, tremendous progress has been made in the field of microRNA (miRNA) research. New miRNA reference databases have emerged, a vast amount of new miRNA candidates has been discovered and the number of experimentally validated target genes has increased considerably. Hence, the demand for a major upgrade of miRPathDB, including extended analysis functionality and intuitive visualizations of query results has emerged. Here, we present the novel release 2.0 of the miRNA Pathway Dictionary Database (miRPathDB) that is freely accessible at https://mpd.bioinf.uni-sb.de/. miRPathDB 2.0 comes with a ten-fold increase of pre-processed data. In total, the updated database provides putative associations between 27 452 (candidate) miRNAs, 28 352 targets and 16 833 pathways for Homo sapiens, as well as interactions of 1978 miRNAs, 24 898 targets and 6511 functional categories for Mus musculus. Additionally, we analyzed publications citing miRPathDB to identify common use-cases and further extensions. Based on this evaluation, we added new functionality for interactive visualizations and down-stream analyses of bulk queries. In summary, the updated version of miRPathDB, with its new custom-tailored features, is one of the most comprehensive and advanced resources for miRNAs and their target pathways.},
  doi          = {10.1093/nar/gkz1022},
  pii          = {10.1093/nar/gkz1022},
}

Since the initial release of miRPathDB, tremendous progress has been made in the field of microRNA (miRNA) research. New miRNA reference databases have emerged, a vast amount of new miRNA candidates has been discovered and the number of experimentally validated target genes has increased considerably. Hence, the demand for a major upgrade of miRPathDB, including extended analysis functionality and intuitive visualizations of query results has emerged. Here, we present the novel release 2.0 of the miRNA Pathway Dictionary Database (miRPathDB) that is freely accessible at https://mpd.bioinf.uni-sb.de/. miRPathDB 2.0 comes with a ten-fold increase of pre-processed data. In total, the updated database provides putative associations between 27 452 (candidate) miRNAs, 28 352 targets and 16 833 pathways for Homo sapiens, as well as interactions of 1978 miRNAs, 24 898 targets and 6511 functional categories for Mus musculus. Additionally, we analyzed publications citing miRPathDB to identify common use-cases and further extensions. Based on this evaluation, we added new functionality for interactive visualizations and down-stream analyses of bulk queries. In summary, the updated version of miRPathDB, with its new custom-tailored features, is one of the most comprehensive and advanced resources for miRNAs and their target pathways.

@Article{Lehallier2019,
  author       = {Benoit Lehallier and David Gate and Nicholas Schaum and Tibor Nanasi and Song Eun Lee and Hanadie Yousef and Patricia Moran Losada and Daniela Berdnik and Andreas Keller and Joe Verghese and Sanish Sathyan and Claudio Franceschi and Sofiya Milman and Nir Barzilai and Tony Wyss-Coray},
  title        = {Undulating changes in human plasma proteome profiles across the lifespan},
  journal      = {Nature Medicine},
  year         = {2019},
  volume       = {25},
  issue        = {12},
  pages        = {1843-1850},
  abstract     = {Aging is a predominant risk factor for several chronic diseases that limit healthspan1. Mechanisms of aging are thus increasingly recognized as potential therapeutic targets. Blood from young mice reverses aspects of aging and disease across multiple tissues2-10, which supports a hypothesis that age-related molecular changes in blood could provide new insights into age-related disease biology. We measured 2,925 plasma proteins from 4,263 young adults to nonagenarians (18-95 years old) and developed a new bioinformatics approach that uncovered marked non-linear alterations in the human plasma proteome with age. Waves of changes in the proteome in the fourth, seventh and eighth decades of life reflected distinct biological pathways and revealed differential associations with the genome and proteome of age-related diseases and phenotypic traits. This new approach to the study of aging led to the identification of unexpected signatures and pathways that might offer potential targets for age-related diseases.},
  doi          = {10.1038/s41591-019-0673-2},
  pii          = {10.1038/s41591-019-0673-2},
}

Aging is a predominant risk factor for several chronic diseases that limit healthspan1. Mechanisms of aging are thus increasingly recognized as potential therapeutic targets. Blood from young mice reverses aspects of aging and disease across multiple tissues2-10, which supports a hypothesis that age-related molecular changes in blood could provide new insights into age-related disease biology. We measured 2,925 plasma proteins from 4,263 young adults to nonagenarians (18-95 years old) and developed a new bioinformatics approach that uncovered marked non-linear alterations in the human plasma proteome with age. Waves of changes in the proteome in the fourth, seventh and eighth decades of life reflected distinct biological pathways and revealed differential associations with the genome and proteome of age-related diseases and phenotypic traits. This new approach to the study of aging led to the identification of unexpected signatures and pathways that might offer potential targets for age-related diseases.

@Article{Meistertzheim2019,
  author       = {Morgane Meistertzheim and Tobias Fehlmann and Franziska Drews and Marcello Pirritano and Gilles Gasparoni and Andreas Keller and Martin Simon},
  title        = {Comparative Analysis of Biochemical Biases by Ligation- and Template-Switch-Based Small RNA Library Preparation Protocols.},
  journal      = {Clinical Chemistry},
  publisher    = {Clinical Chemistry},
  year         = {2019},
  volume       = {65},
  issue        = {12},
  pages        = {1581-1591},
  abstract     = {BACKGROUND: Small RNAs are key players in the regulation of gene expression and differentiation. However, many different classes of small RNAs (sRNAs) have been described with distinct biogenesis pathways and, as a result, with different biochemical properties. To analyze sRNAs by deep sequencing, complementary DNA synthesis requires manipulation of the RNA molecule itself. Thus, enzymatic activities during library preparation bias the library content owing to biochemical criteria. METHODS: We compared 4 different manipulations of RNA for library preparation: (a) a ligation-based procedure allowing only 5'-mono-phosphorylated RNA to enter the library, (b) a ligation-based procedure allowing additional 5'-triphosphates and Cap structures, (c) a ligation-independent, template-switch-based library preparation, and (d) a template-switch-based library preparation allowing 3'-phosphorylated RNAs to enter the library. RESULTS: Our data show large differences between ligation-dependent and ligation-independent libraries in terms of their preference for individual sRNA classes such as microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs), and transfer RNA fragments. Moreover, the miRNA composition is different between both procedures, and more microRNA isoforms (isomiRs) can be identified after pyrophosphatase treatment. piRNAs are enriched in template-switch libraries, and this procedure apparently includes more different RNA species. CONCLUSIONS: Our data indicate that miRNAomics from both methods will hardly be comparable. Ligation-based libraries enrich for canonical miRNAs, which thus may be suitable methods for miRNAomics. Template-switch libraries contain increased numbers and different compositions of fragments and long RNAs. Following different interests for other small RNA species, ligation-independent libraries appear to show a more realistic sRNA landscape with lower bias against biochemical modifications.},
  doi          = {10.1373/clinchem.2019.305045},
  pii          = {10.1373/clinchem.2019.305045},
}

BACKGROUND: Small RNAs are key players in the regulation of gene expression and differentiation. However, many different classes of small RNAs (sRNAs) have been described with distinct biogenesis pathways and, as a result, with different biochemical properties. To analyze sRNAs by deep sequencing, complementary DNA synthesis requires manipulation of the RNA molecule itself. Thus, enzymatic activities during library preparation bias the library content owing to biochemical criteria. METHODS: We compared 4 different manipulations of RNA for library preparation: (a) a ligation-based procedure allowing only 5'-mono-phosphorylated RNA to enter the library, (b) a ligation-based procedure allowing additional 5'-triphosphates and Cap structures, (c) a ligation-independent, template-switch-based library preparation, and (d) a template-switch-based library preparation allowing 3'-phosphorylated RNAs to enter the library. RESULTS: Our data show large differences between ligation-dependent and ligation-independent libraries in terms of their preference for individual sRNA classes such as microRNAs (miRNAs), Piwi-interacting RNAs (piRNAs), and transfer RNA fragments. Moreover, the miRNA composition is different between both procedures, and more microRNA isoforms (isomiRs) can be identified after pyrophosphatase treatment. piRNAs are enriched in template-switch libraries, and this procedure apparently includes more different RNA species. CONCLUSIONS: Our data indicate that miRNAomics from both methods will hardly be comparable. Ligation-based libraries enrich for canonical miRNAs, which thus may be suitable methods for miRNAomics. Template-switch libraries contain increased numbers and different compositions of fragments and long RNAs. Following different interests for other small RNA species, ligation-independent libraries appear to show a more realistic sRNA landscape with lower bias against biochemical modifications.

@Article{10.1093/bib/bbz111,
  author       = {Fabian Kern and Christina Backes and Pascal Hirsch and Tobias Fehlmann and Martin Hart and Eckart Meese and Andreas Keller},
  title        = {What's the target: understanding two decades of in silico microRNA-target prediction.},
  journal      = {Briefings in Bioinformatics},
  year         = {2019},
  abstract     = {Since the initial discovery of microRNAs as post-transcriptional, regulatory key players in the 1990s, a total number of \\$2656\\$ mature microRNAs have been publicly described for Homo sapiens. As discovery of new miRNAs is still on-going, target identification remains to be an essential and challenging step preceding functional annotation analysis. One key challenge for researchers seems to be the selection of the most appropriate tool out of the larger multiverse of published solutions for a given research study set-up.In this review we collectively describe the field of in silico target prediction in the course of time and point out long withstanding principles as well as recent developments. By compiling a catalog of characteristics about the 98 prediction methods and identifying common and exclusive traits, we signpost a simplified mechanism to address the problem of application selection. Going further we devised interpretation strategies for common types of output as generated by frequently used computational methods. To this end, our work specifically aims to make prospective users aware of common mistakes and practical questions that arise during the application of target prediction tools.An interactive implementation of our recommendations including materials shown in the manuscript is freely available at https://www.ccb.uni-saarland.de/mtguide.},
  doi          = {10.1093/bib/bbz111},
  pii          = {10.1093/bib/bbz111},
}

Since the initial discovery of microRNAs as post-transcriptional, regulatory key players in the 1990s, a total number of \$2656\$ mature microRNAs have been publicly described for Homo sapiens. As discovery of new miRNAs is still on-going, target identification remains to be an essential and challenging step preceding functional annotation analysis. One key challenge for researchers seems to be the selection of the most appropriate tool out of the larger multiverse of published solutions for a given research study set-up.In this review we collectively describe the field of in silico target prediction in the course of time and point out long withstanding principles as well as recent developments. By compiling a catalog of characteristics about the 98 prediction methods and identifying common and exclusive traits, we signpost a simplified mechanism to address the problem of application selection. Going further we devised interpretation strategies for common types of output as generated by frequently used computational methods. To this end, our work specifically aims to make prospective users aware of common mistakes and practical questions that arise during the application of target prediction tools.An interactive implementation of our recommendations including materials shown in the manuscript is freely available at https://www.ccb.uni-saarland.de/mtguide.

@Article{10.1371/journal.pone.0226164,
  author       = {Masood Abu-Halima and Josephin Weidinger and Martin Poryo and Dominic Henn and Andreas Keller and Eckart Meese and Hashim Abdul-Khaliq},
  title        = {Micro-RNA signatures in monozygotic twins discordant for congenital heart defects.},
  journal      = {PLOS ONE},
  publisher    = {Public Library of Science},
  year         = {2019},
  volume       = {14},
  issue        = {12},
  pages        = {1-13},
  abstract     = {Background MicroRNAs (miRNAs) are small RNAs regulating gene expression post-transcriptionally. Recent studies demonstrated that miRNAs are involved in the development of congenital heart defects (CHD). In this study, we aimed at identifying the specific patterns of miRNAs in blood of monozygotic twin pairs discordant for CHD and to assess whether miRNAs might be involved in the development or reflect the consequences of CHD.   Methods miRNA microarray analysis and Real-Time Quantitative PCR (RT-qPCR) were employed to determine the miRNA abundance level from 12 monozygotic twins discordant for CHD and their non-CHD co-twins (n = 12). Enrichment analyses of altered miRNAs were performed using bioinformatics tools.   Results Compared with non-CHD co-twins, profiling analysis indicated 34 miRNAs with a significant difference in abundance level (p<0.05, fold change ≥ 1.3), of which 11 miRNAs were up-regulated and 23 miRNAs were down-regulated. Seven miRNAs were validated with RT-qPCR including miR-511-3p, miR-1306-5p, miR-421, miR-4707-3p, miR-4732-3p, miR-5189-3p, and miR-890, and the results were consistent with microarray analysis. Five miRNAs namely miR-511-3p, miR-1306-5p, miR-4732-3p, miR-5189-3p, and miR-890 were found to be significantly up-regulated in twins < 10 years old. Bioinformatics analysis showed that the 7 validated miRNAs were involved in phosphatidylinositol signaling, gap junction signaling, and adrenergic signaling in cardiomyocytes.   Conclusions Our data show deregulated miRNA abundance levels in the peripheral blood of monozygotic twins discordant for CHD, and identify new candidates for further analysis, which may contribute to understanding the development of CHD in the future. Bioinformatics analysis indicated that the target genes of these miRNAs are likely involved in signaling and communication of cardiomyocytes},
  doi          = {10.1371/journal.pone.0226164},
  pii          = {10.1371/journal.pone.0226164},
}

Background MicroRNAs (miRNAs) are small RNAs regulating gene expression post-transcriptionally. Recent studies demonstrated that miRNAs are involved in the development of congenital heart defects (CHD). In this study, we aimed at identifying the specific patterns of miRNAs in blood of monozygotic twin pairs discordant for CHD and to assess whether miRNAs might be involved in the development or reflect the consequences of CHD. Methods miRNA microarray analysis and Real-Time Quantitative PCR (RT-qPCR) were employed to determine the miRNA abundance level from 12 monozygotic twins discordant for CHD and their non-CHD co-twins (n = 12). Enrichment analyses of altered miRNAs were performed using bioinformatics tools. Results Compared with non-CHD co-twins, profiling analysis indicated 34 miRNAs with a significant difference in abundance level (p<0.05, fold change ≥ 1.3), of which 11 miRNAs were up-regulated and 23 miRNAs were down-regulated. Seven miRNAs were validated with RT-qPCR including miR-511-3p, miR-1306-5p, miR-421, miR-4707-3p, miR-4732-3p, miR-5189-3p, and miR-890, and the results were consistent with microarray analysis. Five miRNAs namely miR-511-3p, miR-1306-5p, miR-4732-3p, miR-5189-3p, and miR-890 were found to be significantly up-regulated in twins < 10 years old. Bioinformatics analysis showed that the 7 validated miRNAs were involved in phosphatidylinositol signaling, gap junction signaling, and adrenergic signaling in cardiomyocytes. Conclusions Our data show deregulated miRNA abundance levels in the peripheral blood of monozygotic twins discordant for CHD, and identify new candidates for further analysis, which may contribute to understanding the development of CHD in the future. Bioinformatics analysis indicated that the target genes of these miRNAs are likely involved in signaling and communication of cardiomyocytes

@Article{10.1002/1878-0261.12620,
  author       = {Sinan Uğur Umu and Hilde Langseth and Andreas Keller and Eckart Meese and Åslaug Helland and Robert Lyle and Trine B. Rounge},
  title        = {A 10 year prediagnostic followup study shows that serum RNA signals are highly dynamic in lung carcinogenesis.},
  journal      = {Molecular Oncology},
  year         = {2019},
  abstract     = {The majority of lung cancer (LC) patients are diagnosed at a late stage and survival is poor. Circulating RNA molecules are known to have a role in cancer, however, their involvement before diagnosis remains an open question. In this study, we investigated circulating RNA dynamics in prediagnostic LC samples, focusing on smokers, to identify if and when disease-related signals can be detected in serum. We sequenced small RNAs in 542 serum LC samples donated up to 10 years before diagnosis and 519 matched cancer-free controls coming from 905 individuals in the Janus Serum Bank. This sample size provided sufficient statistical power to independently analyse time-to-diagnosis, stage and histology. The results showed dynamic changes in differentially expressed circulating RNAs specific to LC histology and stage. The greatest number of differentially expressed RNAs were identified around 7 years before diagnosis for early stage LC and 1 to 4 years prior to diagnosis for locally advanced and advanced stage LC, regardless of LC histology. Furthermore, NSCLC and SCLC histologies have distinct prediagnostic signals. The majority of differentially expressed RNAs were associated with cancer-related pathways. The dynamic RNA signals pinpointed different phases of tumor development over time. Stage-specific RNA profiles may be associated with tumor aggressiveness. Our results improve the molecular understanding of carcinogenesis. They indicate substantial opportunity for screening and improved treatment and will guide further research on early detection of LC. However, the dynamic nature of the RNA signals also suggests challenges for prediagnostic biomarker discovery.},
  doi          = {10.1002/1878-0261.12620},
  pii          = {10.1002/1878-0261.12620},
}

The majority of lung cancer (LC) patients are diagnosed at a late stage and survival is poor. Circulating RNA molecules are known to have a role in cancer, however, their involvement before diagnosis remains an open question. In this study, we investigated circulating RNA dynamics in prediagnostic LC samples, focusing on smokers, to identify if and when disease-related signals can be detected in serum. We sequenced small RNAs in 542 serum LC samples donated up to 10 years before diagnosis and 519 matched cancer-free controls coming from 905 individuals in the Janus Serum Bank. This sample size provided sufficient statistical power to independently analyse time-to-diagnosis, stage and histology. The results showed dynamic changes in differentially expressed circulating RNAs specific to LC histology and stage. The greatest number of differentially expressed RNAs were identified around 7 years before diagnosis for early stage LC and 1 to 4 years prior to diagnosis for locally advanced and advanced stage LC, regardless of LC histology. Furthermore, NSCLC and SCLC histologies have distinct prediagnostic signals. The majority of differentially expressed RNAs were associated with cancer-related pathways. The dynamic RNA signals pinpointed different phases of tumor development over time. Stage-specific RNA profiles may be associated with tumor aggressiveness. Our results improve the molecular understanding of carcinogenesis. They indicate substantial opportunity for screening and improved treatment and will guide further research on early detection of LC. However, the dynamic nature of the RNA signals also suggests challenges for prediagnostic biomarker discovery.

@Article{10.1111/and.1350,
  author       = {Abu-Halima, Masood and Galata, Valentina and Backes, Christina and Keller, Andreas and Hammadeh, Mohamad and Meese, Eckart},
  title        = {MicroRNA signature in spermatozoa and seminal plasma of proven fertile men and in testicular tissue of men with obstructive azoospermia},
  journal      = {Andrologia},
  year         = {2019},
  pages        = {e13503},
  abstract     = {Abstract MicroRNAs (miRNAs) have recently received a significant amount of attention due to their remarkable influence on post-transcriptional gene regulation. In this study, we aim to provide a catalogue of miRNAs present in spermatozoa, seminal plasma and testicular tissue. Expression profiles of miRNA in spermatozoa and seminal plasma of 16 proven fertile men and testicular tissue of eight men with morphologically and/or histologically confirmed obstructive azoospermia were determined by microarray and RT-qPCR in combination with bioinformatics analyses. A total of 123, 156 and 133 miRNAs were consistently detected in spermatozoa, seminal plasma and testicular tissue respectively. Sixty-four miRNAs were shared across all sample types. Based on miRNAs expression level present in each group, correlation analysis showed moderate-to-strong correlations within the spermatozoa and seminal plasma samples and a wider range of correlations within the testicular tissue samples. The target genes of known miRNAs appeared to be involved in a wide range of biological processes related to reproduction, development and differentiation of germ cells. Our results suggest that there is a certain similarity between spermatozoa and seminal plasma for the relative miRNA expression changes with respect to testicular tissue and provide an overview of the miRNAs present in each sample type.},
  doi          = {10.1111/and.13503},
  pii          = {10.1111/and.13503},
}

Abstract MicroRNAs (miRNAs) have recently received a significant amount of attention due to their remarkable influence on post-transcriptional gene regulation. In this study, we aim to provide a catalogue of miRNAs present in spermatozoa, seminal plasma and testicular tissue. Expression profiles of miRNA in spermatozoa and seminal plasma of 16 proven fertile men and testicular tissue of eight men with morphologically and/or histologically confirmed obstructive azoospermia were determined by microarray and RT-qPCR in combination with bioinformatics analyses. A total of 123, 156 and 133 miRNAs were consistently detected in spermatozoa, seminal plasma and testicular tissue respectively. Sixty-four miRNAs were shared across all sample types. Based on miRNAs expression level present in each group, correlation analysis showed moderate-to-strong correlations within the spermatozoa and seminal plasma samples and a wider range of correlations within the testicular tissue samples. The target genes of known miRNAs appeared to be involved in a wide range of biological processes related to reproduction, development and differentiation of germ cells. Our results suggest that there is a certain similarity between spermatozoa and seminal plasma for the relative miRNA expression changes with respect to testicular tissue and provide an overview of the miRNAs present in each sample type.

@Article{Amand2019,
  author       = {Jérémy Amand and Tobias Fehlmann and Christina Backes and Andreas Keller},
  title        = {DynaVenn: web-based computation of the most significant overlap between ordered sets.},
  journal      = {BMC Bioinformatics},
  year         = {2019},
  volume       = {20},
  doi          = {10.1186/s12859-019-3320-5},
  pii          = {10.1186/s12859-019-3320-5},
}

@Article{Backes2018,
  author       = {Backes, Christina and Fehlmann, Tobias and Kern, Fabian and Kehl, Tim and Lenhof, Hans-Peter and Meese, Eckart and Keller, Andreas},
  title        = {miRCarta: a central repository for collecting miRNA candidates.},
  journal      = {Nucleic acids research},
  year         = {2018},
  volume       = {46},
  pages        = {D160--D167},
  month        = jan,
  issn         = {1362-4962},
  abstract     = {The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014. As a result, publications describing new miRNA candidates in the last three to five years might have a substantial overlap of candidates without noticing. With miRCarta we implemented a database to collect novel miRNA candidates and augment the information provided by miRBase. In the first stage, miRCarta is thought to be a highly sensitive collection of potential miRNA candidates with a high degree of analysis functionality, annotations and details on each miRNA. We added-besides the full content of the miRBase-12,857 human miRNA precursors to miRCarta. Users can match their own predictions to the entries of miRCarta to reduce potential redundancies in their studies. miRCarta provides the most comprehensive collection of human miRNAs and miRNA candidates to form a basis for further refinement and validation studies. The database is freely accessible at https://mircarta.cs.uni-saarland.de/.},
  country      = {England},
  doi          = {10.1093/nar/gkx851},
  issn-linking = {0305-1048},
  issue        = {D1},
  nlm-id       = {0411011},
  owner        = {NLM},
  pii          = {4191334},
  pmc          = {PMC5753177},
  pmid         = {29036653},
  pubmodel     = {Print},
  pubstatus    = {ppublish},
  revised      = {2018-02-10},
}

The continuous increase of available biological data as consequence of modern high-throughput technologies poses new challenges for analysis techniques and database applications. Especially for miRNAs, one class of small non-coding RNAs, many algorithms have been developed to predict new candidates from next-generation sequencing data. While the amount of publications describing novel miRNA candidates keeps steadily increasing, the current gold standard database for miRNAs - miRBase - has not been updated since June 2014. As a result, publications describing new miRNA candidates in the last three to five years might have a substantial overlap of candidates without noticing. With miRCarta we implemented a database to collect novel miRNA candidates and augment the information provided by miRBase. In the first stage, miRCarta is thought to be a highly sensitive collection of potential miRNA candidates with a high degree of analysis functionality, annotations and details on each miRNA. We added-besides the full content of the miRBase-12,857 human miRNA precursors to miRCarta. Users can match their own predictions to the entries of miRCarta to reduce potential redundancies in their studies. miRCarta provides the most comprehensive collection of human miRNAs and miRNA candidates to form a basis for further refinement and validation studies. The database is freely accessible at https://mircarta.cs.uni-saarland.de/.

@Article{Palmieri2018,
  author       = {Palmieri, Valeria and Backes, Christina and Ludwig, Nicole and Fehlmann, Tobias and Kern, Fabian and Meese, Eckart and Keller, Andreas},
  title        = {IMOTA: an interactive multi-omics tissue atlas for the analysis of human miRNA-target interactions.},
  journal      = {Nucleic acids research},
  year         = {2018},
  volume       = {46},
  pages        = {D770--D775},
  month        = jan,
  issn         = {1362-4962},
  abstract     = {Web repositories for almost all 'omics' types have been generated-detailing the repertoire of representatives across different tissues or cell types. A logical next step is the combination of these valuable sources. With IMOTA (interactive multi omics tissue atlas), we developed a database that includes 23 725 relations between miRNAs and 23 tissues, 310 932 relations between mRNAs and the same tissues as well as 63 043 relations between proteins and the 23 tissues in Homo sapiens. IMOTA also contains data on tissue-specific interactions, e.g. information on 331 413 miRNAs and target gene pairs that are jointly expressed in the considered tissues. By using intuitive filter and visualization techniques, it is with minimal effort possible to answer various questions. These include rather general questions but also requests specific for genes, miRNAs or proteins. An example for a general task could be 'identify all miRNAs, genes and proteins in the lung that are highly expressed and where experimental evidence proves that the miRNAs target the genes'. An example for a specific request for a gene and a miRNA could for example be 'In which tissues is miR-34c and its target gene BCL2 expressed?'. The IMOTA repository is freely available online at https://ccb-web.cs.uni-saarland.de/imota/.},
  country      = {England},
  doi          = {10.1093/nar/gkx701},
  issn-linking = {0305-1048},
  issue        = {D1},
  nlm-id       = {0411011},
  owner        = {NLM},
  pii          = {4081997},
  pmc          = {PMC5753248},
  pmid         = {28977416},
  pubmodel     = {Print},
  pubstatus    = {ppublish},
  revised      = {2018-01-10},
}

Web repositories for almost all 'omics' types have been generated-detailing the repertoire of representatives across different tissues or cell types. A logical next step is the combination of these valuable sources. With IMOTA (interactive multi omics tissue atlas), we developed a database that includes 23 725 relations between miRNAs and 23 tissues, 310 932 relations between mRNAs and the same tissues as well as 63 043 relations between proteins and the 23 tissues in Homo sapiens. IMOTA also contains data on tissue-specific interactions, e.g. information on 331 413 miRNAs and target gene pairs that are jointly expressed in the considered tissues. By using intuitive filter and visualization techniques, it is with minimal effort possible to answer various questions. These include rather general questions but also requests specific for genes, miRNAs or proteins. An example for a general task could be 'identify all miRNAs, genes and proteins in the lung that are highly expressed and where experimental evidence proves that the miRNAs target the genes'. An example for a specific request for a gene and a miRNA could for example be 'In which tissues is miR-34c and its target gene BCL2 expressed?'. The IMOTA repository is freely available online at https://ccb-web.cs.uni-saarland.de/imota/.

@Article{Abu-Halima2018a,
  author       = {Abu-Halima, Masood and Ludwig, Nicole and Rädle-Hurst, Tanja and Keller, Andreas and Motsch, Lars and Marsollek, Ina and El Rahman, Mohammed Abd and Abdul-Khaliq, Hashim and Meese, Eckart},
  title        = {Characterization of micro-RNA Profile in the Blood of Patients with Marfan's Syndrome.},
  journal      = {The Thoracic and cardiovascular surgeon},
  year         = {2018},
  volume       = {66},
  pages        = {116--124},
  month        = jan,
  issn         = {1439-1902},
  abstract     = {Marfan's syndrome (MFS) is an autosomal dominant inheritance disorder with a 1/5,000 live-birth prevalence. It is characterized by a wide range of clinical manifestations with more than 3,000 mutations identified in the   gene. In this study, we aimed to determine if specific patterns of circulating micro-RNAs (miRNAs) are associated with MFS-associated with cardiovascular diseases. Microarray-based miRNA profiling was performed on blood samples of 12 MFS patients, and 12 healthy volunteers (HVs) controls and the differences in miRNA abundance between the two groups were validated using independent cohorts of 22 MFS and of 22 HV controls by real-time quantitative polymerase chain reaction (RT-qPCR). Enrichment analyses of altered miRNA abundance were predicted using bioinformatics tools. Altered miRNA abundance levels were determined between MFS (  = 34) and HVs (  = 34). In a screening phase, we analyzed 12 patients with MFS and 12 HVs by miRNA microarray. We found 198 miRNAs that were significantly altered in MFS patients as compared with HVs, including 16 miRNAs with a more than 1.5-fold change. Out of these 16 miRNAs, 10 showed a decreased abundance and 6 showed an increased abundance. In the validation phase, we analyzed independent cohorts of 22 MFS and of 22 HV controls by RT-qPCR. We confirmed the direction of abundance changes and the significance of different abundances between MFS patients and HVs for four miRNAs, namely, miR-362-5p, miR-339-3p, miR-340-5p, and miR-210-3p. Only the miR-150-5p showed a significant correlation with mitral valve prolapse (  = 0.010). The predicted targets for the validated miRNAs were associated with signal transduction, tissue remodeling, and cellular interaction pathways. The altered abundance level of different miRNAs in whole blood of MFS patients lays the ground to the development of novel diagnostic approaches with altered miRNAs levels associated with MFS with manifestations associated with cardiovascular diseases.},
  country      = {Germany},
  doi          = {10.1055/s-0037-1604083},
  issn-linking = {0171-6425},
  issue        = {1},
  nlm-id       = {7903387},
  owner        = {NLM},
  pmid         = {28679133},
  pubmodel     = {Print-Electronic},
  pubstatus    = {ppublish},
  revised      = {2018-02-22},
}

Marfan's syndrome (MFS) is an autosomal dominant inheritance disorder with a 1/5,000 live-birth prevalence. It is characterized by a wide range of clinical manifestations with more than 3,000 mutations identified in the gene. In this study, we aimed to determine if specific patterns of circulating micro-RNAs (miRNAs) are associated with MFS-associated with cardiovascular diseases. Microarray-based miRNA profiling was performed on blood samples of 12 MFS patients, and 12 healthy volunteers (HVs) controls and the differences in miRNA abundance between the two groups were validated using independent cohorts of 22 MFS and of 22 HV controls by real-time quantitative polymerase chain reaction (RT-qPCR). Enrichment analyses of altered miRNA abundance were predicted using bioinformatics tools. Altered miRNA abundance levels were determined between MFS (  = 34) and HVs (  = 34). In a screening phase, we analyzed 12 patients with MFS and 12 HVs by miRNA microarray. We found 198 miRNAs that were significantly altered in MFS patients as compared with HVs, including 16 miRNAs with a more than 1.5-fold change. Out of these 16 miRNAs, 10 showed a decreased abundance and 6 showed an increased abundance. In the validation phase, we analyzed independent cohorts of 22 MFS and of 22 HV controls by RT-qPCR. We confirmed the direction of abundance changes and the significance of different abundances between MFS patients and HVs for four miRNAs, namely, miR-362-5p, miR-339-3p, miR-340-5p, and miR-210-3p. Only the miR-150-5p showed a significant correlation with mitral valve prolapse (  = 0.010). The predicted targets for the validated miRNAs were associated with signal transduction, tissue remodeling, and cellular interaction pathways. The altered abundance level of different miRNAs in whole blood of MFS patients lays the ground to the development of novel diagnostic approaches with altered miRNAs levels associated with MFS with manifestations associated with cardiovascular diseases.

@Article{Henn2018,
  author       = {Henn, Dominic and Abu-Halima, Masood and Falkner, Florian and Wermke, Dominik and Meme, Lilian G and Kühner, Clemens and Keller, Andreas and Kneser, Ulrich and Meese, Eckart and Schmidt, Volker J},
  title        = {Micro-RNA Regulated Pro-Angiogenic Signaling in Arteriovenous Loops in Patients with Combined Vascular and Soft Tissue Reconstructions - Reisiting the Nutrient Flap Concept.},
  journal      = {Plastic and reconstructive surgery},
  year         = {2018},
  month        = jul,
  issn         = {1529-4242},
  abstract     = {The placement of arteriovenous (AV) loops can enable microvascular anastomoses of free flaps when recipient vessels are scarce. In animal models, elevated fluid shear stress in AV loops promotes neoangiogenesis. Anecdotal reports in patients indicate that vein grafts used in free flap reconstructions of ischemic lower extremities are able to induce capillary formation. However, flow-stimulated angiogenesis has never been systematically investigated in humans and it is unclear whether shear stress alters proangiogenic signaling pathways within the vascular wall of human AV loops. Eight patients with lower extremity soft tissue defects underwent two-stage reconstructions with AV loop placements, and free flap anastomoses to the loops 10-14 days later. MicroRNA and gene expression profiles were determined in tissue samples harvested from vein grafts of AV loops by microarray analysis and quantitative real time polymerase chain reaction. Samples from untreated veins served as controls. A strong deregulation of microRNA and gene expression was detected in AV loops, showing an overexpression of angiopoetic cytokines, oxygenation associated genes, vascular growth factors, as well as connexin-43. We discovered inverse correlations and validated as well as bioinformatically predicted interactions between angiogenesis regulating genes and microRNAs in AV loops. Our findings demonstrate that elevated shear stress triggers pro-angiogenic signaling pathways in human venous tissue, indicating that AV loops may have the ability to induce neoangiogenesis in humans. Our data corroborate the nutrient flap hypothesis and provide a molecular background for AV loop based tissue engineering with potential clinical applications for soft tissue defect reconstruction.},
  country      = {United States},
  doi          = {10.1097/PRS.0000000000004750},
  issn-linking = {0032-1052},
  nlm-id       = {1306050},
  owner        = {NLM},
  pmid         = {29979372},
  pubmodel     = {Print-Electronic},
  pubstatus    = {aheadofprint},
  revised      = {2018-07-09},
}

The placement of arteriovenous (AV) loops can enable microvascular anastomoses of free flaps when recipient vessels are scarce. In animal models, elevated fluid shear stress in AV loops promotes neoangiogenesis. Anecdotal reports in patients indicate that vein grafts used in free flap reconstructions of ischemic lower extremities are able to induce capillary formation. However, flow-stimulated angiogenesis has never been systematically investigated in humans and it is unclear whether shear stress alters proangiogenic signaling pathways within the vascular wall of human AV loops. Eight patients with lower extremity soft tissue defects underwent two-stage reconstructions with AV loop placements, and free flap anastomoses to the loops 10-14 days later. MicroRNA and gene expression profiles were determined in tissue samples harvested from vein grafts of AV loops by microarray analysis and quantitative real time polymerase chain reaction. Samples from untreated veins served as controls. A strong deregulation of microRNA and gene expression was detected in AV loops, showing an overexpression of angiopoetic cytokines, oxygenation associated genes, vascular growth factors, as well as connexin-43. We discovered inverse correlations and validated as well as bioinformatically predicted interactions between angiogenesis regulating genes and microRNAs in AV loops. Our findings demonstrate that elevated shear stress triggers pro-angiogenic signaling pathways in human venous tissue, indicating that AV loops may have the ability to induce neoangiogenesis in humans. Our data corroborate the nutrient flap hypothesis and provide a molecular background for AV loop based tissue engineering with potential clinical applications for soft tissue defect reconstruction.

@Article{Hochfeld2018,
  author       = {Hochfeld, Lara M and Keller, Andreas and Anhalt, Thomas and Fricker, Nadine and Meta-analysis for Androgenetic Alopecia Novel determinants (MAAN) Consortium and Nöthen, Markus M and Heilmann-Heimbach, Stefanie},
  title        = {Insights Into Male Androgenetic Alopecia: Differential Gene Expression Profiling of Plucked Hair Follicles and Integration with Genetic Data.},
  journal      = {The Journal of investigative dermatology},
  year         = {2018},
  month        = jul,
  issn         = {1523-1747},
  country      = {United States},
  doi          = {10.1016/j.jid.2018.06.182},
  issn-linking = {0022-202X},
  nlm-id       = {0426720},
  owner        = {NLM},
  pii          = {S0022-202X(18)32322-4},
  pmid         = {30009830},
  pubmodel     = {Print-Electronic},
  pubstatus    = {aheadofprint},
  revised      = {2018-07-16},
}

@Article{Keller2018,
  author       = {Keller, Andreas and Fehlmann, Tobias and Ludwig, Nicole and Kahraman, Mustafa and Laufer, Thomas and Backes, Christina and Vogelmeier, Claus and Diener, Caroline and Biertz, Frank and Herr, Christian and Jörres, Rudolf A and Lenhof, Hans-Peter and Meese, Eckart and Bals, Robert and COSYCONET Study Group},
  title        = {Genome-wide MicroRNA Expression Profiles in COPD: Early Predictors for Cancer Development.},
  journal      = {Genomics, proteomics \& bioinformatics},
  year         = {2018},
  month        = jul,
  issn         = {2210-3244},
  abstract     = {Chronic obstructive pulmonary disease (COPD) significantly increases the risk of developing cancer. Biomarker studies frequently follow a case-control set-up in which patients diagnosed with a disease are compared to controls. Longitudinal cohort studies such as the COPD-centered German COPD and SYstemic consequences-COmorbidities NETwork (COSYCONET) study provide the patient and biomaterial base for discovering predictive molecular markers. We asked whether microRNA (miRNA) profiles in blood collected from COPD patients prior to a tumor diagnosis could support an early diagnosis of tumor development independent of the tumor type. From 2741 participants of COSYCONET diagnosed with COPD, we selected 534 individuals including 33 patients who developed cancer during the follow-up period of 54 months and 501 patients who did not develop cancer, but had similar age, gender and smoking history. Genome-wide miRNA profiles were generated and evaluated using machine learning techniques. For patients developing cancer we identified nine miRNAs with significantly decreased abundance (two-tailed unpaired t-test adjusted for multiple testing P < 0.05), including members of the miR-320 family. The identified miRNAs regulate different cancer-related pathways including the MAPK pathway (P = 2.3 × 10 ). We also observed the impact of confounding factors on the generated miRNA profiles, underlining the value of our matched analysis. For selected miRNAs, qRT-PCR analysis was applied to validate the results. In conclusion, we identified several miRNAs in blood of COPD patients, which could serve as candidates for biomarkers to help identify COPD patients at risk of developing cancer.},
  country      = {China},
  doi          = {10.1016/j.gpb.2018.06.001},
  issn-linking = {1672-0229},
  keywords     = {Biomarker; COPD; COSYCONET; Cancer; Lung; microRNA},
  nlm-id       = {101197608},
  owner        = {NLM},
  pii          = {S1672-0229(18)30138-4},
  pmid         = {29981854},
  pubmodel     = {Print-Electronic},
  pubstatus    = {aheadofprint},
  revised      = {2018-07-21},
}

Chronic obstructive pulmonary disease (COPD) significantly increases the risk of developing cancer. Biomarker studies frequently follow a case-control set-up in which patients diagnosed with a disease are compared to controls. Longitudinal cohort studies such as the COPD-centered German COPD and SYstemic consequences-COmorbidities NETwork (COSYCONET) study provide the patient and biomaterial base for discovering predictive molecular markers. We asked whether microRNA (miRNA) profiles in blood collected from COPD patients prior to a tumor diagnosis could support an early diagnosis of tumor development independent of the tumor type. From 2741 participants of COSYCONET diagnosed with COPD, we selected 534 individuals including 33 patients who developed cancer during the follow-up period of 54 months and 501 patients who did not develop cancer, but had similar age, gender and smoking history. Genome-wide miRNA profiles were generated and evaluated using machine learning techniques. For patients developing cancer we identified nine miRNAs with significantly decreased abundance (two-tailed unpaired t-test adjusted for multiple testing P < 0.05), including members of the miR-320 family. The identified miRNAs regulate different cancer-related pathways including the MAPK pathway (P = 2.3 × 10 ). We also observed the impact of confounding factors on the generated miRNA profiles, underlining the value of our matched analysis. For selected miRNAs, qRT-PCR analysis was applied to validate the results. In conclusion, we identified several miRNAs in blood of COPD patients, which could serve as candidates for biomarkers to help identify COPD patients at risk of developing cancer.

@Article{Maixner2018,
  author       = {Maixner, Frank and Turaev, Dmitrij and Cazenave-Gassiot, Amaury and Janko, Marek and Krause-Kyora, Ben and Hoopmann, Michael R and Kusebauch, Ulrike and Sartain, Mark and Guerriero, Gea and O'Sullivan, Niall and Teasdale, Matthew and Cipollini, Giovanna and Paladin, Alice and Mattiangeli, Valeria and Samadelli, Marco and Tecchiati, Umberto and Putzer, Andreas and Palazoglu, Mine and Meissen, John and Lösch, Sandra and Rausch, Philipp and Baines, John F and Kim, Bum Jin and An, Hyun-Joo and Gostner, Paul and Egarter-Vigl, Eduard and Malfertheiner, Peter and Keller, Andreas and Stark, Robert W and Wenk, Markus and Bishop, David and Bradley, Daniel G and Fiehn, Oliver and Engstrand, Lars and Moritz, Robert L and Doble, Philip and Franke, Andre and Nebel, Almut and Oeggl, Klaus and Rattei, Thomas and Grimm, Rudolf and Zink, Albert},
  title        = {The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals.},
  journal      = {Current biology : CB},
  year         = {2018},
  month        = jun,
  issn         = {1879-0445},
  abstract     = {The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.},
  country      = {England},
  doi          = {10.1016/j.cub.2018.05.067},
  issn-linking = {0960-9822},
  keywords     = {European Copper Age mummy; Iceman; ancient DNA; diet; last meal; lipidomics; microscopy; multi-omics study; proteomics; stomach content},
  nlm-id       = {9107782},
  owner        = {NLM},
  pii          = {S0960-9822(18)30703-6},
  pmid         = {30017480},
  pubmodel     = {Print-Electronic},
  pubstatus    = {aheadofprint},
  revised      = {2018-07-18},
}

The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.

@Article{Hart2018,
  author       = {Hart, Martin and Kern, Fabian and Backes, Christina and Rheinheimer, Stefanie and Fehlmann, Tobias and Keller, Andreas and Meese, Eckart},
  title        = {The deterministic role of 5-mers in microRNA-gene targeting.},
  journal      = {RNA biology},
  year         = {2018},
  pages        = {1--7},
  month        = may,
  issn         = {1555-8584},
  abstract     = {MiRNAs play a central role in physiological and pathological processes. Both for the biological understanding and for their clinical application, it is essential to understand the interaction of miRNAs and their targets. Target identification largely hinges on in-silico prediction, which requires a complete consideration of miRNA binding sites within the UTRs of target genes. Here, we show that 5-mer sites might also play an essential role for human miRNA-target binding. We implemented and employed an algorithm to all pairs of 2,588 human miRNAs annotated in miRBase and the 3' UTRs of 16725 genes (>43 million combinations). Our in-silico analysis showed a highly significant enrichment (p = 1.4 × 10 ) of 5-mer binding sites in 3' UTRs across all experimentally validated miRNA-target gene pairs. We next confirmed the central role of 5-mer binding sites by reporter assays and demonstrated that two non-canonical 5-mer sites of miR-34a in the 3' UTR of T-cell receptor alpha (TCRA) have a significantly stronger influence on its posttranscriptional regulation than the canonical binding sites. These observations indicate an essential role of 5-mer binding sites for the miRNA targeting in human cells.},
  country      = {United States},
  doi          = {10.1080/15476286.2018.1462652},
  issn-linking = {1547-6286},
  keywords     = {5-mer; T-cell receptor alpha; miR-34a; miRNA; targeting},
  nlm-id       = {101235328},
  owner        = {NLM},
  pmid         = {29749304},
  pubmodel     = {Print-Electronic},
  pubstatus    = {aheadofprint},
  revised      = {2018-05-11},
}

MiRNAs play a central role in physiological and pathological processes. Both for the biological understanding and for their clinical application, it is essential to understand the interaction of miRNAs and their targets. Target identification largely hinges on in-silico prediction, which requires a complete consideration of miRNA binding sites within the UTRs of target genes. Here, we show that 5-mer sites might also play an essential role for human miRNA-target binding. We implemented and employed an algorithm to all pairs of 2,588 human miRNAs annotated in miRBase and the 3' UTRs of 16725 genes (>43 million combinations). Our in-silico analysis showed a highly significant enrichment (p = 1.4 × 10 ) of 5-mer binding sites in 3' UTRs across all experimentally validated miRNA-target gene pairs. We next confirmed the central role of 5-mer binding sites by reporter assays and demonstrated that two non-canonical 5-mer sites of miR-34a in the 3' UTR of T-cell receptor alpha (TCRA) have a significantly stronger influence on its posttranscriptional regulation than the canonical binding sites. These observations indicate an essential role of 5-mer binding sites for the miRNA targeting in human cells.

@Article{Kehl2018,
  author       = {Kehl, Tim and Schneider, Lara and Kattler, Kathrin and Stöckel, Daniel and Wegert, Jenny and Gerstner, Nico and Ludwig, Nicole and Distler, Ute and Schick, Markus and Keller, Ulrich and Tenzer, Stefan and Gessler, Manfred and Walter, Jörn and Keller, Andreas and Graf, Norbert and Meese, Eckart and Lenhof, Hans-Peter},
  title        = {REGGAE: a novel approach for the identification of key transcriptional regulators.},
  journal      = {Bioinformatics (Oxford, England)},
  year         = {2018},
  month        = may,
  issn         = {1367-4811},
  abstract     = {Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Here, we present REGGAE (REGulator-Gene Association Enrichment), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov-Smirnov-like test statistic that implicitly combines associations between regulators and their target genes with an enrichment approach to prioritize the influence of transcriptional regulators. We evaluated our method in two different application scenarios, which demonstrate that REGGAE is well suited for uncovering the influence of transcriptional regulators and is a valuable tool for the elucidation of complex regulatory mechanisms. REGGAE is freely available at https://regulatortrail.bioinf.uni-sb.de. tkehl@bioinf.uni-sb.de. Supplementary data are available at Bioinformatics online.},
  country      = {England},
  doi          = {10.1093/bioinformatics/bty372},
  issn-linking = {1367-4803},
  nlm-id       = {9808944},
  owner        = {NLM},
  pii          = {4993882},
  pmid         = {29741575},
  pubmodel     = {Print-Electronic},
  pubstatus    = {aheadofprint},
  revised      = {2018-05-09},
}

Transcriptional regulators play a major role in most biological processes. Alterations in their activities are associated with a variety of diseases and in particular with tumor development and progression. Hence, it is important to assess the effects of deregulated regulators on pathological processes. Here, we present REGGAE (REGulator-Gene Association Enrichment), a novel method for the identification of key transcriptional regulators that have a significant effect on the expression of a given set of genes, e.g. genes that are differentially expressed between two sample groups. REGGAE uses a Kolmogorov-Smirnov-like test statistic that implicitly combines associations between regulators and their target genes with an enrichment approach to prioritize the influence of transcriptional regulators. We evaluated our method in two different application scenarios, which demonstrate that REGGAE is well suited for uncovering the influence of transcriptional regulators and is a valuable tool for the elucidation of complex regulatory mechanisms. REGGAE is freely available at https://regulatortrail.bioinf.uni-sb.de. tkehl@bioinf.uni-sb.de. Supplementary data are available at Bioinformatics online.

@Article{Ludwig2018,
  author       = {Ludwig, Nicole and Fehlmann, Tobias and Galata, Valentina and Franke, Andre and Backes, Christina and Meese, Eckart and Keller, Andreas},
  title        = {Small ncRNA-Seq Results of Human Tissues: Variations Depending on Sample Integrity.},
  journal      = {Clinical chemistry},
  year         = {2018},
  volume       = {64},
  pages        = {1074--1084},
  month        = jul,
  issn         = {1530-8561},
  abstract     = {Although mature miRNAs are relatively stable in vivo, RNA degradation can have a substantial influence on small noncoding RNA (sncRNA) profiles. Using different tissue storage conditions and RNA isolation procedures, we analyzed the integrity and quality of RNA isolates from human lung and heart tissues. We sequenced a total of 64 RNA samples and quantified the effect of RNA degradation, DNA contamination, and other confounding factors on the sncRNA-seq data. Besides microRNAs, other noncoding RNA species (piRNAs, tRNAs, snoRNAs, rRNAs) were investigated. Consistent with previous results, we found that the tissue specificity of microRNAs is generally well preserved. The distribution of microRNA isoforms was similar to the distribution of canonical forms. New miRNAs were more frequently discovered in degraded samples. sncRNA Reads generated from degraded samples mapped frequently to piRNAs, tRNAs, snoRNAs, or scaRNAs. Sequencing reads that were depleted of sncRNAs showed an increased mapping frequency to bacterial species. Our data emphasize the importance of sample integrity, especially for next-generation sequencing (NGS)-based high-throughput sncRNA profiles. For the prediction of novel miRNAs in particular, only samples with the highest RNA integrity should be used in order to avoid identification of false "miRNAs."},
  country      = {United States},
  doi          = {10.1373/clinchem.2017.285767},
  issn-linking = {0009-9147},
  issue        = {7},
  nlm-id       = {9421549},
  owner        = {NLM},
  pii          = {clinchem.2017.285767},
  pmid         = {29691221},
  pubmodel     = {Print-Electronic},
  pubstatus    = {ppublish},
  revised      = {2018-06-29},
}

Although mature miRNAs are relatively stable in vivo, RNA degradation can have a substantial influence on small noncoding RNA (sncRNA) profiles. Using different tissue storage conditions and RNA isolation procedures, we analyzed the integrity and quality of RNA isolates from human lung and heart tissues. We sequenced a total of 64 RNA samples and quantified the effect of RNA degradation, DNA contamination, and other confounding factors on the sncRNA-seq data. Besides microRNAs, other noncoding RNA species (piRNAs, tRNAs, snoRNAs, rRNAs) were investigated. Consistent with previous results, we found that the tissue specificity of microRNAs is generally well preserved. The distribution of microRNA isoforms was similar to the distribution of canonical forms. New miRNAs were more frequently discovered in degraded samples. sncRNA Reads generated from degraded samples mapped frequently to piRNAs, tRNAs, snoRNAs, or scaRNAs. Sequencing reads that were depleted of sncRNAs showed an increased mapping frequency to bacterial species. Our data emphasize the importance of sample integrity, especially for next-generation sequencing (NGS)-based high-throughput sncRNA profiles. For the prediction of novel miRNAs in particular, only samples with the highest RNA integrity should be used in order to avoid identification of false "miRNAs."

@Article{Abu-Halima2018,
  author       = {Abu-Halima, Masood and Kahraman, Mustafa and Henn, Dominic and Rädle-Hurst, Tanja and Keller, Andreas and Abdul-Khaliq, Hashim and Meese, Eckart},
  title        = {Deregulated microRNA and mRNA expression profiles in the peripheral blood of patients with Marfan syndrome.},
  journal      = {Journal of translational medicine},
  year         = {2018},
  volume       = {16},
  pages        = {60},
  month        = mar,
  issn         = {1479-5876},
  abstract     = {MicroRNAs (miRNAs) are small RNAs regulating gene expression post-transcriptionally. While acquired changes of miRNA and mRNA profiles in cancer have been extensively studied, little is known about expression changes of circulating miRNAs and messenger RNAs (mRNA) in monogenic constitutional anomalies affecting several organ systems, like Marfan syndrome (MFS). We performed integrated miRNA and mRNA expression profiling in blood samples of Marfan patients in order to investigate deregulated miRNA and mRNA networks in these patients which could serve as potential diagnostic and prognostic tools for MFS therapy. MiRNA and mRNA expression profiles were determined in blood samples from MFS patients (n = 7) and from healthy volunteer controls (n = 7) by microarray analysis. Enrichment analyses of altered mRNA expression were identified using bioinformatic tools. A total of 28 miRNAs and 32 mRNAs were found to be significantly altered in MFS patients compared to controls (> 2.0-fold change, adjusted P < 0.05). The expression of 11 miRNA and 6 mRNA candidates was validated by RT-qPCR in an independent cohort of 26 MFS patients and 26 matched HV controls. Significant inverse correlations were evident between 8 miRNAs and 5 mRNAs involved in vascular pathology, inflammation and telomerase regulation. Significant positive correlations were present for 7 miRNAs with age, for 2 miRNAs with the MFS aortic root status (Z-score) and for 7 miRNAs with left ventricular end-diastolic diameter in MFS patients. In addition, miR-331-3p was significantly up-regulated in MFS patients without mitral valve prolapse (MVP) as compared with patients with MVP. Our data show deregulated gene and miRNA expression profiles in the peripheral blood of MFS patients, demonstrating several candidates for prognostic biomarkers for cardiovascular manifestations in MFS as well as targets for novel therapeutic approaches. A deregulation of miRNA expression seems to play an important role in MFS, highlighting the plethora of effects on post-transcriptional regulation of miRNAs and mRNAs initiated by constitutional mutations in single genes. Trial registration Nr: EA2/131/10 . Registered 28 December, 2010.},
  country      = {England},
  doi          = {10.1186/s12967-018-1429-3},
  issn-linking = {1479-5876},
  issue        = {1},
  keywords     = {Fibrillin; Integration analysis; Marfan syndrome; MicroRNA; mRNA},
  nlm-id       = {101190741},
  owner        = {NLM},
  pii          = {10.1186/s12967-018-1429-3},
  pmc          = {PMC5848586},
  pmid         = {29530068},
  pubmodel     = {Electronic},
  pubstatus    = {epublish},
  revised      = {2018-03-22},
}

MicroRNAs (miRNAs) are small RNAs regulating gene expression post-transcriptionally. While acquired changes of miRNA and mRNA profiles in cancer have been extensively studied, little is known about expression changes of circulating miRNAs and messenger RNAs (mRNA) in monogenic constitutional anomalies affecting several organ systems, like Marfan syndrome (MFS). We performed integrated miRNA and mRNA expression profiling in blood samples of Marfan patients in order to investigate deregulated miRNA and mRNA networks in these patients which could serve as potential diagnostic and prognostic tools for MFS therapy. MiRNA and mRNA expression profiles were determined in blood samples from MFS patients (n = 7) and from healthy volunteer controls (n = 7) by microarray analysis. Enrichment analyses of altered mRNA expression were identified using bioinformatic tools. A total of 28 miRNAs and 32 mRNAs were found to be significantly altered in MFS patients compared to controls (> 2.0-fold change, adjusted P < 0.05). The expression of 11 miRNA and 6 mRNA candidates was validated by RT-qPCR in an independent cohort of 26 MFS patients and 26 matched HV controls. Significant inverse correlations were evident between 8 miRNAs and 5 mRNAs involved in vascular pathology, inflammation and telomerase regulation. Significant positive correlations were present for 7 miRNAs with age, for 2 miRNAs with the MFS aortic root status (Z-score) and for 7 miRNAs with left ventricular end-diastolic diameter in MFS patients. In addition, miR-331-3p was significantly up-regulated in MFS patients without mitral valve prolapse (MVP) as compared with patients with MVP. Our data show deregulated gene and miRNA expression profiles in the peripheral blood of MFS patients, demonstrating several candidates for prognostic biomarkers for cardiovascular manifestations in MFS as well as targets for novel therapeutic approaches. A deregulation of miRNA expression seems to play an important role in MFS, highlighting the plethora of effects on post-transcriptional regulation of miRNAs and mRNAs initiated by constitutional mutations in single genes. Trial registration Nr: EA2/131/10 . Registered 28 December, 2010.

@Article{Fehlmann2018,
  author       = {Fehlmann, Tobias and Backes, Christina and Alles, Julia and Fischer, Ulrike and Hart, Martin and Kern, Fabian and Langseth, Hilde and Rounge, Trine and Umu, Sinan Ugur and Kahraman, Mustafa and Laufer, Thomas and Haas, Jan and Staehler, Cord and Ludwig, Nicole and Hübenthal, Matthias and Meder, Benjamin and Franke, Andre and Lenhof, Hans-Peter and Meese, Eckart and Keller, Andreas},
  title        = {A high-resolution map of the human small non-coding transcriptome.},
  journal      = {Bioinformatics (Oxford, England)},
  year         = {2018},
  volume       = {34},
  pages        = {1621--1628},
  month        = may,
  issn         = {1367-4811},
  abstract     = {Although the amount of small non-coding RNA-sequencing data is continuously increasing, it is still unclear to which extent small RNAs are represented in the human genome. In this study we analyzed 303 billion sequencing reads from nearly 25 000 datasets to answer this question. We determined that 0.8% of the human genome are reliably covered by 874 123 regions with an average length of 31 nt. On the basis of these regions, we found that among the known small non-coding RNA classes, microRNAs were the most prevalent. In subsequent steps, we characterized variations of miRNAs and performed a staged validation of 11 877 candidate miRNAs. Of these, many were actually expressed and significantly dysregulated in lung cancer. Selected candidates were finally validated by northern blots. Although isolated miRNAs could still be present in the human genome, our presented set likely contains the largest fraction of human miRNAs. c.backes@mx.uni-saarland.de or andreas.keller@ccb.uni-saarland.de. Supplementary data are available at Bioinformatics online.},
  country      = {England},
  doi          = {10.1093/bioinformatics/btx814},
  issn-linking = {1367-4803},
  issue        = {10},
  nlm-id       = {9808944},
  owner        = {NLM},
  pii          = {4769492},
  pmid         = {29281000},
  pubmodel     = {Print},
  pubstatus    = {ppublish},
  revised      = {2018-05-11},
}

Although the amount of small non-coding RNA-sequencing data is continuously increasing, it is still unclear to which extent small RNAs are represented in the human genome. In this study we analyzed 303 billion sequencing reads from nearly 25 000 datasets to answer this question. We determined that 0.8% of the human genome are reliably covered by 874 123 regions with an average length of 31 nt. On the basis of these regions, we found that among the known small non-coding RNA classes, microRNAs were the most prevalent. In subsequent steps, we characterized variations of miRNAs and performed a staged validation of 11 877 candidate miRNAs. Of these, many were actually expressed and significantly dysregulated in lung cancer. Selected candidates were finally validated by northern blots. Although isolated miRNAs could still be present in the human genome, our presented set likely contains the largest fraction of human miRNAs. c.backes@mx.uni-saarland.de or andreas.keller@ccb.uni-saarland.de. Supplementary data are available at Bioinformatics online.

@Article{Haas2018,
  author       = {Haas, Jan and Mester, Stefan and Lai, Alan and Frese, Karen S and Sedaghat-Hamedani, Farbod and Kayvanpour, Elham and Rausch, Tobias and Nietsch, Rouven and Boeckel, Jes-Niels and Carstensen, Avisha and Völkers, Mirko and Dietrich, Carsten and Pils, Dietmar and Amr, Ali and Holzer, Daniel B and Martins Bordalo, Diana and Oehler, Daniel and Weis, Tanja and Mereles, Derliz and Buss, Sebastian and Riechert, Eva and Wirsz, Emil and Wuerstle, Maximilian and Korbel, Jan O and Keller, Andreas and Katus, Hugo A and Posch, Andreas E and Meder, Benjamin},
  title        = {Genomic structural variations lead to dysregulation of important coding and non-coding RNA species in dilated cardiomyopathy.},
  journal      = {EMBO molecular medicine},
  year         = {2018},
  volume       = {10},
  pages        = {107--120},
  month        = jan,
  issn         = {1757-4684},
  abstract     = {The transcriptome needs to be tightly regulated by mechanisms that include transcription factors, enhancers, and repressors as well as non-coding RNAs. Besides this dynamic regulation, a large part of phenotypic variability of eukaryotes is expressed through changes in gene transcription caused by genetic variation. In this study, we evaluate genome-wide structural genomic variants (SVs) and their association with gene expression in the human heart. We detected 3,898 individual SVs affecting all classes of gene transcripts (e.g., mRNA, miRNA, lncRNA) and regulatory genomic regions (e.g., enhancer or TFBS). In a cohort of patients (  = 50) with dilated cardiomyopathy (DCM), 80,635 non-protein-coding elements of the genome are deleted or duplicated by SVs, containing 3,758 long non-coding RNAs and 1,756 protein-coding transcripts. 65.3% of the SV-eQTLs do not harbor a significant SNV-eQTL, and for the regions with both classes of association, we find similar effect sizes. In case of deleted protein-coding exons, we find downregulation of the associated transcripts, duplication events, however, do not show significant changes over all events. In summary, we are first to describe the genomic variability associated with SVs in heart failure due to DCM and dissect their impact on the transcriptome. Overall, SVs explain up to 7.5% of the variation of cardiac gene expression, underlining the importance to study human myocardial gene expression in the context of the individual genome. This has immediate implications for studies on basic mechanisms of cardiac maladaptation, biomarkers, and (gene) therapeutic studies alike.},
  country      = {England},
  doi          = {10.15252/emmm.201707838},
  issn-linking = {1757-4676},
  issue        = {1},
  keywords     = {cardiac transcriptome; dilated cardiomyopathy; expression quantitative trait locus; genomic structural variation; heart failure},
  nlm-id       = {101487380},
  owner        = {NLM},
  pii          = {emmm.201707838},
  pmc          = {PMC5760848},
  pmid         = {29138229},
  pubmodel     = {Print},
  pubstatus    = {ppublish},
  revised      = {2018-01-11},
}

The transcriptome needs to be tightly regulated by mechanisms that include transcription factors, enhancers, and repressors as well as non-coding RNAs. Besides this dynamic regulation, a large part of phenotypic variability of eukaryotes is expressed through changes in gene transcription caused by genetic variation. In this study, we evaluate genome-wide structural genomic variants (SVs) and their association with gene expression in the human heart. We detected 3,898 individual SVs affecting all classes of gene transcripts (e.g., mRNA, miRNA, lncRNA) and regulatory genomic regions (e.g., enhancer or TFBS). In a cohort of patients (  = 50) with dilated cardiomyopathy (DCM), 80,635 non-protein-coding elements of the genome are deleted or duplicated by SVs, containing 3,758 long non-coding RNAs and 1,756 protein-coding transcripts. 65.3% of the SV-eQTLs do not harbor a significant SNV-eQTL, and for the regions with both classes of association, we find similar effect sizes. In case of deleted protein-coding exons, we find downregulation of the associated transcripts, duplication events, however, do not show significant changes over all events. In summary, we are first to describe the genomic variability associated with SVs in heart failure due to DCM and dissect their impact on the transcriptome. Overall, SVs explain up to 7.5% of the variation of cardiac gene expression, underlining the importance to study human myocardial gene expression in the context of the individual genome. This has immediate implications for studies on basic mechanisms of cardiac maladaptation, biomarkers, and (gene) therapeutic studies alike.

@Article{Altmayer2018,
  author       = {Altmayer, Nora Corinna and Galata, Valentina and Warschburger, Nadine and Keller, Andreas and Meese, Eckart and Fischer, Ulrike},
  title        = {Gene amplification in mesenchymal stem cells and during differentiation towards adipocytes or osteoblasts.},
  journal      = {Oncotarget},
  year         = {2018},
  volume       = {9},
  pages        = {1803--1812},
  month        = jan,
  issn         = {1949-2553},
  abstract     = {Gene amplifications are an attribute of tumor cells and have for long time been overlooked in normal cells. A growing number of investigations describe gene amplifications in normal mammalian cells during development and differentiation. Possibly, tumor cells have rescued the gene amplification mechanism as a physiological attribute of stem cells. Here, we investigated human mesenchymal stem cells (hMSCs) for gene amplification using array-CGH, single cell fluorescence   hybridization and qPCR. Gene amplifications were detected in mesenchymal stem cells and in mesenchymal stem cells during differentiation towards adipocytes and osteoblasts. Undifferentiated hMSCs harbor 12 amplified chromosomal regions, hMSCs that differentiated towards adipocytes 18 amplified chromosome regions, and hMSCs that differentiate towards osteoblasts 19 amplified regions. Specifically, hMSCs that differentiated towards adipocytes or osteoblasts harbor   and   amplifications both of which frequently occur in osteosarcoma and liposarcoma that are both of same cell origin. Beside the amplifications, we identified 36 under-replicated regions in undifferentiated and in differentiating hMSC cells.},
  country      = {United States},
  doi          = {10.18632/oncotarget.22804},
  issn-linking = {1949-2553},
  issue        = {2},
  keywords     = {CDK4; MDM2; adipocyte; gene amplification; osteoblast},
  nlm-id       = {101532965},
  owner        = {NLM},
  pii          = {22804},
  pmc          = {PMC5788600},
  pmid         = {29416732},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2018-03-21},
}

Gene amplifications are an attribute of tumor cells and have for long time been overlooked in normal cells. A growing number of investigations describe gene amplifications in normal mammalian cells during development and differentiation. Possibly, tumor cells have rescued the gene amplification mechanism as a physiological attribute of stem cells. Here, we investigated human mesenchymal stem cells (hMSCs) for gene amplification using array-CGH, single cell fluorescence hybridization and qPCR. Gene amplifications were detected in mesenchymal stem cells and in mesenchymal stem cells during differentiation towards adipocytes and osteoblasts. Undifferentiated hMSCs harbor 12 amplified chromosomal regions, hMSCs that differentiated towards adipocytes 18 amplified chromosome regions, and hMSCs that differentiate towards osteoblasts 19 amplified regions. Specifically, hMSCs that differentiated towards adipocytes or osteoblasts harbor and amplifications both of which frequently occur in osteosarcoma and liposarcoma that are both of same cell origin. Beside the amplifications, we identified 36 under-replicated regions in undifferentiated and in differentiating hMSC cells.

@Article{Galata2018,
  author       = {Galata, Valentina and Backes, Christina and Laczny, Cédric Christian and Hemmrich-Stanisak, Georg and Li, Howard and Smoot, Laura and Posch, Andreas Emanuel and Schmolke, Susanne and Bischoff, Markus and von Müller, Lutz and Plum, Achim and Franke, Andre and Keller, Andreas},
  title        = {Comparing genome versus proteome-based identification of clinical bacterial isolates.},
  journal      = {Briefings in bioinformatics},
  year         = {2018},
  volume       = {19},
  pages        = {495--505},
  month        = may,
  issn         = {1477-4054},
  abstract     = {Whole-genome sequencing (WGS) is gaining importance in the analysis of bacterial cultures derived from patients with infectious diseases. Existing computational tools for WGS-based identification have, however, been evaluated on previously defined data relying thereby unwarily on the available taxonomic information.Here, we newly sequenced 846 clinical gram-negative bacterial isolates representing multiple distinct genera and compared the performance of five tools (CLARK, Kaiju, Kraken, DIAMOND/MEGAN and TUIT). To establish a faithful 'gold standard', the expert-driven taxonomy was compared with identifications based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis. Additionally, the tools were also evaluated using a data set of 200 Staphylococcus aureus isolates.CLARK and Kraken (with k =31) performed best with 626 (100%) and 193 (99.5%) correct species classifications for the gram-negative and S. aureus isolates, respectively. Moreover, CLARK and Kraken demonstrated highest mean F-measure values (85.5/87.9% and 94.4/94.7% for the two data sets, respectively) in comparison with DIAMOND/MEGAN (71 and 85.3%), Kaiju (41.8 and 18.9%) and TUIT (34.5 and 86.5%). Finally, CLARK, Kaiju and Kraken outperformed the other tools by a factor of 30 to 170 fold in terms of runtime.We conclude that the application of nucleotide-based tools using k-mers-e.g. CLARK or Kraken-allows for accurate and fast taxonomic characterization of bacterial isolates from WGS data. Hence, our results suggest WGS-based genotyping to be a promising alternative to the MS-based biotyping in clinical settings. Moreover, we suggest that complementary information should be used for the evaluation of taxonomic classification tools, as public databases may suffer from suboptimal annotations.},
  country      = {England},
  doi          = {10.1093/bib/bbw122},
  issn-linking = {1467-5463},
  issue        = {3},
  nlm-id       = {100912837},
  owner        = {NLM},
  pii          = {bbw122},
  pmid         = {28013236},
  pubmodel     = {Print},
  pubstatus    = {ppublish},
  revised      = {2018-05-17},
}

Whole-genome sequencing (WGS) is gaining importance in the analysis of bacterial cultures derived from patients with infectious diseases. Existing computational tools for WGS-based identification have, however, been evaluated on previously defined data relying thereby unwarily on the available taxonomic information.Here, we newly sequenced 846 clinical gram-negative bacterial isolates representing multiple distinct genera and compared the performance of five tools (CLARK, Kaiju, Kraken, DIAMOND/MEGAN and TUIT). To establish a faithful 'gold standard', the expert-driven taxonomy was compared with identifications based on matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) analysis. Additionally, the tools were also evaluated using a data set of 200 Staphylococcus aureus isolates.CLARK and Kraken (with k =31) performed best with 626 (100%) and 193 (99.5%) correct species classifications for the gram-negative and S. aureus isolates, respectively. Moreover, CLARK and Kraken demonstrated highest mean F-measure values (85.5/87.9% and 94.4/94.7% for the two data sets, respectively) in comparison with DIAMOND/MEGAN (71 and 85.3%), Kaiju (41.8 and 18.9%) and TUIT (34.5 and 86.5%). Finally, CLARK, Kaiju and Kraken outperformed the other tools by a factor of 30 to 170 fold in terms of runtime.We conclude that the application of nucleotide-based tools using k-mers-e.g. CLARK or Kraken-allows for accurate and fast taxonomic characterization of bacterial isolates from WGS data. Hence, our results suggest WGS-based genotyping to be a promising alternative to the MS-based biotyping in clinical settings. Moreover, we suggest that complementary information should be used for the evaluation of taxonomic classification tools, as public databases may suffer from suboptimal annotations.

@Article{Kahraman2018,
  author       = {Kahraman, Mustafa and Röske, Anne and Laufer, Thomas and Fehlmann, Tobias and Backes, Christina and Kern, Fabian and Kohlhaas, Jochen and Schrörs, Hannah and Saiz, Anna and Zabler, Cassandra and Ludwig, Nicole and Fasching, Peter A and Strick, Reiner and Rübner, Matthias and Beckmann, Matthias W and Meese, Eckart and Keller, Andreas and Schrauder, Michael G},
  title        = {{MicroRNA} in diagnosis and therapy monitoring of early-stage triple-negative breast cancer},
  journal      = {Scientific reports},
  year         = {2018},
  volume       = {8},
  number       = {1},
  pages        = {11584},
  month        = aug,
  issn         = {2045-2322},
  abstract     = {Breast cancer is a heterogeneous disease with distinct molecular subtypes including the aggressive subtype triple-negative breast cancer (TNBC). We compared blood-borne miRNA signatures of early-stage basal-like (cytokeratin-CK5-positive) TNBC patients to age-matched controls. The miRNAs of TNBC patients were assessed prior to and following platinum-based neoadjuvant chemotherapy (NCT). After an exploratory genome-wide study on 21 cases and 21 controls using microarrays, the identified signatures were verified independently in two laboratories on the same and a new cohort by RT-qPCR. We differentiated the blood of TNBC patients before NCT from controls with 84% sensitivity. The most significant miRNA for this diagnostic classification was miR-126-5p (two tailed t-test p-value of 1.4 × 10 ). Validation confirmed the microarray results for all tested miRNAs. Comparing cancer patients prior to and post NCT highlighted 321 significant miRNAs (among them miR-34a, p-value of 1.2 × 10 ). Our results also suggest that changes in miRNA expression during NCT may have predictive potential to predict pathological complete response (pCR). In conclusion we report that miRNA expression measured from blood facilitates early and minimally-invasive diagnosis of basal-like TNBC. We also demonstrate that NCT has a significant influence on miRNA expression. Finally, we show that blood-borne miRNA profiles monitored over time have potential to predict pCR.},
  country      = {England},
  doi          = {10.1038/s41598-018-29917-2},
  issn-linking = {2045-2322},
  issue        = {1},
  nlm-id       = {101563288},
  owner        = {NLM},
  pii          = {10.1038/s41598-018-29917-2},
  pmc          = {PMC6072710},
  pmid         = {30072748},
  publisher    = {Springer Nature},
  pubmodel     = {Electronic},
  pubstatus    = {epublish},
  revised      = {2018-08-07},
}

Breast cancer is a heterogeneous disease with distinct molecular subtypes including the aggressive subtype triple-negative breast cancer (TNBC). We compared blood-borne miRNA signatures of early-stage basal-like (cytokeratin-CK5-positive) TNBC patients to age-matched controls. The miRNAs of TNBC patients were assessed prior to and following platinum-based neoadjuvant chemotherapy (NCT). After an exploratory genome-wide study on 21 cases and 21 controls using microarrays, the identified signatures were verified independently in two laboratories on the same and a new cohort by RT-qPCR. We differentiated the blood of TNBC patients before NCT from controls with 84% sensitivity. The most significant miRNA for this diagnostic classification was miR-126-5p (two tailed t-test p-value of 1.4 × 10 ). Validation confirmed the microarray results for all tested miRNAs. Comparing cancer patients prior to and post NCT highlighted 321 significant miRNAs (among them miR-34a, p-value of 1.2 × 10 ). Our results also suggest that changes in miRNA expression during NCT may have predictive potential to predict pathological complete response (pCR). In conclusion we report that miRNA expression measured from blood facilitates early and minimally-invasive diagnosis of basal-like TNBC. We also demonstrate that NCT has a significant influence on miRNA expression. Finally, we show that blood-borne miRNA profiles monitored over time have potential to predict pCR.

@Article{Pirritano2018,
  author       = {Marcello Pirritano and Tobias Fehlmann and Thomas Laufer and Nicole Ludwig and Gilles Gasparoni and Yongping Li and Eckart Meese and Andreas Keller and Martin Simon},
  title        = {Next generation sequencing analysis of total small noncoding RNAs from low input RNA from dried blood sampling},
  journal      = {Analytical chemistry},
  year         = {2018},
  volume       = {90},
  pages        = {11791-11796},
  month        = sep,
  issn         = {11791-11796},
  abstract     = {Circulating miRNAs are favored for biomarker candidates as they can reflect tissue specific miRNA dysregulation in disease contexts. Moreover, they have the additional advantage that they can be monitored in a minimally invasive manner. Blood-borne miRNAs are therefore currently characterized to identify, describe, and validate their potential suitability as biomarkers; however, sampling and as well miRNA detection methods limit these studies in terms of sensitivity but also practicability in clinical, at-home, or low-resource sampling of high-quality circulating RNA samples. We describe here a novel and innovative method of circulating RNA microsampling from minimal volume dried blood samples with direct enrichment for small RNA fractions in combination with ligation free library preparation. We evaluated crucial parameters for efficient library preparation from low RNA inputs of 50 pg for efficient dissection not only of miRNAs but also isomiRs, piRNAs, and lincRNAs. We compared these data to classical microarrays and characterize the technical reproducibility and its sensitivity. We demonstrate and evaluate a method for easy low resource sampling and NGS analysis of circulating RNAs providing a powerful tool for massive cohort and remote patient monitoring.},
  doi          = {10.1021/acs.analchem.8b03557},
  issn-linking = {11791-11796},
  issue        = {20},
  pii          = {10.1021/acs.analchem.8b03557},
  publisher    = {American Chemical Society},
}

Circulating miRNAs are favored for biomarker candidates as they can reflect tissue specific miRNA dysregulation in disease contexts. Moreover, they have the additional advantage that they can be monitored in a minimally invasive manner. Blood-borne miRNAs are therefore currently characterized to identify, describe, and validate their potential suitability as biomarkers; however, sampling and as well miRNA detection methods limit these studies in terms of sensitivity but also practicability in clinical, at-home, or low-resource sampling of high-quality circulating RNA samples. We describe here a novel and innovative method of circulating RNA microsampling from minimal volume dried blood samples with direct enrichment for small RNA fractions in combination with ligation free library preparation. We evaluated crucial parameters for efficient library preparation from low RNA inputs of 50 pg for efficient dissection not only of miRNAs but also isomiRs, piRNAs, and lincRNAs. We compared these data to classical microarrays and characterize the technical reproducibility and its sensitivity. We demonstrate and evaluate a method for easy low resource sampling and NGS analysis of circulating RNAs providing a powerful tool for massive cohort and remote patient monitoring.

@Article{Becker2018,
  author       = {Andre Becker and Giovanna Vella and Christian Herr and Andreas Keller and Cedric Laczny and Christoph Beisswenger and Robert Bals},
  title        = {The pulmonary microbiome in sarcoidosis is similar to other parenchymal lung diseases},
  journal      = {European Respiratory Journal},
  year         = {2018},
  volume       = {52},
  pages        = {1399-3003},
  month        = nov,
  issn         = {1399-3003},
  abstract     = {Sarcoidosis is a chronic inflammatory disease that is characterized by noncaseating granuloma formation and that often affects the lung. The aetiology is largely unclear and there are speculations about a microbial component in the initial activation of adaptive immune mechanisms. The aim of the present study was to determine whether there are differences between the microbiota of patients with sarcoidosis and other parenchymal lung diseases. Patients were recruited at the Department of Internal Medicine V at the Saarland University Medical Center, the study was approved by the ethics committee and informed consent was obtained. Data and biosamples were collected from 31 patients with sarcoidosis and 19 patients with other parenchymal lung diseases (idiopathic pulmonary fibrosis, NSIP). Bronchoalveolar lavage (BAL) was used for the isolation of DNA that was subjected to PCR amplification of the 16sRNA V1V2 and V3V4 gene regions with subsequent sequencing and analysis. The overall quantity of bacterial DNA in all samples was low as compared to samples from patients with acute respiratory tract infection or with chronic obstructive lung disease. Alpha-diversity (Shannon) was not different between the two groups. Also multivariate analysis using principal component analysis (PCA), redundancy analysis (RDA), canonical correspondence analysis (CCA) revealed no significant differences. Microbial community comparisons showed no gross changes of the phyla Firmicutes, Bacteroidetes, Actinobacteria, and others. The data show that the abundance of bacterial DNA in lung samples of patients with sarcoidosis is low and that there are no significant differences between the two patient groups.},
  doi          = {10.1183/13993003.congress-2018.PA5208},
  issn-linking = {1399-3003},
  issue        = {suppl 62},
  pii          = {10.1183/13993003.congress-2018.PA5208},
  publisher    = {European Respiratory Society},
}

Sarcoidosis is a chronic inflammatory disease that is characterized by noncaseating granuloma formation and that often affects the lung. The aetiology is largely unclear and there are speculations about a microbial component in the initial activation of adaptive immune mechanisms. The aim of the present study was to determine whether there are differences between the microbiota of patients with sarcoidosis and other parenchymal lung diseases. Patients were recruited at the Department of Internal Medicine V at the Saarland University Medical Center, the study was approved by the ethics committee and informed consent was obtained. Data and biosamples were collected from 31 patients with sarcoidosis and 19 patients with other parenchymal lung diseases (idiopathic pulmonary fibrosis, NSIP). Bronchoalveolar lavage (BAL) was used for the isolation of DNA that was subjected to PCR amplification of the 16sRNA V1V2 and V3V4 gene regions with subsequent sequencing and analysis. The overall quantity of bacterial DNA in all samples was low as compared to samples from patients with acute respiratory tract infection or with chronic obstructive lung disease. Alpha-diversity (Shannon) was not different between the two groups. Also multivariate analysis using principal component analysis (PCA), redundancy analysis (RDA), canonical correspondence analysis (CCA) revealed no significant differences. Microbial community comparisons showed no gross changes of the phyla Firmicutes, Bacteroidetes, Actinobacteria, and others. The data show that the abundance of bacterial DNA in lung samples of patients with sarcoidosis is low and that there are no significant differences between the two patient groups.

@Article{Rupf2018,
  author       = {Stefan Rupf and Cedric C Laczny and Valentina Galata and Christina Backes and Andreas Keller and Natalia Umanskaya and Arzu Erol and Sascha Tierling and Christina Lo Porto and Jörn Walter and Jasmin Kirsch and Matthias Hannig and Christian Hannig},
  title        = {Comparison of initial oral microbiomes of young adults with and without cavitated dentin caries lesions using an in situ biofilm model},
  journal      = {Scientific reports},
  year         = {2018},
  volume       = {8},
  pages        = {14010},
  month        = sep,
  issn         = {14010},
  issn-linking = {14010},
  abstract     = {Dental caries is caused by acids released from bacterial biofilms. However, the in vivo formation of initial biofilms in relation to caries remains largely unexplored. The aim of this study was to compare the oral microbiome during the initial phase of bacterial colonization for individuals with (CC) and without (NC) cavitated dentin caries lesions. Bovine enamel slabs on acrylic splints were worn by the volunteers (CC: 14, NC: 13) for in situ biofilm formation (2 h, 4 h, 8 h, 1 ml saliva as reference). Sequencing of the V1/V2 regions of the 16S rRNA gene was performed (MiSeq). The relative abundances of individual operational taxonomic units (OTUs) were compared between samples from the CC group and the NC group. Random forests models were furthermore trained to separate the groups. While the overall heterogeneity did not differ substantially between CC and NC individuals, several individual OTUs were found to have significantly different relative abundances. For the 8 h samples, most of the significant OTUs showed higher relative abundances in the CC group, while the majority of significant OTUs in the saliva samples were more abundant in the NC group. Furthermore, using OTU signatures enabled a separation between both groups, with area-under-the-curve (AUC) values of ~0.8. In summary, the results suggest that initial oral biofilms provide the potential to differentiate between CC and NC individuals.},
  doi          = {10.1038/s41598-018-32361-x},
  issue        = {1},
  pii          = {10.1038/s41598-018-32361-x},
}

Dental caries is caused by acids released from bacterial biofilms. However, the in vivo formation of initial biofilms in relation to caries remains largely unexplored. The aim of this study was to compare the oral microbiome during the initial phase of bacterial colonization for individuals with (CC) and without (NC) cavitated dentin caries lesions. Bovine enamel slabs on acrylic splints were worn by the volunteers (CC: 14, NC: 13) for in situ biofilm formation (2 h, 4 h, 8 h, 1 ml saliva as reference). Sequencing of the V1/V2 regions of the 16S rRNA gene was performed (MiSeq). The relative abundances of individual operational taxonomic units (OTUs) were compared between samples from the CC group and the NC group. Random forests models were furthermore trained to separate the groups. While the overall heterogeneity did not differ substantially between CC and NC individuals, several individual OTUs were found to have significantly different relative abundances. For the 8 h samples, most of the significant OTUs showed higher relative abundances in the CC group, while the majority of significant OTUs in the saliva samples were more abundant in the NC group. Furthermore, using OTU signatures enabled a separation between both groups, with area-under-the-curve (AUC) values of  0.8. In summary, the results suggest that initial oral biofilms provide the potential to differentiate between CC and NC individuals.

@Article{Diener2018,
  author       = {Caroline Diener and Martin Hart and Dalia Alansary and Vanessa Poth and Barbara Walch-Rückheim and Jennifer Menegatti and Friedrich Grässer and Tobias Fehlmann and Stefanie Rheinheimer and Barbara A Niemeyer and Hans-Peter Lenhof and Andreas Keller and Eckart Meese},
  title        = {Modulation of intracellular calcium signaling by microRNA-34a-5p},
  journal      = {Cell death & disease},
  year         = {2018},
  volume       = {9},
  pages        = {1008},
  month        = sep,
  issn         = {1008},
  abstract     = {Adjusting intracellular calcium signaling is an important feature in the regulation of immune cell function and survival. Here we show that miR-34a-5p, a small non-coding RNA that is deregulated in many common diseases, is a regulator of store-operated Ca2+ entry (SOCE) and calcineurin signaling. Upon miR-34a-5p overexpression, we observed both a decreased depletion of ER calcium content and a decreased Ca2+ influx through Ca2+ release-activated Ca2+ channels. Based on an in silico target prediction we identified multiple miR-34a-5p target genes within both pathways that are implicated in the balance between T-cell activation and apoptosis including ITPR2, CAMLG, STIM1, ORAI3, RCAN1, PPP3R1, and NFATC4. Functional analysis revealed a decrease in Ca2+ activated calcineurin pathway activity measured by a reduced IL-2 secretion due to miR-34a-5p overexpression. Impacting SOCE and/or downstream calcineurin/NFAT signaling by miR-34a-5p offers a possible future approach to manipulate immune cells for clinical interventions.},
  doi          = {10.1038/s41419-018-1050-7},
  issn-linking = {1008},
  issue        = {10},
  pii          = {10.1038/s41419-018-1050-7},
  publisher    = {Nature Publishing Group},
}

Adjusting intracellular calcium signaling is an important feature in the regulation of immune cell function and survival. Here we show that miR-34a-5p, a small non-coding RNA that is deregulated in many common diseases, is a regulator of store-operated Ca2+ entry (SOCE) and calcineurin signaling. Upon miR-34a-5p overexpression, we observed both a decreased depletion of ER calcium content and a decreased Ca2+ influx through Ca2+ release-activated Ca2+ channels. Based on an in silico target prediction we identified multiple miR-34a-5p target genes within both pathways that are implicated in the balance between T-cell activation and apoptosis including ITPR2, CAMLG, STIM1, ORAI3, RCAN1, PPP3R1, and NFATC4. Functional analysis revealed a decrease in Ca2+ activated calcineurin pathway activity measured by a reduced IL-2 secretion due to miR-34a-5p overexpression. Impacting SOCE and/or downstream calcineurin/NFAT signaling by miR-34a-5p offers a possible future approach to manipulate immune cells for clinical interventions.

@Article{Henn2018,
  author       = {Dominic Henn and Masood Abu-Halima and Florian Falkner and Dominik Wermke and Lilian G Meme and Clemens Kühner and Andreas Keller and Ulrich Kneser and Eckart Meese and Volker J Schmidt},
  title        = {Micro-RNA–Regulated Proangiogenic Signaling in Arteriovenous Loops in Patients with Combined Vascular and Soft-Tissue Reconstructions: Revisiting the Nutrient Flap Concept},
  journal      = {Plastic and reconstructive surgery},
  year         = {2018},
  volume       = {142},
  pages        = {489e-502e},
  month        = oct,
  issn         = {489e-502e},
  abstract     = {Background: The placement of arteriovenous loops can enable microvascular anastomoses of free flaps when recipient vessels are scarce. In animal models, elevated fluid shear stress in arteriovenous loops promotes neoangiogenesis. Anecdotal reports in patients indicate that vein grafts used in free flap reconstructions of ischemic lower extremities are able to induce capillary formation. However, flow-stimulated angiogenesis has never been systematically investigated in humans, and it is unclear whether shear stress alters proangiogenic signaling pathways within the vascular wall of human arteriovenous loops. Methods: Eight patients with lower extremity soft-tissue defects underwent two-stage reconstruction with arteriovenous loop placement, and free flap anastomoses to the loops 10 to 14 days later. Micro-RNA (miRNA) and gene expression profiles were determined in tissue samples harvested from vein grafts of arteriovenous loops by microarray analysis and quantitative real-time polymerase chain reaction. Samples from untreated veins served as controls. Results: A strong deregulation of miRNA and gene expression was detected in arteriovenous loops, showing an overexpression of angiopoietic cytokines, oxygenation-associated genes, vascular growth factors, and connexin-43. The authors discovered inverse correlations along with validated and bioinformatically predicted interactions between angiogenesis-regulating genes and miRNAs in arteriovenous loops. Conclusions: The authors’ findings demonstrate that elevated shear stress triggers proangiogenic signaling pathways in human venous tissue, indicating that arteriovenous loops may have the ability to induce neoangiogenesis in humans. The authors’ data corroborate the nutrient flap hypothesis and provide a molecular background for arteriovenous loop–based tissue engineering with potential clinical applications for soft-tissue defect reconstruction.},
  doi          = {10.1097/PRS.0000000000004750},
  issn-linking = {489e-502e},
  issue        = {4},
  pii          = {10.1097/PRS.0000000000004750},
  publisher    = {LWW},
}

Background: The placement of arteriovenous loops can enable microvascular anastomoses of free flaps when recipient vessels are scarce. In animal models, elevated fluid shear stress in arteriovenous loops promotes neoangiogenesis. Anecdotal reports in patients indicate that vein grafts used in free flap reconstructions of ischemic lower extremities are able to induce capillary formation. However, flow-stimulated angiogenesis has never been systematically investigated in humans, and it is unclear whether shear stress alters proangiogenic signaling pathways within the vascular wall of human arteriovenous loops. Methods: Eight patients with lower extremity soft-tissue defects underwent two-stage reconstruction with arteriovenous loop placement, and free flap anastomoses to the loops 10 to 14 days later. Micro-RNA (miRNA) and gene expression profiles were determined in tissue samples harvested from vein grafts of arteriovenous loops by microarray analysis and quantitative real-time polymerase chain reaction. Samples from untreated veins served as controls. Results: A strong deregulation of miRNA and gene expression was detected in arteriovenous loops, showing an overexpression of angiopoietic cytokines, oxygenation-associated genes, vascular growth factors, and connexin-43. The authors discovered inverse correlations along with validated and bioinformatically predicted interactions between angiogenesis-regulating genes and miRNAs in arteriovenous loops. Conclusions: The authors’ findings demonstrate that elevated shear stress triggers proangiogenic signaling pathways in human venous tissue, indicating that arteriovenous loops may have the ability to induce neoangiogenesis in humans. The authors’ data corroborate the nutrient flap hypothesis and provide a molecular background for arteriovenous loop–based tissue engineering with potential clinical applications for soft-tissue defect reconstruction.

@Article{Galata2018,
  author       = {Valentina Galata and Tobias Fehlmann and Christina Backes and Andreas Keller},
  title        = {PLSDB: a resource of complete bacterial plasmids},
  journal      = {Nucleic acids research},
  publisher    = {Oxford University Press},
  year         = {2018},
  volume       = {47},
  issue        = {D1},
  pages        = {D195-D202},
  issn         = {D195-D202},
  issn-linking = {D195-D202},
  month        = oct,
  abstract     = {The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial interest as they contribute to the dissemination of antibiotic resistance. As the number of newly sequenced bacterial genomes is growing a comprehensive resource is required which will allow to browse and filter the available plasmids, and to perform sequence analyses. Here, we present PLSDB, a resource containing 13 789 plasmid records collected from the NCBI nucleotide database. The web server provides an interactive view of all obtained plasmids with additional meta information such as sequence characteristics, sample-related information and taxonomy. Moreover, nucleotide sequence data can be uploaded to search for short nucleotide sequences (e.g. specific genes) in the plasmids, to compare a given plasmid to the records in the collection or to determine whether a sample contains one or multiple of the known plasmids (containment analysis). The resource is freely accessible under https://ccb-microbe.cs.uni-saarland.de/plsdb/.},
  doi          = {10.1093/nar/gky1050},
  pii          = {10.1093/nar/gky1050},
}

The study of bacterial isolates or communities requires the analysis of the therein included plasmids in order to provide an extensive characterization of the organisms. Plasmids harboring resistance and virulence factors are of especial interest as they contribute to the dissemination of antibiotic resistance. As the number of newly sequenced bacterial genomes is growing a comprehensive resource is required which will allow to browse and filter the available plasmids, and to perform sequence analyses. Here, we present PLSDB, a resource containing 13 789 plasmid records collected from the NCBI nucleotide database. The web server provides an interactive view of all obtained plasmids with additional meta information such as sequence characteristics, sample-related information and taxonomy. Moreover, nucleotide sequence data can be uploaded to search for short nucleotide sequences (e.g. specific genes) in the plasmids, to compare a given plasmid to the records in the collection or to determine whether a sample contains one or multiple of the known plasmids (containment analysis). The resource is freely accessible under https://ccb-microbe.cs.uni-saarland.de/plsdb/.

@Article{Christofyllakis2018,
  author       = {Konstantinos Christofyllakis, Frank Neumann, Stephan Stilgenbauer, Dominic Kaddu-Mulindwa, Evi Regitz, Moritz Bewarder, Andreas Keller, Jörg Thomas Bittenbring},
  title        = {Gene Set Enrichment Analysis Suggests That Increased Rituximab-Mediated NK Cell Cytotoxicity after Vitamin D Substitution Is Driven By Upregulation of Interferon Alpha (IFN-a) Isoforms},
  journal      = {blood},
  publisher    = {American Society of Hematology},
  year         = {2018},
  volume       = {132},
  issue        = {Suppl 1},
  pages        = {3696},
  issn         = {3696},
  issn-linking = {3696},
  month        = nov,
  abstract     = {Introduction: We recently showed that vitamin D deficiency leads to decreased overall survival of DLBCL-patients treated with rituximab-chemotherapy (Bittenbring et al, JCO, 2014). We hypothesized that rituximab-mediated NK cell-cytotoxicity is more effective at higher vitamin D levels. This was confirmed by vitamin D substitution of healthy volunteers, which increased their rituximab-mediated cytotoxicity in vitro against the Daudi lymphoma cell line. To unveil the molecular mechanisms behind this finding, resting NK cells before and after vitamin D supplementation were isolated from those volunteers and a whole transcriptome analysis was performed. Methods: We collected PBMCs from eight healthy volunteers with vitamin D deficiency before and after vitamin D substitution to > 30 ng/ml 25-OH vitamin D3. NK cells were isolated from PBMCs by magnetic depletion of all non-NK cells. Purity of the CD16+ cells was confirmed by flow cytometry. After isolating total RNA, we performed a microarray analysis using an Affymetrix Gene-Chip 2.0 ™. The signals were normalized using the LMA algorithm. For pathway analysis, gene set enrichment analysis (GSEA) was used. A two-step approach was chosen. Firstly, we separated 7.705 genes due to their involvement in the NK cell-mediated immune response according to the Gene Ontology database, irrespective of their differential expression. This dataset was used separately for specific analysis of the NK cell-cytotoxicity pathway to increase sensitivity. Secondly, the complete data set of 48.145 genes was used in an exploratory analysis in an attempt to screen for other dysregulated pathways involved in the immune response and vitamin D homeostasis. We used gene sets provided from the Molecular Signature Database. A significance level of < 0.05 for p and False Discovery Rate (FDR) was chosen. Real-time quantitative PCR was performed to confirm the results. Results: The NK cell-associated cytotoxicity pathway was found to be significantly upregulated after restoration of normal vitamin D levels in the specific analysis. The most significantly overexpressed genes in the gene set were five IFN-α subtypes (IFN-α2, IFN-α4, IFN-α6, IFN-α7, and IFN-α10) as well as IFN-κ. The exploratory analysis showed an upregulation of the response to type I interferon pathway and regulation of type I interferon mediated signaling pathway. The most upregulated genes in those pathways were again the IFN-α subtypes mentioned above. Other pathways involved in the immune response were found to be downregulated after vitamin D substitution, like interferon gamma response; cytokine production and chemotaxis. The common denominator of these pathways was the downregulation of three toll-like receptor genes (TLR-8, TLR-7, TLR-2). Conclusion: The increased expression of specific IFN-α subtypes could explain the increased rituximab-mediated NK cell-cytotoxicity after vitamin D substitution in deficient individuals. To the best of our knowledge, this is the first study to suggest a role for vitamin D in IFN-α regulation. TLRs are known to stimulate cytokine production in NK cells including IFN-α. It can be assumed, that the observed upregulation of IFN-α genes after vitamin D substitution leads to a negative feedback on positive regulators of cytokine production like TLR, causing their downregulation once vitamin D levels are restored. This implies a comprehensive role of vitamin D in IFN-α biosynthesis in human NK cells.},
  doi          = {10.1182/blood-2018-99-111817},
  pii          = {10.1182/blood-2018-99-111817},
}

Introduction: We recently showed that vitamin D deficiency leads to decreased overall survival of DLBCL-patients treated with rituximab-chemotherapy (Bittenbring et al, JCO, 2014). We hypothesized that rituximab-mediated NK cell-cytotoxicity is more effective at higher vitamin D levels. This was confirmed by vitamin D substitution of healthy volunteers, which increased their rituximab-mediated cytotoxicity in vitro against the Daudi lymphoma cell line. To unveil the molecular mechanisms behind this finding, resting NK cells before and after vitamin D supplementation were isolated from those volunteers and a whole transcriptome analysis was performed. Methods: We collected PBMCs from eight healthy volunteers with vitamin D deficiency before and after vitamin D substitution to > 30 ng/ml 25-OH vitamin D3. NK cells were isolated from PBMCs by magnetic depletion of all non-NK cells. Purity of the CD16+ cells was confirmed by flow cytometry. After isolating total RNA, we performed a microarray analysis using an Affymetrix Gene-Chip 2.0 ™. The signals were normalized using the LMA algorithm. For pathway analysis, gene set enrichment analysis (GSEA) was used. A two-step approach was chosen. Firstly, we separated 7.705 genes due to their involvement in the NK cell-mediated immune response according to the Gene Ontology database, irrespective of their differential expression. This dataset was used separately for specific analysis of the NK cell-cytotoxicity pathway to increase sensitivity. Secondly, the complete data set of 48.145 genes was used in an exploratory analysis in an attempt to screen for other dysregulated pathways involved in the immune response and vitamin D homeostasis. We used gene sets provided from the Molecular Signature Database. A significance level of < 0.05 for p and False Discovery Rate (FDR) was chosen. Real-time quantitative PCR was performed to confirm the results. Results: The NK cell-associated cytotoxicity pathway was found to be significantly upregulated after restoration of normal vitamin D levels in the specific analysis. The most significantly overexpressed genes in the gene set were five IFN-α subtypes (IFN-α2, IFN-α4, IFN-α6, IFN-α7, and IFN-α10) as well as IFN-κ. The exploratory analysis showed an upregulation of the response to type I interferon pathway and regulation of type I interferon mediated signaling pathway. The most upregulated genes in those pathways were again the IFN-α subtypes mentioned above. Other pathways involved in the immune response were found to be downregulated after vitamin D substitution, like interferon gamma response; cytokine production and chemotaxis. The common denominator of these pathways was the downregulation of three toll-like receptor genes (TLR-8, TLR-7, TLR-2). Conclusion: The increased expression of specific IFN-α subtypes could explain the increased rituximab-mediated NK cell-cytotoxicity after vitamin D substitution in deficient individuals. To the best of our knowledge, this is the first study to suggest a role for vitamin D in IFN-α regulation. TLRs are known to stimulate cytokine production in NK cells including IFN-α. It can be assumed, that the observed upregulation of IFN-α genes after vitamin D substitution leads to a negative feedback on positive regulators of cytokine production like TLR, causing their downregulation once vitamin D levels are restored. This implies a comprehensive role of vitamin D in IFN-α biosynthesis in human NK cells.

@Article{Abu-Halima2018,
  author       = {Masood Abu-Halima and Mustafa Kahraman and Dominic Henn and Tanja Rädle-Hurst and Andreas Keller and Hashim Abdul-Khaliq and Eckart Meese},
  title        = {Deregulated microRNA and mRNA expression profiles in the peripheral blood of patients with Marfan syndrome},
  journal      = {Journal of translational medicine},
  publisher    = {BioMed Central},
  year         = {2018},
  volume       = {16},
  issue        = {1},
  pages        = {60},
  issn         = {60},
  issn-linking = {60},
  month        = dec,
  abstract     = {Background: MicroRNAs (miRNAs) are small RNAs regulating gene expression post-transcriptionally. While acquired changes of miRNA and mRNA profiles in cancer have been extensively studied, little is known about expression changes of circulating miRNAs and messenger RNAs (mRNA) in monogenic constitutional anomalies affecting several organ systems, like Marfan syndrome (MFS). We performed integrated miRNA and mRNA expression profiling in blood samples of Marfan patients in order to investigate deregulated miRNA and mRNA networks in these patients which could serve as potential diagnostic and prognostic tools for MFS therapy. Methods: MiRNA and mRNA expression profiles were determined in blood samples from MFS patients (n = 7) and from healthy volunteer controls (n = 7) by microarray analysis. Enrichment analyses of altered mRNA expression were identified using bioinformatic tools. Results: A total of 28 miRNAs and 32 mRNAs were found to be significantly altered in MFS patients compared to controls (> 2.0-fold change, adjusted P < 0.05). The expression of 11 miRNA and 6 mRNA candidates was validated by RT-qPCR in an independent cohort of 26 MFS patients and 26 matched HV controls. Significant inverse correlations were evident between 8 miRNAs and 5 mRNAs involved in vascular pathology, inflammation and telomerase regulation. Significant positive correlations were present for 7 miRNAs with age, for 2 miRNAs with the MFS aortic root status (Z-score) and for 7 miRNAs with left ventricular end-diastolic diameter in MFS patients. In addition, miR-331-3p was significantly up-regulated in MFS patients without mitral valve prolapse (MVP) as compared with patients with MVP.Conclusions: Our data show deregulated gene and miRNA expression profiles in the peripheral blood of MFS patients, demonstrating several candidates for prognostic biomarkers for cardiovascular manifestations in MFS as well as targets for novel therapeutic approaches. A deregulation of miRNA expression seems to play an important role in MFS, highlighting the plethora of effects on post-transcriptional regulation of miRNAs and mRNAs initiated by constitutional mutations in single genes.},
  doi          = {10.1186/s12967-018-1429-3},
  pii          = {10.1186/s12967-018-1429-3},
}

Background: MicroRNAs (miRNAs) are small RNAs regulating gene expression post-transcriptionally. While acquired changes of miRNA and mRNA profiles in cancer have been extensively studied, little is known about expression changes of circulating miRNAs and messenger RNAs (mRNA) in monogenic constitutional anomalies affecting several organ systems, like Marfan syndrome (MFS). We performed integrated miRNA and mRNA expression profiling in blood samples of Marfan patients in order to investigate deregulated miRNA and mRNA networks in these patients which could serve as potential diagnostic and prognostic tools for MFS therapy. Methods: MiRNA and mRNA expression profiles were determined in blood samples from MFS patients (n = 7) and from healthy volunteer controls (n = 7) by microarray analysis. Enrichment analyses of altered mRNA expression were identified using bioinformatic tools. Results: A total of 28 miRNAs and 32 mRNAs were found to be significantly altered in MFS patients compared to controls (> 2.0-fold change, adjusted P < 0.05). The expression of 11 miRNA and 6 mRNA candidates was validated by RT-qPCR in an independent cohort of 26 MFS patients and 26 matched HV controls. Significant inverse correlations were evident between 8 miRNAs and 5 mRNAs involved in vascular pathology, inflammation and telomerase regulation. Significant positive correlations were present for 7 miRNAs with age, for 2 miRNAs with the MFS aortic root status (Z-score) and for 7 miRNAs with left ventricular end-diastolic diameter in MFS patients. In addition, miR-331-3p was significantly up-regulated in MFS patients without mitral valve prolapse (MVP) as compared with patients with MVP.Conclusions: Our data show deregulated gene and miRNA expression profiles in the peripheral blood of MFS patients, demonstrating several candidates for prognostic biomarkers for cardiovascular manifestations in MFS as well as targets for novel therapeutic approaches. A deregulation of miRNA expression seems to play an important role in MFS, highlighting the plethora of effects on post-transcriptional regulation of miRNAs and mRNAs initiated by constitutional mutations in single genes.

@Article{Rounge2018,
  author       = {Trine B Rounge and Sinan U Umu and Andreas Keller and Eckart Meese and Giske Ursin and Steinar Tretli and Robert Lyle and Hilde Langseth},
  title        = {Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity},
  journal      = {Scientific reports},
  publisher    = {Nature Publishing Group},
  year         = {2018},
  volume       = {8},
  issue        = {1},
  pages        = {17650},
  issn         = {17650},
  issn-linking = {17650},
  month        = dec,
  abstract     = {Small non-coding RNAs (sncRNA) are regulators of cell functions and circulating sncRNAs from the majority of RNA classes are potential non-invasive biomarkers. Understanding how common traits influence ncRNA expression is essential for assessing their biomarker potential. In this study, we identify associations between sncRNA expression and common traits (sex, age, self-reported smoking, body mass, self-reported physical activity). We used RNAseq data from 526 serum samples from the Janus Serum Bank and traits from health examination surveys. Ageing showed the strongest association with sncRNA expression, both in terms of statistical significance and number of RNAs, regardless of RNA class. piRNAs were abundant in the serum samples and they were associated to sex. Interestingly, smoking cessation generally restored RNA expression to non-smoking levels, although for some sncRNAs smoking-related expression levels persisted. Pathway analysis suggests that smoking-related sncRNAs target the cholinergic synapses and may therefore potentially play a role in smoking addiction. Our results show that common traits influence circulating sncRNA expression. It is clear that sncRNA biomarker analyses should be adjusted for age and sex. In addition, for specific sncRNAs, analyses should also be adjusted for body mass, smoking, physical activity and technical factors.},
  doi          = {10.1038/s41598-018-35974-4},
  pii          = {10.1038/s41598-018-35974-4},
}

Small non-coding RNAs (sncRNA) are regulators of cell functions and circulating sncRNAs from the majority of RNA classes are potential non-invasive biomarkers. Understanding how common traits influence ncRNA expression is essential for assessing their biomarker potential. In this study, we identify associations between sncRNA expression and common traits (sex, age, self-reported smoking, body mass, self-reported physical activity). We used RNAseq data from 526 serum samples from the Janus Serum Bank and traits from health examination surveys. Ageing showed the strongest association with sncRNA expression, both in terms of statistical significance and number of RNAs, regardless of RNA class. piRNAs were abundant in the serum samples and they were associated to sex. Interestingly, smoking cessation generally restored RNA expression to non-smoking levels, although for some sncRNAs smoking-related expression levels persisted. Pathway analysis suggests that smoking-related sncRNAs target the cholinergic synapses and may therefore potentially play a role in smoking addiction. Our results show that common traits influence circulating sncRNA expression. It is clear that sncRNA biomarker analyses should be adjusted for age and sex. In addition, for specific sncRNAs, analyses should also be adjusted for body mass, smoking, physical activity and technical factors.

@Article{Sharbati2017,
  author       = {Sharbati, Jutta and Bohmer, Marc and Bohmer, Nils and Keller, Andreas and Backes, Christina and Franke, Andre and Steinberg, Pablo and Zeljenková, Dagmar and Einspanier, Ralf},
  title        = {Transcriptomic Analysis of Intestinal Tissues from Two 90-Day Feeding Studies in Rats Using Genetically Modified MON810 Maize Varieties.},
  journal      = {Frontiers in genetics},
  year         = {2017},
  volume       = {8},
  pages        = {222},
  issn         = {1664-8021},
  abstract     = { Global as well as specific expression profiles of selected rat tissues were characterized to assess the safety of genetically modified (GM) maize MON810 containing the insecticidal protein Cry1Ab. Gene expression was evaluated by use of Next Generation Sequencing (NGS) as well as RT-qPCR within rat intestinal tissues based on mandatory 90-day rodent feeding studies. In parallel to two 90-day feeding studies, the transcriptional response of rat tissues was assessed as another endpoint to enhance the mechanistic interpretation of GM feeding studies and/or to facilitate the generation of a targeted hypothesis. Rats received diets containing 33% GM maize (MON810) or near-isogenic control maize. As a site of massive exposure to ingested feed the transcriptomic response of ileal and colonic tissue was profiled via RT-qPCR arrays targeting apoptosis, DNA-damage/repair, unfolded protein response (UPR). For global RNA profiling of rat ileal tissue, we applied NGS.   No biological response to the GM-diet was observed in male and in female rat tissues. Transcriptome wide analysis of gene expression by RNA-seq confirmed these findings. Nevertheless, gene ontology (GO) analysis clearly associated a set of distinctly regulated transcripts with circadian rhythms. We confirmed differential expression of circadian clock genes using RT-qPCR and immunoassays for selected factors, thereby indicating physiological effects caused by the time point of sampling.   Prediction of potential unintended effects of GM-food/feed by transcriptome based profiling of intestinal tissue presents a novel approach to complement classical toxicological testing procedures. Including the detection of alterations in signaling pathways in toxicity testing procedures may enhance the confidence in outcomes of toxicological trials. In this study, no significant GM-related changes in intestinal expression profiles were found in rats fed GM-maize MON810. Relevant alterations of selected cellular pathways (apoptosis, DNA damage and repair, UPR) pointing toward intestinal toxicity of the diets were not observed. Transcriptomic profiles did not reveal perturbations of pathways associated with toxicity, underlining the study results revealed by classical OECD endpoints.},
  country      = {Switzerland},
  doi          = {10.3389/fgene.2017.00222},
  issn-linking = {1664-8021},
  keywords     = {GM-plant; MON810-maize; pathway-analysis; rat feeding-trial; transcriptomics profiles},
  nlm-id       = {101560621},
  owner        = {NLM},
  pmc          = {PMC5742243},
  pmid         = {29312443},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2018-01-11},
}

Global as well as specific expression profiles of selected rat tissues were characterized to assess the safety of genetically modified (GM) maize MON810 containing the insecticidal protein Cry1Ab. Gene expression was evaluated by use of Next Generation Sequencing (NGS) as well as RT-qPCR within rat intestinal tissues based on mandatory 90-day rodent feeding studies. In parallel to two 90-day feeding studies, the transcriptional response of rat tissues was assessed as another endpoint to enhance the mechanistic interpretation of GM feeding studies and/or to facilitate the generation of a targeted hypothesis. Rats received diets containing 33% GM maize (MON810) or near-isogenic control maize. As a site of massive exposure to ingested feed the transcriptomic response of ileal and colonic tissue was profiled via RT-qPCR arrays targeting apoptosis, DNA-damage/repair, unfolded protein response (UPR). For global RNA profiling of rat ileal tissue, we applied NGS. No biological response to the GM-diet was observed in male and in female rat tissues. Transcriptome wide analysis of gene expression by RNA-seq confirmed these findings. Nevertheless, gene ontology (GO) analysis clearly associated a set of distinctly regulated transcripts with circadian rhythms. We confirmed differential expression of circadian clock genes using RT-qPCR and immunoassays for selected factors, thereby indicating physiological effects caused by the time point of sampling. Prediction of potential unintended effects of GM-food/feed by transcriptome based profiling of intestinal tissue presents a novel approach to complement classical toxicological testing procedures. Including the detection of alterations in signaling pathways in toxicity testing procedures may enhance the confidence in outcomes of toxicological trials. In this study, no significant GM-related changes in intestinal expression profiles were found in rats fed GM-maize MON810. Relevant alterations of selected cellular pathways (apoptosis, DNA damage and repair, UPR) pointing toward intestinal toxicity of the diets were not observed. Transcriptomic profiles did not reveal perturbations of pathways associated with toxicity, underlining the study results revealed by classical OECD endpoints.

@Article{Umu2017,
  author    = {Sinan U{\u{g}}ur Umu and Hilde Langseth and Cecilie Bucher-Johannessen and Bastian Fromm and Andreas Keller and Eckart Meese and Marianne Lauritzen and Magnus Leithaug and Robert Lyle and Trine B. Rounge},
  title     = {A comprehensive profile of circulating {RNAs} in human serum},
  journal   = {{RNA} Biology},
  year      = {2017},
  volume    = {15},
  number    = {2},
  pages     = {242--250},
  month     = {dec},
  doi       = {10.1080/15476286.2017.1403003},
  publisher = {Informa {UK} Limited},
}

@Article{Sedaghat-Hamedani2017,
  author    = {Farbod Sedaghat-Hamedani and Jan Haas and Feng Zhu and Christian Geier and Elham Kayvanpour and Martin Liss and Alan Lai and Karen Frese and Regina Pribe-Wolferts and Ali Amr and Daniel Tian Li and Omid Shirvani Samani and Avisha Carstensen and Diana Martins Bordalo and Marion Müller and Christine Fischer and Jing Shao and Jing Wang and Ming Nie and Li Yuan and Sabine Ha{\ss}feld and Christine Schwartz and Min Zhou and Zihua Zhou and Yanwen Shu and Min Wang and Kai Huang and Qiutang Zeng and Longxian Cheng and Tobias Fehlmann and Philipp Ehlermann and Andreas Keller and Christoph Dieterich and Katrin Streckfu{\ss}-Bömeke and Yuhua Liao and Michael Gotthardt and Hugo A Katus and Benjamin Meder},
  title     = {Clinical genetics and outcome of left ventricular non-compaction cardiomyopathy},
  journal   = {European Heart Journal},
  year      = {2017},
  volume    = {38},
  number    = {46},
  pages     = {3449--3460},
  month     = {oct},
  doi       = {10.1093/eurheartj/ehx545},
  publisher = {Oxford University Press ({OUP})},
}

@Article{Juzenas2017,
  author    = {Simonas Juzenas and Geetha Venkatesh and Matthias Hübenthal and Marc P. Hoeppner and Zhipei Gracie Du and Maren Paulsen and Philip Rosenstiel and Philipp Senger and Martin Hofmann-Apitius and Andreas Keller and Limas Kupcinskas and Andre Franke and Georg Hemmrich-Stanisak},
  title     = {A comprehensive, cell specific {microRNA} catalogue of human peripheral blood},
  journal   = {Nucleic Acids Research},
  year      = {2017},
  volume    = {45},
  number    = {16},
  pages     = {9290--9301},
  month     = {aug},
  doi       = {10.1093/nar/gkx706},
  publisher = {Oxford University Press ({OUP})},
}

@Article{Keller2017,
  author          = {Keller, Andreas and Kreis, Stephanie and Leidinger, Petra and Maixner, Frank and Ludwig, Nicole and Backes, Christina and Galata, Valentina and Guerriero, Gea and Fehlmann, Tobias and Franke, Andre and Meder, Benjamin and Zink, Albert and Meese, Eckart},
  title           = {miRNAs in Ancient Tissue Specimens of the Tyrolean Iceman.},
  journal         = {Molecular biology and evolution},
  year            = {2017},
  volume          = {34},
  pages           = {793--801},
  month           = apr,
  issn            = {1537-1719},
  abstract        = {The analysis of nucleic acids in ancient samples is largely limited to DNA. Small noncoding RNAs (microRNAs) are known to be evolutionary conserved and stable. To gain knowledge on miRNAs measured from ancient samples, we profiled microRNAs in cryoconserved mummies. First, we established the approach on a World War One warrior, the "Kaiserjäger", which has been preserved for almost one century. Then, we profiled seven ancient tissue specimens including skeletal muscle, stomach mucosa, stomach content and two corpus organ tissues of the 5,300-year-old copper age mummy Iceman and compared these profiles to the presence of organ-specific miRNAs in modern tissues. Our analyses suggest the presence of specific miRNAs in the different Iceman's tissues. Of 1,066 analyzed human miRNAs, 31 were discovered across all biopsies and 87 miRNAs were detected only in a single sample. To check for potential microbiological contaminations, all miRNAs detected in Iceman samples and not present in ancient samples were mapped to 14,582 bacterial and viral genomes. We detected few hits (3.9% of miRNAs compared with 3.6% of miRNAs). Interestingly, the miRNAs with higher abundance across all ancient tissues were significantly enriched for Guanine (P value of 10-13) and Cytosine (P value of 10-7). The same pattern was observed for modern tissues. Comparing miRNAs measured from ancient organs to modern tissue patterns highlighted significant similarities, e.g., for miRNAs present in the muscle. Our first comprehensive analysis of microRNAs in ancient human tissues indicates that these stable molecules can be detected in tissue specimens after 5,300 years.},
  chemicals       = {DNA, Ancient, MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-07-24},
  country         = {United States},
  doi             = {10.1093/molbev/msw291},
  issn-linking    = {0737-4038},
  issue           = {4},
  keywords        = {DNA, Ancient, analysis; Humans; MicroRNAs, analysis, genetics; Mummies; Nucleic Acid Amplification Techniques, methods; Iceman; ancient; miRNA},
  nlm-id          = {8501455},
  owner           = {NLM},
  pii             = {msw291},
  pmid            = {28025275},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2018-07-16},
}

The analysis of nucleic acids in ancient samples is largely limited to DNA. Small noncoding RNAs (microRNAs) are known to be evolutionary conserved and stable. To gain knowledge on miRNAs measured from ancient samples, we profiled microRNAs in cryoconserved mummies. First, we established the approach on a World War One warrior, the "Kaiserjäger", which has been preserved for almost one century. Then, we profiled seven ancient tissue specimens including skeletal muscle, stomach mucosa, stomach content and two corpus organ tissues of the 5,300-year-old copper age mummy Iceman and compared these profiles to the presence of organ-specific miRNAs in modern tissues. Our analyses suggest the presence of specific miRNAs in the different Iceman's tissues. Of 1,066 analyzed human miRNAs, 31 were discovered across all biopsies and 87 miRNAs were detected only in a single sample. To check for potential microbiological contaminations, all miRNAs detected in Iceman samples and not present in ancient samples were mapped to 14,582 bacterial and viral genomes. We detected few hits (3.9% of miRNAs compared with 3.6% of miRNAs). Interestingly, the miRNAs with higher abundance across all ancient tissues were significantly enriched for Guanine (P value of 10-13) and Cytosine (P value of 10-7). The same pattern was observed for modern tissues. Comparing miRNAs measured from ancient organs to modern tissue patterns highlighted significant similarities, e.g., for miRNAs present in the muscle. Our first comprehensive analysis of microRNAs in ancient human tissues indicates that these stable molecules can be detected in tissue specimens after 5,300 years.

@Article{Fehlmann2017,
  author       = {Fehlmann, Tobias and Sahay, Shashwat and Keller, Andreas and Backes, Christina},
  title        = {A review of databases predicting the effects of SNPs in miRNA genes or miRNA-binding sites.},
  journal      = {Briefings in bioinformatics},
  year         = {2017},
  month        = nov,
  issn         = {1477-4054},
  abstract     = {Modern precision medicine comprises the knowledge and understanding of individual differences in the genomic sequence of patients to provide tailor-made treatments. Regularly, such variants are considered in coding regions only, and their effects are predicted based on their impact on the amino acid sequence of expressed proteins. However, assessing the effects of variants in noncoding elements, in particular microRNAs (miRNAs) and their binding sites, is important as well, as a single miRNA can influence the expression patterns of many genes at the same time. To analyze the effects of variants in miRNAs and their target sites, several databases storing variant impact predictions have been published. In this review, we will compare the core functionalities and features of these databases and discuss the importance of up-to-date data resources in the context of web applications. Finally, we will outline some recommendations for future developments in the field.},
  country      = {England},
  doi          = {10.1093/bib/bbx155},
  issn-linking = {1467-5463},
  keywords     = {SNPs; databases; miRNAs; target sites},
  nlm-id       = {100912837},
  owner        = {NLM},
  pii          = {4665691},
  pmid         = {29186316},
  pubmodel     = {Print-Electronic},
  pubstatus    = {aheadofprint},
  revised      = {2017-11-29},
}

Modern precision medicine comprises the knowledge and understanding of individual differences in the genomic sequence of patients to provide tailor-made treatments. Regularly, such variants are considered in coding regions only, and their effects are predicted based on their impact on the amino acid sequence of expressed proteins. However, assessing the effects of variants in noncoding elements, in particular microRNAs (miRNAs) and their binding sites, is important as well, as a single miRNA can influence the expression patterns of many genes at the same time. To analyze the effects of variants in miRNAs and their target sites, several databases storing variant impact predictions have been published. In this review, we will compare the core functionalities and features of these databases and discuss the importance of up-to-date data resources in the context of web applications. Finally, we will outline some recommendations for future developments in the field.

@Article{Kehl2017,
  author       = {Kehl, Tim and Backes, Christina and Kern, Fabian and Fehlmann, Tobias and Ludwig, Nicole and Meese, Eckart and Lenhof, Hans-Peter and Keller, Andreas},
  title        = {About miRNAs, miRNA seeds, target genes and target pathways.},
  journal      = {Oncotarget},
  year         = {2017},
  volume       = {8},
  pages        = {107167--107175},
  month        = dec,
  issn         = {1949-2553},
  abstract     = {miRNAs are typically repressing gene expression by binding to the 3' UTR, leading to degradation of the mRNA. This process is dominated by the eight-base seed region of the miRNA. Further, miRNAs are known not only to target genes but also to target significant parts of pathways. A logical line of thoughts is: miRNAs with similar (seed) sequence target similar sets of genes and thus similar sets of pathways. By calculating similarity scores for all 3.25 million pairs of 2,550 human miRNAs, we found that this pattern frequently holds, while we also observed exceptions. Respective results were obtained for both, predicted target genes as well as experimentally validated targets. We note that miRNAs target gene set similarity follows a bimodal distribution, pointing at a set of 282 miRNAs that seems to target genes with very high specificity. Further, we discuss miRNAs with different (seed) sequences that nonetheless regulate similar gene sets or pathways. Most intriguingly, we found miRNA pairs that regulate different gene sets but similar pathways such as miR-6886-5p and miR-3529-5p. These are jointly targeting different parts of the MAPK signaling cascade. The main goal of this study is to provide a general overview on the results, to highlight a selection of relevant results on miRNAs, miRNA seeds, target genes and target pathways and to raise awareness for artifacts in respective comparisons. The full set of information that allows to infer detailed results on each miRNA has been included in miRPathDB, the miRNA target pathway database (https://mpd.bioinf.uni-sb.de).},
  country      = {United States},
  doi          = {10.18632/oncotarget.22363},
  issn-linking = {1949-2553},
  issue        = {63},
  keywords     = {microRNA; non-coding RNA; systems biology; target gene},
  nlm-id       = {101532965},
  owner        = {NLM},
  pii          = {22363},
  pmc          = {PMC5739805},
  pmid         = {29291020},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2018-01-03},
}

miRNAs are typically repressing gene expression by binding to the 3' UTR, leading to degradation of the mRNA. This process is dominated by the eight-base seed region of the miRNA. Further, miRNAs are known not only to target genes but also to target significant parts of pathways. A logical line of thoughts is: miRNAs with similar (seed) sequence target similar sets of genes and thus similar sets of pathways. By calculating similarity scores for all 3.25 million pairs of 2,550 human miRNAs, we found that this pattern frequently holds, while we also observed exceptions. Respective results were obtained for both, predicted target genes as well as experimentally validated targets. We note that miRNAs target gene set similarity follows a bimodal distribution, pointing at a set of 282 miRNAs that seems to target genes with very high specificity. Further, we discuss miRNAs with different (seed) sequences that nonetheless regulate similar gene sets or pathways. Most intriguingly, we found miRNA pairs that regulate different gene sets but similar pathways such as miR-6886-5p and miR-3529-5p. These are jointly targeting different parts of the MAPK signaling cascade. The main goal of this study is to provide a general overview on the results, to highlight a selection of relevant results on miRNAs, miRNA seeds, target genes and target pathways and to raise awareness for artifacts in respective comparisons. The full set of information that allows to infer detailed results on each miRNA has been included in miRPathDB, the miRNA target pathway database (https://mpd.bioinf.uni-sb.de).

@Article{Freis2017,
  author          = {Freis, Alexander and Keller, Andreas and Ludwig, Nicole and Meese, Eckart and Jauckus, Julia and Rehnitz, Julia and Capp, Edison and Strowitzki, Thomas and Germeyer, Ariane},
  title           = {Altered miRNA-profile dependent on ART outcome in early pregnancy targets Wnt-pathway.},
  journal         = {Reproduction (Cambridge, England)},
  year            = {2017},
  volume          = {154},
  pages           = {799--805},
  month           = dec,
  issn            = {1741-7899},
  abstract        = {Main goal of this study is to detect the possible alterations in microRNA (miRNA) expression and the pathway targeted in plasma at the time of embryo transfer and pregnancy testing dependent on the assisted reproductive treatment (ART) outcome after ovarian hyperstimulation for   fertilization. Changes in miRNA expression in plasma of women, who became pregnant (  = 6) vs women who failed implantation (  = 6) following day 5 embryo transfer (ET), were investigated at the day of ET and pregnancy testing (PT). Protein expression to validate the finding was performed with a sample size of   = 20 (10 per group) using enzyme-linked immunosorbent assay. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using DIANA-miRPath, v3.0 software based on predicted targets by DIANA-microT-CDS. 4 miRNAs could be identified as possible biomarkers for implantation success. The 11 miRNAs showing the highest significant alterations were all associated with the regulation of WNT3 and WNT7a. While WNT7a presented with a significant decrease between ET and PT in case of ongoing pregnancy, women with implantation failure showed unaltered concentrations. WNT3 presented with a significant decrease in both groups. However, the loss of WNT3 between ET and PT was significantly higher in patients who became pregnant. Main limitation of this prospective study is its small sample size, defining it as a pilot analysis. To conclude, we could demonstrate a significant change in miRNA profile dependent on the ART outcome affecting Wnt pathway. Our findings indicate a possible prospective use of miRNA as biomarkers for implantation success.},
  chemicals       = {MicroRNAs, WNT3 protein, human, WNT7A protein, human, Wnt Proteins, Wnt3 Protein},
  citation-subset = {IM},
  completed       = {2018-06-25},
  country         = {England},
  doi             = {10.1530/REP-17-0396},
  issn-linking    = {1470-1626},
  issue           = {6},
  keywords        = {Adult; Embryo Culture Techniques; Embryo Implantation; Embryo Transfer, adverse effects; Female; Fertility; Fertilization in Vitro, adverse effects; Gene Expression Regulation, Developmental; Humans; Infertility, genetics, metabolism, physiopathology, therapy; MicroRNAs, genetics, metabolism; Pilot Projects; Pregnancy; Pregnancy Rate; Prospective Studies; Sperm Injections, Intracytoplasmic; Time Factors; Transcriptome; Treatment Outcome; Wnt Proteins, genetics, metabolism; Wnt Signaling Pathway, genetics; Wnt3 Protein, genetics, metabolism; Young Adult},
  nlm-id          = {100966036},
  owner           = {NLM},
  pii             = {REP-17-0396},
  pmid            = {28971890},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-07-16},
}

Main goal of this study is to detect the possible alterations in microRNA (miRNA) expression and the pathway targeted in plasma at the time of embryo transfer and pregnancy testing dependent on the assisted reproductive treatment (ART) outcome after ovarian hyperstimulation for fertilization. Changes in miRNA expression in plasma of women, who became pregnant (  = 6) vs women who failed implantation (  = 6) following day 5 embryo transfer (ET), were investigated at the day of ET and pregnancy testing (PT). Protein expression to validate the finding was performed with a sample size of  = 20 (10 per group) using enzyme-linked immunosorbent assay. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed using DIANA-miRPath, v3.0 software based on predicted targets by DIANA-microT-CDS. 4 miRNAs could be identified as possible biomarkers for implantation success. The 11 miRNAs showing the highest significant alterations were all associated with the regulation of WNT3 and WNT7a. While WNT7a presented with a significant decrease between ET and PT in case of ongoing pregnancy, women with implantation failure showed unaltered concentrations. WNT3 presented with a significant decrease in both groups. However, the loss of WNT3 between ET and PT was significantly higher in patients who became pregnant. Main limitation of this prospective study is its small sample size, defining it as a pilot analysis. To conclude, we could demonstrate a significant change in miRNA profile dependent on the ART outcome affecting Wnt pathway. Our findings indicate a possible prospective use of miRNA as biomarkers for implantation success.

@Article{Abu-Halima2017b,
  author          = {Abu-Halima, Masood and Meese, Eckart and Keller, Andreas and Abdul-Khaliq, Hashim and Rädle-Hurst, Tanja},
  title           = {Analysis of circulating microRNAs in patients with repaired Tetralogy of Fallot with and without heart failure.},
  journal         = {Journal of translational medicine},
  year            = {2017},
  volume          = {15},
  pages           = {156},
  month           = jul,
  issn            = {1479-5876},
  abstract        = {MicroRNAs (miRNAs) are a class of regulatory RNAs that regulate gene expression post-transcriptionally. Little, however, is known on the expression profile of circulating miRNAs in Tetralogy of Fallot (TOF) patients late after surgical repair. In this study, we aimed to identify the specific patterns of circulating miRNAs in blood of patients with repaired, non-syndromic TOF and to assess whether these specific miRNAs may be useful to differentiate patients with and without heart failure. SurePrint™ 8 × 60 K Human v16 miRNA arrays were used to determine miRNA expression profiles in 15 healthy controls and 37 patients after TOF repair of whom 3 had symptomatic right heart failure. The expression levels of selected miRNAs have been validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Enrichment analyses of altered miRNA expression were predicted using bioinformatic tools. Compared with healthy controls, a total of 49, 58 and 77 miRNAs were found to be significantly altered in TOF patients (TOF-all), TOF patients with (TOF-HF) and without symptomatic right heart failure (TOF-noHF) (>2.0-fold change, adjusted P < 0.05), respectively. Three miRNAs namely miR-181d-5p, miR-206 and miR-625-5p were validated by RT-qPCR in all TOF groups. The area under the receiver operating characteristic curve (AUC) for miR-181d-5p, miR-206 and miR-625-5p were 0.987, 0.993 and 0.769 in TOF-all and 0.990, 0.994 and 0.749 in TOF-noHF, respectively. Moreover, expression levels of miR-625-5p, miR-1233-3p and miR-421 were lower in TOF-HF compared to TOF-noHF (P = 0.012). Altered expression levels of circulating miRNAs were found in TOF patients late after surgical repair and are different to those seen in the right ventricular myocardium of infants with TOF. Expression levels of miR-421, miR-1233-3p and miR-625-5p are lower in TOF patients with symptomatic right heart failure and thus may indicate disease progression in these patients.},
  chemicals       = {Circulating MicroRNA},
  citation-subset = {IM},
  completed       = {2018-03-30},
  country         = {England},
  doi             = {10.1186/s12967-017-1255-z},
  issn-linking    = {1479-5876},
  issue           = {1},
  keywords        = {Adult; Circulating MicroRNA, genetics, metabolism; Female; Gene Expression Profiling; Heart Failure, blood, complications, genetics; Humans; Male; Real-Time Polymerase Chain Reaction; Reproducibility of Results; Tetralogy of Fallot, blood, complications, genetics; Congenital heart defects; Heart failure; MicroRNA; Tetralogy of Fallot},
  nlm-id          = {101190741},
  owner           = {NLM},
  pii             = {10.1186/s12967-017-1255-z},
  pmc             = {PMC5504636},
  pmid            = {28693530},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2018-07-12},
}

MicroRNAs (miRNAs) are a class of regulatory RNAs that regulate gene expression post-transcriptionally. Little, however, is known on the expression profile of circulating miRNAs in Tetralogy of Fallot (TOF) patients late after surgical repair. In this study, we aimed to identify the specific patterns of circulating miRNAs in blood of patients with repaired, non-syndromic TOF and to assess whether these specific miRNAs may be useful to differentiate patients with and without heart failure. SurePrint™ 8 × 60 K Human v16 miRNA arrays were used to determine miRNA expression profiles in 15 healthy controls and 37 patients after TOF repair of whom 3 had symptomatic right heart failure. The expression levels of selected miRNAs have been validated by quantitative reverse transcription polymerase chain reaction (RT-qPCR). Enrichment analyses of altered miRNA expression were predicted using bioinformatic tools. Compared with healthy controls, a total of 49, 58 and 77 miRNAs were found to be significantly altered in TOF patients (TOF-all), TOF patients with (TOF-HF) and without symptomatic right heart failure (TOF-noHF) (>2.0-fold change, adjusted P < 0.05), respectively. Three miRNAs namely miR-181d-5p, miR-206 and miR-625-5p were validated by RT-qPCR in all TOF groups. The area under the receiver operating characteristic curve (AUC) for miR-181d-5p, miR-206 and miR-625-5p were 0.987, 0.993 and 0.769 in TOF-all and 0.990, 0.994 and 0.749 in TOF-noHF, respectively. Moreover, expression levels of miR-625-5p, miR-1233-3p and miR-421 were lower in TOF-HF compared to TOF-noHF (P = 0.012). Altered expression levels of circulating miRNAs were found in TOF patients late after surgical repair and are different to those seen in the right ventricular myocardium of infants with TOF. Expression levels of miR-421, miR-1233-3p and miR-625-5p are lower in TOF patients with symptomatic right heart failure and thus may indicate disease progression in these patients.

@Article{Laczny2017,
  author       = {Laczny, Cedric C and Galata, Valentina and Plum, Achim and Posch, Andreas E and Keller, Andreas},
  title        = {Assessing the heterogeneity of in silico plasmid predictions based on whole-genome-sequenced clinical isolates.},
  journal      = {Briefings in bioinformatics},
  year         = {2017},
  month        = dec,
  issn         = {1477-4054},
  abstract     = {High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data. Heterogeneity, sensitivity and precision were evaluated by reference-independent and reference-dependent benchmarking using 846 Gram-negative clinical isolates. Interestingly, the majority of predicted sequences were tool-specific, resulting in a pronounced heterogeneity across tools for the reference-independent assessment. In the reference-dependent assessment, sensitivity and precision values were found to substantially vary between tools and across taxa, with cBar exhibiting the highest median sensitivity (87.45%) but a low median precision (27.05%). Furthermore, integrating the individual tools into an ensemble approach showed increased sensitivity (95.55%) while reducing the precision (25.62%). CBar and plasmidSPAdes exhibited the strongest concordance with respect to identified antibiotic resistance factors. Moreover, false-positive plasmid predictions typically contained only few antibiotic resistance factors. In conclusion, while high degrees of heterogeneity and variation in sensitivity and precision were observed across the different tools and taxa, existing tools are valuable for investigating the plasmid-borne resistome. Nevertheless, additional studies on representative clinical data sets will be necessary to translate in silico plasmid prediction approaches from research to clinical application.},
  country      = {England},
  doi          = {10.1093/bib/bbx162},
  issn-linking = {1467-5463},
  keywords     = {bacteria; next-generation sequencing; plasmids; prediction},
  nlm-id       = {100912837},
  owner        = {NLM},
  pii          = {4696344},
  pmid         = {29220507},
  pubmodel     = {Print-Electronic},
  pubstatus    = {aheadofprint},
  revised      = {2017-12-08},
}

High-throughput next-generation shotgun sequencing of pathogenic bacteria is growing in clinical relevance, especially for chromosomal DNA-based taxonomic identification and for antibiotic resistance prediction. Genetic exchange is facilitated for extrachromosomal DNA, e.g. plasmid-borne antibiotic resistance genes. Consequently, accurate identification of plasmids from whole-genome sequencing (WGS) data remains one of the major challenges for sequencing-based precision medicine in infectious diseases. Here, we assess the heterogeneity of four state-of-the-art tools (cBar, PlasmidFinder, plasmidSPAdes and Recycler) for the in silico prediction of plasmid-derived sequences from WGS data. Heterogeneity, sensitivity and precision were evaluated by reference-independent and reference-dependent benchmarking using 846 Gram-negative clinical isolates. Interestingly, the majority of predicted sequences were tool-specific, resulting in a pronounced heterogeneity across tools for the reference-independent assessment. In the reference-dependent assessment, sensitivity and precision values were found to substantially vary between tools and across taxa, with cBar exhibiting the highest median sensitivity (87.45%) but a low median precision (27.05%). Furthermore, integrating the individual tools into an ensemble approach showed increased sensitivity (95.55%) while reducing the precision (25.62%). CBar and plasmidSPAdes exhibited the strongest concordance with respect to identified antibiotic resistance factors. Moreover, false-positive plasmid predictions typically contained only few antibiotic resistance factors. In conclusion, while high degrees of heterogeneity and variation in sensitivity and precision were observed across the different tools and taxa, existing tools are valuable for investigating the plasmid-borne resistome. Nevertheless, additional studies on representative clinical data sets will be necessary to translate in silico plasmid prediction approaches from research to clinical application.

@Article{Abu-Halima2017,
  author       = {Abu-Halima, Masood and Häusler, Sebastian and Backes, Christina and Fehlmann, Tobias and Staib, Claudia and Nestel, Sigrun and Nazarenko, Irina and Meese, Eckart and Keller, Andreas},
  title        = {Micro-ribonucleic acids and extracellular vesicles repertoire in the spent culture media is altered in women undergoing In Vitro Fertilization.},
  journal      = {Scientific reports},
  year         = {2017},
  volume       = {7},
  pages        = {13525},
  month        = oct,
  issn         = {2045-2322},
  abstract     = {MicroRNAs (miRNAs) are class of small RNA molecules with major impact on gene regulation. We analyzed the potential of miRNAs secreted from pre-implantation embryos into the embryonic culture media as biomarkers to predict successful pregnancy. Using microarray analysis, we profiled the miRNome of the 56 spent culture media (SCM) after embryos transfer and found a total of 621 miRNAs in the SCM. On average, we detected 163 miRNAs in SCM of samples with failed pregnancies, but only 149 SCM miRNAs of embryos leading to pregnancies. MiR-634 predicted an embryo transfer leading to a positive pregnancy with an accuracy of 71% and a sensitivity of 85%. Among the 621 miRNAs, 102 (16.4%) showed a differential expression between positive and negative outcome of pregnancy with miR-29c-3p as the most significantly differentially expressed miRNA. The number of extracellular vehicles was lower in SCM with positive outcomes (3.8 × 10 /mL EVs), as compared to a negative outcome (7.35 × 10 /mL EVs) possibly explaining the reduced number of miRNAs in the SCM associated with failed pregnancies. The analysis of the miRNome in the SCM of couples undergoing fertility treatment lays the ground towards development of biomarkers to predict successful pregnancy and towards understanding the role of embryonic miRNAs found in the SCM.},
  country      = {England},
  doi          = {10.1038/s41598-017-13683-8},
  issn-linking = {2045-2322},
  issue        = {1},
  nlm-id       = {101563288},
  owner        = {NLM},
  pii          = {10.1038/s41598-017-13683-8},
  pmc          = {PMC5648749},
  pmid         = {29051527},
  pubmodel     = {Electronic},
  pubstatus    = {epublish},
  revised      = {2017-12-19},
}

MicroRNAs (miRNAs) are class of small RNA molecules with major impact on gene regulation. We analyzed the potential of miRNAs secreted from pre-implantation embryos into the embryonic culture media as biomarkers to predict successful pregnancy. Using microarray analysis, we profiled the miRNome of the 56 spent culture media (SCM) after embryos transfer and found a total of 621 miRNAs in the SCM. On average, we detected 163 miRNAs in SCM of samples with failed pregnancies, but only 149 SCM miRNAs of embryos leading to pregnancies. MiR-634 predicted an embryo transfer leading to a positive pregnancy with an accuracy of 71% and a sensitivity of 85%. Among the 621 miRNAs, 102 (16.4%) showed a differential expression between positive and negative outcome of pregnancy with miR-29c-3p as the most significantly differentially expressed miRNA. The number of extracellular vehicles was lower in SCM with positive outcomes (3.8 × 10 /mL EVs), as compared to a negative outcome (7.35 × 10 /mL EVs) possibly explaining the reduced number of miRNAs in the SCM associated with failed pregnancies. The analysis of the miRNome in the SCM of couples undergoing fertility treatment lays the ground towards development of biomarkers to predict successful pregnancy and towards understanding the role of embryonic miRNAs found in the SCM.

@Article{Abu-Halima2017a,
  author          = {Abu-Halima, Masood and Poryo, Martin and Ludwig, Nicole and Mark, Janine and Marsollek, Ina and Giebels, Christian and Petersen, Johannes and Schäfers, Hans-Joachim and Grundmann, Ulrich and Pickardt, Thomas and Keller, Andreas and Meese, Eckart and Abdul-Khaliq, Hashim},
  title           = {Differential expression of microRNAs following cardiopulmonary bypass in children with congenital heart diseases.},
  journal         = {Journal of translational medicine},
  year            = {2017},
  volume          = {15},
  pages           = {117},
  month           = may,
  issn            = {1479-5876},
  abstract        = {Children with congenital heart defects (CHDs) are at high risk for myocardial failure after operative procedures with cardiopulmonary bypass (CPB). Recent studies suggest that microRNAs (miRNA) are involved in the development of CHDs and myocardial failure. Therefore, the aim of this study was to determine alterations in the miRNA profile in heart tissue after cardiac surgery using CPB. In total, 14 tissue samples from right atrium were collected from patients before and after connection of the CPB. SurePrint™ 8 × 60K Human v21 miRNA array and quantitative reverse transcription-polymerase chain reaction (RT-qPCR) were employed to determine the miRNA expression profile from three patients before and after connection of the CPB. Enrichment analyses of altered miRNA expression were predicted using bioinformatic tools. According to miRNA array, a total of 90 miRNAs were significantly altered including 29 miRNAs with increased and 61 miRNAs with decreased expression after de-connection of CPB (n = 3) compared to before CPB (n = 3). Seven miRNAs had been validated using RT-qPCR in an independent cohort of 11 patients. Enrichment analyses applying the KEGG database displayed the highest correlation for signaling pathways, cellular community, cardiovascular disease and circulatory system. Our result identified the overall changes of the miRNome in right atrium tissue of patients with CHDs after CPB. The differentially altered miRNAs lay a good foundation for further understanding of the molecular function of changed miRNAs in regulating CHDs and after CPB in particular.},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2018-03-22},
  country         = {England},
  doi             = {10.1186/s12967-017-1213-9},
  issn-linking    = {1479-5876},
  issue           = {1},
  keywords        = {Cardiopulmonary Bypass; Child; Child, Preschool; Cluster Analysis; Cohort Studies; Computational Biology; Female; Gene Expression Profiling; Gene Expression Regulation; Heart Atria, metabolism; Heart Defects, Congenital, metabolism; Humans; Infant; Male; MicroRNAs, metabolism; Myocardium, pathology; Oligonucleotide Array Sequence Analysis; Time Factors; Tissue Distribution; Atrial myocardium; Cardiopulmonary bypass; Congenital heart disease; MicroRNA},
  nlm-id          = {101190741},
  owner           = {NLM},
  pii             = {10.1186/s12967-017-1213-9},
  pmc             = {PMC5450060},
  pmid            = {28558735},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2018-07-12},
}

Children with congenital heart defects (CHDs) are at high risk for myocardial failure after operative procedures with cardiopulmonary bypass (CPB). Recent studies suggest that microRNAs (miRNA) are involved in the development of CHDs and myocardial failure. Therefore, the aim of this study was to determine alterations in the miRNA profile in heart tissue after cardiac surgery using CPB. In total, 14 tissue samples from right atrium were collected from patients before and after connection of the CPB. SurePrint™ 8 × 60K Human v21 miRNA array and quantitative reverse transcription-polymerase chain reaction (RT-qPCR) were employed to determine the miRNA expression profile from three patients before and after connection of the CPB. Enrichment analyses of altered miRNA expression were predicted using bioinformatic tools. According to miRNA array, a total of 90 miRNAs were significantly altered including 29 miRNAs with increased and 61 miRNAs with decreased expression after de-connection of CPB (n = 3) compared to before CPB (n = 3). Seven miRNAs had been validated using RT-qPCR in an independent cohort of 11 patients. Enrichment analyses applying the KEGG database displayed the highest correlation for signaling pathways, cellular community, cardiovascular disease and circulatory system. Our result identified the overall changes of the miRNome in right atrium tissue of patients with CHDs after CPB. The differentially altered miRNAs lay a good foundation for further understanding of the molecular function of changed miRNAs in regulating CHDs and after CPB in particular.

@Article{Fehlmann2017a,
  author          = {Fehlmann, Tobias and Backes, Christina and Kahraman, Mustafa and Haas, Jan and Ludwig, Nicole and Posch, Andreas E and Würstle, Maximilian L and Hübenthal, Matthias and Franke, Andre and Meder, Benjamin and Meese, Eckart and Keller, Andreas},
  title           = {Web-based NGS data analysis using miRMaster: a large-scale meta-analysis of human miRNAs.},
  journal         = {Nucleic acids research},
  year            = {2017},
  volume          = {45},
  pages           = {8731--8744},
  month           = sep,
  issn            = {1362-4962},
  abstract        = {The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data we implemented the fast, accurate and comprehensive web-based tool miRMaster. Our toolbox provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%. An integrative analysis of small RNAs from 1836 data sets (20 billion reads) indicated that context-specific miRNAs (e.g. miRNAs present only in one or few different tissues / cell types) still remain to be discovered while broadly expressed miRNAs appear to be largely known. In total, our analysis of known and novel miRNAs indicated nearly 22 000 candidates of precursors with one or two mature forms. Based on these, we designed a custom microarray comprising 11 872 potential mature miRNAs to assess the quality of our prediction. MiRMaster is a convenient-to-use tool for the comprehensive and fast analysis of miRNA NGS data. In addition, our predicted miRNA candidates provided as custom array will allow researchers to perform in depth validation of candidates interesting to them.},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-11-07},
  country         = {England},
  doi             = {10.1093/nar/gkx595},
  issn-linking    = {0305-1048},
  issue           = {15},
  keywords        = {Computational Biology, methods, statistics & numerical data; Data Interpretation, Statistical; High-Throughput Nucleotide Sequencing, methods, statistics & numerical data; Humans; Internet; MicroRNAs, analysis, genetics; Microarray Analysis, methods; Sequence Analysis, RNA, methods, statistics & numerical data; Transcriptome; Validation Studies as Topic},
  nlm-id          = {0411011},
  owner           = {NLM},
  pii             = {3956630},
  pmc             = {PMC5587802},
  pmid            = {28911107},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2017-11-07},
}

The analysis of small RNA NGS data together with the discovery of new small RNAs is among the foremost challenges in life science. For the analysis of raw high-throughput sequencing data we implemented the fast, accurate and comprehensive web-based tool miRMaster. Our toolbox provides a wide range of modules for quantification of miRNAs and other non-coding RNAs, discovering new miRNAs, isomiRs, mutations, exogenous RNAs and motifs. Use-cases comprising hundreds of samples are processed in less than 5 h with an accuracy of 99.4%. An integrative analysis of small RNAs from 1836 data sets (20 billion reads) indicated that context-specific miRNAs (e.g. miRNAs present only in one or few different tissues / cell types) still remain to be discovered while broadly expressed miRNAs appear to be largely known. In total, our analysis of known and novel miRNAs indicated nearly 22 000 candidates of precursors with one or two mature forms. Based on these, we designed a custom microarray comprising 11 872 potential mature miRNAs to assess the quality of our prediction. MiRMaster is a convenient-to-use tool for the comprehensive and fast analysis of miRNA NGS data. In addition, our predicted miRNA candidates provided as custom array will allow researchers to perform in depth validation of candidates interesting to them.

@Article{Meder2017,
  author          = {Meder, Benjamin and Haas, Jan and Sedaghat-Hamedani, Farbod and Kayvanpour, Elham and Frese, Karen and Lai, Alan and Nietsch, Rouven and Scheiner, Christina and Mester, Stefan and Bordalo, Diana Martins and Amr, Ali and Dietrich, Carsten and Pils, Dietmar and Siede, Dominik and Hund, Hauke and Bauer, Andrea and Holzer, Daniel Benjamin and Ruhparwar, Arjang and Mueller-Hennessen, Matthias and Weichenhan, Dieter and Plass, Christoph and Weis, Tanja and Backs, Johannes and Wuerstle, Maximilian and Keller, Andreas and Katus, Hugo A and Posch, Andreas E},
  title           = {Epigenome-Wide Association Study Identifies Cardiac Gene Patterning and a Novel Class of Biomarkers for Heart Failure.},
  journal         = {Circulation},
  year            = {2017},
  volume          = {136},
  pages           = {1528--1544},
  month           = oct,
  issn            = {1524-4539},
  abstract        = {Biochemical DNA modification resembles a crucial regulatory layer among genetic information, environmental factors, and the transcriptome. To identify epigenetic susceptibility regions and novel biomarkers linked to myocardial dysfunction and heart failure, we performed the first multi-omics study in myocardial tissue and blood of patients with dilated cardiomyopathy and controls. Infinium human methylation 450 was used for high-density epigenome-wide mapping of DNA methylation in left-ventricular biopsies and whole peripheral blood of living probands. RNA deep sequencing was performed on the same samples in parallel. Whole-genome sequencing of all patients allowed exclusion of promiscuous genotype-induced methylation calls. In the screening stage, we detected 59 epigenetic loci that are significantly associated with dilated cardiomyopathy (false discovery corrected  ≤0.05), with 3 of them reaching epigenome-wide significance at  ≤5×10 . Twenty-seven (46%) of these loci could be replicated in independent cohorts, underlining the role of epigenetic regulation of key cardiac transcription regulators. Using a staged multi-omics study design, we link a subset of 517 epigenetic loci with dilated cardiomyopathy and cardiac gene expression. Furthermore, we identified distinct epigenetic methylation patterns that are conserved across tissues, rendering these CpGs novel epigenetic biomarkers for heart failure. The present study provides to our knowledge the first epigenome-wide association study in living patients with heart failure using a multi-omics approach.},
  chemicals       = {Genetic Markers, RNA, Messenger},
  citation-subset = {AIM, IM},
  completed       = {2017-10-24},
  country         = {United States},
  doi             = {10.1161/CIRCULATIONAHA.117.027355},
  issn-linking    = {0009-7322},
  issue           = {16},
  keywords        = {Cardiomyopathy, Dilated, blood, diagnosis, genetics; Case-Control Studies; CpG Islands; DNA Methylation; Epigenesis, Genetic; Epigenomics, methods; Gene Expression Profiling; Genetic Loci; Genetic Markers; Genetic Predisposition to Disease; Genome-Wide Association Study; Heart Failure, blood, diagnosis, genetics; Heart Ventricles, chemistry; High-Throughput Nucleotide Sequencing; Humans; Phenotype; RNA, Messenger, genetics; Sequence Analysis, RNA; DNA methylation; biomarker; dilated cardiomyopathy; epigenetics; heart failure; natriuretic peptides},
  nlm-id          = {0147763},
  owner           = {NLM},
  pii             = {CIRCULATIONAHA.117.027355},
  pmid            = {28838933},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-10-24},
}

Biochemical DNA modification resembles a crucial regulatory layer among genetic information, environmental factors, and the transcriptome. To identify epigenetic susceptibility regions and novel biomarkers linked to myocardial dysfunction and heart failure, we performed the first multi-omics study in myocardial tissue and blood of patients with dilated cardiomyopathy and controls. Infinium human methylation 450 was used for high-density epigenome-wide mapping of DNA methylation in left-ventricular biopsies and whole peripheral blood of living probands. RNA deep sequencing was performed on the same samples in parallel. Whole-genome sequencing of all patients allowed exclusion of promiscuous genotype-induced methylation calls. In the screening stage, we detected 59 epigenetic loci that are significantly associated with dilated cardiomyopathy (false discovery corrected ≤0.05), with 3 of them reaching epigenome-wide significance at ≤5×10 . Twenty-seven (46%) of these loci could be replicated in independent cohorts, underlining the role of epigenetic regulation of key cardiac transcription regulators. Using a staged multi-omics study design, we link a subset of 517 epigenetic loci with dilated cardiomyopathy and cardiac gene expression. Furthermore, we identified distinct epigenetic methylation patterns that are conserved across tissues, rendering these CpGs novel epigenetic biomarkers for heart failure. The present study provides to our knowledge the first epigenome-wide association study in living patients with heart failure using a multi-omics approach.

@Article{Kahraman2017,
  author          = {Kahraman, Mustafa and Laufer, Thomas and Backes, Christina and Schrörs, Hannah and Fehlmann, Tobias and Ludwig, Nicole and Kohlhaas, Jochen and Meese, Eckart and Wehler, Thomas and Bals, Robert and Keller, Andreas},
  title           = {Technical Stability and Biological Variability in MicroRNAs from Dried Blood Spots: A Lung Cancer Therapy-Monitoring Showcase.},
  journal         = {Clinical chemistry},
  year            = {2017},
  volume          = {63},
  pages           = {1476--1488},
  month           = sep,
  issn            = {1530-8561},
  abstract        = {Different work flows have been proposed to use miRNAs as blood-borne biomarkers. In particular, the method used for collecting blood from patients can considerably influence the diagnostic results. We explored whether dried blood spots (DBSs) facilitate stable miRNA measurements and compared its technical stability with biological variability. First, we tested the stability of DBS samples by generating from 1 person 18 whole-genome-wide miRNA profiles of DBS samples that were exposed to different temperature and humidity conditions. Second, we investigated technical reproducibility by performing 7 replicates of DBS again from 1 person. Third, we investigated DBS samples from 53 patients with lung cancer undergoing different therapies. Across these 3 stages, 108 genome-wide miRNA profiles from DBS were generated and evaluated biostatistically. In the stability analysis, we observed that temperature and humidity had an overall limited influence on the miRNomes (average correlation between the different conditions of 0.993). Usage of a silica gel slightly diminished DBS' technical reproducibility. The 7 technical replicates had an average correlation of 0.996. The correlation with whole-blood PAXGene miRNomes of the same individual was remarkable (correlation of 0.88). Finally, evaluation of the samples from the 53 patients with lung cancer exposed to different therapies showed that the biological variations exceeded the technical variability significantly (  < 0.0001), yielding 51 dysregulated miRNAs. We present a stable work flow for profiling of whole miRNomes on the basis of samples collected from DBS. Biological variations exceeded technical variations significantly. DBS-based miRNA profiles will potentially further the translational character of miRNA biomarker studies.},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-09-07},
  country         = {United States},
  doi             = {10.1373/clinchem.2017.271619},
  issn-linking    = {0009-9147},
  issue           = {9},
  keywords        = {Computational Biology; Dried Blood Spot Testing, standards; Humans; Lung Neoplasms, diagnosis; MicroRNAs, analysis, chemistry; RNA Stability; Reproducibility of Results},
  nlm-id          = {9421549},
  owner           = {NLM},
  pii             = {clinchem.2017.271619},
  pmid            = {28679647},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-09-07},
}

Different work flows have been proposed to use miRNAs as blood-borne biomarkers. In particular, the method used for collecting blood from patients can considerably influence the diagnostic results. We explored whether dried blood spots (DBSs) facilitate stable miRNA measurements and compared its technical stability with biological variability. First, we tested the stability of DBS samples by generating from 1 person 18 whole-genome-wide miRNA profiles of DBS samples that were exposed to different temperature and humidity conditions. Second, we investigated technical reproducibility by performing 7 replicates of DBS again from 1 person. Third, we investigated DBS samples from 53 patients with lung cancer undergoing different therapies. Across these 3 stages, 108 genome-wide miRNA profiles from DBS were generated and evaluated biostatistically. In the stability analysis, we observed that temperature and humidity had an overall limited influence on the miRNomes (average correlation between the different conditions of 0.993). Usage of a silica gel slightly diminished DBS' technical reproducibility. The 7 technical replicates had an average correlation of 0.996. The correlation with whole-blood PAXGene miRNomes of the same individual was remarkable (correlation of 0.88). Finally, evaluation of the samples from the 53 patients with lung cancer exposed to different therapies showed that the biological variations exceeded the technical variability significantly ( < 0.0001), yielding 51 dysregulated miRNAs. We present a stable work flow for profiling of whole miRNomes on the basis of samples collected from DBS. Biological variations exceeded technical variations significantly. DBS-based miRNA profiles will potentially further the translational character of miRNA biomarker studies.

@Article{Kayvanpour2017,
  author          = {Kayvanpour, Elham and Sedaghat-Hamedani, Farbod and Amr, Ali and Lai, Alan and Haas, Jan and Holzer, Daniel B and Frese, Karen S and Keller, Andreas and Jensen, Katrin and Katus, Hugo A and Meder, Benjamin},
  title           = {Genotype-phenotype associations in dilated cardiomyopathy: meta-analysis on more than 8000 individuals.},
  journal         = {Clinical research in cardiology : official journal of the German Cardiac Society},
  year            = {2017},
  volume          = {106},
  pages           = {127--139},
  month           = feb,
  issn            = {1861-0692},
  abstract        = {Routine genetic testing in Dilated Cardiomyopathy (DCM) has recently become reality using Next-Generation Sequencing. Several studies have explored the relationship between genotypes and clinical phenotypes to support risk estimation and therapeutic decisions, however, most studies are small or restricted to a few genes. This study provides to our knowledge the first systematic meta-analysis on genotype-phenotype associations in DCM. We retrieved PubMed/Medline literature on genotype-phenotype associations in patients with DCM and mutations in LMNA, PLN, RBM20, MYBPC3, MYH7, TNNT2 and TNNI3. We summarized and extensively reviewed all studies that passed selection criteria and performed a meta-analysis on key phenotypic parameters. Together, 48 studies with 8097 patients were included. Furthermore, we reviewed recent studies investigating genotype-phenotype associations in DCM patients with TTN mutations. The average frequency of mutations in the investigated genes was between 1 and 5 %. The mean age of DCM onset was the beginning of the fifth decade for all genes. Heart transplantation (HTx) rate was highest in LMNA mutation carriers (27 %), while RBM20 mutation carriers were transplanted at a markedly younger age (mean 28.5 years). While 73 % of DCM patients with LMNA mutations showed cardiac conduction diseases, low voltage was the reported ECG hallmark in PLN mutation carriers. The frequency of ventricular arrhythmia in DCM patients with LMNA (50 %) and PLN (43 %) mutations was significantly higher. The penetrance of DCM phenotype in subjects with TTN truncating variants increased with age and reached 100 % by age of 70. A pooled analysis of available genotype-phenotype data shows a higher prevalence of sudden cardiac death (SCD), cardiac transplantation, or ventricular arrhythmias in LMNA and PLN mutation carriers compared to sarcomeric gene mutations. This study will further support the clinical interpretation of genetic findings.},
  chemicals       = {Genetic Markers},
  citation-subset = {IM},
  completed       = {2017-02-21},
  country         = {Germany},
  doi             = {10.1007/s00392-016-1033-6},
  issn-linking    = {1861-0684},
  issue           = {2},
  keywords        = {Adult; Age Factors; Arrhythmias, Cardiac, genetics, mortality, physiopathology; Cardiomyopathy, Dilated, genetics, mortality, physiopathology, surgery; Death, Sudden, Cardiac, etiology; Female; Gene Frequency; Genetic Association Studies; Genetic Markers; Genetic Predisposition to Disease; Heart Transplantation; Humans; Male; Middle Aged; Mutation; Phenotype; Prognosis; Risk Assessment; Risk Factors; Sex Factors; DCM; Meta-analysis; Phenotype-genotype associations},
  nlm-id          = {101264123},
  owner           = {NLM},
  pii             = {10.1007/s00392-016-1033-6},
  pmid            = {27576561},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-09-28},
}

Routine genetic testing in Dilated Cardiomyopathy (DCM) has recently become reality using Next-Generation Sequencing. Several studies have explored the relationship between genotypes and clinical phenotypes to support risk estimation and therapeutic decisions, however, most studies are small or restricted to a few genes. This study provides to our knowledge the first systematic meta-analysis on genotype-phenotype associations in DCM. We retrieved PubMed/Medline literature on genotype-phenotype associations in patients with DCM and mutations in LMNA, PLN, RBM20, MYBPC3, MYH7, TNNT2 and TNNI3. We summarized and extensively reviewed all studies that passed selection criteria and performed a meta-analysis on key phenotypic parameters. Together, 48 studies with 8097 patients were included. Furthermore, we reviewed recent studies investigating genotype-phenotype associations in DCM patients with TTN mutations. The average frequency of mutations in the investigated genes was between 1 and 5 %. The mean age of DCM onset was the beginning of the fifth decade for all genes. Heart transplantation (HTx) rate was highest in LMNA mutation carriers (27 %), while RBM20 mutation carriers were transplanted at a markedly younger age (mean 28.5 years). While 73 % of DCM patients with LMNA mutations showed cardiac conduction diseases, low voltage was the reported ECG hallmark in PLN mutation carriers. The frequency of ventricular arrhythmia in DCM patients with LMNA (50 %) and PLN (43 %) mutations was significantly higher. The penetrance of DCM phenotype in subjects with TTN truncating variants increased with age and reached 100 % by age of 70. A pooled analysis of available genotype-phenotype data shows a higher prevalence of sudden cardiac death (SCD), cardiac transplantation, or ventricular arrhythmias in LMNA and PLN mutation carriers compared to sarcomeric gene mutations. This study will further support the clinical interpretation of genetic findings.

@Article{Alles2017,
  author       = {Alles, Julia and Ludwig, Nicole and Rheinheimer, Stefanie and Leidinger, Petra and Grässer, Friedrich A and Keller, Andreas and Meese, Eckart},
  title        = {MiR-148a impairs Ras/ERK signaling in B lymphocytes by targeting SOS proteins.},
  journal      = {Oncotarget},
  year         = {2017},
  volume       = {8},
  pages        = {56417--56427},
  month        = aug,
  issn         = {1949-2553},
  abstract     = {Although microRNAs have been recognized as central cellular regulators, there is an evident lack of knowledge about their targets. Here, we analyzed potential target genes for miR-148a functioning in Ras signaling in B cells, including SOS1 and SOS2. A dual-luciferase reporter assay showed significantly decreased luciferase activity upon ectopic overexpression of miR-148a in HEK-293T cells that were co-transfected with the 3'UTR of either SOS1 or SOS2. Each of the 3'UTRs of SOS1 and SOS2 contained two binding sites for miR-148a both of which were necessary for the decreased luciferase activity. MiR-148a overexpression in HEK-293T lead to significantly reduced levels of both endogenous SOS1 and SOS2 proteins. Likewise, reduced levels of SOS proteins were found in two B cell lines that were transfected with miR-148a. The level of ERK1/2 phosphorylation as one of the most relevant downstream members of the Ras/ERK signaling pathway was also reduced in cells with miR-148a overexpression. The data show that miR-148a impairs the Ras/ERK signaling pathway via SOS1 and SOS2 proteins in B cells.},
  completed    = {2017-09-25},
  country      = {United States},
  doi          = {10.18632/oncotarget.17662},
  issn-linking = {1949-2553},
  issue        = {34},
  keywords     = {B cells; ERK; SOS; miR-148a; microRNA},
  nlm-id       = {101532965},
  owner        = {NLM},
  pii          = {17662},
  pmc          = {PMC5593572},
  pmid         = {28915601},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2017-09-25},
}

Although microRNAs have been recognized as central cellular regulators, there is an evident lack of knowledge about their targets. Here, we analyzed potential target genes for miR-148a functioning in Ras signaling in B cells, including SOS1 and SOS2. A dual-luciferase reporter assay showed significantly decreased luciferase activity upon ectopic overexpression of miR-148a in HEK-293T cells that were co-transfected with the 3'UTR of either SOS1 or SOS2. Each of the 3'UTRs of SOS1 and SOS2 contained two binding sites for miR-148a both of which were necessary for the decreased luciferase activity. MiR-148a overexpression in HEK-293T lead to significantly reduced levels of both endogenous SOS1 and SOS2 proteins. Likewise, reduced levels of SOS proteins were found in two B cell lines that were transfected with miR-148a. The level of ERK1/2 phosphorylation as one of the most relevant downstream members of the Ras/ERK signaling pathway was also reduced in cells with miR-148a overexpression. The data show that miR-148a impairs the Ras/ERK signaling pathway via SOS1 and SOS2 proteins in B cells.

@Article{Keller2017a,
  author       = {Keller, Andreas and Rounge, Trine and Backes, Christina and Ludwig, Nicole and Gislefoss, Randi and Leidinger, Petra and Langseth, Hilde and Meese, Eckart},
  title        = {Sources to variability in circulating human miRNA signatures.},
  journal      = {RNA biology},
  year         = {2017},
  volume       = {14},
  pages        = {1791--1798},
  month        = dec,
  issn         = {1555-8584},
  abstract     = {An increasing number of studies propose circulating microRNAs (miRNAs) as biomarkers for a large number of human diseases including cancer, cardiovascular diseases, neurologic pathologies and others. To further validate miRNA as biomarkers it is indispensable to understand the variability of circulating miRNAs in healthy individuals. We determined the longitudinal miRNomes of 90 serum samples from the Janus Serum Bank in Norway, which have been stored between 23 and 40 y at -25 °Celsius. We profiled 3 serum samples with microarrays for 30 individuals, each. For each individual the samples were collected with a time interval of approximately 5 y. This design allowed insights into inter-individual variability, age dependent miRNA variability and the impact of storage length and pre-processing. A significant proportion of the miRNome was affected by the age of the blood donor and a not negligible, albeit small, part of the miRNome by the storage time. A substantial part of miRNAs was differentially abundant between individuals, independent of the time when samples were collected. Stepwise filtering of the 529 miRNAs that were detected in the serum samples showed 168 miRNAs with differential abundance depending on the time point analyzed, 56 miRNAs differentially abundant between individuals, and 169 miRNAs with an abundance depending on the sampling procedure. While these groups of miRNAs contain generally interesting and biologically important miRNAs, the remaining 135 miRNAs constitute very promising biomarker candidates as they show an overall low variability between healthy individuals, a likewise overall low variability across a longer life span, and a high independence of the sampling process and the storage length.},
  country      = {United States},
  doi          = {10.1080/15476286.2017.1367888},
  issn-linking = {1547-6286},
  issue        = {12},
  keywords     = {circulating biomarkers; control signatures; miRNA; serum},
  nlm-id       = {101235328},
  owner        = {NLM},
  pmc          = {PMC5731815},
  pmid         = {28820329},
  pubmodel     = {Print-Electronic},
  pubstatus    = {ppublish},
  revised      = {2017-12-20},
}

An increasing number of studies propose circulating microRNAs (miRNAs) as biomarkers for a large number of human diseases including cancer, cardiovascular diseases, neurologic pathologies and others. To further validate miRNA as biomarkers it is indispensable to understand the variability of circulating miRNAs in healthy individuals. We determined the longitudinal miRNomes of 90 serum samples from the Janus Serum Bank in Norway, which have been stored between 23 and 40 y at -25 °Celsius. We profiled 3 serum samples with microarrays for 30 individuals, each. For each individual the samples were collected with a time interval of approximately 5 y. This design allowed insights into inter-individual variability, age dependent miRNA variability and the impact of storage length and pre-processing. A significant proportion of the miRNome was affected by the age of the blood donor and a not negligible, albeit small, part of the miRNome by the storage time. A substantial part of miRNAs was differentially abundant between individuals, independent of the time when samples were collected. Stepwise filtering of the 529 miRNAs that were detected in the serum samples showed 168 miRNAs with differential abundance depending on the time point analyzed, 56 miRNAs differentially abundant between individuals, and 169 miRNAs with an abundance depending on the sampling procedure. While these groups of miRNAs contain generally interesting and biologically important miRNAs, the remaining 135 miRNAs constitute very promising biomarker candidates as they show an overall low variability between healthy individuals, a likewise overall low variability across a longer life span, and a high independence of the sampling process and the storage length.

@Article{Belkacemi2017,
  author          = {Belkacemi, Thabet and Niermann, Alexander and Hofmann, Laura and Wissenbach, Ulrich and Birnbaumer, Lutz and Leidinger, Petra and Backes, Christina and Meese, Eckart and Keller, Andreas and Bai, Xianshu and Scheller, Anja and Kirchhoff, Frank and Philipp, Stephan E and Weissgerber, Petra and Flockerzi, Veit and Beck, Andreas},
  title           = {TRPC1- and TRPC3-dependent Ca, javax.xml.bind.JAXBElement@c75b5d8, signaling in mouse cortical astrocytes affects injury-evoked astrogliosis in vivo.},
  journal         = {Glia},
  year            = {2017},
  volume          = {65},
  pages           = {1535--1549},
  month           = sep,
  issn            = {1098-1136},
  abstract        = {Following brain injury astrocytes change into a reactive state, proliferate and grow into the site of lesion, a process called astrogliosis, initiated and regulated by changes in cytoplasmic Ca  . Transient receptor potential canonical (TRPC) channels may contribute to Ca  influx but their presence and possible function in astrocytes is not known. By RT-PCR and RNA sequencing we identified transcripts of Trpc1, Trpc2, Trpc3, and Trpc4 in FACS-sorted glutamate aspartate transporter (GLAST)-positive cultured mouse cortical astrocytes and subcloned full-length Trpc1 and Trpc3 cDNAs from these cells. Ca  entry in cortical astrocytes depended on TRPC3 and was increased in the absence of Trpc1. After co-expression of Trpc1 and Trpc3 in HEK-293 cells both proteins co-immunoprecipitate and form functional heteromeric channels, with TRPC1 reducing TRPC3 activity. In vitro, lack of Trpc3 reduced astrocyte proliferation and migration whereas the TRPC3 gain-of-function moonwalker mutation and Trpc1 deficiency increased astrocyte migration. In vivo, astrogliosis and cortex edema following stab wound injury were reduced in Trpc3  but increased in Trpc1  mice. In summary, our results show a decisive contribution of TRPC3 to astrocyte Ca  signaling, which is even augmented in the absence of Trpc1, in particular following brain injury. Targeted therapies to reduce TRPC3 channel activity in astrocytes might therefore be beneficial in traumatic brain injury.},
  chemicals       = {TRPC Cation Channels, TRPC3 cation channel, Trpc5 protein, mouse, Trpc6 protein, mouse, transient receptor potential cation channel, subfamily C, member 1},
  citation-subset = {IM},
  completed       = {2018-04-12},
  country         = {United States},
  doi             = {10.1002/glia.23180},
  issn-linking    = {0894-1491},
  issue           = {9},
  keywords        = {Animals; Astrocytes, metabolism, pathology; Brain Edema, etiology, metabolism, pathology; Calcium Signaling, physiology; Cell Movement, physiology; Cell Proliferation, physiology; Cerebral Cortex, injuries, metabolism, pathology; Disease Models, Animal; Gliosis, etiology, metabolism, pathology; HEK293 Cells; Humans; Male; Mice, 129 Strain; Mice, Inbred C57BL; Mice, Knockout; TRPC Cation Channels, genetics, metabolism; Wounds, Stab, metabolism, pathology; glia; ion channels; membrane currents; migration; proliferation; stab wound injury},
  mid             = {NIHMS881833},
  nlm-id          = {8806785},
  owner           = {NLM},
  pmc             = {PMC5526095},
  pmid            = {28636132},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-05-17},
}

Following brain injury astrocytes change into a reactive state, proliferate and grow into the site of lesion, a process called astrogliosis, initiated and regulated by changes in cytoplasmic Ca . Transient receptor potential canonical (TRPC) channels may contribute to Ca influx but their presence and possible function in astrocytes is not known. By RT-PCR and RNA sequencing we identified transcripts of Trpc1, Trpc2, Trpc3, and Trpc4 in FACS-sorted glutamate aspartate transporter (GLAST)-positive cultured mouse cortical astrocytes and subcloned full-length Trpc1 and Trpc3 cDNAs from these cells. Ca entry in cortical astrocytes depended on TRPC3 and was increased in the absence of Trpc1. After co-expression of Trpc1 and Trpc3 in HEK-293 cells both proteins co-immunoprecipitate and form functional heteromeric channels, with TRPC1 reducing TRPC3 activity. In vitro, lack of Trpc3 reduced astrocyte proliferation and migration whereas the TRPC3 gain-of-function moonwalker mutation and Trpc1 deficiency increased astrocyte migration. In vivo, astrogliosis and cortex edema following stab wound injury were reduced in Trpc3 but increased in Trpc1 mice. In summary, our results show a decisive contribution of TRPC3 to astrocyte Ca signaling, which is even augmented in the absence of Trpc1, in particular following brain injury. Targeted therapies to reduce TRPC3 channel activity in astrocytes might therefore be beneficial in traumatic brain injury.

@Article{Ludwig2017,
  author       = {Ludwig, Nicole and Becker, Meike and Schumann, Timo and Speer, Timo and Fehlmann, Tobias and Keller, Andreas and Meese, Eckart},
  title        = {Bias in recent miRBase annotations potentially associated with RNA quality issues.},
  journal      = {Scientific reports},
  year         = {2017},
  volume       = {7},
  pages        = {5162},
  month        = jul,
  issn         = {2045-2322},
  abstract     = {Although microRNAs are supposed to be stable in-vivo, degradation processes potentially blur our knowledge on the small oligonucleotides. We set to quantify the effect of degradation on microRNAs in mouse to identify causes for distorted microRNAs patterns. In liver, we found 298, 99 and 8 microRNAs whose expression significantly correlated to RNA integrity, storage time at room temperature and storage time at 4 °C, respectively. Expression levels of 226 microRNAs significantly differed between liver samples with high RNA integrity compared to liver samples with low RNA integrity by more than two-fold. Especially the 157 microRNAs with increased expression in tissue samples with low RNA integrity were most recently added to miRBase. Testing potentially confounding sources, e.g. in-vitro degraded RNA depleted of small RNAs, we detected signals for 350 microRNAs, suggesting cross-hybridization of fragmented RNAs. Therefore, we conclude that especially microRNAs added in the latest miRBase versions might be artefacts due to RNA degradation. The results facilitate differentiation between degradation-resilient microRNAs, degradation-sensitive microRNAs, and likely erroneously annotated microRNAs. The latter were largely identified by NGS but not experimentally validated and can severely bias microRNA biomarker research and impact the value of microRNAs as diagnostic, prognostic or therapeutic tools.},
  country      = {England},
  doi          = {10.1038/s41598-017-05070-0},
  issn-linking = {2045-2322},
  issue        = {1},
  nlm-id       = {101563288},
  owner        = {NLM},
  pii          = {10.1038/s41598-017-05070-0},
  pmc          = {PMC5507985},
  pmid         = {28701729},
  pubmodel     = {Electronic},
  pubstatus    = {epublish},
  revised      = {2017-08-26},
}

Although microRNAs are supposed to be stable in-vivo, degradation processes potentially blur our knowledge on the small oligonucleotides. We set to quantify the effect of degradation on microRNAs in mouse to identify causes for distorted microRNAs patterns. In liver, we found 298, 99 and 8 microRNAs whose expression significantly correlated to RNA integrity, storage time at room temperature and storage time at 4 °C, respectively. Expression levels of 226 microRNAs significantly differed between liver samples with high RNA integrity compared to liver samples with low RNA integrity by more than two-fold. Especially the 157 microRNAs with increased expression in tissue samples with low RNA integrity were most recently added to miRBase. Testing potentially confounding sources, e.g. in-vitro degraded RNA depleted of small RNAs, we detected signals for 350 microRNAs, suggesting cross-hybridization of fragmented RNAs. Therefore, we conclude that especially microRNAs added in the latest miRBase versions might be artefacts due to RNA degradation. The results facilitate differentiation between degradation-resilient microRNAs, degradation-sensitive microRNAs, and likely erroneously annotated microRNAs. The latter were largely identified by NGS but not experimentally validated and can severely bias microRNA biomarker research and impact the value of microRNAs as diagnostic, prognostic or therapeutic tools.

@Article{Laczny2017a,
  author       = {Laczny, Cedric C and Kiefer, Christina and Galata, Valentina and Fehlmann, Tobias and Backes, Christina and Keller, Andreas},
  title        = {BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation.},
  journal      = {Nucleic acids research},
  year         = {2017},
  volume       = {45},
  pages        = {W171--W179},
  month        = jul,
  issn         = {1362-4962},
  abstract     = {Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02-95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee.},
  country      = {England},
  doi          = {10.1093/nar/gkx348},
  issn-linking = {0305-1048},
  issue        = {W1},
  nlm-id       = {0411011},
  owner        = {NLM},
  pii          = {3787850},
  pmc          = {PMC5570254},
  pmid         = {28472498},
  pubmodel     = {Print},
  pubstatus    = {ppublish},
  revised      = {2018-01-25},
}

Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02-95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee.

@Article{Kehl2017a,
  author       = {Kehl, Tim and Schneider, Lara and Schmidt, Florian and Stöckel, Daniel and Gerstner, Nico and Backes, Christina and Meese, Eckart and Keller, Andreas and Schulz, Marcel H and Lenhof, Hans-Peter},
  title        = {RegulatorTrail: a web service for the identification of key transcriptional regulators.},
  journal      = {Nucleic acids research},
  year         = {2017},
  volume       = {45},
  pages        = {W146--W153},
  month        = jul,
  issn         = {1362-4962},
  abstract     = {Transcriptional regulators such as transcription factors and chromatin modifiers play a central role in most biological processes. Alterations in their activities have been observed in many diseases, e.g. cancer. Hence, it is of utmost importance to evaluate and assess the effects of transcriptional regulators on natural and pathogenic processes. Here, we present RegulatorTrail, a web service that provides rich functionality for the identification and prioritization of key transcriptional regulators that have a strong impact on, e.g. pathological processes. RegulatorTrail offers eight methods that use regulator binding information in combination with transcriptomic or epigenomic data to infer the most influential regulators. Our web service not only provides an intuitive web interface, but also a well-documented RESTful API that allows for a straightforward integration into third-party workflows. The presented case studies highlight the capabilities of our web service and demonstrate its potential for the identification of influential regulators: we successfully identified regulators that might explain the increased malignancy in metastatic melanoma compared to primary tumors, as well as important regulators in macrophages. RegulatorTrail is freely accessible at: https://regulatortrail.bioinf.uni-sb.de/.},
  country      = {England},
  doi          = {10.1093/nar/gkx350},
  issn-linking = {0305-1048},
  issue        = {W1},
  nlm-id       = {0411011},
  owner        = {NLM},
  pii          = {3787856},
  pmc          = {PMC5570139},
  pmid         = {28472408},
  pubmodel     = {Print},
  pubstatus    = {ppublish},
  revised      = {2018-01-25},
}

Transcriptional regulators such as transcription factors and chromatin modifiers play a central role in most biological processes. Alterations in their activities have been observed in many diseases, e.g. cancer. Hence, it is of utmost importance to evaluate and assess the effects of transcriptional regulators on natural and pathogenic processes. Here, we present RegulatorTrail, a web service that provides rich functionality for the identification and prioritization of key transcriptional regulators that have a strong impact on, e.g. pathological processes. RegulatorTrail offers eight methods that use regulator binding information in combination with transcriptomic or epigenomic data to infer the most influential regulators. Our web service not only provides an intuitive web interface, but also a well-documented RESTful API that allows for a straightforward integration into third-party workflows. The presented case studies highlight the capabilities of our web service and demonstrate its potential for the identification of influential regulators: we successfully identified regulators that might explain the increased malignancy in metastatic melanoma compared to primary tumors, as well as important regulators in macrophages. RegulatorTrail is freely accessible at: https://regulatortrail.bioinf.uni-sb.de/.

@Article{Bethune2017,
  author       = {Bethune, Jörn and Kraemer, Lars and Thomsen, Ingo and Keller, Andreas and Ellinghaus, David and Franke, Andre},
  title        = {LitDB - Keeping Track of Research Papers From Your Institute Made Simple.},
  journal      = {Source code for biology and medicine},
  year         = {2017},
  volume       = {12},
  pages        = {5},
  issn         = {1751-0473},
  abstract     = {In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities. We here describe LitDB, a novel open source literature database solution for easy maintenance of publication lists assigned to various topics. In the last 2 years more than 50 users have been using LitDB at our research institute. The LitDB system is accessed via a web browser. Publications can be uploaded through direct exports from reference manager libraries or by entering PubMed IDs. Single users or user groups can track their citation counts, h-index and impact factor statistics and gain insights into the publication records of other users. It offers various visualization functions like coauthor networks and provides ways to organize publications from dedicated projects and user groups. The latter is in particular beneficial to manage publication lists of large research groups and research initiatives through a "crowd-sourcing" effort. Keeping track of papers authored and published by a research group, institute or university is an important and non-trivial task. By using a centralized web-based platform for publication management such as LitDB the compilation of project- and group-related publication lists becomes easily manageable and it is less likely that papers are forgotten along the way.},
  country      = {England},
  doi          = {10.1186/s13029-017-0065-2},
  issn-linking = {1751-0473},
  keywords     = {Citations; Database; Impact factor; Management of project-related publication lists; Open source; Web browser interface},
  nlm-id       = {101276533},
  owner        = {NLM},
  pii          = {65},
  pmc          = {PMC5361695},
  pmid         = {28344641},
  pubmodel     = {Electronic-eCollection},
  pubstatus    = {epublish},
  revised      = {2017-08-16},
}

In science peer-reviewed publications serve as an important indicator of scientific excellence and productivity. Therefore, every scientist and institution must carefully maintain and update records of their scientific publications. However, in most institutions and universities articles are often managed in a redundant file-based and non-central way. Whereas excellent reference management software packages such as Zotero, Endnote or Mendeley exist to manage bibliographies and references when writing scientific articles, we are not aware of any open source database solution keeping track of publication records from large scientific groups, entire institutions and/or universities. We here describe LitDB, a novel open source literature database solution for easy maintenance of publication lists assigned to various topics. In the last 2 years more than 50 users have been using LitDB at our research institute. The LitDB system is accessed via a web browser. Publications can be uploaded through direct exports from reference manager libraries or by entering PubMed IDs. Single users or user groups can track their citation counts, h-index and impact factor statistics and gain insights into the publication records of other users. It offers various visualization functions like coauthor networks and provides ways to organize publications from dedicated projects and user groups. The latter is in particular beneficial to manage publication lists of large research groups and research initiatives through a "crowd-sourcing" effort. Keeping track of papers authored and published by a research group, institute or university is an important and non-trivial task. By using a centralized web-based platform for publication management such as LitDB the compilation of project- and group-related publication lists becomes easily manageable and it is less likely that papers are forgotten along the way.

@Article{Werner2017,
  author          = {Werner, Tamara V and Hart, Martin and Nickels, Ruth and Kim, Yoo-Jin and Menger, Michael D and Bohle, Rainer M and Keller, Andreas and Ludwig, Nicole and Meese, Eckart},
  title           = {MiR-34a-3p alters proliferation and apoptosis of meningioma cells , javax.xml.bind.JAXBElement@3565bad6, and is directly targeting SMAD4, FRAT1 and BCL2.},
  journal         = {Aging},
  year            = {2017},
  volume          = {9},
  pages           = {932--954},
  month           = mar,
  issn            = {1945-4589},
  abstract        = {Micro (mi)RNAs are short, noncoding RNAs and deregulation of miRNAs and their targets are implicated in tumor generation and progression in many cancers. Meningiomas are mostly benign, slow growing tumors of the central nervous system with a small percentage showing a malignant phenotype.Following   prediction of potential targets of miR-34a-3p,  ,  , and   have been confirmed as targets by dual luciferase assays with co-expression of miR-34a-3p and reporter gene constructs containing the respective 3'UTRs. Disruption of the miR-34a-3p binding sites in the 3'UTRs resulted in loss of responsiveness to miR-34a-3p overexpression. In meningioma cells, overexpression of miR-34a-3p resulted in decreased protein levels of SMAD4, FRAT1 and BCL2, while inhibition of miR-34a-3p led to increased levels of these proteins as confirmed by Western blotting. Furthermore, deregulation of miR-34a-3p altered cell proliferation and apoptosis of meningioma cells  .We show that  ,   and   are direct targets of miR-34a-3p and that deregulation of miR-34a-3p alters proliferation and apoptosis of meningioma cells  . As part of their respective signaling pathways, which are known to play a role in meningioma genesis and progression, deregulation of  ,   and   might contribute to the aberrant activation of these signaling pathways leading to increased proliferation and inhibition of apoptosis in meningiomas.},
  chemicals       = {BCL2 protein, human, FRAT1 protein, human, Intracellular Signaling Peptides and Proteins, MIRN34 microRNA, human, MicroRNAs, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-bcl-2, Smad4 Protein},
  citation-subset = {IM},
  completed       = {2017-11-16},
  country         = {United States},
  doi             = {10.18632/aging.101201},
  issn-linking    = {1945-4589},
  issue           = {3},
  keywords        = {Apoptosis, genetics; Cell Line, Tumor; Cell Proliferation, genetics; Computer Simulation; Gene Expression Regulation, Neoplastic; Humans; Intracellular Signaling Peptides and Proteins, genetics, metabolism; Meningeal Neoplasms, genetics, metabolism, pathology; Meningioma, genetics, metabolism, pathology; MicroRNAs, genetics, metabolism; Proto-Oncogene Proteins, genetics, metabolism; Proto-Oncogene Proteins c-bcl-2, genetics, metabolism; Signal Transduction, genetics; Smad4 Protein, genetics, metabolism; BCL2; FRAT1; SMAD4; meningioma; miR-34a-3p},
  nlm-id          = {101508617},
  owner           = {NLM},
  pii             = {101201},
  pmc             = {PMC5391240},
  pmid            = {28340489},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2017-11-28},
}

Micro (mi)RNAs are short, noncoding RNAs and deregulation of miRNAs and their targets are implicated in tumor generation and progression in many cancers. Meningiomas are mostly benign, slow growing tumors of the central nervous system with a small percentage showing a malignant phenotype.Following prediction of potential targets of miR-34a-3p, , , and have been confirmed as targets by dual luciferase assays with co-expression of miR-34a-3p and reporter gene constructs containing the respective 3'UTRs. Disruption of the miR-34a-3p binding sites in the 3'UTRs resulted in loss of responsiveness to miR-34a-3p overexpression. In meningioma cells, overexpression of miR-34a-3p resulted in decreased protein levels of SMAD4, FRAT1 and BCL2, while inhibition of miR-34a-3p led to increased levels of these proteins as confirmed by Western blotting. Furthermore, deregulation of miR-34a-3p altered cell proliferation and apoptosis of meningioma cells .We show that , and are direct targets of miR-34a-3p and that deregulation of miR-34a-3p alters proliferation and apoptosis of meningioma cells . As part of their respective signaling pathways, which are known to play a role in meningioma genesis and progression, deregulation of , and might contribute to the aberrant activation of these signaling pathways leading to increased proliferation and inhibition of apoptosis in meningiomas.

@Article{Fischer2017,
  author          = {Fischer, Ulrike and Kim, Ella and Keller, Andreas and Meese, Eckart},
  title           = {Specific amplifications and copy number decreases during human neural stem cells differentiation towards astrocytes, neurons and oligodendrocytes.},
  journal         = {Oncotarget},
  year            = {2017},
  volume          = {8},
  pages           = {25872--25884},
  month           = apr,
  issn            = {1949-2553},
  abstract        = {There is growing evidence that gene amplifications are an attribute of normal cells during development and differentiation. During neural progenitor cell differentiation half of the genome is involved in amplification process. To answer the question how specific amplifications occur at different stages and in different lineages of differentiation we analyzed the genes CDK4, MDM2, EGFR, GINS2, GFAP, TP53, DDB1 and MDM4 in human neural stem cells that were induced to differentiate towards astrocytes, neurons and oligodendrocytes. We found specific amplification pattern for each of the eight analyzed genes both in undifferentiated neural stem and progenitor cells and in cells that were induced for differentiation. Different amplification patterns were also found between adherently grown neural stem cells and cells that were grown as spheres. The most frequently amplified genes were MDM2 and CDK4 with the latter amplified in all three lineages at all analyzed stages. Amplification of the analyzed genes was also found in four glioma stem-like cells. The combined amplification data of stem cells and of tumor stem cells can help to define cell populations at the origin of the tumor. Furthermore, we detected a decrease of gene copies at specific differentiation stages most frequently for MDM4. This study shows specific amplification pattern in defined stem cell populations within specific time windows during differentiation processes indicating that amplifications occur in an orderly sequence during the differentiation of human neural stem and progenitor cells.},
  chemicals       = {Biomarkers, DDB1 protein, human, DNA-Binding Proteins, MDM4 protein, human, Nuclear Proteins, Proto-Oncogene Proteins, Proto-Oncogene Proteins c-mdm2, Cyclin-Dependent Kinase 4},
  citation-subset = {IM},
  completed       = {2018-03-05},
  country         = {United States},
  doi             = {10.18632/oncotarget.15980},
  issn-linking    = {1949-2553},
  issue           = {16},
  keywords        = {Astrocytes, cytology, metabolism; Biomarkers; Cell Differentiation, genetics; Cyclin-Dependent Kinase 4, genetics; DNA-Binding Proteins, genetics; Gene Amplification; Gene Dosage; Glioma, genetics; Humans; In Situ Hybridization, Fluorescence; Neural Stem Cells, cytology, metabolism; Neurons, cytology, metabolism; Nuclear Proteins, genetics; Oligodendroglia, cytology, metabolism; Proto-Oncogene Proteins, genetics; Proto-Oncogene Proteins c-mdm2, genetics; CDK4; EGFR; MDM2; Neuroscience; astrocytes; gene amplification},
  nlm-id          = {101532965},
  owner           = {NLM},
  pii             = {15980},
  pmc             = {PMC5432223},
  pmid            = {28415661},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2018-03-05},
}

There is growing evidence that gene amplifications are an attribute of normal cells during development and differentiation. During neural progenitor cell differentiation half of the genome is involved in amplification process. To answer the question how specific amplifications occur at different stages and in different lineages of differentiation we analyzed the genes CDK4, MDM2, EGFR, GINS2, GFAP, TP53, DDB1 and MDM4 in human neural stem cells that were induced to differentiate towards astrocytes, neurons and oligodendrocytes. We found specific amplification pattern for each of the eight analyzed genes both in undifferentiated neural stem and progenitor cells and in cells that were induced for differentiation. Different amplification patterns were also found between adherently grown neural stem cells and cells that were grown as spheres. The most frequently amplified genes were MDM2 and CDK4 with the latter amplified in all three lineages at all analyzed stages. Amplification of the analyzed genes was also found in four glioma stem-like cells. The combined amplification data of stem cells and of tumor stem cells can help to define cell populations at the origin of the tumor. Furthermore, we detected a decrease of gene copies at specific differentiation stages most frequently for MDM4. This study shows specific amplification pattern in defined stem cell populations within specific time windows during differentiation processes indicating that amplifications occur in an orderly sequence during the differentiation of human neural stem and progenitor cells.

@Article{Fehlmann2017b,
  author       = {Fehlmann, Tobias and Meese, Eckart and Keller, Andreas},
  title        = {Exploring ncRNAs in Alzheimer's disease by miRMaster.},
  journal      = {Oncotarget},
  year         = {2017},
  volume       = {8},
  pages        = {3771--3772},
  month        = jan,
  issn         = {1949-2553},
  country      = {United States},
  doi          = {10.18632/oncotarget.14054},
  issn-linking = {1949-2553},
  issue        = {3},
  keywords     = {NGS; miRNA; microRNA; nc-RNA},
  nlm-id       = {101532965},
  owner        = {NLM},
  pii          = {14054},
  pmc          = {PMC5354793},
  pmid         = {28030833},
  pubmodel     = {Print},
  pubstatus    = {ppublish},
  revised      = {2017-04-25},
}

@Article{Backes2017,
  author          = {Backes, Christina and Kehl, Tim and Stöckel, Daniel and Fehlmann, Tobias and Schneider, Lara and Meese, Eckart and Lenhof, Hans-Peter and Keller, Andreas},
  title           = {miRPathDB: a new dictionary on microRNAs and target pathways.},
  journal         = {Nucleic acids research},
  year            = {2017},
  volume          = {45},
  pages           = {D90--D96},
  month           = jan,
  issn            = {1362-4962},
  abstract        = {In the last decade, miRNAs and their regulatory mechanisms have been intensively studied and many tools for the analysis of miRNAs and their targets have been developed. We previously presented a dictionary on single miRNAs and their putative target pathways. Since then, the number of miRNAs has tripled and the knowledge on miRNAs and targets has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs, their target genes and related pathways. Here, we introduce the miRNA Pathway Dictionary Database (miRPathDB), freely accessible at https://mpd.bioinf.uni-sb.de/ With the database we aim to complement available target pathway web-servers by providing researchers easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific these regulations are. The database contains a large number of miRNAs (2595 human miRNAs), different miRNA target sets (14 773 experimentally validated target genes as well as 19 281 predicted targets genes) and a broad selection of functional biochemical categories (KEGG-, WikiPathways-, BioCarta-, SMPDB-, PID-, Reactome pathways, functional categories from gene ontology (GO), protein families from Pfam and chromosomal locations totaling 12 875 categories). In addition to Homo sapiens, also Mus musculus data are stored and can be compared to human target pathways.},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-07-10},
  country         = {England},
  doi             = {10.1093/nar/gkw926},
  issn-linking    = {0305-1048},
  issue           = {D1},
  keywords        = {Animals; Databases, Nucleic Acid; Gene Expression Regulation; Humans; Mice; MicroRNAs, metabolism},
  nlm-id          = {0411011},
  owner           = {NLM},
  pii             = {gkw926},
  pmc             = {PMC5210630},
  pmid            = {27742822},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-07-13},
}

In the last decade, miRNAs and their regulatory mechanisms have been intensively studied and many tools for the analysis of miRNAs and their targets have been developed. We previously presented a dictionary on single miRNAs and their putative target pathways. Since then, the number of miRNAs has tripled and the knowledge on miRNAs and targets has grown substantially. This, along with changes in pathway resources such as KEGG, leads to an improved understanding of miRNAs, their target genes and related pathways. Here, we introduce the miRNA Pathway Dictionary Database (miRPathDB), freely accessible at https://mpd.bioinf.uni-sb.de/ With the database we aim to complement available target pathway web-servers by providing researchers easy access to the information which pathways are regulated by a miRNA, which miRNAs target a pathway and how specific these regulations are. The database contains a large number of miRNAs (2595 human miRNAs), different miRNA target sets (14 773 experimentally validated target genes as well as 19 281 predicted targets genes) and a broad selection of functional biochemical categories (KEGG-, WikiPathways-, BioCarta-, SMPDB-, PID-, Reactome pathways, functional categories from gene ontology (GO), protein families from Pfam and chromosomal locations totaling 12 875 categories). In addition to Homo sapiens, also Mus musculus data are stored and can be compared to human target pathways.

@Article{Pichler2017,
  author          = {Pichler, Sabrina and Gu, Wei and Hartl, Daniela and Gasparoni, Gilles and Leidinger, Petra and Keller, Andreas and Meese, Eckart and Mayhaus, Manuel and Hampel, Harald and Riemenschneider, Matthias},
  title           = {The miRNome of Alzheimer's disease: consistent downregulation of the miR-132/212 cluster.},
  journal         = {Neurobiology of aging},
  year            = {2017},
  volume          = {50},
  pages           = {167.e1--167.e10},
  month           = feb,
  issn            = {1558-1497},
  abstract        = {MicroRNAs (miRNAs) are small noncoding RNA molecules, with essential functions in RNA silencing and post-transcriptional regulation of gene expression. miRNAs appear to regulate the development and function of the nervous system. Alterations of miRNA expression have been associated with Alzheimer's disease (AD). To characterize the AD miRNA signature, we examined genome-wide miRNA and mRNA expression patterns in the temporal cortex of AD and control samples. We validated our miRNA results by semiquantitative real-time polymerase chain reaction (PCR) in independent prefrontal cortex. Furthermore, we separated gray and white matter brain sections to identify the cellular origin of the altered miRNA expression. We observed genome-wide downregulation of hsa-miR-132-3p and hsa-miR-212-3p in AD with a stronger decrease in gray matter AD samples. We further identified 10 differently expressed transcripts achieving genome-wide levels of significance. Significantly deregulated miRNAs and mRNAs were correlated and examined for potential binding sites (in silico). This miRNome-wide study in AD provides supportive evidence and corroborates an important contribution of miR-132/212 and corresponding target mRNAs to the pathogenesis of AD.},
  chemicals       = {MIRN132 microRNA, human, MIRN212 microRNA, human, MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-10-06},
  country         = {United States},
  doi             = {10.1016/j.neurobiolaging.2016.09.019},
  issn-linking    = {0197-4580},
  keywords        = {Aged; Aged, 80 and over; Alzheimer Disease, genetics; Binding Sites; Down-Regulation; Female; Gene Expression; Genome-Wide Association Study; Gray Matter, metabolism; Humans; Male; MicroRNAs, genetics, metabolism; Multigene Family, genetics; Alzheimer's disease; Hsa-miR-132; Hsa-miR-212; Human cortical brain tissue; mRNA; microRNA},
  nlm-id          = {8100437},
  owner           = {NLM},
  pii             = {S0197-4580(16)30233-0},
  pmid            = {27816213},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-10-06},
}

MicroRNAs (miRNAs) are small noncoding RNA molecules, with essential functions in RNA silencing and post-transcriptional regulation of gene expression. miRNAs appear to regulate the development and function of the nervous system. Alterations of miRNA expression have been associated with Alzheimer's disease (AD). To characterize the AD miRNA signature, we examined genome-wide miRNA and mRNA expression patterns in the temporal cortex of AD and control samples. We validated our miRNA results by semiquantitative real-time polymerase chain reaction (PCR) in independent prefrontal cortex. Furthermore, we separated gray and white matter brain sections to identify the cellular origin of the altered miRNA expression. We observed genome-wide downregulation of hsa-miR-132-3p and hsa-miR-212-3p in AD with a stronger decrease in gray matter AD samples. We further identified 10 differently expressed transcripts achieving genome-wide levels of significance. Significantly deregulated miRNAs and mRNAs were correlated and examined for potential binding sites (in silico). This miRNome-wide study in AD provides supportive evidence and corroborates an important contribution of miR-132/212 and corresponding target mRNAs to the pathogenesis of AD.

@Article{pmid27895807,
   Author="Fehlmann, T.  and Reinheimer, S.  and Geng, C.  and Su, X.  and Drmanac, S.  and Alexeev, A.  and Zhang, C.  and Backes, C.  and Ludwig, N.  and Hart, M.  and An, D.  and Zhu, Z.  and Xu, C.  and Chen, A.  and Ni, M.  and Liu, J.  and Li, Y.  and Poulter, M.  and Li, Y.  and Stahler, C.  and Drmanac, R.  and Xu, X.  and Meese, E.  and Keller, A. ",
   Title="{c{P}{A}{S}-based sequencing on the {B}{G}{I}{S}{E}{Q}-500 to explore small non-coding {R}{N}{A}s}",
   Journal="Clin Epigenetics",
   Year="2016",
   Volume="8",
   Pages="123"
}

@Article{pmid27987355,
   Author="Kappel, A.  and Keller, A. ",
   Title="{mi{R}{N}{A} assays in the clinical laboratory: {W}orkflow, detection technologies and automation aspects}",
   Journal="Clin. Chem. Lab. Med.",
   Year="2016",
   Month="Dec"
}

@Article{pmid27497711,
   Author="Meder, B.  and Katus, H. A.  and Keller, A. ",
   Title="{{C}omputational {C}ardiology - {A} {N}ew {D}iscipline of {T}ranslational {R}esearch}",
   Journal="Genomics Proteomics Bioinformatics",
   Year="2016",
   Volume="14",
   Number="4",
   Pages="177--178",
   Month="Aug"
}

@Article{pmid27687236,
   Author="Fehlmann, T.  and Ludwig, N.  and Backes, C.  and Meese, E.  and Keller, A. ",
   Title="{{D}istribution of micro{R}{N}{A} biomarker candidates in solid tissues and body fluids}",
   Journal="RNA Biol",
   Year="2016",
   Volume="13",
   Number="11",
   Pages="1084--1088",
   Month="Nov"
}

@Article{pmid27588394,
   Author="Backes, C.  and Ludwig, N.  and Leidinger, P.  and Huwer, H.  and Tenzer, S.  and Fehlmann, T.  and Franke, A.  and Meese, E.  and Lenhof, H. P.  and Keller, A. ",
   Title="{{P}aired proteomics, transcriptomics and mi{R}{N}omics in non-small cell lung cancers: known and novel signaling cascades}",
   Journal="Oncotarget",
   Year="2016",
   Pages=" ",
   Month="Aug"
}

@Article{pmid27456854,
   Author="Hecksteden, A.  and Leidinger, P.  and Backes, C.  and Rheinheimer, S.  and Pfeiffer, M.  and Ferrauti, A.  and Kellmann, M.  and Sedaghat, F.  and Meder, B.  and Meese, E.  and Meyer, T.  and Keller, A. ",
   Title="{mi{R}{N}{A}s and sports: tracking training status and potentially confounding diagnoses}",
   Journal="J Transl Med",
   Year="2016",
   Volume="14",
   Number="1",
   Pages="219"
}

@Article{pmid27429792,
   Author="Zur Bruegge, J.  and Backes, C.  and Golz, G.  and Hemmrich-Stanisak, G.  and Scharek-Tedin, L.  and Franke, A.  and Alter, T.  and Einspanier, R.  and Keller, A.  and Sharbati, S. ",
   Title="{{M}icro{R}{N}{A} {R}esponse of {P}rimary {H}uman {M}acrophages to {A}rcobacter {B}utzleri {I}nfection}",
   Journal="Eur. J. Microbiol. Immunol.",
   Year="2016",
   Volume="6",
   Number="2",
   Pages="99--108",
   Month="Jun"
}

@Article{pmid27144431,
   Author="Hart, M.  and Rheinheimer, S.  and Leidinger, P.  and Backes, C.  and Menegatti, J.  and Fehlmann, T.  and Grasser, F.  and Keller, A.  and Meese, E. ",
   Title="{{I}dentification of mi{R}-34a-target interactions by a combined network based and experimental approach}",
   Journal="Oncotarget",
   Year="2016",
   Pages=" ",
   Month="Apr"
}

@Article{pmid27094127,
   Author="Bhat, S. S.  and Friedmann, K. S.  and Knorck, A.  and Hoxha, C.  and Leidinger, P.  and Backes, C.  and Meese, E.  and Keller, A.  and Rettig, J.  and Hoth, M.  and Qu, B.  and Schwarz, E. C. ",
   Title="{{S}yntaxin 8 is required for efficient lytic granule trafficking in cytotoxic {T} lymphocytes}",
   Journal="Biochim. Biophys. Acta",
   Year="2016",
   Volume="1863",
   Number="7 Pt A",
   Pages="1653--1664",
   Month="Apr"
}

@Article{pmid27131362,
   Author="Backes, C.  and Khaleeq, Q. T.  and Meese, E.  and Keller, A. ",
   Title="{mi{E}{A}{A}: micro{R}{N}{A} enrichment analysis and annotation}",
   Journal="Nucleic Acids Res.",
   Year="2016",
   Pages=" ",
   Month="Apr"
}

@Article{pmid27089332,
   Author="Hamberg, M.  and Backes, C.  and Fehlmann, T.  and Hart, M.  and Meder, B.  and Meese, E.  and Keller, A. ",
   Title="{mi{R}{T}arget{L}ink-mi{R}{N}{A}s, {G}enes and {I}nteraction {N}etworks}",
   Journal="Int J Mol Sci",
   Year="2016",
   Volume="17",
   Number="4",
   Pages=" "
}

@Article{pmid27043538,
   Author="Ludwig, N.  and Werner, T. V.  and Backes, C.  and Trampert, P.  and Gessler, M.  and Keller, A.  and Lenhof, H. P.  and Graf, N.  and Meese, E. ",
   Title="{{C}ombining mi{R}{N}{A} and m{R}{N}{A} {E}xpression {P}rofiles in {W}ilms {T}umor {S}ubtypes}",
   Journal="Int J Mol Sci",
   Year="2016",
   Volume="17",
   Number="4",
   Pages=" "
}

@Article{pmid27153685,
   Author="Mueller, S. C.  and Backes, C.  and Gress, A.  and Baumgarten, N.  and Kalinina, O. V.  and Moll, A.  and Kohlbacher, O.  and Meese, E.  and Keller, A. ",
   Title="{{B}{A}{L}{L}-{S}{N}{P}gp-from genetic variants toward computational diagnostics}",
   Journal="Bioinformatics",
   Year="2016",
   Pages=" ",
   Month="Feb"
}

@Article{pmid27150811,
   Author="Gress, A.  and Ramensky, V.  and Buch, J.  and Keller, A.  and Kalinina, O. V. ",
   Title="{{S}truct{M}{A}n: annotation of single-nucleotide polymorphisms in the structural context}",
   Journal="Nucleic Acids Res.",
   Year="2016",
   Pages=" ",
   Month="May"
}

@Article{pmid26930711,
   Author="Tenzer, S.  and Leidinger, P.  and Backes, C.  and Huwer, H.  and Hildebrandt, A.  and Lenhof, H. P.  and Wesse, T.  and Franke, A.  and Meese, E.  and Keller, A. ",
   Title="{{I}ntegrated quantitative proteomic and transcriptomic analysis of lung tumor and control tissue: a lung cancer showcase}",
   Journal="Oncotarget",
   Year="2016",
   Pages=" ",
   Month="Feb"
}

@Article{pmid26831660,
   Author="Leidinger, P.  and Hart, M.  and Backes, C.  and Rheinheimer, S.  and Keck, B.  and Wullich, B.  and Keller, A.  and Meese, E. ",
   Title="{{D}ifferential blood-based diagnosis between benign prostatic hyperplasia and prostate cancer: mi{R}{N}{A} as source for biomarkers independent of {P}{S}{A} level, {G}leason score, or {T}{N}{M} status}",
   Journal="Tumour Biol.",
   Year="2016",
   Pages=" ",
   Month="Jan"
}

@Article{pmid26760198,
   Author="Backes, C.  and Sedaghat-Hamedani, F.  and Frese, K.  and Hart, M.  and Ludwig, N.  and Meder, B.  and Meese, E.  and Keller, A. ",
   Title="{{B}ias in {H}igh-{T}hroughput {A}nalysis of mi{R}{N}{A}s and {I}mplications for {B}iomarker {S}tudies}",
   Journal="Anal. Chem.",
   Year="2016",
   Pages=" ",
   Month="Jan"
}

@Article{pmid26787660,
   Author="Stoeckel, D.  and Kehl, T.  and Trampert, P.  and Schneider, L.  and Backes, C.  and Ludwig, N.  and Gerasch, A.  and Kaufmann, M.  and Gessler, M.  and Graf, N.  and Meese, E.  and Keller, A.  and Lenhof, H. P. ",
   Title="{{M}ulti-omics {E}nrichment {A}nalysis using the {G}ene{T}rail2 {W}eb {S}ervice}",
   Journal="Bioinformatics",
   Year="2016",
   Pages=" ",
   Month="Jan"
}

@Article{pmid26829645,
   Author="Marx, Alexander  and Backes, Christina  and Meese, Eckart  and Lenhof, Hans-Peter  and Keller, Andreas",
   Title="{{E}{D}{I}{S}{O}{N}-{W}{M}{W}: {E}xact {D}ynamic {P}rograming {S}olution of the {W}ilcoxon-{M}ann-{W}hitney {T}est}",
   Journal="Genomics Proteomics Bioinformatics",
   Year="2016",
   Volume="14",
   Number="1",
   Pages="55--61",
   Month="Feb"
}

@Article{Abu-Halima2016,
  author          = {Abu-Halima, Masood and Ludwig, Nicole and Hart, Martin and Leidinger, Petra and Backes, Christina and Keller, Andreas and Hammadeh, Mohamad and Meese, Eckart},
  title           = {Altered micro-ribonucleic acid expression profiles of extracellular microvesicles in the seminal plasma of patients with oligoasthenozoospermia.},
  journal         = {Fertility and sterility},
  year            = {2016},
  volume          = {106},
  pages           = {1061--1069.e3},
  month           = oct,
  issn            = {1556-5653},
  abstract        = {To determine whether microRNA (miRNA) expression profile is different in extracellular microvesicles collected from seminal plasma of men with oligoasthenozoospermia, to gain further insight into molecular mechanisms underlying male infertility. Microarray with quantitative real-time polymerase chain reaction validation and Western blot analysis confirmation. University research and clinical institutes. A total of 24 men, including 12 oligoasthenozoospermic subfertile men and 12 normozoospermic men. None. Statistically significant altered miRNA expression profiles in oligoasthenozoospermic subfertile men compared with normozoospermic fertile men. Extracellular microvesicles including exosomes were isolated from seminal plasma by ultracentrifugation. Presence of exosome-specific proteins was confirmed by Western blotting. In the extracellular microvesicles, we analyzed 1,205 miRNAs by microarray and identified 36 miRNAs with altered expression levels in oligoasthenozoospermic compared with normozoospermic fertile men. Seven miRNAs were overexpressed and 29 miRNAs were underexpressed in oligoasthenozoospermic men. Using quantitative real-time polymerase chain reaction as an independent method, we confirmed the significantly higher expression levels of miR-765 and miR-1275 and the significantly lower expression level of miR-15a in oligoasthenozoospermic subfertile men as compared with the normozoospermic men. We identified altered expression levels of miRNAs in extracellular microvesicles from seminal plasma as part of the molecular events in the male genital tract. These miRNAs may help to understand the molecular mechanisms underlying male infertility.},
  chemicals       = {Genetic Markers, MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-05-30},
  country         = {United States},
  doi             = {10.1016/j.fertnstert.2016.06.030},
  issn-linking    = {0015-0282},
  issue           = {5},
  keywords        = {Adult; Asthenozoospermia, diagnosis, genetics, physiopathology; Blotting, Western; Case-Control Studies; Cell-Derived Microparticles, genetics; Exosomes, genetics; Fertility, genetics; Gene Expression Profiling, methods; Gene Regulatory Networks; Genetic Markers; Genetic Predisposition to Disease; Germany; Humans; Male; MicroRNAs, genetics; Oligonucleotide Array Sequence Analysis; Oligospermia, diagnosis, genetics; Phenotype; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; Semen, chemistry; Transcriptome; Young Adult; Exosomes; male infertility; microRNA; seminal plasma; spermatogenesis},
  nlm-id          = {0372772},
  owner           = {NLM},
  pii             = {S0015-0282(16)61385-7},
  pmid            = {27424049},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-05-30},
}

To determine whether microRNA (miRNA) expression profile is different in extracellular microvesicles collected from seminal plasma of men with oligoasthenozoospermia, to gain further insight into molecular mechanisms underlying male infertility. Microarray with quantitative real-time polymerase chain reaction validation and Western blot analysis confirmation. University research and clinical institutes. A total of 24 men, including 12 oligoasthenozoospermic subfertile men and 12 normozoospermic men. None. Statistically significant altered miRNA expression profiles in oligoasthenozoospermic subfertile men compared with normozoospermic fertile men. Extracellular microvesicles including exosomes were isolated from seminal plasma by ultracentrifugation. Presence of exosome-specific proteins was confirmed by Western blotting. In the extracellular microvesicles, we analyzed 1,205 miRNAs by microarray and identified 36 miRNAs with altered expression levels in oligoasthenozoospermic compared with normozoospermic fertile men. Seven miRNAs were overexpressed and 29 miRNAs were underexpressed in oligoasthenozoospermic men. Using quantitative real-time polymerase chain reaction as an independent method, we confirmed the significantly higher expression levels of miR-765 and miR-1275 and the significantly lower expression level of miR-15a in oligoasthenozoospermic subfertile men as compared with the normozoospermic men. We identified altered expression levels of miRNAs in extracellular microvesicles from seminal plasma as part of the molecular events in the male genital tract. These miRNAs may help to understand the molecular mechanisms underlying male infertility.

@Article{Nietsch2016,
  author          = {Nietsch, Rouven and Haas, Jan and Lai, Alan and Oehler, Daniel and Mester, Stefan and Frese, Karen S and Sedaghat-Hamedani, Farbod and Kayvanpour, Elham and Keller, Andreas and Meder, Benjamin},
  title           = {The Role of Quality Control in Targeted Next-generation Sequencing Library Preparation.},
  journal         = {Genomics, proteomics \& bioinformatics},
  year            = {2016},
  volume          = {14},
  pages           = {200--206},
  month           = aug,
  issn            = {2210-3244},
  abstract        = {Next-generation sequencing (NGS) is getting routinely used in the diagnosis of hereditary diseases, such as human cardiomyopathies. Hence, it is of utter importance to secure high quality sequencing data, enabling the identification of disease-relevant mutations or the conclusion of negative test results. During the process of sample preparation, each protocol for target enrichment library preparation has its own requirements for quality control (QC); however, there is little evidence on the actual impact of these guidelines on resulting data quality. In this study, we analyzed the impact of QC during the diverse library preparation steps of Agilent SureSelect XT target enrichment and Illumina sequencing. We quantified the parameters for a cohort of around 600 samples, which include starting amount of DNA, amount of sheared DNA, smallest and largest fragment size of the starting DNA; amount of DNA after the pre-PCR, and smallest and largest fragment size of the resulting DNA; as well as the amount of the final library, the corresponding smallest and largest fragment size, and the number of detected variants. Intriguingly, there is a high tolerance for variations in all QC steps, meaning that within the boundaries proposed in the current study, a considerable variance at each step of QC can be well tolerated without compromising NGS quality.},
  chemicals       = {DNA},
  citation-subset = {IM},
  completed       = {2017-05-23},
  country         = {China},
  doi             = {10.1016/j.gpb.2016.04.007},
  issn-linking    = {1672-0229},
  issue           = {4},
  keywords        = {DNA, chemistry, genetics, metabolism; Gene Library; High-Throughput Nucleotide Sequencing, methods, standards; Humans; Quality Control; Sequence Analysis, DNA, methods, standards; Library preparation; Next-generation sequencing; Quality control; Sequence variants; Target enrichment},
  nlm-id          = {101197608},
  owner           = {NLM},
  pii             = {S1672-0229(16)30107-3},
  pmc             = {PMC4996852},
  pmid            = {27475404},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-02-17},
}

Next-generation sequencing (NGS) is getting routinely used in the diagnosis of hereditary diseases, such as human cardiomyopathies. Hence, it is of utter importance to secure high quality sequencing data, enabling the identification of disease-relevant mutations or the conclusion of negative test results. During the process of sample preparation, each protocol for target enrichment library preparation has its own requirements for quality control (QC); however, there is little evidence on the actual impact of these guidelines on resulting data quality. In this study, we analyzed the impact of QC during the diverse library preparation steps of Agilent SureSelect XT target enrichment and Illumina sequencing. We quantified the parameters for a cohort of around 600 samples, which include starting amount of DNA, amount of sheared DNA, smallest and largest fragment size of the starting DNA; amount of DNA after the pre-PCR, and smallest and largest fragment size of the resulting DNA; as well as the amount of the final library, the corresponding smallest and largest fragment size, and the number of detected variants. Intriguingly, there is a high tolerance for variations in all QC steps, meaning that within the boundaries proposed in the current study, a considerable variance at each step of QC can be well tolerated without compromising NGS quality.

@Article{Schwarz2016,
  author          = {Schwarz, Eva C and Backes, Christina and Knörck, Arne and Ludwig, Nicole and Leidinger, Petra and Hoxha, Cora and Schwär, Gertrud and Grossmann, Thomas and Müller, Sabine C and Hart, Martin and Haas, Jan and Galata, Valentina and Müller, Isabelle and Fehlmann, Tobias and Eichler, Hermann and Franke, Andre and Meder, Benjamin and Meese, Eckart and Hoth, Markus and Keller, Andreas},
  title           = {Deep characterization of blood cell miRNomes by NGS.},
  journal         = {Cellular and molecular life sciences : CMLS},
  year            = {2016},
  volume          = {73},
  pages           = {3169--3181},
  month           = aug,
  issn            = {1420-9071},
  abstract        = {A systematic understanding of different factors influencing cell type specific microRNA profiles is essential for state-of-the art biomarker research. We carried out a comprehensive analysis of the biological variability and changes in cell type pattern over time for different cell types and different isolation approaches in technical replicates. All combinations of the parameters mentioned above have been measured, resulting in 108 miRNA profiles that were evaluated by next-generation-sequencing. The largest miRNA variability was due to inter-individual differences (34 %), followed by the cell types (23.4 %) and the isolation technique (17.2 %). The change over time in cell miRNA composition was moderate (<3 %) being close to the technical variations (<1 %). Largest variability (including technical and biological variance) was observed for CD8 cells while CD3 and CD4 cells showed significantly lower variations. ANOVA highlighted that 51.5 % of all miRNAs were significantly influenced by the purification technique. While CD4 cells were least affected, especially miRNA profiles of CD8 cells were fluctuating depending on the cell purification approach. To provide researchers access to the profiles and to allow further analyses of the tested conditions we implemented a dynamic web resource.},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-08-03},
  country         = {Switzerland},
  doi             = {10.1007/s00018-016-2154-9},
  issn-linking    = {1420-682X},
  issue           = {16},
  keywords        = {Base Sequence; Blood Cells, metabolism; Cluster Analysis; Gene Expression Profiling, methods; High-Throughput Nucleotide Sequencing, methods; Humans; MicroRNAs, genetics, isolation & purification; Principal Component Analysis; Blood cells; FACS; Next-generation sequencing; microRNA},
  nlm-id          = {9705402},
  owner           = {NLM},
  pii             = {10.1007/s00018-016-2154-9},
  pmid            = {26874686},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-01-30},
}

A systematic understanding of different factors influencing cell type specific microRNA profiles is essential for state-of-the art biomarker research. We carried out a comprehensive analysis of the biological variability and changes in cell type pattern over time for different cell types and different isolation approaches in technical replicates. All combinations of the parameters mentioned above have been measured, resulting in 108 miRNA profiles that were evaluated by next-generation-sequencing. The largest miRNA variability was due to inter-individual differences (34 %), followed by the cell types (23.4 %) and the isolation technique (17.2 %). The change over time in cell miRNA composition was moderate (<3 %) being close to the technical variations (<1 %). Largest variability (including technical and biological variance) was observed for CD8 cells while CD3 and CD4 cells showed significantly lower variations. ANOVA highlighted that 51.5 % of all miRNAs were significantly influenced by the purification technique. While CD4 cells were least affected, especially miRNA profiles of CD8 cells were fluctuating depending on the cell purification approach. To provide researchers access to the profiles and to allow further analyses of the tested conditions we implemented a dynamic web resource.

@Article{Keller2016,
  author          = {Keller, Andreas and Backes, Christina and Haas, Jan and Leidinger, Petra and Maetzler, Walter and Deuschle, Christian and Berg, Daniela and Ruschil, Christoph and Galata, Valentina and Ruprecht, Klemens and Stähler, Cord and Würstle, Maximilian and Sickert, Daniel and Gogol, Manfred and Meder, Benjamin and Meese, Eckart},
  title           = {Validating Alzheimer's disease micro RNAs using next-generation sequencing.},
  journal         = {Alzheimer's \& dementia : the journal of the Alzheimer's Association},
  year            = {2016},
  volume          = {12},
  pages           = {565--576},
  month           = may,
  issn            = {1552-5279},
  abstract        = {Molecular biomarkers for Alzheimer's disease (AD) can support detection and improved care for patients, but novel candidates require verification. We previously reported a 12-micro RNA (miRNA) blood-based signature using next-generation sequencing (NGS) of 54 AD cases and 22 controls. We performed validation of 49 AD cases and 55 controls using NGS and also included 20 mild cognitive impairment and 90 multiple sclerosis samples to identify nonspecific markers. Thus, 103 AD cases, 77 unaffected controls, and 110 diseased controls were sequenced. Although the initial cohort came predominantly from the United States, the validation samples were collected in Germany. Five hundred eighty miRNAs were detected in the blood. In the initial cohort, we observed 203, in the validation cohort, 146 dysregulated miRNAs at a significance level of 0.05. With 68 miRNAs, the overlap was significant (P = .0003). Likewise, the area under the receiver operator characteristic curve values of the miRNAs correlated (correlation of 0.93; 95% confidence interval 0.89-0.96; P <10(-16)). MiRNAs have the potential to support AD diagnosis and patient care.},
  chemicals       = {Biomarkers, MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-10-23},
  country         = {United States},
  doi             = {10.1016/j.jalz.2015.12.012},
  issn-linking    = {1552-5260},
  issue           = {5},
  keywords        = {Aged; Alzheimer Disease, blood, genetics; Biomarkers, blood; Cognitive Dysfunction; Female; Germany; Humans; Male; MicroRNAs, blood, genetics; Sequence Analysis, methods; United States; Up-Regulation; Alzheimer's disease; Biomarker; Validation; miRNA},
  nlm-id          = {101231978},
  owner           = {NLM},
  pii             = {S1552-5260(15)03036-8},
  pmid            = {26806387},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2018-03-02},
}

Molecular biomarkers for Alzheimer's disease (AD) can support detection and improved care for patients, but novel candidates require verification. We previously reported a 12-micro RNA (miRNA) blood-based signature using next-generation sequencing (NGS) of 54 AD cases and 22 controls. We performed validation of 49 AD cases and 55 controls using NGS and also included 20 mild cognitive impairment and 90 multiple sclerosis samples to identify nonspecific markers. Thus, 103 AD cases, 77 unaffected controls, and 110 diseased controls were sequenced. Although the initial cohort came predominantly from the United States, the validation samples were collected in Germany. Five hundred eighty miRNAs were detected in the blood. In the initial cohort, we observed 203, in the validation cohort, 146 dysregulated miRNAs at a significance level of 0.05. With 68 miRNAs, the overlap was significant (P = .0003). Likewise, the area under the receiver operator characteristic curve values of the miRNAs correlated (correlation of 0.93; 95% confidence interval 0.89-0.96; P <10(-16)). MiRNAs have the potential to support AD diagnosis and patient care.

@Article{Mueller2016,
  author          = {Mueller, Sabine C and Sommer, Björn and Backes, Christina and Haas, Jan and Meder, Benjamin and Meese, Eckart and Keller, Andreas},
  title           = {From Single Variants to Protein Cascades: MULTISCALE MODELING OF SINGLE NUCLEOTIDE VARIANT SETS IN GENETIC DISORDERS.},
  journal         = {The Journal of biological chemistry},
  year            = {2016},
  volume          = {291},
  pages           = {1582--1590},
  month           = jan,
  issn            = {1083-351X},
  abstract        = {Understanding the role of genetics in disease has become a central part of medical research. Non-synonymous single nucleotide variants (nsSNVs) in coding regions of human genes frequently lead to pathological phenotypes. Beyond single variations, the individual combination of nsSNVs may add to pathogenic processes. We developed a multiscale pipeline to systematically analyze the existence of quantitative effects of multiple nsSNVs and gene combinations in single individuals on pathogenicity. Based on this pipeline, we detected in a data set of 842 nsSNVs discovered in 76 genes related to cardiomyopathies, associated nsSNV combinations in seven genes present in at least 70% of all 639 patient samples, but not in a control cohort of healthy humans. Structural analyses of these revealed primarily an influence on the protein stability. For amino acid substitutions located at the protein surface, we generally observed a proximity to putative binding pockets. To computationally analyze cumulative effects and their impact, pathogenicity methods are currently being developed. Our approach supports this process, as shown on the example of a cardiac phenotype but can be likewise applied to other diseases such as cancer. },
  chemicals       = {Proteins},
  citation-subset = {IM},
  completed       = {2016-08-22},
  country         = {United States},
  doi             = {10.1074/jbc.M115.695247},
  issn-linking    = {0021-9258},
  issue           = {4},
  keywords        = {Amino Acid Substitution; Cardiomyopathies, genetics, metabolism; Cohort Studies; Computational Biology; Gene Regulatory Networks; Genetic Diseases, Inborn, genetics, metabolism; Humans; Polymorphism, Single Nucleotide; Proteins, genetics, metabolism; bioinformatics; cardiomyopathy; computational biology; genetic polymorphism; molecular genetics},
  nlm-id          = {2985121R},
  owner           = {NLM},
  pii             = {M115.695247},
  pmc             = {PMC4722441},
  pmid            = {26601959},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-02-20},
}

Understanding the role of genetics in disease has become a central part of medical research. Non-synonymous single nucleotide variants (nsSNVs) in coding regions of human genes frequently lead to pathological phenotypes. Beyond single variations, the individual combination of nsSNVs may add to pathogenic processes. We developed a multiscale pipeline to systematically analyze the existence of quantitative effects of multiple nsSNVs and gene combinations in single individuals on pathogenicity. Based on this pipeline, we detected in a data set of 842 nsSNVs discovered in 76 genes related to cardiomyopathies, associated nsSNV combinations in seven genes present in at least 70% of all 639 patient samples, but not in a control cohort of healthy humans. Structural analyses of these revealed primarily an influence on the protein stability. For amino acid substitutions located at the protein surface, we generally observed a proximity to putative binding pockets. To computationally analyze cumulative effects and their impact, pathogenicity methods are currently being developed. Our approach supports this process, as shown on the example of a cardiac phenotype but can be likewise applied to other diseases such as cancer.

@Article{Leidinger2016,
  author          = {Leidinger, Petra and Brefort, Thomas and Backes, Christina and Krapp, Medea and Galata, Valentina and Beier, Markus and Kohlhaas, Jochen and Huwer, Hanno and Meese, Eckart and Keller, Andreas},
  title           = {High-throughput qRT-PCR validation of blood microRNAs in non-small cell lung cancer.},
  journal         = {Oncotarget},
  year            = {2016},
  volume          = {7},
  pages           = {4611--4623},
  month           = jan,
  issn            = {1949-2553},
  abstract        = {Validation of biomarkers is essential to advance the translational process to clinical application. Although there exists an increasing number of reports on small non-coding RNAs (microRNAs) as minimally-invasive markers from blood, serum or plasma, just a limited number is verified in follow-up studies. We used qRT-PCR to evaluate a known miRNA signature measured from blood that allowed for separation between patients with non-small cell lung cancer (NSCLC), COPD and healthy controls.From the data of our previous microarray studies we selected a panel of 235 miRNAs related to lung cancer and COPD. We observed a high concordance between the AUC values of our initial microarray screening and the qRT-PCR data (correlation of 0.704, p < 10-16). Overall, 90.3% of markers were successfully validated. Among the top markers that were concordant between both studies we found hsa-miR-20b-5p, hsa-miR-20a-5p, hsa-miR-17-5p, and hsa-miR-106a-5p. The qRT-PCR analysis also confirmed that non-small cell lung cancer patients could be accurately differentiated from unaffected controls: a subset of five markers was sufficient to separate NSCLC patients from unaffected controls with accuracy of 94.5% (specificity and sensitivity of 98% and 91%). Beyond differentiation from controls, we also succeeded in separating NSCLC patients from patients with COPD. MiRNAs that were identified as relevant for the separation between lung cancer and COPD by both qRT-PCR and the array-based studies included hsa-miR-26a-5p, hsa-miR-328-3p and hsa-miR-1224-3p. Although for differentiation between NSCLC patients from COPD patients more markers were required, still high accuracy rates were obtained (5 markers: 78.8%; 10 markers: 83.9%; 50 markers: 87.6%).},
  chemicals       = {Biomarkers, Tumor, MicroRNAs, RNA, Messenger},
  citation-subset = {IM},
  completed       = {2016-10-27},
  country         = {United States},
  doi             = {10.18632/oncotarget.6566},
  issn-linking    = {1949-2553},
  issue           = {4},
  keywords        = {Aged; Biomarkers, Tumor, blood, genetics; Carcinoma, Non-Small-Cell Lung, blood, genetics; Case-Control Studies; Cohort Studies; Female; Gene Expression Profiling; High-Throughput Screening Assays; Humans; Lung Neoplasms, blood, genetics; Male; MicroRNAs, blood, genetics; Middle Aged; Prognosis; Pulmonary Disease, Chronic Obstructive, blood, genetics; RNA, Messenger, genetics; Real-Time Polymerase Chain Reaction; Reverse Transcriptase Polymerase Chain Reaction; NSCLC; diagnosis; miRNA; qRT-PCR},
  nlm-id          = {101532965},
  owner           = {NLM},
  pii             = {6566},
  pmc             = {PMC4826230},
  pmid            = {26672767},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2017-02-20},
}

Validation of biomarkers is essential to advance the translational process to clinical application. Although there exists an increasing number of reports on small non-coding RNAs (microRNAs) as minimally-invasive markers from blood, serum or plasma, just a limited number is verified in follow-up studies. We used qRT-PCR to evaluate a known miRNA signature measured from blood that allowed for separation between patients with non-small cell lung cancer (NSCLC), COPD and healthy controls.From the data of our previous microarray studies we selected a panel of 235 miRNAs related to lung cancer and COPD. We observed a high concordance between the AUC values of our initial microarray screening and the qRT-PCR data (correlation of 0.704, p < 10-16). Overall, 90.3% of markers were successfully validated. Among the top markers that were concordant between both studies we found hsa-miR-20b-5p, hsa-miR-20a-5p, hsa-miR-17-5p, and hsa-miR-106a-5p. The qRT-PCR analysis also confirmed that non-small cell lung cancer patients could be accurately differentiated from unaffected controls: a subset of five markers was sufficient to separate NSCLC patients from unaffected controls with accuracy of 94.5% (specificity and sensitivity of 98% and 91%). Beyond differentiation from controls, we also succeeded in separating NSCLC patients from patients with COPD. MiRNAs that were identified as relevant for the separation between lung cancer and COPD by both qRT-PCR and the array-based studies included hsa-miR-26a-5p, hsa-miR-328-3p and hsa-miR-1224-3p. Although for differentiation between NSCLC patients from COPD patients more markers were required, still high accuracy rates were obtained (5 markers: 78.8%; 10 markers: 83.9%; 50 markers: 87.6%).

@Article{Backes2016a,
  author          = {Backes, Christina and Meder, Benjamin and Hart, Martin and Ludwig, Nicole and Leidinger, Petra and Vogel, Britta and Galata, Valentina and Roth, Patrick and Menegatti, Jennifer and Grässer, Friedrich and Ruprecht, Klemens and Kahraman, Mustafa and Grossmann, Thomas and Haas, Jan and Meese, Eckart and Keller, Andreas},
  title           = {Prioritizing and selecting likely novel miRNAs from NGS data.},
  journal         = {Nucleic acids research},
  year            = {2016},
  volume          = {44},
  pages           = {e53},
  month           = apr,
  issn            = {1362-4962},
  abstract        = {Small non-coding RNAs play a key role in many physiological and pathological processes. Since 2004, miRNA sequences have been catalogued in miRBase, which is currently in its 21st version. We investigated sequence and structural features of miRNAs annotated in the miRBase and compared them between different versions of this reference database. We have identified that the two most recent releases (v20 and v21) are influenced by next-generation sequencing based miRNA predictions and show significant deviation from miRNAs discovered prior to the high-throughput profiling period. From the analysis of miRBase, we derived a set of key characteristics to predict new miRNAs and applied the implemented algorithm to evaluate novel blood-borne miRNA candidates. We carried out 705 individual whole miRNA sequencings of blood cells and collected a total of 9.7 billion reads. Using miRDeep2 we initially predicted 1452 potentially novel miRNAs. After excluding false positives, 518 candidates remained. These novel candidates were ranked according to their distance to the features in the early miRBase versions allowing for an easier selection of a subset of putative miRNAs for validation. Selected candidates were successfully validated by qRT-PCR and northern blotting. In addition, we implemented a web-server for ranking potential miRNA candidates, which is available at:www.ccb.uni-saarland.de/novomirank. },
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2016-08-29},
  country         = {England},
  doi             = {10.1093/nar/gkv1335},
  issn-linking    = {0305-1048},
  issue           = {6},
  keywords        = {Algorithms; Base Sequence; Blood Cells, chemistry, metabolism; Blotting, Northern; Computational Biology, methods; Gene Expression Profiling; High-Throughput Nucleotide Sequencing; Humans; MicroRNAs, blood, genetics; Molecular Sequence Data; Real-Time Polymerase Chain Reaction; Sequence Analysis, RNA, statistics & numerical data; Software; Transcriptome},
  nlm-id          = {0411011},
  owner           = {NLM},
  pii             = {gkv1335},
  pmc             = {PMC4824081},
  pmid            = {26635395},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2016-04-09},
}

Small non-coding RNAs play a key role in many physiological and pathological processes. Since 2004, miRNA sequences have been catalogued in miRBase, which is currently in its 21st version. We investigated sequence and structural features of miRNAs annotated in the miRBase and compared them between different versions of this reference database. We have identified that the two most recent releases (v20 and v21) are influenced by next-generation sequencing based miRNA predictions and show significant deviation from miRNAs discovered prior to the high-throughput profiling period. From the analysis of miRBase, we derived a set of key characteristics to predict new miRNAs and applied the implemented algorithm to evaluate novel blood-borne miRNA candidates. We carried out 705 individual whole miRNA sequencings of blood cells and collected a total of 9.7 billion reads. Using miRDeep2 we initially predicted 1452 potentially novel miRNAs. After excluding false positives, 518 candidates remained. These novel candidates were ranked according to their distance to the features in the early miRBase versions allowing for an easier selection of a subset of putative miRNAs for validation. Selected candidates were successfully validated by qRT-PCR and northern blotting. In addition, we implemented a web-server for ranking potential miRNA candidates, which is available at:www.ccb.uni-saarland.de/novomirank.

@Article{Ludwig2016,
  author          = {Ludwig, Nicole and Leidinger, Petra and Becker, Kurt and Backes, Christina and Fehlmann, Tobias and Pallasch, Christian and Rheinheimer, Steffi and Meder, Benjamin and Stähler, Cord and Meese, Eckart and Keller, Andreas},
  title           = {Distribution of {miRNA} expression across human tissues},
  journal         = {Nucleic acids research},
  year            = {2016},
  volume          = {44},
  number          = {8},
  pages           = {3865--3877},
  month           = may,
  issn            = {1362-4962},
  abstract        = {We present a human miRNA tissue atlas by determining the abundance of 1997 miRNAs in 61 tissue biopsies of different organs from two individuals collected post-mortem. One thousand three hundred sixty-four miRNAs were discovered in at least one tissue, 143 were present in each tissue. To define the distribution of miRNAs, we utilized a tissue specificity index (TSI). The majority of miRNAs (82.9%) fell in a middle TSI range i.e. were neither specific for single tissues (TSI > 0.85) nor housekeeping miRNAs (TSI < 0.5). Nonetheless, we observed many different miRNAs and miRNA families that were predominantly expressed in certain tissues. Clustering of miRNA abundances revealed that tissues like several areas of the brain clustered together. Considering -3p and -5p mature forms we observed miR-150 with different tissue specificity. Analysis of additional lung and prostate biopsies indicated that inter-organism variability was significantly lower than inter-organ variability. Tissue-specific differences between the miRNA patterns appeared not to be significantly altered by storage as shown for heart and lung tissue. MiRNAs TSI values of human tissues were significantly (P = 10(-8)) correlated with those of rats; miRNAs that were highly abundant in certain human tissues were likewise abundant in according rat tissues. We implemented a web-based repository enabling scientists to access and browse the data (https://ccb-web.cs.uni-saarland.de/tissueatlas).},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-06-05},
  country         = {England},
  doi             = {10.1093/nar/gkw116},
  issn-linking    = {0305-1048},
  issue           = {8},
  keywords        = {Adult; Aged; Animals; Databases, Nucleic Acid; Humans; Male; MicroRNAs, classification, metabolism; Organ Specificity; Rats; Reproducibility of Results; Tissue Distribution},
  nlm-id          = {0411011},
  owner           = {NLM},
  pii             = {gkw116},
  pmc             = {PMC4856985},
  pmid            = {26921406},
  publisher       = {Oxford University Press ({OUP})},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-11-01},
}

We present a human miRNA tissue atlas by determining the abundance of 1997 miRNAs in 61 tissue biopsies of different organs from two individuals collected post-mortem. One thousand three hundred sixty-four miRNAs were discovered in at least one tissue, 143 were present in each tissue. To define the distribution of miRNAs, we utilized a tissue specificity index (TSI). The majority of miRNAs (82.9%) fell in a middle TSI range i.e. were neither specific for single tissues (TSI > 0.85) nor housekeeping miRNAs (TSI < 0.5). Nonetheless, we observed many different miRNAs and miRNA families that were predominantly expressed in certain tissues. Clustering of miRNA abundances revealed that tissues like several areas of the brain clustered together. Considering -3p and -5p mature forms we observed miR-150 with different tissue specificity. Analysis of additional lung and prostate biopsies indicated that inter-organism variability was significantly lower than inter-organ variability. Tissue-specific differences between the miRNA patterns appeared not to be significantly altered by storage as shown for heart and lung tissue. MiRNAs TSI values of human tissues were significantly (P = 10(-8)) correlated with those of rats; miRNAs that were highly abundant in certain human tissues were likewise abundant in according rat tissues. We implemented a web-based repository enabling scientists to access and browse the data (https://ccb-web.cs.uni-saarland.de/tissueatlas).

@Article{Backes2016,
  author          = {Backes, Christina and Meese, Eckart and Keller, Andreas},
  title           = {Specific {miRNA} Disease Biomarkers in Blood, Serum and Plasma: Challenges and Prospects},
  journal         = {Molecular diagnosis \& therapy},
  year            = {2016},
  volume          = {20},
  number          = {6},
  pages           = {509--518},
  month           = dec,
  issn            = {1179-2000},
  abstract        = {Significant effort has been devoted to discovering microRNA (miRNA) disease biomarkers. In particular, miRNAs in whole blood or specific blood components are candidates for improving the diagnosis of diseases, including life-threatening pathologies. This review covers the challenges crucial for the translation of miRNAs in body fluids (circulating miRNAs) from a research setting into a clinical care scenario. First, we discuss the specificity of miRNA biomarkers for the diagnosis of a disease. While single miRNAs such as miR-20a, miR-21, miR-155, and miR-126 are frequently not disease specific, miRNA signatures that consist of a plurality of different miRNAs may help to improve differentiation between pathologies. Second, we discuss the degree of reproducibility and highlight selected validation studies. While single miRNA markers are often confirmed by independent studies, miRNA signatures are less frequently verified. Third, we address challenges to the profiling of miRNAs in high-throughput settings and we discuss the appropriateness of various analytical platforms and bioinformatics towards a clinical application of miRNAs. Finally, we shed light on the suitability of enriched miRNA sources, e.g. fractionation of body fluids for extracellular vesicles such as exosomes or blood cells, to develop miRNA signatures. With an increasing number of verified miRNA signatures and with the advance of matured medium-throughput approaches in clinical settings, specific miRNA markers are increasingly likely to contribute to human healthcare.},
  chemicals       = {Biomarkers, MicroRNAs},
  citation-subset = {IM},
  completed       = {2017-10-16},
  country         = {New Zealand},
  doi             = {10.1007/s40291-016-0221-4},
  issn-linking    = {1177-1062},
  issue           = {6},
  keywords        = {Biomarkers, blood; Computational Biology; Gene Expression Profiling; Gene Expression Regulation; High-Throughput Nucleotide Sequencing; Humans; MicroRNAs, blood, genetics; Reproducibility of Results; Sensitivity and Specificity},
  nlm-id          = {101264260},
  owner           = {NLM},
  pii             = {10.1007/s40291-016-0221-4},
  pmid            = {27378479},
  publisher       = {Springer Nature},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2018-01-08},
}

Significant effort has been devoted to discovering microRNA (miRNA) disease biomarkers. In particular, miRNAs in whole blood or specific blood components are candidates for improving the diagnosis of diseases, including life-threatening pathologies. This review covers the challenges crucial for the translation of miRNAs in body fluids (circulating miRNAs) from a research setting into a clinical care scenario. First, we discuss the specificity of miRNA biomarkers for the diagnosis of a disease. While single miRNAs such as miR-20a, miR-21, miR-155, and miR-126 are frequently not disease specific, miRNA signatures that consist of a plurality of different miRNAs may help to improve differentiation between pathologies. Second, we discuss the degree of reproducibility and highlight selected validation studies. While single miRNA markers are often confirmed by independent studies, miRNA signatures are less frequently verified. Third, we address challenges to the profiling of miRNAs in high-throughput settings and we discuss the appropriateness of various analytical platforms and bioinformatics towards a clinical application of miRNAs. Finally, we shed light on the suitability of enriched miRNA sources, e.g. fractionation of body fluids for extracellular vesicles such as exosomes or blood cells, to develop miRNA signatures. With an increasing number of verified miRNA signatures and with the advance of matured medium-throughput approaches in clinical settings, specific miRNA markers are increasingly likely to contribute to human healthcare.

@Article{pmid26670867,
   Author="Keller, A.  and Meese, E. ",
   Title="{{C}an circulating mi{R}{N}{A}s live up to the promise of being minimal invasive biomarkers in clinical settings?}",
   Journal="Wiley Interdiscip Rev RNA",
   Year="2015",
   Pages=" ",
   Month="Dec"
}

@Article{pmid26240298,
   Author="Sedaghat-Hamedani, F.  and Kayvanpour, E.  and Frankenstein, L.  and Mereles, D.  and Amr, A.  and Buss, S.  and Keller, A.  and Giannitsis, E.  and Jensen, K.  and Katus, H. A.  and Meder, B. ",
   Title="{{B}iomarker changes after strenuous exercise can mimic pulmonary embolism and cardiac injury--a metaanalysis of 45 studies}",
   Journal="Clin. Chem.",
   Year="2015",
   Volume="61",
   Number="10",
   Pages="1246--1255",
   Month="Oct"
}

@Article{pmid26599228,
   Author="Leidinger, P.  and Backes, C.  and Rheinheimer, S.  and Keller, A.  and Meese, E. ",
   Title="{{T}owards {C}linical {A}pplications of {B}lood-{B}orne mi{R}{N}{A} {S}ignatures: {T}he {I}nfluence of the {A}nticoagulant {E}{D}{T}{A} on mi{R}{N}{A} {A}bundance}",
   Journal="PLoS ONE",
   Year="2015",
   Volume="10",
   Number="11",
   Pages="e0143321"
}

@Article{pmid26547721,
   Author="Backes, C.  and Meder, B.  and Lai, A.  and Stoll, M.  and Ruhle, F.  and Katus, H. A.  and Keller, A. ",
   Title="{{P}athway-based variant enrichment analysis on the example of dilated cardiomyopathy}",
   Journal="Hum. Genet.",
   Year="2015",
   Pages=" ",
   Month="Nov"
}

@Article{pmid26501925,
   Author="Schneider, L.  and Stoeckel, D.  and Kehl, T.  and Gerasch, A.  and Ludwig, N.  and Leidinger, P.  and Huwer, H.  and Tenzer, S.  and Kohlbacher, O.  and Hildebrandt, A.  and Kaufmann, M.  and Gessler, M.  and Keller, A.  and Meese, E.  and Graf, N.  and Lenhof, H. P. ",
   Title="{{D}rug{T}arget{I}nspector: {A}n assistance tool for patient treatment stratification}",
   Journal="Int. J. Cancer",
   Year="2015",
   Pages=" ",
   Month="Oct"
}

@Article{pmid26484209,
   Author="Fischer, U.  and Ludwig, N.  and Keller, A.  and Backes, C.  and Meese, E. ",
   Title="{{G}enome-wide copy number profiling of mouse neural stem cells during differentiation}",
   Journal="Genom. Data",
   Year="2015",
   Volume="5",
   Pages="3--6",
   Month="Sep"
}

@Article{pmid26466382,
   Author="Hubenthal, M.  and Hemmrich-Stanisak, G.  and Degenhardt, F.  and Szymczak, S.  and Du, Z.  and Elsharawy, A.  and Keller, A.  and Schreiber, S.  and Franke, A. ",
   Title="{{S}parse {M}odeling {R}eveals mi{R}{N}{A} {S}ignatures for {D}iagnostics of {I}nflammatory {B}owel {D}isease}",
   Journal="PLoS ONE",
   Year="2015",
   Volume="10",
   Number="10",
   Pages="e0140155"
}

@Article{pmid26207298,
   Author="Backes, C.  and Leidinger, P.  and Altmann, G.  and Wuerstle, M.  and Meder, B.  and Galata, V.  and Mueller, S. C.  and Sickert, D.  and Stahler, C.  and Meese, E.  and Keller, A. ",
   Title="{{I}nfluence of next-generation sequencing and storage conditions on mi{R}{N}{A} patterns generated from {P}{A}{X}gene blood}",
   Journal="Anal. Chem.",
   Year="2015",
   Volume="87",
   Number="17",
   Pages="8910--8916",
   Month="Sep"
}

@Article{pmid26193622,
   Author="Kelsen, J. R.  and Dawany, N.  and Moran, C. J.  and Petersen, B. S.  and Sarmady, M.  and Sasson, A.  and Pauly-Hubbard, H.  and Martinez, A.  and Maurer, K.  and Soong, J.  and Rappaport, E.  and Franke, A.  and Keller, A.  and Winter, H. S.  and Mamula, P.  and Piccoli, D.  and Artis, D.  and Sonnenberg, G. F.  and Daly, M.  and Sullivan, K. E.  and Baldassano, R. N.  and Devoto, M. ",
   Title="{{E}xome {S}equencing {A}nalysis {R}eveals {V}ariants in {P}rimary {I}mmunodeficiency {G}enes in {P}atients {W}ith {V}ery {E}arly {O}nset {I}nflammatory {B}owel {D}isease}",
   Journal="Gastroenterology",
   Year="2015",
   Volume="149",
   Number="6",
   Pages="1415--1424",
   Month="Nov"
}

@Article{pmid26191084,
   Author="Mueller, S. C.  and Backes, C.  and Kalinina, O. V.  and Meder, B.  and Stoeckel, D.  and Lenhof, H. P.  and Meese, E.  and Keller, A. ",
   Title="{{B}{A}{L}{L}-{S}{N}{P}: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms}",
   Journal="Genome Med.",
   Year="2015",
   Volume="7",
   Number="1",
   Pages="65"
}

@Article{pmid26169798,
   Author="Zafari, S.  and Backes, C.  and Leidinger, P.  and Meese, E.  and Keller, A. ",
   Title="{{R}egulatory micro{R}{N}{A} networks: complex patterns of target pathways for disease-related and housekeeping micro{R}{N}{A}s}",
   Journal="Genomics Proteomics Bioinformatics",
   Year="2015",
   Volume="13",
   Number="3",
   Pages="159--168",
   Month="Jun"
}

@Article{pmid26078336,
   Author="Leidinger, P.  and Galata, V.  and Backes, C.  and Stahler, C.  and Rheinheimer, S.  and Huwer, H.  and Meese, E.  and Keller, A. ",
   Title="{{L}ongitudinal study on circulating mi{R}{N}{A}s in patients after lung cancer resection}",
   Journal="Oncotarget",
   Year="2015",
   Volume="6",
   Number="18",
   Pages="16674--16685",
   Month="Jun"
}

@Article{pmid26039628,
   Author="Leidinger, P.  and Keller, A.  and Milchram, L.  and Harz, C.  and Hart, M.  and Werth, A.  and Lenhof, H. P.  and Weinhausel, A.  and Keck, B.  and Wullich, B.  and Ludwig, N.  and Meese, E. ",
   Title="{{C}ombination of {A}utoantibody {S}ignature with {P}{S}{A} {L}evel {E}nables a {H}ighly {A}ccurate {B}lood-{B}ased {D}ifferentiation of {P}rostate {C}ancer {P}atients from {P}atients with {B}enign {P}rostatic {H}yperplasia}",
   Journal="PLoS ONE",
   Year="2015",
   Volume="10",
   Number="6",
   Pages="e0128235"
}

@Article{pmid25979944,
   Author="Backes, C.  and Keller, A. ",
   Title="{{R}eanalysis of 3,707 novel human micro{R}{N}{A} candidates}",
   Journal="Proc. Natl. Acad. Sci. U.S.A.",
   Year="2015",
   Volume="112",
   Number="22",
   Pages="E2849--2850",
   Month="Jun"
}

@Article{pmid25787821,
   Author="Ludwig, N.  and Nourkami-Tutdibi, N.  and Backes, C.  and Lenhof, H. P.  and Graf, N.  and Keller, A.  and Meese, E. ",
   Title="{{C}irculating serum mi{R}{N}{A}s as potential biomarkers for nephroblastoma}",
   Journal="Pediatr. Blood Cancer",
   Year="2015",
   Volume="62",
   Number="8",
   Pages="1360--1367",
   Month="Aug"
}

@Article{pmid25760141,
   Author="Fischer, U.  and Backes, C.  and Raslan, A.  and Keller, A.  and Meier, C.  and Meese, E. ",
   Title="{{G}ene amplification during differentiation of mammalian neural stem cells in vitro and in vivo}",
   Journal="Oncotarget",
   Year="2015",
   Volume="6",
   Number="9",
   Pages="7023--7039",
   Month="Mar"
}

@Article{pmid25720553,
   Author="Zafari, S.  and Backes, C.  and Meese, E.  and Keller, A. ",
   Title="{{C}irculating {B}iomarker {P}anels in {A}lzheimer's {D}isease}",
   Journal="Gerontology",
   Year="2015",
   Volume="61",
   Number="6",
   Pages="497--503"
}

@Article{pmid25681310,
   Author="Ludwig, N.  and Kim, Y. J.  and Mueller, S. C.  and Backes, C.  and Werner, T. V.  and Galata, V.  and Sartorius, E.  and Bohle, R. M.  and Keller, A.  and Meese, E. ",
   Title="{{P}osttranscriptional deregulation of signaling pathways in meningioma subtypes by differential expression of mi{R}{N}{A}s}",
   Journal="Neuro Oncol.",
   Year="2015",
   Volume="17",
   Number="9",
   Pages="1250--1260",
   Month="Sep"
}

@Article{pmid25670083,
   Author="Wegert, J.  and Ishaque, N.  and Vardapour, R.  and Georg, C.  and Gu, Z.  and Bieg, M.  and Ziegler, B.  and Bausenwein, S.  and Nourkami, N.  and Ludwig, N.  and Keller, A.  and Grimm, C.  and Kneitz, S.  and Williams, R. D.  and Chagtai, T.  and Pritchard-Jones, K.  and van Sluis, P.  and Volckmann, R.  and Koster, J.  and Versteeg, R.  and Acha, T.  and O'Sullivan, M. J.  and Bode, P. K.  and Niggli, F.  and Tytgat, G. A.  and van Tinteren, H.  and van den Heuvel-Eibrink, M. M.  and Meese, E.  and Vokuhl, C.  and Leuschner, I.  and Graf, N.  and Eils, R.  and Pfister, S. M.  and Kool, M.  and Gessler, M. ",
   Title="{{M}utations in the {S}{I}{X}1{/}2 pathway and the {D}{R}{O}{S}{H}{A}{/}{D}{G}{C}{R}8 mi{R}{N}{A} microprocessor complex underlie high-risk blastemal type {W}ilms tumors}",
   Journal="Cancer Cell",
   Year="2015",
   Volume="27",
   Number="2",
   Pages="298--311",
   Month="Feb"
}

@Article{pmid25642434,
   Author="Ingwersen, J.  and Menge, T.  and Wingerath, B.  and Kaya, D.  and Graf, J.  and Prozorovski, T.  and Keller, A.  and Backes, C.  and Beier, M.  and Scheffler, M.  and Dehmel, T.  and Kieseier, B. C.  and Hartung, H. P.  and Kury, P.  and Aktas, O. ",
   Title="{{N}atalizumab restores aberrant mi{R}{N}{A} expression profile in multiple sclerosis and reveals a critical role for mi{R}-20b}",
   Journal="Ann. Clin. Transl. Neurol.",
   Year="2015",
   Volume="2",
   Number="1",
   Pages="43--55",
   Month="Jan"
}

@Article{pmid25617425,
   Author="Kappel, A.  and Backes, C.  and Huang, Y.  and Zafari, S.  and Leidinger, P.  and Meder, B.  and Schwarz, H.  and Gumbrecht, W.  and Meese, E.  and Staehler, C. F.  and Keller, A. ",
   Title="{{M}icro{R}{N}{A} in vitro diagnostics using immunoassay analyzers}",
   Journal="Clin. Chem.",
   Year="2015",
   Volume="61",
   Number="4",
   Pages="600--607",
   Month="Apr"
}

@Article{pmid25537509,
   Author="Backes, C.  and Harz, C.  and Fischer, U.  and Schmitt, J.  and Ludwig, N.  and Petersen, B. S.  and Mueller, S. C.  and Kim, Y. J.  and Wolf, N. M.  and Katus, H. A.  and Meder, B.  and Furtwangler, R.  and Franke, A.  and Bohle, R.  and Henn, W.  and Graf, N.  and Keller, A.  and Meese, E. ",
   Title="{{N}ew insights into the genetics of glioblastoma multiforme by familial exome sequencing}",
   Journal="Oncotarget",
   Year="2015",
   Volume="6",
   Number="8",
   Pages="5918--5931",
   Month="Mar"
}

@Article{pmid25534293,
   Author="Roth, P.  and Keller, A.  and Hoheisel, J. D.  and Codo, P.  and Bauer, A. S.  and Backes, C.  and Leidinger, P.  and Meese, E.  and Thiel, E.  and Korfel, A.  and Weller, M. ",
   Title="{{D}ifferentially regulated mi{R}{N}{A}s as prognostic biomarkers in the blood of primary {C}{N}{S} lymphoma patients}",
   Journal="Eur. J. Cancer",
   Year="2015",
   Volume="51",
   Number="3",
   Pages="382--390",
   Month="Feb"
}

@Article{pmid24572142,
   Author="Zeissig, Y.  and Petersen, B. S.  and Milutinovic, S.  and Bosse, E.  and Mayr, G.  and Peuker, K.  and Hartwig, J.  and Keller, A.  and Kohl, M.  and Laass, M. W.  and Billmann-Born, S.  and Brandau, H.  and Feller, A. C.  and Rocken, C.  and Schrappe, M.  and Rosenstiel, P.  and Reed, J. C.  and Schreiber, S.  and Franke, A.  and Zeissig, S. ",
   Title="{{X}{I}{A}{P} variants in male {C}rohn's disease}",
   Journal="Gut",
   Year="2015",
   Volume="64",
   Number="1",
   Pages="66--76",
   Month="Jan"
}

@Article{Hofmann2015,
  author          = {Hofmann, Stefan and Huang, Yiwei and Paulicka, Peter and Kappel, Andreas and Katus, Hugo A and Keller, Andreas and Meder, Benjamin and Stähler, Cord Friedrich and Gumbrecht, Walter},
  title           = {Double-Stranded Ligation Assay for the Rapid Multiplex Quantification of MicroRNAs.},
  journal         = {Analytical chemistry},
  year            = {2015},
  volume          = {87},
  pages           = {12104--12111},
  month           = dec,
  issn            = {1520-6882},
  abstract        = {MicroRNAs are auspicious candidates for a new generation of biomarkers. The detection of microRNA panels in body fluids promises early diagnosis of many diseases, including cancer or acute coronary syndrome. For a fast, sensitive, and specific detection of microRNA panels on the bedside, medical point-of-care systems that measure those biomarkers are required. As microchips are promising technical tools for a robust signal measurement at biochemical interfaces, we developed an assay for the electrochemical multiplex quantification of microRNAs on a CMOS chip with interdigitated gold electrode sensor positions. The method is based on the formation of a tripartite hybridization complex and subsequent both-sided ligation of the target nucleic acid to a reporter and capture strand. With a time to results of 30 min, the reported assay achieves a limit of detection below 1 pM, at a specificity down to single mismatch discrimination. It also offers very good signal dynamics between 1 pM and 1 nM, thus, allowing reliable quantification of the detected microRNAs and easy implementation into automated devices due to a simple workflow. },
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2016-09-01},
  country         = {United States},
  doi             = {10.1021/acs.analchem.5b02850},
  issn-linking    = {0003-2700},
  issue           = {24},
  keywords        = {Genetic Techniques; Limit of Detection; MicroRNAs, analysis, genetics; Molecular Diagnostic Techniques; Time Factors},
  nlm-id          = {0370536},
  owner           = {NLM},
  pmid            = {26574152},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2015-12-15},
}

MicroRNAs are auspicious candidates for a new generation of biomarkers. The detection of microRNA panels in body fluids promises early diagnosis of many diseases, including cancer or acute coronary syndrome. For a fast, sensitive, and specific detection of microRNA panels on the bedside, medical point-of-care systems that measure those biomarkers are required. As microchips are promising technical tools for a robust signal measurement at biochemical interfaces, we developed an assay for the electrochemical multiplex quantification of microRNAs on a CMOS chip with interdigitated gold electrode sensor positions. The method is based on the formation of a tripartite hybridization complex and subsequent both-sided ligation of the target nucleic acid to a reporter and capture strand. With a time to results of 30 min, the reported assay achieves a limit of detection below 1 pM, at a specificity down to single mismatch discrimination. It also offers very good signal dynamics between 1 pM and 1 nM, thus, allowing reliable quantification of the detected microRNAs and easy implementation into automated devices due to a simple workflow.

@Article{Latorre2015,
  author          = {Latorre, Irene and Leidinger, Petra and Backes, Christina and Domínguez, Jose and de Souza-Galvão, Maria Luiza and Maldonado, Jose and Prat, Cristina and Ruiz-Manzano, Juan and Sánchez, Francisca and Casas, Irma and Keller, Andreas and von Briesen, Hagen and Knobel, Hernando and Meese, Eckart and Meyerhans, Andreas},
  title           = {A novel whole-blood miRNA signature for a rapid diagnosis of pulmonary tuberculosis.},
  journal         = {The European respiratory journal},
  year            = {2015},
  volume          = {45},
  pages           = {1173--1176},
  month           = apr,
  issn            = {1399-3003},
  chemicals       = {Biomarkers, MicroRNAs},
  citation-subset = {IM},
  completed       = {2015-12-31},
  country         = {England},
  doi             = {10.1183/09031936.00221514},
  issn-linking    = {0903-1936},
  issue           = {4},
  keywords        = {Adult; Bacteriological Techniques; Biomarkers, blood; Case-Control Studies; Female; Humans; Latent Tuberculosis, blood, diagnosis; Male; MicroRNAs, blood; Middle Aged; Mycobacterium tuberculosis, isolation & purification; Real-Time Polymerase Chain Reaction, methods; Sensitivity and Specificity; Spain; Time Factors; Tuberculosis, Pulmonary, blood, diagnosis},
  nlm-id          = {8803460},
  owner           = {NLM},
  pii             = {09031936.00221514},
  pmid            = {25657026},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2015-04-01},
}

@Article{Keller2015,
  author          = {Keller, Andreas and Leidinger, Petra and Meese, Eckart and Haas, Jan and Backes, Christina and Rasche, Ludwig and Behrens, Janina R and Pfuhl, Catherina and Wakonig, Katharina and Gieß, René M and Jarius, Sven and Meder, Benjamin and Bellmann-Strobl, Judith and Paul, Friedemann and Pache, Florence C and Ruprecht, Klemens},
  title           = {Next-generation sequencing identifies altered whole blood microRNAs in neuromyelitis optica spectrum disorder which may permit discrimination from multiple sclerosis.},
  journal         = {Journal of neuroinflammation},
  year            = {2015},
  volume          = {12},
  pages           = {196},
  month           = oct,
  issn            = {1742-2094},
  abstract        = {Neuromyelitis optica spectrum disorder (NMOSD) and multiple sclerosis (MS) have a similar clinical phenotype but represent distinct diseases, requiring different therapies. MicroRNAs (miRNAs) are short non-coding RNAs whose expression profiles can serve as diagnostic biomarkers and which may be involved in the pathophysiology of neuroinflammatory diseases. Here, we analyzed miRNA profiles in serum and whole blood of patients with NMOSD and clinically isolated syndrome (CIS)/relapsing-remitting MS (RRMS) as well as healthy controls by next-generation sequencing (NGS). MiRNA expression profiles were determined by NGS in sera of patients with aquaporin-4 antibody-positive NMOSD (n = 20), CIS/RRMS (n = 20), and healthy controls (n = 20) and in whole blood of patients with NMOSD (n = 11), CIS/RRMS (n = 60), and healthy controls (n = 43). Differentially expressed miRNAs were calculated by analysis of variance and t tests. All significance values were corrected for multiple testing. Selected miRNAs were validated in whole blood of patients with NMOSD (n = 18) and CIS/RRMS (n = 19) by quantitative real-time polymerase chain reaction (qRT-PCR). None of 261 miRNAs detected in serum but 178 of 416 miRNAs detected in whole blood showed significantly different expression levels among the three groups. Pairwise comparisons revealed 115 (NMOSD vs. CIS/RRMS), 141 (NMOSD vs. healthy controls), and 44 (CIS/RRMS vs. healthy controls) miRNAs in whole blood with significantly different expression levels. qRT-PCR confirmed different expression levels in whole blood of patients with NMOSD and CIS/RRMS for 9 out of 10 exemplarily chosen miRNAs. In silico enrichment analysis demonstrated an accumulation of altered miRNAs in NMOSD in particular in CD15(+) cells (i.e., neutrophils and eosinophils). This study identifies a set of miRNAs in whole blood, which may have the potential to discriminate NMOSD from CIS/RRMS and healthy controls. In contrast, miRNA profiles in serum do not appear to be promising diagnostic biomarkers for NMOSD. Enrichment of altered miRNAs in CD15(+) neutrophils and eosinophils, which were previously implicated in the pathophysiology of NMOSD, suggests that miRNAs could be involved in the regulation of these cells in NMOSD.},
  chemicals       = {Aquaporin 4, Lewis X Antigen, MicroRNAs},
  citation-subset = {IM},
  completed       = {2016-03-22},
  country         = {England},
  doi             = {10.1186/s12974-015-0418-1},
  issn-linking    = {1742-2094},
  keywords        = {Adolescent; Adult; Aged; Aquaporin 4, immunology; Computational Biology; Computer Simulation; Female; Gene Library; Humans; Lewis X Antigen, metabolism; Male; MicroRNAs, blood, genetics; Middle Aged; Multiple Sclerosis, blood, genetics; Neuromyelitis Optica, blood, genetics; Polymerase Chain Reaction; Sequence Analysis, RNA; Young Adult},
  nlm-id          = {101222974},
  owner           = {NLM},
  pii             = {10.1186/s12974-015-0418-1},
  pmc             = {PMC4628234},
  pmid            = {26521232},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2017-11-16},
}

Neuromyelitis optica spectrum disorder (NMOSD) and multiple sclerosis (MS) have a similar clinical phenotype but represent distinct diseases, requiring different therapies. MicroRNAs (miRNAs) are short non-coding RNAs whose expression profiles can serve as diagnostic biomarkers and which may be involved in the pathophysiology of neuroinflammatory diseases. Here, we analyzed miRNA profiles in serum and whole blood of patients with NMOSD and clinically isolated syndrome (CIS)/relapsing-remitting MS (RRMS) as well as healthy controls by next-generation sequencing (NGS). MiRNA expression profiles were determined by NGS in sera of patients with aquaporin-4 antibody-positive NMOSD (n = 20), CIS/RRMS (n = 20), and healthy controls (n = 20) and in whole blood of patients with NMOSD (n = 11), CIS/RRMS (n = 60), and healthy controls (n = 43). Differentially expressed miRNAs were calculated by analysis of variance and t tests. All significance values were corrected for multiple testing. Selected miRNAs were validated in whole blood of patients with NMOSD (n = 18) and CIS/RRMS (n = 19) by quantitative real-time polymerase chain reaction (qRT-PCR). None of 261 miRNAs detected in serum but 178 of 416 miRNAs detected in whole blood showed significantly different expression levels among the three groups. Pairwise comparisons revealed 115 (NMOSD vs. CIS/RRMS), 141 (NMOSD vs. healthy controls), and 44 (CIS/RRMS vs. healthy controls) miRNAs in whole blood with significantly different expression levels. qRT-PCR confirmed different expression levels in whole blood of patients with NMOSD and CIS/RRMS for 9 out of 10 exemplarily chosen miRNAs. In silico enrichment analysis demonstrated an accumulation of altered miRNAs in NMOSD in particular in CD15(+) cells (i.e., neutrophils and eosinophils). This study identifies a set of miRNAs in whole blood, which may have the potential to discriminate NMOSD from CIS/RRMS and healthy controls. In contrast, miRNA profiles in serum do not appear to be promising diagnostic biomarkers for NMOSD. Enrichment of altered miRNAs in CD15(+) neutrophils and eosinophils, which were previously implicated in the pathophysiology of NMOSD, suggests that miRNAs could be involved in the regulation of these cells in NMOSD.

@Article{Kayvanpour2015,
  author          = {Kayvanpour, Elham and Mansi, Tommaso and Sedaghat-Hamedani, Farbod and Amr, Ali and Neumann, Dominik and Georgescu, Bogdan and Seegerer, Philipp and Kamen, Ali and Haas, Jan and Frese, Karen S and Irawati, Maria and Wirsz, Emil and King, Vanessa and Buss, Sebastian and Mereles, Derliz and Zitron, Edgar and Keller, Andreas and Katus, Hugo A and Comaniciu, Dorin and Meder, Benjamin},
  title           = {Towards Personalized Cardiology: Multi-Scale Modeling of the Failing Heart.},
  journal         = {PloS one},
  year            = {2015},
  volume          = {10},
  pages           = {e0134869},
  issn            = {1932-6203},
  abstract        = {Despite modern pharmacotherapy and advanced implantable cardiac devices, overall prognosis and quality of life of HF patients remain poor. This is in part due to insufficient patient stratification and lack of individualized therapy planning, resulting in less effective treatments and a significant number of non-responders. State-of-the-art clinical phenotyping was acquired, including magnetic resonance imaging (MRI) and biomarker assessment. An individualized, multi-scale model of heart function covering cardiac anatomy, electrophysiology, biomechanics and hemodynamics was estimated using a robust framework. The model was computed on n=46 HF patients, showing for the first time that advanced multi-scale models can be fitted consistently on large cohorts. Novel multi-scale parameters derived from the model of all cases were analyzed and compared against clinical parameters, cardiac imaging, lab tests and survival scores to evaluate the explicative power of the model and its potential for better patient stratification. Model validation was pursued by comparing clinical parameters that were not used in the fitting process against model parameters. This paper illustrates how advanced multi-scale models can complement cardiovascular imaging and how they could be applied in patient care. Based on obtained results, it becomes conceivable that, after thorough validation, such heart failure models could be applied for patient management and therapy planning in the future, as we illustrate in one patient of our cohort who received CRT-D implantation.},
  citation-subset = {IM},
  completed       = {2016-04-25},
  country         = {United States},
  doi             = {10.1371/journal.pone.0134869},
  issn-linking    = {1932-6203},
  issue           = {7},
  keywords        = {Heart Failure, pathology, physiopathology, therapy; Humans; Precision Medicine},
  nlm-id          = {101285081},
  owner           = {NLM},
  pii             = {PONE-D-15-06628},
  pmc             = {PMC4521877},
  pmid            = {26230546},
  pubmodel        = {Electronic-eCollection},
  pubstatus       = {epublish},
  revised         = {2017-02-20},
}

Despite modern pharmacotherapy and advanced implantable cardiac devices, overall prognosis and quality of life of HF patients remain poor. This is in part due to insufficient patient stratification and lack of individualized therapy planning, resulting in less effective treatments and a significant number of non-responders. State-of-the-art clinical phenotyping was acquired, including magnetic resonance imaging (MRI) and biomarker assessment. An individualized, multi-scale model of heart function covering cardiac anatomy, electrophysiology, biomechanics and hemodynamics was estimated using a robust framework. The model was computed on n=46 HF patients, showing for the first time that advanced multi-scale models can be fitted consistently on large cohorts. Novel multi-scale parameters derived from the model of all cases were analyzed and compared against clinical parameters, cardiac imaging, lab tests and survival scores to evaluate the explicative power of the model and its potential for better patient stratification. Model validation was pursued by comparing clinical parameters that were not used in the fitting process against model parameters. This paper illustrates how advanced multi-scale models can complement cardiovascular imaging and how they could be applied in patient care. Based on obtained results, it becomes conceivable that, after thorough validation, such heart failure models could be applied for patient management and therapy planning in the future, as we illustrate in one patient of our cohort who received CRT-D implantation.

@Article{Backes2015,
  author          = {Backes, Christina and Haas, Jan and Leidinger, Petra and Frese, Karen and Großmann, Thomas and Ruprecht, Klemens and Meder, Benjamin and Meese, Eckart and Keller, Andreas},
  title           = {miFRame: analysis and visualization of miRNA sequencing data in neurological disorders.},
  journal         = {Journal of translational medicine},
  year            = {2015},
  volume          = {13},
  pages           = {224},
  month           = jul,
  issn            = {1479-5876},
  abstract        = {While in the past decades nucleic acid analysis has been predominantly carried out using quantitative low- and high-throughput approaches such as qRT-PCR and microarray technology, next-generation sequencing (NGS) with its single base resolution is now frequently applied in DNA and RNA testing. Especially for small non-coding RNAs such as microRNAs there is a need for analysis and visualization tools that facilitate interpretation of the results also for clinicians. We developed miFRame, which supports the analysis of human small RNA NGS data. Our tool carries out different data analyses for known as well as predicted novel mature microRNAs from known precursors and presents the results in a well interpretable manner. Analyses include among others expression analysis of precursors and mature miRNAs, detection of novel precursors and detection of potential iso-microRNAs. Aggregation of results from different users moreover allows for evaluation whether remarkable results, such as novel mature miRNAs, are indeed specific for the respective experimental set-up or are frequently detected across a broad range of experiments. We demonstrate the capabilities of miFRame, which is freely available at http://www.ccb.uni-saarland.de/miframe on two studies, circulating biomarker screening for Multiple Sclerosis (cohort includes clinically isolated syndrome, relapse remitting MS, matched controls) as well as Alzheimer Disease (cohort includes Alzheimer Disease, Mild Cognitive Impairment, matched controls). Here, our tool allowed for an improved biomarker discovery by identifying likely false positive marker candidates.},
  chemicals       = {MicroRNAs, Protein Isoforms},
  citation-subset = {IM},
  completed       = {2016-03-17},
  country         = {England},
  doi             = {10.1186/s12967-015-0594-x},
  issn-linking    = {1479-5876},
  keywords        = {Alzheimer Disease, genetics; Base Sequence; Computational Biology, methods; Gene Expression Profiling; Humans; MicroRNAs, genetics, metabolism; Multiple Sclerosis, genetics; Nervous System Diseases, genetics; Protein Isoforms, genetics, metabolism; Sequence Analysis, RNA, methods; Software},
  nlm-id          = {101190741},
  owner           = {NLM},
  pii             = {10.1186/s12967-015-0594-x},
  pmc             = {PMC4501052},
  pmid            = {26169944},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2015-07-19},
}

While in the past decades nucleic acid analysis has been predominantly carried out using quantitative low- and high-throughput approaches such as qRT-PCR and microarray technology, next-generation sequencing (NGS) with its single base resolution is now frequently applied in DNA and RNA testing. Especially for small non-coding RNAs such as microRNAs there is a need for analysis and visualization tools that facilitate interpretation of the results also for clinicians. We developed miFRame, which supports the analysis of human small RNA NGS data. Our tool carries out different data analyses for known as well as predicted novel mature microRNAs from known precursors and presents the results in a well interpretable manner. Analyses include among others expression analysis of precursors and mature miRNAs, detection of novel precursors and detection of potential iso-microRNAs. Aggregation of results from different users moreover allows for evaluation whether remarkable results, such as novel mature miRNAs, are indeed specific for the respective experimental set-up or are frequently detected across a broad range of experiments. We demonstrate the capabilities of miFRame, which is freely available at http://www.ccb.uni-saarland.de/miframe on two studies, circulating biomarker screening for Multiple Sclerosis (cohort includes clinically isolated syndrome, relapse remitting MS, matched controls) as well as Alzheimer Disease (cohort includes Alzheimer Disease, Mild Cognitive Impairment, matched controls). Here, our tool allowed for an improved biomarker discovery by identifying likely false positive marker candidates.

@Article{Frese2015,
  author          = {Frese, Karen S and Meder, Benjamin and Keller, Andreas and Just, Steffen and Haas, Jan and Vogel, Britta and Fischer, Simon and Backes, Christina and Matzas, Mark and Köhler, Doreen and Benes, Vladimir and Katus, Hugo A and Rottbauer, Wolfgang},
  title           = {RNA splicing regulated by RBFOX1 is essential for cardiac function in zebrafish.},
  journal         = {Journal of cell science},
  year            = {2015},
  volume          = {128},
  pages           = {3030--3040},
  month           = aug,
  issn            = {1477-9137},
  abstract        = {Alternative splicing is one of the major mechanisms through which the proteomic and functional diversity of eukaryotes is achieved. However, the complex nature of the splicing machinery, its associated splicing regulators and the functional implications of alternatively spliced transcripts are only poorly understood. Here, we investigated the functional role of the splicing regulator rbfox1 in vivo using the zebrafish as a model system. We found that loss of rbfox1 led to progressive cardiac contractile dysfunction and heart failure. By using deep-transcriptome sequencing and quantitative real-time PCR, we show that depletion of rbfox1 in zebrafish results in an altered isoform expression of several crucial target genes, such as actn3a and hug. This study underlines that tightly regulated splicing is necessary for unconstrained cardiac function and renders the splicing regulator rbfox1 an interesting target for investigation in human heart failure and cardiomyopathy. },
  chemicals       = {Neuropeptides, RBFOX1 protein, human, RNA Splicing Factors, RNA-Binding Proteins, Actinin},
  citation-subset = {IM},
  completed       = {2016-05-31},
  country         = {England},
  doi             = {10.1242/jcs.166850},
  issn-linking    = {0021-9533},
  issue           = {16},
  keywords        = {Actinin, genetics, metabolism; Alternative Splicing, genetics; Animals; Cardiomyopathies, genetics, pathology; Heart Failure, genetics, physiopathology; High-Throughput Nucleotide Sequencing; Humans; Neuropeptides, genetics; RNA Splicing Factors; RNA-Binding Proteins, biosynthesis, genetics; Transcriptome, genetics; Zebrafish, genetics; Deep sequencing; Dilated cardiomyopathy; Genetics; Splicing; Zebrafish},
  nlm-id          = {0052457},
  owner           = {NLM},
  pii             = {jcs.166850},
  pmc             = {PMC4541041},
  pmid            = {26116573},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2016-11-25},
}

Alternative splicing is one of the major mechanisms through which the proteomic and functional diversity of eukaryotes is achieved. However, the complex nature of the splicing machinery, its associated splicing regulators and the functional implications of alternatively spliced transcripts are only poorly understood. Here, we investigated the functional role of the splicing regulator rbfox1 in vivo using the zebrafish as a model system. We found that loss of rbfox1 led to progressive cardiac contractile dysfunction and heart failure. By using deep-transcriptome sequencing and quantitative real-time PCR, we show that depletion of rbfox1 in zebrafish results in an altered isoform expression of several crucial target genes, such as actn3a and hug. This study underlines that tightly regulated splicing is necessary for unconstrained cardiac function and renders the splicing regulator rbfox1 an interesting target for investigation in human heart failure and cardiomyopathy.

@Article{Mueller2015,
  author          = {Mueller, Sabine C and Backes, Christina and Haas, Jan and INHERITANCE Study Group and Katus, Hugo A and Meder, Benjamin and Meese, Eckart and Keller, Andreas},
  title           = {Pathogenicity prediction of non-synonymous single nucleotide variants in dilated cardiomyopathy.},
  journal         = {Briefings in bioinformatics},
  year            = {2015},
  volume          = {16},
  pages           = {769--779},
  month           = sep,
  issn            = {1477-4054},
  abstract        = {Non-synonymous single nucleotide variants (nsSNVs) in coding DNA regions can result in phenotypic differences between individuals; however, only some nsSNVs are causative for a certain disease. As just a fraction of respective nsSNVs is annotated in databases, computational biology tools are applied to predict the pathogenicity in silico. In addition to applications in oncology, novel molecular diagnostic tests have been developed for cardiovascular disorders as a leading cause of morbidity and mortality in industrialized nations. We explored the concordance and performance of 13 nsSNV pathogenicity prediction tools on panel sequencing results of dilated cardiomyopathy. The analyzed data set from the INHERITANCE study contained 842 nsSNVs discovered in 639 patients, screened for the full sequence of 76 genes related to cardiomyopathies. The single tools prediction revealed a surprisingly high heterogeneity and discordance based on the implemented prediction method. Known disease associations were not reported by the tools, limiting usability in clinics. Because different tools have different advantages, we combined their results. By clustering of correlated methods using similar prediction strategies and calculating a majority vote-based consensus, we found that the prediction accuracy and sensitivity can be further improved. Although challenges remain, different in silico tools bear the potential to predict the malignancy of nsSNVs, especially if different algorithms are combined. Most tools rely mainly on sequence features; beyond these, structural information is important to analyze the relationship of nsSNVs with disease phenotypes. Likewise, current tools consider single nsSNVs, which may, however, show a cumulative effect and turn neutral mutations in an ensemble into pathogenic variants. },
  citation-subset = {IM},
  completed       = {2016-07-12},
  country         = {England},
  doi             = {10.1093/bib/bbu054},
  issn-linking    = {1467-5463},
  issue           = {5},
  keywords        = {Cardiomyopathy, Dilated, genetics; Humans; Polymorphism, Single Nucleotide; DCM; concordance; nsSNVs; pathogenicity prediction; performance quality},
  nlm-id          = {100912837},
  owner           = {NLM},
  pii             = {bbu054},
  pmid            = {25638801},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2015-09-16},
}

Non-synonymous single nucleotide variants (nsSNVs) in coding DNA regions can result in phenotypic differences between individuals; however, only some nsSNVs are causative for a certain disease. As just a fraction of respective nsSNVs is annotated in databases, computational biology tools are applied to predict the pathogenicity in silico. In addition to applications in oncology, novel molecular diagnostic tests have been developed for cardiovascular disorders as a leading cause of morbidity and mortality in industrialized nations. We explored the concordance and performance of 13 nsSNV pathogenicity prediction tools on panel sequencing results of dilated cardiomyopathy. The analyzed data set from the INHERITANCE study contained 842 nsSNVs discovered in 639 patients, screened for the full sequence of 76 genes related to cardiomyopathies. The single tools prediction revealed a surprisingly high heterogeneity and discordance based on the implemented prediction method. Known disease associations were not reported by the tools, limiting usability in clinics. Because different tools have different advantages, we combined their results. By clustering of correlated methods using similar prediction strategies and calculating a majority vote-based consensus, we found that the prediction accuracy and sensitivity can be further improved. Although challenges remain, different in silico tools bear the potential to predict the malignancy of nsSNVs, especially if different algorithms are combined. Most tools rely mainly on sequence features; beyond these, structural information is important to analyze the relationship of nsSNVs with disease phenotypes. Likewise, current tools consider single nsSNVs, which may, however, show a cumulative effect and turn neutral mutations in an ensemble into pathogenic variants.

@Article{Haas2015,
  author          = {Haas, Jan and Frese, Karen S and Peil, Barbara and Kloos, Wanda and Keller, Andreas and Nietsch, Rouven and Feng, Zhu and Müller, Sabine and Kayvanpour, Elham and Vogel, Britta and Sedaghat-Hamedani, Farbod and Lim, Wei-Keat and Zhao, Xiaohong and Fradkin, Dmitriy and Köhler, Doreen and Fischer, Simon and Franke, Jennifer and Marquart, Sabine and Barb, Ioana and Li, Daniel Tian and Amr, Ali and Ehlermann, Philipp and Mereles, Derliz and Weis, Tanja and Hassel, Sarah and Kremer, Andreas and King, Vanessa and Wirsz, Emil and Isnard, Richard and Komajda, Michel and Serio, Alessandra and Grasso, Maurizia and Syrris, Petros and Wicks, Eleanor and Plagnol, Vincent and Lopes, Luis and Gadgaard, Tenna and Eiskjær, Hans and Jørgensen, Mads and Garcia-Giustiniani, Diego and Ortiz-Genga, Martin and Crespo-Leiro, Maria G and Deprez, Rondal H Lekanne Dit and Christiaans, Imke and van Rijsingen, Ingrid A and Wilde, Arthur A and Waldenstrom, Anders and Bolognesi, Martino and Bellazzi, Riccardo and Mörner, Stellan and Bermejo, Justo Lorenzo and Monserrat, Lorenzo and Villard, Eric and Mogensen, Jens and Pinto, Yigal M and Charron, Philippe and Elliott, Perry and Arbustini, Eloisa and Katus, Hugo A and Meder, Benjamin},
  title           = {Atlas of the clinical genetics of human dilated cardiomyopathy.},
  journal         = {European heart journal},
  year            = {2015},
  volume          = {36},
  pages           = {1123--135a},
  month           = may,
  issn            = {1522-9645},
  abstract        = {Numerous genes are known to cause dilated cardiomyopathy (DCM). However, until now technological limitations have hindered elucidation of the contribution of all clinically relevant disease genes to DCM phenotypes in larger cohorts. We now utilized next-generation sequencing to overcome these limitations and screened all DCM disease genes in a large cohort. In this multi-centre, multi-national study, we have enrolled 639 patients with sporadic or familial DCM. To all samples, we applied a standardized protocol for ultra-high coverage next-generation sequencing of 84 genes, leading to 99.1% coverage of the target region with at least 50-fold and a mean read depth of 2415. In this well characterized cohort, we find the highest number of known cardiomyopathy mutations in plakophilin-2, myosin-binding protein C-3, and desmoplakin. When we include yet unknown but predicted disease variants, we find titin, plakophilin-2, myosin-binding protein-C 3, desmoplakin, ryanodine receptor 2, desmocollin-2, desmoglein-2, and SCN5A variants among the most commonly mutated genes. The overlap between DCM, hypertrophic cardiomyopathy (HCM), and channelopathy causing mutations is considerably high. Of note, we find that >38% of patients have compound or combined mutations and 12.8% have three or even more mutations. When comparing patients recruited in the eight participating European countries we find remarkably little differences in mutation frequencies and affected genes. This is to our knowledge, the first study that comprehensively investigated the genetics of DCM in a large-scale cohort and across a broad gene panel of the known DCM genes. Our results underline the high analytical quality and feasibility of Next-Generation Sequencing in clinical genetic diagnostics and provide a sound database of the genetic causes of DCM.},
  chemicals       = {Genetic Markers},
  citation-subset = {IM},
  completed       = {2016-02-01},
  country         = {England},
  doi             = {10.1093/eurheartj/ehu301},
  issn-linking    = {0195-668X},
  issue           = {18},
  keywords        = {Cardiomyopathy, Dilated, diagnosis, genetics; Europe; Feasibility Studies; Female; Genetic Markers, genetics; Genotype; Heterozygote; Humans; Male; Mutation, genetics; Phenotype; Residence Characteristics; Sequence Analysis, DNA, methods; Cardiomyopathy; Diagnosis; Genetics; Patients},
  nlm-id          = {8006263},
  owner           = {NLM},
  pii             = {ehu301},
  pmid            = {25163546},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2015-05-08},
}

Numerous genes are known to cause dilated cardiomyopathy (DCM). However, until now technological limitations have hindered elucidation of the contribution of all clinically relevant disease genes to DCM phenotypes in larger cohorts. We now utilized next-generation sequencing to overcome these limitations and screened all DCM disease genes in a large cohort. In this multi-centre, multi-national study, we have enrolled 639 patients with sporadic or familial DCM. To all samples, we applied a standardized protocol for ultra-high coverage next-generation sequencing of 84 genes, leading to 99.1% coverage of the target region with at least 50-fold and a mean read depth of 2415. In this well characterized cohort, we find the highest number of known cardiomyopathy mutations in plakophilin-2, myosin-binding protein C-3, and desmoplakin. When we include yet unknown but predicted disease variants, we find titin, plakophilin-2, myosin-binding protein-C 3, desmoplakin, ryanodine receptor 2, desmocollin-2, desmoglein-2, and SCN5A variants among the most commonly mutated genes. The overlap between DCM, hypertrophic cardiomyopathy (HCM), and channelopathy causing mutations is considerably high. Of note, we find that >38% of patients have compound or combined mutations and 12.8% have three or even more mutations. When comparing patients recruited in the eight participating European countries we find remarkably little differences in mutation frequencies and affected genes. This is to our knowledge, the first study that comprehensively investigated the genetics of DCM in a large-scale cohort and across a broad gene panel of the known DCM genes. Our results underline the high analytical quality and feasibility of Next-Generation Sequencing in clinical genetic diagnostics and provide a sound database of the genetic causes of DCM.

@Article{pmid26484086,
   Author="Fischer, U.  and Keller, A.  and Backes, C.  and Meese, E. ",
   Title="{{G}enome-wide copy number profiling to detect gene amplifications in neural progenitor cells}",
   Journal="Genom. Data",
   Year="2014",
   Volume="2",
   Pages="162--165",
   Month="Dec"
}

@Article{pmid25344866,
   Author="Leidinger, P.  and Backes, C.  and Dahmke, I. N.  and Galata, V.  and Huwer, H.  and Stehle, I.  and Bals, R.  and Keller, A.  and Meese, E. ",
   Title="{{W}hat makes a blood cell based mi{R}{N}{A} expression pattern disease specific? -- a mi{R}{N}ome analysis of blood cell subsets in lung cancer patients and healthy controls}",
   Journal="Oncotarget",
   Year="2014",
   Volume="5",
   Number="19",
   Pages="9484--9497",
   Month="Oct"
}

@Article{pmid25175044,
   Author="Leidinger, P.  and Backes, C.  and Blatt, M.  and Keller, A.  and Huwer, H.  and Lepper, P.  and Bals, R.  and Meese, E. ",
   Title="{{T}he blood-borne mi{R}{N}{A} signature of lung cancer patients is independent of histology but influenced by metastases}",
   Journal="Mol. Cancer",
   Year="2014",
   Volume="13",
   Pages="202"
}

@Article{pmid25122923,
   Author="Harz, C.  and Ludwig, N.  and Lang, S.  and Werner, T. V.  and Galata, V.  and Backes, C.  and Schmitt, K.  and Nickels, R.  and Krause, E.  and Jung, M.  and Rettig, J.  and Keller, A.  and Menger, M.  and Zimmermann, R.  and Meese, E. ",
   Title="{{S}ecretion and immunogenicity of the meningioma-associated antigen {T}{X}{N}{D}{C}16}",
   Journal="J. Immunol.",
   Year="2014",
   Volume="193",
   Number="6",
   Pages="3146--3154",
   Month="Sep"
}

@Article{pmid25030422,
   Author="Chandran, P. A.  and Keller, A.  and Weinmann, L.  and Seida, A. A.  and Braun, M.  and Andreev, K.  and Fischer, B.  and Horn, E.  and Schwinn, S.  and Junker, M.  and Houben, R.  and Dombrowski, Y.  and Dietl, J.  and Finotto, S.  and Wolfl, M.  and Meister, G.  and Wischhusen, J. ",
   Title="{{T}he {T}{G}{F}-$\beta$-inducible mi{R}-23a cluster attenuates {I}{F}{N}-$\gamma$ levels and antigen-specific cytotoxicity in human {C}{D}8\textsuperscript{+} {T} cells}",
   Journal="J. Leukoc. Biol.",
   Year="2014",
   Volume="96",
   Number="4",
   Pages="633--645",
   Month="Oct"
}

@Article{pmid25010680,
   Author="Backes, C.  and Leidinger, P.  and Keller, A.  and Hart, M.  and Meyer, T.  and Meese, E.  and Hecksteden, A. ",
   Title="{{B}lood born mi{R}{N}{A}s signatures that can serve as disease specific biomarkers are not significantly affected by overall fitness and exercise}",
   Journal="PLoS ONE",
   Year="2014",
   Volume="9",
   Number="7",
   Pages="e102183"
}

@Article{pmid24928098,
   Author="Leidinger, P.  and Backes, C.  and Meder, B.  and Meese, E.  and Keller, A. ",
   Title="{{T}he human mi{R}{N}{A} repertoire of different blood compounds}",
   Journal="BMC Genomics",
   Year="2014",
   Volume="15",
   Pages="474"
}

@Article{pmid23836875,
   Author="Keller, A.  and Leidinger, P.  and Steinmeyer, F.  and Stahler, C.  and Franke, A.  and Hemmrich-Stanisak, G.  and Kappel, A.  and Wright, I.  and Dorr, J.  and Paul, F.  and Diem, R.  and Tocariu-Krick, B.  and Meder, B.  and Backes, C.  and Meese, E.  and Ruprecht, K. ",
   Title="{{C}omprehensive analysis of micro{R}{N}{A} profiles in multiple sclerosis including next-generation sequencing}",
   Journal="Mult. Scler.",
   Year="2014",
   Volume="20",
   Number="3",
   Pages="295--303",
   Month="Mar"
}

@article{bar02,
    Title="{{Evaluation of microRNAs by molecular imaging for novel diagnostics and therapeutics}}",
    Author="Kloos, W. and Keller, A. and Katus, H. A. and Meder, B",
    Year=2014,
    Journal="Heart Metab.",
    Volume={65},
    Pages="15-20",
}

@Article{Sikora2014,
  author          = {Sikora, Martin and Carpenter, Meredith L and Moreno-Estrada, Andres and Henn, Brenna M and Underhill, Peter A and Sánchez-Quinto, Federico and Zara, Ilenia and Pitzalis, Maristella and Sidore, Carlo and Busonero, Fabio and Maschio, Andrea and Angius, Andrea and Jones, Chris and Mendoza-Revilla, Javier and Nekhrizov, Georgi and Dimitrova, Diana and Theodossiev, Nikola and Harkins, Timothy T and Keller, Andreas and Maixner, Frank and Zink, Albert and Abecasis, Goncalo and Sanna, Serena and Cucca, Francesco and Bustamante, Carlos D},
  title           = {Population genomic analysis of ancient and modern genomes yields new insights into the genetic ancestry of the Tyrolean Iceman and the genetic structure of Europe.},
  journal         = {PLoS genetics},
  year            = {2014},
  volume          = {10},
  pages           = {e1004353},
  month           = may,
  issn            = {1553-7404},
  abstract        = {Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture. },
  citation-subset = {IM},
  completed       = {2014-11-25},
  country         = {United States},
  doi             = {10.1371/journal.pgen.1004353},
  issn-linking    = {1553-7390},
  issue           = {5},
  keywords        = {Europe; Female; Fossils; Genetics, Population; Genome, Human; Humans; Polymorphism, Single Nucleotide},
  nlm-id          = {101239074},
  owner           = {NLM},
  pii             = {PGENETICS-D-13-03438},
  pmc             = {PMC4014435},
  pmid            = {24809476},
  pubmodel        = {Electronic-eCollection},
  pubstatus       = {epublish},
  revised         = {2017-02-20},
}

Genome sequencing of the 5,300-year-old mummy of the Tyrolean Iceman, found in 1991 on a glacier near the border of Italy and Austria, has yielded new insights into his origin and relationship to modern European populations. A key finding of that study was an apparent recent common ancestry with individuals from Sardinia, based largely on the Y chromosome haplogroup and common autosomal SNP variation. Here, we compiled and analyzed genomic datasets from both modern and ancient Europeans, including genome sequence data from over 400 Sardinians and two ancient Thracians from Bulgaria, to investigate this result in greater detail and determine its implications for the genetic structure of Neolithic Europe. Using whole-genome sequencing data, we confirm that the Iceman is, indeed, most closely related to Sardinians. Furthermore, we show that this relationship extends to other individuals from cultural contexts associated with the spread of agriculture during the Neolithic transition, in contrast to individuals from a hunter-gatherer context. We hypothesize that this genetic affinity of ancient samples from different parts of Europe with Sardinians represents a common genetic component that was geographically widespread across Europe during the Neolithic, likely related to migrations and population expansions associated with the spread of agriculture.

@Article{Zink2014,
  author          = {Zink, Albert and Wann, L Samuel and Thompson, Randall C and Keller, Andreas and Maixner, Frank and Allam, Adel H and Finch, Caleb E and Frohlich, Bruno and Kaplan, Hillard and Lombardi, Guido P and Sutherland, M Linda and Sutherland, James D and Watson, Lucia and Cox, Samantha L and Miyamoto, Michael I and Narula, Jagat and Stewart, Alexandre F R and Thomas, Gregory S and Krause, Johannes},
  title           = {Genomic correlates of atherosclerosis in ancient humans.},
  journal         = {Global heart},
  year            = {2014},
  volume          = {9},
  pages           = {203--209},
  month           = jun,
  issn            = {2211-8179},
  abstract        = {Paleogenetics offers a unique opportunity to study human evolution, population dynamics, and disease evolution in situ. Although histologic and computed x-ray tomographic investigations of ancient mummies have clearly shown that atherosclerosis has been present in humans for more than 5,000 years, limited data are available on the presence of genetic predisposition for cardiovascular disease in ancient human populations. In a previous whole-genome study of the Tyrolean Iceman, a 5,300-year-old glacier mummy from the Alps, an increased risk for coronary heart disease was detected. The Iceman's genome revealed several single nucleotide polymorphisms that are linked with cardiovascular disease in genome-wide association studies. Future genetic studies of ancient humans from various geographic origins and time periods have the potential to provide more insights into the presence and possible changes of genetic risk factors in our ancestors. The study of ancient humans and a better understanding of the interaction between environmental and genetic influences on the development of heart diseases may lead to a more effective prevention and treatment of the most common cause of death in the modern world.},
  citation-subset = {IM},
  completed       = {2015-11-05},
  country         = {England},
  doi             = {10.1016/j.gheart.2014.03.2453},
  issue           = {2},
  keywords        = {Atherosclerosis, diagnostic imaging, genetics; Egypt; Genomics; Humans; Imaging, Three-Dimensional; Italy; Mummies; Tomography, X-Ray Computed},
  nlm-id          = {101584391},
  owner           = {NLM},
  pii             = {S2211-8160(14)02496-X},
  pmid            = {25667090},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2016-11-25},
}

Paleogenetics offers a unique opportunity to study human evolution, population dynamics, and disease evolution in situ. Although histologic and computed x-ray tomographic investigations of ancient mummies have clearly shown that atherosclerosis has been present in humans for more than 5,000 years, limited data are available on the presence of genetic predisposition for cardiovascular disease in ancient human populations. In a previous whole-genome study of the Tyrolean Iceman, a 5,300-year-old glacier mummy from the Alps, an increased risk for coronary heart disease was detected. The Iceman's genome revealed several single nucleotide polymorphisms that are linked with cardiovascular disease in genome-wide association studies. Future genetic studies of ancient humans from various geographic origins and time periods have the potential to provide more insights into the presence and possible changes of genetic risk factors in our ancestors. The study of ancient humans and a better understanding of the interaction between environmental and genetic influences on the development of heart diseases may lead to a more effective prevention and treatment of the most common cause of death in the modern world.

@Article{Meder2014,
  author          = {Meder, Benjamin and Rühle, Frank and Weis, Tanja and Homuth, Georg and Keller, Andreas and Franke, Jennifer and Peil, Barbara and Lorenzo Bermejo, Justo and Frese, Karen and Huge, Andreas and Witten, Anika and Vogel, Britta and Haas, Jan and Völker, Uwe and Ernst, Florian and Teumer, Alexander and Ehlermann, Philipp and Zugck, Christian and Friedrichs, Frauke and Kroemer, Heyo and Dörr, Marcus and Hoffmann, Wolfgang and Maisch, Bernhard and Pankuweit, Sabine and Ruppert, Volker and Scheffold, Thomas and Kühl, Uwe and Schultheiss, Hans-Peter and Kreutz, Reinhold and Ertl, Georg and Angermann, Christiane and Charron, Philippe and Villard, Eric and Gary, Françoise and Isnard, Richard and Komajda, Michel and Lutz, Matthias and Meitinger, Thomas and Sinner, Moritz F and Wichmann, H-Erich and Krawczak, Michael and Ivandic, Boris and Weichenhan, Dieter and Gelbrich, Goetz and El-Mokhtari, Nour-Eddine and Schreiber, Stefan and Felix, Stephan B and Hasenfuß, Gerd and Pfeufer, Arne and Hübner, Norbert and Kääb, Stefan and Arbustini, Eloisa and Rottbauer, Wolfgang and Frey, Norbert and Stoll, Monika and Katus, Hugo A},
  title           = {A genome-wide association study identifies 6p21 as novel risk locus for dilated cardiomyopathy.},
  journal         = {European heart journal},
  year            = {2014},
  volume          = {35},
  pages           = {1069--1077},
  month           = apr,
  issn            = {1522-9645},
  abstract        = {Dilated cardiomyopathy (DCM) is one of the leading causes for cardiac transplantations and accounts for up to one-third of all heart failure cases. Since extrinsic and monogenic causes explain only a fraction of all cases, common genetic variants are suspected to contribute to the pathogenesis of DCM, its age of onset, and clinical progression. By a large-scale case-control genome-wide association study we aimed here to identify novel genetic risk loci for DCM. Applying a three-staged study design, we analysed more than 4100 DCM cases and 7600 controls. We identified and successfully replicated multiple single nucleotide polymorphism on chromosome 6p21. In the combined analysis, the most significant association signal was obtained for rs9262636 (P = 4.90 × 10(-9)) located in HCG22, which could again be replicated in an independent cohort. Taking advantage of expression quantitative trait loci (eQTL) as molecular phenotypes, we identified rs9262636 as an eQTL for several closely located genes encoding class I and class II major histocompatibility complex heavy chain receptors. The present study reveals a novel genetic susceptibility locus that clearly underlines the role of genetically driven, inflammatory processes in the pathogenesis of idiopathic DCM.},
  chemicals       = {HLA-C Antigens},
  citation-subset = {IM},
  completed       = {2014-12-16},
  country         = {England},
  doi             = {10.1093/eurheartj/eht251},
  issn-linking    = {0195-668X},
  issue           = {16},
  keywords        = {Cardiomyopathy, Dilated, genetics, physiopathology; Case-Control Studies; Chromosomes, Human, Pair 6, genetics; Female; Genetic Predisposition to Disease, genetics; Genome-Wide Association Study; Genotype; HLA-C Antigens, genetics; Humans; Male; Middle Aged; Polymorphism, Single Nucleotide, genetics; Stroke Volume, physiology; DCM; Dilated cardiomyopathy; Genome-wide association study},
  nlm-id          = {8006263},
  owner           = {NLM},
  pii             = {eht251},
  pmid            = {23853074},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2014-04-22},
}

Dilated cardiomyopathy (DCM) is one of the leading causes for cardiac transplantations and accounts for up to one-third of all heart failure cases. Since extrinsic and monogenic causes explain only a fraction of all cases, common genetic variants are suspected to contribute to the pathogenesis of DCM, its age of onset, and clinical progression. By a large-scale case-control genome-wide association study we aimed here to identify novel genetic risk loci for DCM. Applying a three-staged study design, we analysed more than 4100 DCM cases and 7600 controls. We identified and successfully replicated multiple single nucleotide polymorphism on chromosome 6p21. In the combined analysis, the most significant association signal was obtained for rs9262636 (P = 4.90 × 10(-9)) located in HCG22, which could again be replicated in an independent cohort. Taking advantage of expression quantitative trait loci (eQTL) as molecular phenotypes, we identified rs9262636 as an eQTL for several closely located genes encoding class I and class II major histocompatibility complex heavy chain receptors. The present study reveals a novel genetic susceptibility locus that clearly underlines the role of genetically driven, inflammatory processes in the pathogenesis of idiopathic DCM.

@Article{Okada2014,
  author          = {Okada, Nobuhiro and Lin, Chao-Po and Ribeiro, Marcelo C and Biton, Anne and Lai, Gregory and He, Xingyue and Bu, Pengcheng and Vogel, Hannes and Jablons, David M and Keller, Andreas C and Wilkinson, J Erby and He, Biao and Speed, Terry P and He, Lin},
  title           = {A positive feedback between p53 and miR-34 miRNAs mediates tumor suppression.},
  journal         = {Genes \& development},
  year            = {2014},
  volume          = {28},
  pages           = {438--450},
  month           = mar,
  issn            = {1549-5477},
  abstract        = {As bona fide p53 transcriptional targets, miR-34 microRNAs (miRNAs) exhibit frequent alterations in many human tumor types and elicit multiple p53 downstream effects upon overexpression. Unexpectedly, miR-34 deletion alone fails to impair multiple p53-mediated tumor suppressor effects in mice, possibly due to the considerable redundancy in the p53 pathway. Here, we demonstrate that miR-34a represses HDM4, a potent negative regulator of p53, creating a positive feedback loop acting on p53. In a Kras-induced mouse lung cancer model, miR-34a deficiency alone does not exhibit a strong oncogenic effect. However, miR-34a deficiency strongly promotes tumorigenesis when p53 is haploinsufficient, suggesting that the defective p53-miR-34 feedback loop can enhance oncogenesis in a specific context. The importance of the p53/miR-34/HDM4 feedback loop is further confirmed by an inverse correlation between miR-34 and full-length HDM4 in human lung adenocarcinomas. In addition, human lung adenocarcinomas generate an elevated level of a short HDM4 isoform through alternative polyadenylation. This short HDM4 isoform lacks miR-34-binding sites in the 3' untranslated region (UTR), thereby evading miR-34 regulation to disable the p53-miR-34 positive feedback. Taken together, our results elucidated the intricate cross-talk between p53 and miR-34 miRNAs and revealed an important tumor suppressor effect generated by this positive feedback loop. },
  chemicals       = {MIRN34 microRNA, human, MIRN34 microRNA, mouse, MicroRNAs, Proto-Oncogene Proteins, Tumor Suppressor Protein p53, ras Proteins},
  citation-subset = {IM},
  completed       = {2014-04-21},
  country         = {United States},
  doi             = {10.1101/gad.233585.113},
  issn-linking    = {0890-9369},
  issue           = {5},
  keywords        = {Adenocarcinoma, physiopathology; Animals; Cell Line, Tumor; Feedback, Physiological; Gene Deletion; Gene Expression Regulation, Neoplastic; Haploinsufficiency; Humans; Lung Neoplasms, physiopathology; Mice; MicroRNAs, genetics, metabolism; Proto-Oncogene Proteins, genetics, metabolism; Tumor Cells, Cultured; Tumor Suppressor Protein p53, genetics, metabolism; ras Proteins, genetics, metabolism; HDM4; Mdm4; miR-34; microRNAs; p53},
  nlm-id          = {8711660},
  owner           = {NLM},
  pii             = {gad.233585.113},
  pmc             = {PMC3950342},
  pmid            = {24532687},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2016-10-19},
}

As bona fide p53 transcriptional targets, miR-34 microRNAs (miRNAs) exhibit frequent alterations in many human tumor types and elicit multiple p53 downstream effects upon overexpression. Unexpectedly, miR-34 deletion alone fails to impair multiple p53-mediated tumor suppressor effects in mice, possibly due to the considerable redundancy in the p53 pathway. Here, we demonstrate that miR-34a represses HDM4, a potent negative regulator of p53, creating a positive feedback loop acting on p53. In a Kras-induced mouse lung cancer model, miR-34a deficiency alone does not exhibit a strong oncogenic effect. However, miR-34a deficiency strongly promotes tumorigenesis when p53 is haploinsufficient, suggesting that the defective p53-miR-34 feedback loop can enhance oncogenesis in a specific context. The importance of the p53/miR-34/HDM4 feedback loop is further confirmed by an inverse correlation between miR-34 and full-length HDM4 in human lung adenocarcinomas. In addition, human lung adenocarcinomas generate an elevated level of a short HDM4 isoform through alternative polyadenylation. This short HDM4 isoform lacks miR-34-binding sites in the 3' untranslated region (UTR), thereby evading miR-34 regulation to disable the p53-miR-34 positive feedback. Taken together, our results elucidated the intricate cross-talk between p53 and miR-34 miRNAs and revealed an important tumor suppressor effect generated by this positive feedback loop.

@Article{Abu-Halima2014,
  author          = {Abu-Halima, Masood and Hammadeh, Mohamad and Backes, Christina and Fischer, Ulrike and Leidinger, Petra and Lubbad, Abdel Monem and Keller, Andreas and Meese, Eckart},
  title           = {Panel of five microRNAs as potential biomarkers for the diagnosis and assessment of male infertility.},
  journal         = {Fertility and sterility},
  year            = {2014},
  volume          = {102},
  pages           = {989--997.e1},
  month           = oct,
  issn            = {1556-5653},
  abstract        = {To validate a set of five microRNAs (miRNAs) as specific biomarkers for the assessment of male infertility. Quantitative real-time polymerase chain reaction (qRT-PCR) validation study. University research and clinical institutes. Two hundred twenty-six men presenting at an infertility clinic. None. Validation analysis of a set of miRNAs in human purified spermatozoa and testicular biopsies. Five miRNAs (hsa-miR-34b*, hsa-miR-34b, hsa-miR-34c-5p, hsa-miR-429, and hsa-miR-122) were confirmed with the use of qRT-PCR analysis in validation sets in patients with different forms of spermatogenic impairments (subfertile and nonobstructive azoospermia [NOA]) and control subjects. We found that hsa-miR-429 was significantly increased and the four other miRNAs were decreased in both tested groups compared with normal control subjects. Computing the area under the receiver operating characteristic curve (AUC) value for each of the five miRNAs, we showed that they separated the tested groups with high accuracy (range 0.777-0.988), except for hsa-miR-429 (AUC 0.475), in patient samples with NOA. Furthermore, with the use of support vector machine classification combining these five miRNAs, we found that they discriminated individuals with, respectively, subfertility and NOA from control subjects with an accuracy of 98.65% and 99.91%, a specificity of 98.44% and 99.69%, and a sensitivity of 98.83% and 100%. Our finding suggests that these five miRNAs have potential as novel noninvasive biomarkers to diagnose patients with subfertility. Except for hsa-miR-429, the combination of these miRNAs with other conventional tests would improve the diagnostic accuracy for detecting patients with different forms of NOA.},
  chemicals       = {Genetic Markers, MicroRNAs},
  citation-subset = {IM},
  completed       = {2014-11-28},
  country         = {United States},
  doi             = {10.1016/j.fertnstert.2014.07.001},
  issn-linking    = {0015-0282},
  issue           = {4},
  keywords        = {Case-Control Studies; Genetic Markers; Genetic Predisposition to Disease; Genetic Testing, methods; Humans; Infertility, Male, diagnosis, genetics, physiopathology; Male; MicroRNAs, genetics; Phenotype; Predictive Value of Tests; Real-Time Polymerase Chain Reaction; Reproducibility of Results; Spermatogenesis, genetics; Spermatozoa, chemistry; Testis, chemistry; male infertility; microRNA; nonobstructive azoospermia; seminal plasma; spermatozoa},
  nlm-id          = {0372772},
  owner           = {NLM},
  pii             = {S0015-0282(14)00596-2},
  pmid            = {25108464},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2014-10-02},
}

To validate a set of five microRNAs (miRNAs) as specific biomarkers for the assessment of male infertility. Quantitative real-time polymerase chain reaction (qRT-PCR) validation study. University research and clinical institutes. Two hundred twenty-six men presenting at an infertility clinic. None. Validation analysis of a set of miRNAs in human purified spermatozoa and testicular biopsies. Five miRNAs (hsa-miR-34b*, hsa-miR-34b, hsa-miR-34c-5p, hsa-miR-429, and hsa-miR-122) were confirmed with the use of qRT-PCR analysis in validation sets in patients with different forms of spermatogenic impairments (subfertile and nonobstructive azoospermia [NOA]) and control subjects. We found that hsa-miR-429 was significantly increased and the four other miRNAs were decreased in both tested groups compared with normal control subjects. Computing the area under the receiver operating characteristic curve (AUC) value for each of the five miRNAs, we showed that they separated the tested groups with high accuracy (range 0.777-0.988), except for hsa-miR-429 (AUC 0.475), in patient samples with NOA. Furthermore, with the use of support vector machine classification combining these five miRNAs, we found that they discriminated individuals with, respectively, subfertility and NOA from control subjects with an accuracy of 98.65% and 99.91%, a specificity of 98.44% and 99.69%, and a sensitivity of 98.83% and 100%. Our finding suggests that these five miRNAs have potential as novel noninvasive biomarkers to diagnose patients with subfertility. Except for hsa-miR-429, the combination of these miRNAs with other conventional tests would improve the diagnostic accuracy for detecting patients with different forms of NOA.

@Article{Abu-Halima2014a,
  author          = {Abu-Halima, Masood and Backes, Christina and Leidinger, Petra and Keller, Andreas and Lubbad, Abdel Monem and Hammadeh, Mohamad and Meese, Eckart},
  title           = {MicroRNA expression profiles in human testicular tissues of infertile men with different histopathologic patterns.},
  journal         = {Fertility and sterility},
  year            = {2014},
  volume          = {101},
  pages           = {78--86.e2},
  month           = jan,
  issn            = {1556-5653},
  abstract        = {To investigate the expression profiles of microRNA (miRNA) in human testes showing different histopathological patterns. Microarray with quantitative real-time polymerase chain reaction (qRT-PCR) validation. University research and clinical institutes. Azoospermic men who underwent testicular biopsy for sperm recovery in preparation for intracytoplasmic sperm injection. Testicular biopsies. Statistically significantly altered miRNA expression profiles among the testicular histopathologic patterns groups compared with normal pattern group. According to miRNA array, a total of 197, 68, and 46 miRNAs were found to be differentially expressed when comparing the samples from Sertoli cell only (SCO), mixed atrophy (MA), and germ cell arrest (GA) groups, respectively, with normal spermatogenesis (N). Five miRNAs have been validated using qRT-PCR, and the results were consistent with miRNA array analysis. Bioinformatics analysis showed that five microRNAs (hsa-mir-34b*, hsa-mir-34b, hsa-mir-34c-5p, hsa-mir-449a, and hsa-mir-449b*) were involved in apoptosis, cell proliferation, and differentiation. Notably, potential target genes of these five miRNAs were involved in the spermatogenesis process. This study provides new insights into specific miRNAs that are expressed in infertile men with different histopathologic patterns, suggesting a role of miRNAs in regulating male germ and somatic cells and that their alteration is associated with reproductive abnormalities.},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2014-02-24},
  country         = {United States},
  doi             = {10.1016/j.fertnstert.2013.09.009},
  issn-linking    = {0015-0282},
  issue           = {1},
  keywords        = {Adult; Gene Expression Regulation; Humans; Infertility, Male, diagnosis, genetics, metabolism; Male; MicroRNAs, biosynthesis, genetics; Real-Time Polymerase Chain Reaction, methods; Testis, metabolism, pathology; Transcriptome, physiology; Young Adult; MicroRNA; male infertility; nonobstructive azoospermia; small noncoding RNA; testis},
  nlm-id          = {0372772},
  owner           = {NLM},
  pii             = {S0015-0282(13)03059-8},
  pmid            = {24140040},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2014-01-02},
}

To investigate the expression profiles of microRNA (miRNA) in human testes showing different histopathological patterns. Microarray with quantitative real-time polymerase chain reaction (qRT-PCR) validation. University research and clinical institutes. Azoospermic men who underwent testicular biopsy for sperm recovery in preparation for intracytoplasmic sperm injection. Testicular biopsies. Statistically significantly altered miRNA expression profiles among the testicular histopathologic patterns groups compared with normal pattern group. According to miRNA array, a total of 197, 68, and 46 miRNAs were found to be differentially expressed when comparing the samples from Sertoli cell only (SCO), mixed atrophy (MA), and germ cell arrest (GA) groups, respectively, with normal spermatogenesis (N). Five miRNAs have been validated using qRT-PCR, and the results were consistent with miRNA array analysis. Bioinformatics analysis showed that five microRNAs (hsa-mir-34b*, hsa-mir-34b, hsa-mir-34c-5p, hsa-mir-449a, and hsa-mir-449b*) were involved in apoptosis, cell proliferation, and differentiation. Notably, potential target genes of these five miRNAs were involved in the spermatogenesis process. This study provides new insights into specific miRNAs that are expressed in infertile men with different histopathologic patterns, suggesting a role of miRNAs in regulating male germ and somatic cells and that their alteration is associated with reproductive abnormalities.

@Article{Keller2014,
  author          = {Keller, Andreas and Leidinger, Petra and Vogel, Britta and Backes, Christina and ElSharawy, Abdou and Galata, Valentina and Mueller, Sabine C and Marquart, Sabine and Schrauder, Michael G and Strick, Reiner and Bauer, Andrea and Wischhusen, Jörg and Beier, Markus and Kohlhaas, Jochen and Katus, Hugo A and Hoheisel, Jörg and Franke, Andre and Meder, Benjamin and Meese, Eckart},
  title           = {miRNAs can be generally associated with human pathologies as exemplified for miR-144.},
  journal         = {BMC medicine},
  year            = {2014},
  volume          = {12},
  pages           = {224},
  month           = dec,
  issn            = {1741-7015},
  abstract        = {miRNA profiles are promising biomarker candidates for a manifold of human pathologies, opening new avenues for diagnosis and prognosis. Beyond studies that describe miRNAs frequently as markers for specific traits, we asked whether a general pattern for miRNAs across many diseases exists. We evaluated genome-wide circulating profiles of 1,049 patients suffering from 19 different cancer and non-cancer diseases as well as unaffected controls. The results were validated on 319 individuals using qRT-PCR. We discovered 34 miRNAs with strong disease association. Among those, we found substantially decreased levels of hsa-miR-144* and hsa-miR-20b with AUC of 0.751 (95% CI: 0.703-0.799), respectively. We also discovered a set of miRNAs, including hsa-miR-155*, as rather stable markers, offering reasonable control miRNAs for future studies. The strong downregulation of hsa-miR-144* and the less variable pattern of hsa-miR-155* has been validated in a cohort of 319 samples in three different centers. Here, breast cancer as an additional disease phenotype not included in the screening phase has been included as the 20th trait. Our study on 1,368 patients including 1,049 genome-wide miRNA profiles and 319 qRT-PCR validations further underscores the high potential of specific blood-borne miRNA patterns as molecular biomarkers. Importantly, we highlight 34 miRNAs that are generally dysregulated in human pathologies. Although these markers are not specific to certain diseases they may add to the diagnosis in combination with other markers, building a specific signature. Besides these dysregulated miRNAs, we propose a set of constant miRNAs that may be used as control markers.},
  chemicals       = {Biomarkers, Tumor, MIRN144 microRNA, human, MicroRNAs},
  citation-subset = {IM},
  completed       = {2015-09-21},
  country         = {England},
  doi             = {10.1186/s12916-014-0224-0},
  issn-linking    = {1741-7015},
  keywords        = {Biomarkers, Tumor, genetics; Breast Neoplasms, genetics, pathology; Female; Gene Expression Regulation, Neoplastic; Humans; Male; MicroRNAs, genetics; Middle Aged; Neoplasms, genetics, pathology; Phenotype; Prognosis},
  nlm-id          = {101190723},
  owner           = {NLM},
  pii             = {s12916-014-0224-0},
  pmc             = {PMC4268797},
  pmid            = {25465851},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2015-11-19},
}

miRNA profiles are promising biomarker candidates for a manifold of human pathologies, opening new avenues for diagnosis and prognosis. Beyond studies that describe miRNAs frequently as markers for specific traits, we asked whether a general pattern for miRNAs across many diseases exists. We evaluated genome-wide circulating profiles of 1,049 patients suffering from 19 different cancer and non-cancer diseases as well as unaffected controls. The results were validated on 319 individuals using qRT-PCR. We discovered 34 miRNAs with strong disease association. Among those, we found substantially decreased levels of hsa-miR-144* and hsa-miR-20b with AUC of 0.751 (95% CI: 0.703-0.799), respectively. We also discovered a set of miRNAs, including hsa-miR-155*, as rather stable markers, offering reasonable control miRNAs for future studies. The strong downregulation of hsa-miR-144* and the less variable pattern of hsa-miR-155* has been validated in a cohort of 319 samples in three different centers. Here, breast cancer as an additional disease phenotype not included in the screening phase has been included as the 20th trait. Our study on 1,368 patients including 1,049 genome-wide miRNA profiles and 319 qRT-PCR validations further underscores the high potential of specific blood-borne miRNA patterns as molecular biomarkers. Importantly, we highlight 34 miRNAs that are generally dysregulated in human pathologies. Although these markers are not specific to certain diseases they may add to the diagnosis in combination with other markers, building a specific signature. Besides these dysregulated miRNAs, we propose a set of constant miRNAs that may be used as control markers.

@Article{Backes2014,
  author          = {Backes, Christina and Rühle, Frank and Stoll, Monika and Haas, Jan and Frese, Karen and Franke, Andre and Lieb, Wolfgang and Wichmann, H-Erich and Weis, Tanja and Kloos, Wanda and Lenhof, Hans-Peter and Meese, Eckart and Katus, Hugo and Meder, Benjamin and Keller, Andreas},
  title           = {Systematic permutation testing in GWAS pathway analyses: identification of genetic networks in dilated cardiomyopathy and ulcerative colitis.},
  journal         = {BMC genomics},
  year            = {2014},
  volume          = {15},
  pages           = {622},
  month           = jul,
  issn            = {1471-2164},
  abstract        = {Genome wide association studies (GWAS) are applied to identify genetic loci, which are associated with complex traits and human diseases. Analogous to the evolution of gene expression analyses, pathway analyses have emerged as important tools to uncover functional networks of genome-wide association data. Usually, pathway analyses combine statistical methods with a priori available biological knowledge. To determine significance thresholds for associated pathways, correction for multiple testing and over-representation permutation testing is applied. We systematically investigated the impact of three different permutation test approaches for over-representation analysis to detect false positive pathway candidates and evaluate them on genome-wide association data of Dilated Cardiomyopathy (DCM) and Ulcerative Colitis (UC). Our results provide evidence that the gold standard - permuting the case-control status - effectively improves specificity of GWAS pathway analysis. Although permutation of SNPs does not maintain linkage disequilibrium (LD), these permutations represent an alternative for GWAS data when case-control permutations are not possible. Gene permutations, however, did not add significantly to the specificity. Finally, we provide estimates on the required number of permutations for the investigated approaches. To discover potential false positive functional pathway candidates and to support the results from standard statistical tests such as the Hypergeometric test, permutation tests of case control data should be carried out. The most reasonable alternative was case-control permutation, if this is not possible, SNP permutations may be carried out. Our study also demonstrates that significance values converge rapidly with an increasing number of permutations. By applying the described statistical framework we were able to discover axon guidance, focal adhesion and calcium signaling as important DCM-related pathways and Intestinal immune network for IgA production as most significant UC pathway.},
  citation-subset = {IM},
  completed       = {2015-03-31},
  country         = {England},
  doi             = {10.1186/1471-2164-15-622},
  issn-linking    = {1471-2164},
  keywords        = {Cardiomyopathy, Dilated, genetics, pathology; Colitis, Ulcerative, genetics, pathology; Gene Regulatory Networks; Genome-Wide Association Study; Genomics, methods; Humans; Polymorphism, Single Nucleotide, genetics; Signal Transduction, genetics},
  nlm-id          = {100965258},
  owner           = {NLM},
  pii             = {1471-2164-15-622},
  pmc             = {PMC4223581},
  pmid            = {25052024},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2017-02-20},
}

Genome wide association studies (GWAS) are applied to identify genetic loci, which are associated with complex traits and human diseases. Analogous to the evolution of gene expression analyses, pathway analyses have emerged as important tools to uncover functional networks of genome-wide association data. Usually, pathway analyses combine statistical methods with a priori available biological knowledge. To determine significance thresholds for associated pathways, correction for multiple testing and over-representation permutation testing is applied. We systematically investigated the impact of three different permutation test approaches for over-representation analysis to detect false positive pathway candidates and evaluate them on genome-wide association data of Dilated Cardiomyopathy (DCM) and Ulcerative Colitis (UC). Our results provide evidence that the gold standard - permuting the case-control status - effectively improves specificity of GWAS pathway analysis. Although permutation of SNPs does not maintain linkage disequilibrium (LD), these permutations represent an alternative for GWAS data when case-control permutations are not possible. Gene permutations, however, did not add significantly to the specificity. Finally, we provide estimates on the required number of permutations for the investigated approaches. To discover potential false positive functional pathway candidates and to support the results from standard statistical tests such as the Hypergeometric test, permutation tests of case control data should be carried out. The most reasonable alternative was case-control permutation, if this is not possible, SNP permutations may be carried out. Our study also demonstrates that significance values converge rapidly with an increasing number of permutations. By applying the described statistical framework we were able to discover axon guidance, focal adhesion and calcium signaling as important DCM-related pathways and Intestinal immune network for IgA production as most significant UC pathway.

@Article{Meder2014a,
  author          = {Meder, Benjamin and Backes, Christina and Haas, Jan and Leidinger, Petra and Stähler, Cord and Großmann, Thomas and Vogel, Britta and Frese, Karen and Giannitsis, Evangelos and Katus, Hugo A and Meese, Eckart and Keller, Andreas},
  title           = {Influence of the confounding factors age and sex on microRNA profiles from peripheral blood.},
  journal         = {Clinical chemistry},
  year            = {2014},
  volume          = {60},
  pages           = {1200--1208},
  month           = sep,
  issn            = {1530-8561},
  abstract        = {MicroRNAs (miRNAs) measured from blood samples are promising minimally invasive biomarker candidates that have been extensively studied in several case-control studies. However, the influence of age and sex as confounding variables remains largely unknown. We systematically explored the impact of age and sex on miRNAs in a cohort of 109 physiologically unaffected individuals whose blood was characterized by microarray technology (stage 1). We also investigated an independent cohort from a different institution consisting of 58 physiologically unaffected individuals having a similar mean age but with a smaller age distribution. These samples were measured by use of high-throughput sequencing (stage 2). We detected 318 miRNAs that were significantly correlated with age in stage 1 and, after adjustment for multiple testing of 35 miRNAs, remained statistically significant. Regarding sex, 144 miRNAs showed significant dysregulation. Here, no miRNA remained significant after adjustment for multiple testing. In the high-throughput datasets of stage 2, we generally observed a smaller number of significant associations, mainly as an effect of the smaller cohort size and age distribution. Nevertheless, we found 7 miRNAs that were correlated with age, of which 5 were concordant with stage 1. The age distribution of individuals recruited for case-control studies needs to be carefully considered, whereas sex may be less confounding. To support the translation of miRNAs into clinical application, we offer a web-based application (http://www.ccb.uni-saarland.de/mirnacon) to test individual miRNAs or miRNA signatures for their likelihood of being influenced.},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2014-10-28},
  country         = {United States},
  doi             = {10.1373/clinchem.2014.224238},
  issn-linking    = {0009-9147},
  issue           = {9},
  keywords        = {Adult; Age Factors; Aged; Aged, 80 and over; Female; Gene Expression Regulation; Humans; Male; MicroRNAs, blood; Microarray Analysis; Middle Aged; Reference Standards; Sex Factors; Transcriptome},
  nlm-id          = {9421549},
  owner           = {NLM},
  pii             = {clinchem.2014.224238},
  pmid            = {24987111},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2014-08-29},
}

MicroRNAs (miRNAs) measured from blood samples are promising minimally invasive biomarker candidates that have been extensively studied in several case-control studies. However, the influence of age and sex as confounding variables remains largely unknown. We systematically explored the impact of age and sex on miRNAs in a cohort of 109 physiologically unaffected individuals whose blood was characterized by microarray technology (stage 1). We also investigated an independent cohort from a different institution consisting of 58 physiologically unaffected individuals having a similar mean age but with a smaller age distribution. These samples were measured by use of high-throughput sequencing (stage 2). We detected 318 miRNAs that were significantly correlated with age in stage 1 and, after adjustment for multiple testing of 35 miRNAs, remained statistically significant. Regarding sex, 144 miRNAs showed significant dysregulation. Here, no miRNA remained significant after adjustment for multiple testing. In the high-throughput datasets of stage 2, we generally observed a smaller number of significant associations, mainly as an effect of the smaller cohort size and age distribution. Nevertheless, we found 7 miRNAs that were correlated with age, of which 5 were concordant with stage 1. The age distribution of individuals recruited for case-control studies needs to be carefully considered, whereas sex may be less confounding. To support the translation of miRNAs into clinical application, we offer a web-based application (http://www.ccb.uni-saarland.de/mirnacon) to test individual miRNAs or miRNA signatures for their likelihood of being influenced.

@Article{pmid23864135,
   Author="Vogel, B.  and Keller, A.  and Frese, K. S.  and Leidinger, P.  and Sedaghat-Hamedani, F.  and Kayvanpour, E.  and Kloos, W.  and Backe, C.  and Thanaraj, A.  and Brefort, T.  and Beier, M.  and Hardt, S.  and Meese, E.  and Katus, H. A.  and Meder, B. ",
   Title="{{M}ultivariate mi{R}{N}{A} signatures as biomarkers for non-ischaemic systolic heart failure}",
   Journal="Eur. Heart J.",
   Year="2013",
   Volume="34",
   Number="36",
   Pages="2812--2822",
   Month="Sep"
}

@Article{pmid23826261,
   Author="Hoeke, L.  and Sharbati, J.  and Pawar, K.  and Keller, A.  and Einspanier, R.  and Sharbati, S. ",
   Title="{{I}ntestinal {S}almonella typhimurium infection leads to mi{R}-29a induced caveolin 2 regulation}",
   Journal="PLoS ONE",
   Year="2013",
   Volume="8",
   Number="6",
   Pages="e67300"
}

@Article{pmid23739949,
   Author="Maixner, F.  and Overath, T.  and Linke, D.  and Janko, M.  and Guerriero, G.  and van den Berg, B. H.  and Stade, B.  and Leidinger, P.  and Backes, C.  and Jaremek, M.  and Kneissl, B.  and Meder, B.  and Franke, A.  and Egarter-Vigl, E.  and Meese, E.  and Schwarz, A.  and Tholey, A.  and Zink, A.  and Keller, A. ",
   Title="{{P}aleoproteomic study of the {I}ceman's brain tissue}",
   Journal="Cell. Mol. Life Sci.",
   Year="2013",
   Volume="70",
   Number="19",
   Pages="3709--3722",
   Month="Oct"
}

@Article{pmid23625999,
   Author="Stoeckel, D.  and Mueller, O.  and Kehl, T.  and Gerasch, A.  and Backes, C.  and Rurainski, A.  and Keller, A.  and Kaufmann, M.  and Lenhof, H. P. ",
   Title="{{N}etwork{T}rail--a web service for identifying and visualizing deregulated subnetworks}",
   Journal="Bioinformatics",
   Year="2013",
   Volume="29",
   Number="13",
   Pages="1702--1703",
   Month="Jul"
}

@Article{pmid23624108,
   Author="Ellinghaus, D.  and Zhang, H.  and Zeissig, S.  and Lipinski, S.  and Till, A.  and Jiang, T.  and Stade, B.  and Bromberg, Y.  and Ellinghaus, E.  and Keller, A.  and Rivas, M. A.  and Skieceviciene, J.  and Doncheva, N. T.  and Liu, X.  and Liu, Q.  and Jiang, F.  and Forster, M.  and Mayr, G.  and Albrecht, M.  and Hasler, R.  and Boehm, B. O.  and Goodall, J.  and Berzuini, C. R.  and Lee, J.  and Andersen, V.  and Vogel, U.  and Kupcinskas, L.  and Kayser, M.  and Krawczak, M.  and Nikolaus, S.  and Weersma, R. K.  and Ponsioen, C. Y.  and Sans, M.  and Wijmenga, C.  and Strachan, D. P.  and McArdle, W. L.  and Vermeire, S.  and Rutgeerts, P.  and Sanderson, J. D.  and Mathew, C. G.  and Vatn, M. H.  and Wang, J.  and Nothen, M. M.  and Duerr, R. H.  and Buning, C.  and Brand, S.  and Glas, J.  and Winkelmann, J.  and Illig, T.  and Latiano, A.  and Annese, V.  and Halfvarson, J.  and D'Amato, M.  and Daly, M. J.  and Nothnagel, M.  and Karlsen, T. H.  and Subramani, S.  and Rosenstiel, P.  and Schreiber, S.  and Parkes, M.  and Franke, A. ",
   Title="{{A}ssociation between variants of {P}{R}{D}{M}1 and {N}{D}{P}52 and {C}rohn's disease, based on exome sequencing and functional studies}",
   Journal="Gastroenterology",
   Year="2013",
   Volume="145",
   Number="2",
   Pages="339--347",
   Month="Aug"
}

@Article{pmid23483977,
   Author="Becker, A.  and Ludwig, N.  and Keller, A.  and Tackenberg, B.  and Eienbroker, C.  and Oertel, W. H.  and Fassbender, K.  and Meese, E.  and Ruprecht, K. ",
   Title="{{M}yasthenia gravis: analysis of serum autoantibody reactivities to 1827 potential human autoantigens by protein macroarrays}",
   Journal="PLoS ONE",
   Year="2013",
   Volume="8",
   Number="3",
   Pages="e58095"
}

@Article{pmid23255549,
   Author="Vogel, B.  and Keller, A.  and Frese, K. S.  and Kloos, W.  and Kayvanpour, E.  and Sedaghat-Hamedani, F.  and Hassel, S.  and Marquart, S.  and Beier, M.  and Giannitis, E.  and Hardt, S.  and Katus, H. A.  and Meder, B. ",
   Title="{{R}efining diagnostic micro{R}{N}{A} signatures by whole-mi{R}{N}ome kinetic analysis in acute myocardial infarction}",
   Journal="Clin. Chem.",
   Year="2013",
   Volume="59",
   Number="2",
   Pages="410--418",
   Month="Feb"
}

@Article{pmid22965131,
   Author="Forster, M.  and Forster, P.  and Elsharawy, A.  and Hemmrich, G.  and Kreck, B.  and Wittig, M.  and Thomsen, I.  and Stade, B.  and Barann, M.  and Ellinghaus, D.  and Petersen, B. S.  and May, S.  and Melum, E.  and Schilhabel, M. B.  and Keller, A.  and Schreiber, S.  and Rosenstiel, P.  and Franke, A. ",
   Title="{{F}rom next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software}",
   Journal="Nucleic Acids Res.",
   Year="2013",
   Volume="41",
   Number="1",
   Pages="e16",
   Month="Jan"
}

@Article{Leidinger2013,
  author          = {Leidinger, Petra and Backes, Christina and Deutscher, Stephanie and Schmitt, Katja and Mueller, Sabine C and Frese, Karen and Haas, Jan and Ruprecht, Klemens and Paul, Friedemann and Stähler, Cord and Lang, Christoph J G and Meder, Benjamin and Bartfai, Tamas and Meese, Eckart and Keller, Andreas},
  title           = {A blood based 12-miRNA signature of Alzheimer disease patients.},
  journal         = {Genome biology},
  year            = {2013},
  volume          = {14},
  pages           = {R78},
  month           = jul,
  issn            = {1474-760X},
  abstract        = {Alzheimer disease (AD) is the most common form of dementia but the identification of reliable, early and non-invasive biomarkers remains a major challenge. We present a novel miRNA-based signature for detecting AD from blood samples. We apply next-generation sequencing to miRNAs from blood samples of 48 AD patients and 22 unaffected controls, yielding a total of 140 unique mature miRNAs with significantly changed expression levels. Of these, 82 have higher and 58 have lower abundance in AD patient samples. We selected a panel of 12 miRNAs for an RT-qPCR analysis on a larger cohort of 202 samples, comprising not only AD patients and healthy controls but also patients with other CNS illnesses. These included mild cognitive impairment, which is assumed to represent a transitional period before the development of AD, as well as multiple sclerosis, Parkinson disease, major depression, bipolar disorder and schizophrenia. miRNA target enrichment analysis of the selected 12 miRNAs indicates an involvement of miRNAs in nervous system development, neuron projection, neuron projection development and neuron projection morphogenesis. Using this 12-miRNA signature, we differentiate between AD and controls with an accuracy of 93%, a specificity of 95% and a sensitivity of 92%. The differentiation of AD from other neurological diseases is possible with accuracies between 74% and 78%. The differentiation of the other CNS disorders from controls yields even higher accuracies. The data indicate that deregulated miRNAs in blood might be used as biomarkers in the diagnosis of AD or other neurological diseases.},
  chemicals       = {Biomarkers, MicroRNAs},
  citation-subset = {IM},
  completed       = {2015-03-13},
  country         = {England},
  doi             = {10.1186/gb-2013-14-7-r78},
  issn-linking    = {1474-7596},
  issue           = {7},
  keywords        = {Adult; Aged; Aged, 80 and over; Alzheimer Disease, blood, genetics; Biomarkers, blood; Brain, metabolism; Case-Control Studies; Gene Expression Profiling; Gene Expression Regulation; High-Throughput Nucleotide Sequencing; Humans; MicroRNAs, blood, genetics; Middle Aged; Real-Time Polymerase Chain Reaction; Reproducibility of Results},
  nlm-id          = {100960660},
  owner           = {NLM},
  pii             = {gb-2013-14-7-r78},
  pmc             = {PMC4053778},
  pmid            = {23895045},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2017-02-20},
}

Alzheimer disease (AD) is the most common form of dementia but the identification of reliable, early and non-invasive biomarkers remains a major challenge. We present a novel miRNA-based signature for detecting AD from blood samples. We apply next-generation sequencing to miRNAs from blood samples of 48 AD patients and 22 unaffected controls, yielding a total of 140 unique mature miRNAs with significantly changed expression levels. Of these, 82 have higher and 58 have lower abundance in AD patient samples. We selected a panel of 12 miRNAs for an RT-qPCR analysis on a larger cohort of 202 samples, comprising not only AD patients and healthy controls but also patients with other CNS illnesses. These included mild cognitive impairment, which is assumed to represent a transitional period before the development of AD, as well as multiple sclerosis, Parkinson disease, major depression, bipolar disorder and schizophrenia. miRNA target enrichment analysis of the selected 12 miRNAs indicates an involvement of miRNAs in nervous system development, neuron projection, neuron projection development and neuron projection morphogenesis. Using this 12-miRNA signature, we differentiate between AD and controls with an accuracy of 93%, a specificity of 95% and a sensitivity of 92%. The differentiation of AD from other neurological diseases is possible with accuracies between 74% and 78%. The differentiation of the other CNS disorders from controls yields even higher accuracies. The data indicate that deregulated miRNAs in blood might be used as biomarkers in the diagnosis of AD or other neurological diseases.

@Article{Shah2013,
  author          = {Shah, Aftab Ali and Leidinger, Petra and Backes, Christina and Keller, Andreas and Karpinski, Pawel and Sasiadek, Maria M and Blin, Nikolaus and Meese, Eckart},
  title           = {A set of specific miRNAs is connected with murine and human gastric cancer.},
  journal         = {Genes, chromosomes \& cancer},
  year            = {2013},
  volume          = {52},
  pages           = {237--249},
  month           = mar,
  issn            = {1098-2264},
  abstract        = {MircoRNAs as a new class of regulatory molecules have been investigated in many specific cells and organs in healthy and diseased conditions. Although miRNA signatures can be directly assessed in patients' affected tissues such as tumor sections, recent studies revealed that miRNA profiles can also be obtained indirectly, that is, from the patients' peripheral blood. For better understanding of miRNA's contribution to gastric carcinoma (one of the leading causes of cancer-related mortality worldwide), we screened for deregulated miRNAs in blood collected from human cancer patients and compared the expression patterns with a gastric carcinoma mouse model (Tff1 knock-out). The profiles were assessed using species-specific miRNA microarrays. Among many dozens of deregulated miRNAs (219 in H. sapiens; 75 in M. musculus), a subset of eight miRNAs comparable in sequence from both species was noted. By in silico analysis, their involvement in targeting neoplastic and MAPkinase pathways was demonstrated. We found a high probability of linkage of all noted miRNAs to pathways in cancer with P-values of 0.013 and 0.018 in mice and humans, respectively. Linkage to the MAPK-signaling pathway in mice was observed with a P-value of 0.01. Moreover, when comparing the 219 deregulated miRNAs obtained from blood with deregulated miRNAs derived from gastric cancer (GC) tissues, as published previously, 24 miRNAs were identical. If confirmed in a larger patient pool, these miRNAs could constitute appropriate blood-born biomarkers for GC.},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2013-06-12},
  country         = {United States},
  doi             = {10.1002/gcc.22024},
  issn-linking    = {1045-2257},
  issue           = {3},
  keywords        = {Animals; Disease Models, Animal; Female; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Humans; Male; Mice; Mice, Knockout; MicroRNAs, genetics; Stomach Neoplasms, genetics, pathology},
  nlm-id          = {9007329},
  owner           = {NLM},
  pmid            = {23124995},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2013-01-14},
}

MircoRNAs as a new class of regulatory molecules have been investigated in many specific cells and organs in healthy and diseased conditions. Although miRNA signatures can be directly assessed in patients' affected tissues such as tumor sections, recent studies revealed that miRNA profiles can also be obtained indirectly, that is, from the patients' peripheral blood. For better understanding of miRNA's contribution to gastric carcinoma (one of the leading causes of cancer-related mortality worldwide), we screened for deregulated miRNAs in blood collected from human cancer patients and compared the expression patterns with a gastric carcinoma mouse model (Tff1 knock-out). The profiles were assessed using species-specific miRNA microarrays. Among many dozens of deregulated miRNAs (219 in H. sapiens; 75 in M. musculus), a subset of eight miRNAs comparable in sequence from both species was noted. By in silico analysis, their involvement in targeting neoplastic and MAPkinase pathways was demonstrated. We found a high probability of linkage of all noted miRNAs to pathways in cancer with P-values of 0.013 and 0.018 in mice and humans, respectively. Linkage to the MAPK-signaling pathway in mice was observed with a P-value of 0.01. Moreover, when comparing the 219 deregulated miRNAs obtained from blood with deregulated miRNAs derived from gastric cancer (GC) tissues, as published previously, 24 miRNAs were identical. If confirmed in a larger patient pool, these miRNAs could constitute appropriate blood-born biomarkers for GC.

@Article{Haas2013,
  author          = {Haas, Jan and Frese, Karen S and Park, Yoon Jung and Keller, Andreas and Vogel, Britta and Lindroth, Anders M and Weichenhan, Dieter and Franke, Jennifer and Fischer, Simon and Bauer, Andrea and Marquart, Sabine and Sedaghat-Hamedani, Farbod and Kayvanpour, Elham and Köhler, Doreen and Wolf, Nadine M and Hassel, Sarah and Nietsch, Rouven and Wieland, Thomas and Ehlermann, Philipp and Schultz, Jobst-Hendrik and Dösch, Andreas and Mereles, Derliz and Hardt, Stefan and Backs, Johannes and Hoheisel, Jörg D and Plass, Christoph and Katus, Hugo A and Meder, Benjamin},
  title           = {Alterations in cardiac DNA methylation in human dilated cardiomyopathy.},
  journal         = {EMBO molecular medicine},
  year            = {2013},
  volume          = {5},
  pages           = {413--429},
  month           = mar,
  issn            = {1757-4684},
  abstract        = {Dilated cardiomyopathies (DCM) show remarkable variability in their age of onset, phenotypic presentation, and clinical course. Hence, disease mechanisms must exist that modify the occurrence and progression of DCM, either by genetic or epigenetic factors that may interact with environmental stimuli. In the present study, we examined genome-wide cardiac DNA methylation in patients with idiopathic DCM and controls. We detected methylation differences in pathways related to heart disease, but also in genes with yet unknown function in DCM or heart failure, namely Lymphocyte antigen 75 (LY75), Tyrosine kinase-type cell surface receptor HER3 (ERBB3), Homeobox B13 (HOXB13) and Adenosine receptor A2A (ADORA2A). Mass-spectrometric analysis and bisulphite-sequencing enabled confirmation of the observed DNA methylation changes in independent cohorts. Aberrant DNA methylation in DCM patients was associated with significant changes in LY75 and ADORA2A mRNA expression, but not in ERBB3 and HOXB13. In vivo studies of orthologous ly75 and adora2a in zebrafish demonstrate a functional role of these genes in adaptive or maladaptive pathways in heart failure.},
  chemicals       = {Antigens, CD, DEC-205 receptor, Lectins, C-Type, Minor Histocompatibility Antigens, RNA, Messenger, Receptor, Adenosine A2A, Receptors, Cell Surface, Zebrafish Proteins},
  citation-subset = {IM},
  completed       = {2013-07-22},
  country         = {England},
  doi             = {10.1002/emmm.201201553},
  issn-linking    = {1757-4676},
  issue           = {3},
  keywords        = {Adult; Aged; Animals; Antigens, CD, genetics, metabolism; Biopsy; Cardiomyopathy, Dilated, genetics, metabolism, physiopathology; Case-Control Studies; Cluster Analysis; DNA Methylation; Epigenesis, Genetic; Female; Gene Expression Regulation; Gene Knockdown Techniques; Genetic Predisposition to Disease; HEK293 Cells; Humans; Lectins, C-Type, genetics, metabolism; Male; Mass Spectrometry; Middle Aged; Minor Histocompatibility Antigens; Molecular Sequence Data; Myocardium, metabolism; Phenotype; RNA, Messenger, metabolism; Rats; Receptor, Adenosine A2A, genetics, metabolism; Receptors, Cell Surface, genetics, metabolism; Reproducibility of Results; Sequence Analysis, DNA, methods; Sequence Analysis, Protein; Transfection; Zebrafish, genetics, metabolism; Zebrafish Proteins, genetics, metabolism},
  nlm-id          = {101487380},
  owner           = {NLM},
  pmc             = {PMC3598081},
  pmid            = {23341106},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2016-11-25},
}

Dilated cardiomyopathies (DCM) show remarkable variability in their age of onset, phenotypic presentation, and clinical course. Hence, disease mechanisms must exist that modify the occurrence and progression of DCM, either by genetic or epigenetic factors that may interact with environmental stimuli. In the present study, we examined genome-wide cardiac DNA methylation in patients with idiopathic DCM and controls. We detected methylation differences in pathways related to heart disease, but also in genes with yet unknown function in DCM or heart failure, namely Lymphocyte antigen 75 (LY75), Tyrosine kinase-type cell surface receptor HER3 (ERBB3), Homeobox B13 (HOXB13) and Adenosine receptor A2A (ADORA2A). Mass-spectrometric analysis and bisulphite-sequencing enabled confirmation of the observed DNA methylation changes in independent cohorts. Aberrant DNA methylation in DCM patients was associated with significant changes in LY75 and ADORA2A mRNA expression, but not in ERBB3 and HOXB13. In vivo studies of orthologous ly75 and adora2a in zebrafish demonstrate a functional role of these genes in adaptive or maladaptive pathways in heart failure.

@Article{Abu-Halima2013,
  author          = {Abu-Halima, Masood and Hammadeh, Mohamad and Schmitt, Jana and Leidinger, Petra and Keller, Andreas and Meese, Eckart and Backes, Christina},
  title           = {Altered microRNA expression profiles of human spermatozoa in patients with different spermatogenic impairments.},
  journal         = {Fertility and sterility},
  year            = {2013},
  volume          = {99},
  pages           = {1249--1255.e16},
  month           = apr,
  issn            = {1556-5653},
  abstract        = {To determine whether microRNAs are differentially expressed in men with normal versus impaired spermatogenesis, and to find a biomarker for accurate diagnosis of male infertility. Microarray with real-time polymerase chain reaction (RT-PCR) validation. University research and clinical institutes. Male partner of selected couples (n = 27) who were undergoing assisted reproduction techniques for infertility treatment. None. Statistically significantly altered microRNA expression profiles in normozoospermic versus asthenozoospermic and oligoasthenozoospermic men. There were 50 miRNAs up-regulated and 27 miRNAs down-regulated in asthenozoospermic males. In oligoasthenozoospermic males, 42 miRNAs were up-regulated and 44 miRNAs down-regulated when compared with normozoospermic males. The miRNAs that exhibited the highest fold changes and area under the receiver operating characteristic curve were miR-34b, miR-122, and miR-1973 in samples from asthenozoospermic men and miR-34b, miR-34b*, miR-15b, miR-34c-5p, miR-122, miR-449a, miR-1973, miR-16, and miR-19a in samples from oligoasthenozoospermic men. Furthermore, quantitative RT-PCR assays on specific miRNAs, including miR-141, miR-200a, miR-122, miR-34b, miR-34c-5p, and miR-16, yielded results that were largely consistent with the microarray data. Our results reveal an extended number of miRNAs that were differentially expressed in asthenozoospermic and oligoasthenozoospermic males compared with normozoospermic males. These data provide evidence for analysis of miRNA profiles as a future diagnosing tool for male infertility.},
  chemicals       = {MicroRNAs, RNA, Small Untranslated},
  citation-subset = {IM},
  completed       = {2013-06-28},
  country         = {United States},
  doi             = {10.1016/j.fertnstert.2012.11.054},
  issn-linking    = {0015-0282},
  issue           = {5},
  keywords        = {Adult; Asthenozoospermia, diagnosis, genetics; Down-Regulation, genetics; Fertility, genetics; Humans; Male; MicroRNAs, genetics; Oligospermia, diagnosis, genetics; RNA, Small Untranslated, genetics; Real-Time Polymerase Chain Reaction, methods, standards; Reproducibility of Results; Reproductive Techniques, Assisted; Spermatogenesis, genetics; Spermatozoa, physiology; Transcriptome; Up-Regulation, genetics},
  nlm-id          = {0372772},
  owner           = {NLM},
  pii             = {S0015-0282(12)02496-X},
  pmid            = {23312218},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2013-04-01},
}

To determine whether microRNAs are differentially expressed in men with normal versus impaired spermatogenesis, and to find a biomarker for accurate diagnosis of male infertility. Microarray with real-time polymerase chain reaction (RT-PCR) validation. University research and clinical institutes. Male partner of selected couples (n = 27) who were undergoing assisted reproduction techniques for infertility treatment. None. Statistically significantly altered microRNA expression profiles in normozoospermic versus asthenozoospermic and oligoasthenozoospermic men. There were 50 miRNAs up-regulated and 27 miRNAs down-regulated in asthenozoospermic males. In oligoasthenozoospermic males, 42 miRNAs were up-regulated and 44 miRNAs down-regulated when compared with normozoospermic males. The miRNAs that exhibited the highest fold changes and area under the receiver operating characteristic curve were miR-34b, miR-122, and miR-1973 in samples from asthenozoospermic men and miR-34b, miR-34b*, miR-15b, miR-34c-5p, miR-122, miR-449a, miR-1973, miR-16, and miR-19a in samples from oligoasthenozoospermic men. Furthermore, quantitative RT-PCR assays on specific miRNAs, including miR-141, miR-200a, miR-122, miR-34b, miR-34c-5p, and miR-16, yielded results that were largely consistent with the microarray data. Our results reveal an extended number of miRNAs that were differentially expressed in asthenozoospermic and oligoasthenozoospermic males compared with normozoospermic males. These data provide evidence for analysis of miRNA profiles as a future diagnosing tool for male infertility.

@Article{pmid23200138,
   Author="Staehler, C. F.  and Keller, A.  and Leidinger, P.  and Backes, C.  and Chandran, A.  and Wischhusen, J.  and Meder, B.  and Meese, E. ",
   Title="{{W}hole mi{R}{N}ome-wide differential co-expression of micro{R}{N}{A}s}",
   Journal="Genomics Proteomics Bioinformatics",
   Year="2012",
   Volume="10",
   Number="5",
   Pages="285--294",
   Month="Oct"
}

@Article{pmid22913592,
   Author="Elsharawy, A.  and Forster, M.  and Schracke, N.  and Keller, A.  and Thomsen, I.  and Petersen, B. S.  and Stade, B.  and Stahler, P.  and Schreiber, S.  and Rosenstiel, P.  and Franke, A. ",
   Title="{{I}mproving mapping and {S}{N}{P}-calling performance in multiplexed targeted next-generation sequencing}",
   Journal="BMC Genomics",
   Year="2012",
   Volume="13",
   Pages="417"
}

@Article{pmid22871070,
   Author="Schmitt, J.  and Backes, C.  and Nourkami-Tutdibi, N.  and Leidinger, P.  and Deutscher, S.  and Beier, M.  and Gessler, M.  and Graf, N.  and Lenhof, H. P.  and Keller, A.  and Meese, E. ",
   Title="{{T}reatment-independent mi{R}{N}{A} signature in blood of {W}ilms tumor patients}",
   Journal="BMC Genomics",
   Year="2012",
   Volume="13",
   Pages="379"
}

@Article{pmid22619067,
   Author="Schmitt, J.  and Fischer, U.  and Heisel, S.  and Strickfaden, H.  and Backes, C.  and Ruggieri, A.  and Keller, A.  and Chang, P.  and Meese, E. ",
   Title="{{G}{A}{S}41 amplification results in overexpression of a new spindle pole protein}",
   Journal="Genes Chromosomes Cancer",
   Year="2012",
   Volume="51",
   Number="9",
   Pages="868--880",
   Month="Sep"
}

@Article{pmid22606362,
   Author="Fischer, U.  and Keller, A.  and Voss, M.  and Backes, C.  and Welter, C.  and Meese, E. ",
   Title="{{G}enome-wide gene amplification during differentiation of neural progenitor cells in vitro}",
   Journal="PLoS ONE",
   Year="2012",
   Volume="7",
   Number="5",
   Pages="e37422"
}

@Article{pmid22533606,
   Author="ElSharawy, A.  and Keller, A.  and Flachsbart, F.  and Wendschlag, A.  and Jacobs, G.  and Kefer, N.  and Brefort, T.  and Leidinger, P.  and Backes, C.  and Meese, E.  and Schreiber, S.  and Rosenstiel, P.  and Franke, A.  and Nebel, A. ",
   Title="{{G}enome-wide mi{R}{N}{A} signatures of human longevity}",
   Journal="Aging Cell",
   Year="2012",
   Volume="11",
   Number="4",
   Pages="607--616",
   Month="Aug"
}

@Article{pmid22511932,
   Author="Bauer, A. S.  and Keller, A.  and Costello, E.  and Greenhalf, W.  and Bier, M.  and Borries, A.  and Beier, M.  and Neoptolemos, J.  and Buchler, M.  and Werner, J.  and Giese, N.  and Hoheisel, J. D. ",
   Title="{{D}iagnosis of pancreatic ductal adenocarcinoma and chronic pancreatitis by measurement of micro{R}{N}{A} abundance in blood and tissue}",
   Journal="PLoS ONE",
   Year="2012",
   Volume="7",
   Number="4",
   Pages="e34151"
}

@Article{pmid22384141,
   Author="Jiao, L. R.  and Frampton, A. E.  and Jacob, J.  and Pellegrino, L.  and Krell, J.  and Giamas, G.  and Tsim, N.  and Vlavianos, P.  and Cohen, P.  and Ahmad, R.  and Keller, A.  and Habib, N. A.  and Stebbing, J.  and Castellano, L. ",
   Title="{{M}icro{R}{N}{A}s targeting oncogenes are down-regulated in pancreatic malignant transformation from benign tumors}",
   Journal="PLoS ONE",
   Year="2012",
   Volume="7",
   Number="2",
   Pages="e32068"
}

@Article{pmid22364731,
   Author="Ludwig, N.  and Keller, A.  and Leidinger, P.  and Harz, C.  and Backes, C.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{I}s there a general autoantibody signature for cancer?}",
   Journal="Eur. J. Cancer",
   Year="2012",
   Volume="48",
   Number="15",
   Pages="2451--2461",
   Month="Oct"
}

@Article{pmid21913182,
   Author="Schmitt, J.  and Heisel, S.  and Keller, A.  and Leidinger, P.  and Ludwig, N.  and Habel, N.  and Furtwangler, R.  and Nourkami-Tutdibi, N.  and Wegert, J.  and Grundy, P.  and Gessler, M.  and Graf, N.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{M}ulticenter study identified molecular blood-born protein signatures for {W}ilms {T}umor}",
   Journal="Int. J. Cancer",
   Year="2012",
   Volume="131",
   Number="3",
   Pages="673--682",
   Month="Aug"
}

@Article{pmid21601932,
   Author="Meder, B.  and Bergmann, C. E.  and Keller, A.  and Just, S.  and Katus, H. A.  and Hoefer, I. E.  and Buschmann, I. R. ",
   Title="{{Q}uantification of collateral artery growth by automated fluorescent microsphere perfusion}",
   Journal="Int. J. Cardiol.",
   Year="2012",
   Volume="161",
   Number="2",
   Pages="88--92",
   Month="Nov"
}

@Article{pmid22664918,
   Author="Leidinger, P.  and Keller, A.  and Backes, C.  and Huwer, H.  and Meese, E. ",
   Title="{{M}icro{R}{N}{A} expression changes after lung cancer resection: a follow-up study}",
   Journal="RNA Biol",
   Year="2012",
   Volume="9",
   Number="6",
   Pages="900--910",
   Month="Jun"
}

@Article{Shah2012,
  author          = {Shah, Aftab Ali and Leidinger, Petra and Keller, Andreas and Wendschlag, Anke and Meese, Eckart and Blin, Nikolaus},
  title           = {Altered miRNA expression patterns in Tff2 knock-out mice correlate with cellular pathways of neoplastic development and caloric metabolism.},
  journal         = {International journal of molecular medicine},
  year            = {2012},
  volume          = {29},
  pages           = {637--643},
  month           = apr,
  issn            = {1791-244X},
  abstract        = {The trefoil peptide family, consisting in mammals of three members namely TFF1, 2 and 3, plays a cytoprotective role in epithelial cells of various tissues, mainly in the digestive tract. Tff1, Tff2 or Tff3 knock-out mouse models developed various kinds of gastrointestinal impairment. microRNAs are known to be novel gene regulators. We aimed to investigate the physiological role of such miRNAs in Tff2 knock-out mice. Whole miRNome profiling and in silico analysis were performed for Tff2-KO and WT mice. Our latest data explored the role of miRNAs in the regulatory cascades and molecular processes of Tff2-/- mice. As much as 6% of the Tff2-KO mice miRNome was significantly dys-regulated. Further in silico analysis suggests that the respective dys-regulated part of the miRNome is involved in human pathological processes, including pancreatic, colorectal and basal cell cancer. Additionally, the dys-regulated miRNome targets pathways involved in carbohydrate metabolism and adipocytokine signaling. The latter links deficient caloric maintenance in Tff2 and previous observation in Tff3-KO mice with miRNAs. In summary, our proof-of-concept study indicates that miRNAs may play an important role in the regulatory processes of the trefoil peptide family, especially in the regulation of cancer-related cascades.},
  chemicals       = {Adipokines, MicroRNAs, Mucins, Muscle Proteins, Peptides, TFF2 protein, human, TFF2 protein, mouse, Trefoil Factor-2},
  citation-subset = {IM},
  completed       = {2012-05-29},
  country         = {Greece},
  doi             = {10.3892/ijmm.2012.881},
  issn-linking    = {1107-3756},
  issue           = {4},
  keywords        = {Adipokines, genetics, metabolism; Animals; Carbohydrate Metabolism, genetics; Gene Expression Profiling; Gene Expression Regulation, Neoplastic; Genes, Regulator; Mice; Mice, Knockout; MicroRNAs, genetics, metabolism; Mucins, genetics, metabolism; Muscle Proteins, genetics, metabolism; Peptides, genetics, metabolism; Signal Transduction; Trefoil Factor-2},
  nlm-id          = {9810955},
  owner           = {NLM},
  pmc             = {PMC3573770},
  pmid            = {22245972},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2016-11-25},
}

The trefoil peptide family, consisting in mammals of three members namely TFF1, 2 and 3, plays a cytoprotective role in epithelial cells of various tissues, mainly in the digestive tract. Tff1, Tff2 or Tff3 knock-out mouse models developed various kinds of gastrointestinal impairment. microRNAs are known to be novel gene regulators. We aimed to investigate the physiological role of such miRNAs in Tff2 knock-out mice. Whole miRNome profiling and in silico analysis were performed for Tff2-KO and WT mice. Our latest data explored the role of miRNAs in the regulatory cascades and molecular processes of Tff2-/- mice. As much as 6% of the Tff2-KO mice miRNome was significantly dys-regulated. Further in silico analysis suggests that the respective dys-regulated part of the miRNome is involved in human pathological processes, including pancreatic, colorectal and basal cell cancer. Additionally, the dys-regulated miRNome targets pathways involved in carbohydrate metabolism and adipocytokine signaling. The latter links deficient caloric maintenance in Tff2 and previous observation in Tff3-KO mice with miRNAs. In summary, our proof-of-concept study indicates that miRNAs may play an important role in the regulatory processes of the trefoil peptide family, especially in the regulation of cancer-related cascades.

@Article{Backes2012,
  author          = {Backes, Christina and Rurainski, Alexander and Klau, Gunnar W and Müller, Oliver and Stöckel, Daniel and Gerasch, Andreas and Küntzer, Jan and Maisel, Daniela and Ludwig, Nicole and Hein, Matthias and Keller, Andreas and Burtscher, Helmut and Kaufmann, Michael and Meese, Eckart and Lenhof, Hans-Peter},
  title           = {An integer linear programming approach for finding deregulated subgraphs in regulatory networks.},
  journal         = {Nucleic acids research},
  year            = {2012},
  volume          = {40},
  pages           = {e43},
  month           = mar,
  issn            = {1362-4962},
  abstract        = {Deregulation of cell signaling pathways plays a crucial role in the development of tumors. The identification of such pathways requires effective analysis tools that facilitate the interpretation of expression differences. Here, we present a novel and highly efficient method for identifying deregulated subnetworks in a regulatory network. Given a score for each node that measures the degree of deregulation of the corresponding gene or protein, the algorithm computes the heaviest connected subnetwork of a specified size reachable from a designated root node. This root node can be interpreted as a molecular key player responsible for the observed deregulation. To demonstrate the potential of our approach, we analyzed three gene expression data sets. In one scenario, we compared expression profiles of non-malignant primary mammary epithelial cells derived from BRCA1 mutation carriers and of epithelial cells without BRCA1 mutation. Our results suggest that oxidative stress plays an important role in epithelial cells of BRCA1 mutation carriers and that the activation of stress proteins may result in avoidance of apoptosis leading to an increased overall survival of cells with genetic alterations. In summary, our approach opens new avenues for the elucidation of pathogenic mechanisms and for the detection of molecular key players.},
  citation-subset = {IM},
  completed       = {2012-05-29},
  country         = {England},
  doi             = {10.1093/nar/gkr1227},
  issn-linking    = {0305-1048},
  issue           = {6},
  keywords        = {Adenocarcinoma, genetics, metabolism; Algorithms; Breast, cytology, metabolism; Cell Line, Tumor; Colorectal Neoplasms, genetics, metabolism; Epithelial Cells, metabolism; Female; Gene Expression Profiling; Gene Expression Regulation; Gene Regulatory Networks; Genes, BRCA1; Glioma, genetics, metabolism; Humans; Mutation; Programming, Linear; Protein Interaction Maps; Signal Transduction},
  nlm-id          = {0411011},
  owner           = {NLM},
  pii             = {gkr1227},
  pmc             = {PMC3315310},
  pmid            = {22210863},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2015-01-29},
}

Deregulation of cell signaling pathways plays a crucial role in the development of tumors. The identification of such pathways requires effective analysis tools that facilitate the interpretation of expression differences. Here, we present a novel and highly efficient method for identifying deregulated subnetworks in a regulatory network. Given a score for each node that measures the degree of deregulation of the corresponding gene or protein, the algorithm computes the heaviest connected subnetwork of a specified size reachable from a designated root node. This root node can be interpreted as a molecular key player responsible for the observed deregulation. To demonstrate the potential of our approach, we analyzed three gene expression data sets. In one scenario, we compared expression profiles of non-malignant primary mammary epithelial cells derived from BRCA1 mutation carriers and of epithelial cells without BRCA1 mutation. Our results suggest that oxidative stress plays an important role in epithelial cells of BRCA1 mutation carriers and that the activation of stress proteins may result in avoidance of apoptosis leading to an increased overall survival of cells with genetic alterations. In summary, our approach opens new avenues for the elucidation of pathogenic mechanisms and for the detection of molecular key players.

@Article{Keller2012,
  author          = {Keller, Andreas and Graefen, Angela and Ball, Markus and Matzas, Mark and Boisguerin, Valesca and Maixner, Frank and Leidinger, Petra and Backes, Christina and Khairat, Rabab and Forster, Michael and Stade, Björn and Franke, Andre and Mayer, Jens and Spangler, Jessica and McLaughlin, Stephen and Shah, Minita and Lee, Clarence and Harkins, Timothy T and Sartori, Alexander and Moreno-Estrada, Andres and Henn, Brenna and Sikora, Martin and Semino, Ornella and Chiaroni, Jacques and Rootsi, Siiri and Myres, Natalie M and Cabrera, Vicente M and Underhill, Peter A and Bustamante, Carlos D and Vigl, Eduard Egarter and Samadelli, Marco and Cipollini, Giovanna and Haas, Jan and Katus, Hugo and O'Connor, Brian D and Carlson, Marc R J and Meder, Benjamin and Blin, Nikolaus and Meese, Eckart and Pusch, Carsten M and Zink, Albert},
  title           = {New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing.},
  journal         = {Nature communications},
  year            = {2012},
  volume          = {3},
  pages           = {698},
  month           = feb,
  issn            = {2041-1723},
  abstract        = {The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to ~60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.},
  chemicals       = {DNA, Mitochondrial},
  citation-subset = {IM},
  completed       = {2012-08-02},
  country         = {England},
  doi             = {10.1038/ncomms1701},
  issn-linking    = {2041-1723},
  keywords        = {Base Sequence; Borrelia burgdorferi, genetics; Chromosome Mapping; DNA, Mitochondrial, genetics; Genetic Predisposition to Disease; Genome, Human; Genome, Mitochondrial; History, Ancient; Humans; Lyme Disease, history; Mitochondria, genetics; Mummies, microbiology; Paleontology; Phenotype; Sequence Analysis, DNA; Vascular Calcification},
  nlm-id          = {101528555},
  owner           = {NLM},
  pii             = {ncomms1701},
  pmid            = {22426219},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2017-02-20},
}

The Tyrolean Iceman, a 5,300-year-old Copper age individual, was discovered in 1991 on the Tisenjoch Pass in the Italian part of the Ötztal Alps. Here we report the complete genome sequence of the Iceman and show 100% concordance between the previously reported mitochondrial genome sequence and the consensus sequence generated from our genomic data. We present indications for recent common ancestry between the Iceman and present-day inhabitants of the Tyrrhenian Sea, that the Iceman probably had brown eyes, belonged to blood group O and was lactose intolerant. His genetic predisposition shows an increased risk for coronary heart disease and may have contributed to the development of previously reported vascular calcifications. Sequences corresponding to  60% of the genome of Borrelia burgdorferi are indicative of the earliest human case of infection with the pathogen for Lyme borreliosis.

@Article{Laczny2012,
  author          = {Laczny, Cedric and Leidinger, Petra and Haas, Jan and Ludwig, Nicole and Backes, Christina and Gerasch, Andreas and Kaufmann, Michael and Vogel, Britta and Katus, Hugo A and Meder, Benjamin and Stähler, Cord and Meese, Eckart and Lenhof, Hans-Peter and Keller, Andreas},
  title           = {miRTrail--a comprehensive webserver for analyzing gene and miRNA patterns to enhance the understanding of regulatory mechanisms in diseases.},
  journal         = {BMC bioinformatics},
  year            = {2012},
  volume          = {13},
  pages           = {36},
  month           = feb,
  issn            = {1471-2105},
  abstract        = {Expression profiling provides new insights into regulatory and metabolic processes and in particular into pathogenic mechanisms associated with diseases. Besides genes, non-coding transcripts as microRNAs (miRNAs) gained increasing relevance in the last decade. To understand the regulatory processes of miRNAs on genes, integrative computer-aided approaches are essential, especially in the light of complex human diseases as cancer. Here, we present miRTrail, an integrative tool that allows for performing comprehensive analyses of interactions of genes and miRNAs based on expression profiles. The integrated analysis of mRNA and miRNA data should generate more robust and reliable results on deregulated pathogenic processes and may also offer novel insights into the regulatory interactions between miRNAs and genes. Our web-server excels in carrying out gene sets analysis, analysis of miRNA sets as well as the combination of both in a systems biology approach. To this end, miRTrail integrates information on 20.000 genes, almost 1.000 miRNAs, and roughly 280.000 putative interactions, for Homo sapiens and accordingly for Mus musculus and Danio rerio. The well-established, classical Chi-squared test is one of the central techniques of our tool for the joint consideration of miRNAs and their targets. For interactively visualizing obtained results, it relies on the network analyzers and viewers BiNA or Cytoscape-web, also enabling direct access to relevant literature. We demonstrated the potential of miRTrail by applying our tool to mRNA and miRNA data of malignant melanoma. MiRTrail identified several deregulated miRNAs that target deregulated mRNAs including miRNAs hsa-miR-23b and hsa-miR-223, which target the highest numbers of deregulated mRNAs and regulate the pathway "basal cell carcinoma". In addition, both miRNAs target genes like PTCH1 and RASA1 that are involved in many oncogenic processes. The application on melanoma samples demonstrates that the miRTrail platform may open avenues for investigating the regulatory interactions between genes and miRNAs for a wide range of human diseases. Moreover, miRTrail cannot only be applied to microarray based expression profiles, but also to NGS-based transcriptomic data. The program is freely available as web-server at mirtrail.bioinf.uni-sb.de.},
  chemicals       = {MicroRNAs, RNA, Messenger},
  citation-subset = {IM},
  completed       = {2012-11-19},
  country         = {England},
  doi             = {10.1186/1471-2105-13-36},
  issn-linking    = {1471-2105},
  keywords        = {Animals; Computers; Gene Expression Regulation; Humans; Internet; Melanoma, genetics; Mice; MicroRNAs, genetics, metabolism, physiology; RNA, Messenger, genetics, metabolism; Skin Neoplasms, genetics; Transcriptome; Zebrafish},
  nlm-id          = {100965194},
  owner           = {NLM},
  pii             = {1471-2105-13-36},
  pmc             = {PMC3352041},
  pmid            = {22356618},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2017-02-20},
}

Expression profiling provides new insights into regulatory and metabolic processes and in particular into pathogenic mechanisms associated with diseases. Besides genes, non-coding transcripts as microRNAs (miRNAs) gained increasing relevance in the last decade. To understand the regulatory processes of miRNAs on genes, integrative computer-aided approaches are essential, especially in the light of complex human diseases as cancer. Here, we present miRTrail, an integrative tool that allows for performing comprehensive analyses of interactions of genes and miRNAs based on expression profiles. The integrated analysis of mRNA and miRNA data should generate more robust and reliable results on deregulated pathogenic processes and may also offer novel insights into the regulatory interactions between miRNAs and genes. Our web-server excels in carrying out gene sets analysis, analysis of miRNA sets as well as the combination of both in a systems biology approach. To this end, miRTrail integrates information on 20.000 genes, almost 1.000 miRNAs, and roughly 280.000 putative interactions, for Homo sapiens and accordingly for Mus musculus and Danio rerio. The well-established, classical Chi-squared test is one of the central techniques of our tool for the joint consideration of miRNAs and their targets. For interactively visualizing obtained results, it relies on the network analyzers and viewers BiNA or Cytoscape-web, also enabling direct access to relevant literature. We demonstrated the potential of miRTrail by applying our tool to mRNA and miRNA data of malignant melanoma. MiRTrail identified several deregulated miRNAs that target deregulated mRNAs including miRNAs hsa-miR-23b and hsa-miR-223, which target the highest numbers of deregulated mRNAs and regulate the pathway "basal cell carcinoma". In addition, both miRNAs target genes like PTCH1 and RASA1 that are involved in many oncogenic processes. The application on melanoma samples demonstrates that the miRTrail platform may open avenues for investigating the regulatory interactions between genes and miRNAs for a wide range of human diseases. Moreover, miRTrail cannot only be applied to microarray based expression profiles, but also to NGS-based transcriptomic data. The program is freely available as web-server at mirtrail.bioinf.uni-sb.de.

@Article{pmid22194956,
   Author="Schmitt, J.  and Keller, A.  and Nourkami-Tutdibi, N.  and Heisel, S.  and Habel, N.  and Leidinger, P.  and Ludwig, N.  and Gessler, M.  and Graf, N.  and Berthold, F.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{A}utoantibody signature differentiates {W}ilms tumor patients from neuroblastoma patients}",
   Journal="PLoS ONE",
   Year="2011",
   Volume="6",
   Number="12",
   Pages="e28951"
}

@Article{pmid22027949,
   Author="Keller, A.  and Backes, C.  and Leidinger, P.  and Kefer, N.  and Boisguerin, V.  and Barbacioru, C.  and Vogel, B.  and Matzas, M.  and Huwer, H.  and Katus, H. A.  and Stahler, C.  and Meder, B.  and Meese, E. ",
   Title="{{N}ext-generation sequencing identifies novel micro{R}{N}{A}s in peripheral blood of lung cancer patients}",
   Journal="Mol. Biosyst.",
   Year="2011",
   Volume="7",
   Number="12",
   Pages="3187--3199",
   Month="Dec"
}

@Article{pmid21730303,
   Author="Just, S.  and Berger, I. M.  and Meder, B.  and Backs, J.  and Keller, A.  and Marquart, S.  and Frese, K.  and Patzel, E.  and Rauch, G. J.  and Katus, H. A.  and Rottbauer, W. ",
   Title="{{P}rotein kinase {D}2 controls cardiac valve formation in zebrafish by regulating histone deacetylase 5 activity}",
   Journal="Circulation",
   Year="2011",
   Volume="124",
   Number="3",
   Pages="324--334",
   Month="Jul"
}

@Article{pmid21695249,
   Author="Keller, A.  and Harz, C.  and Matzas, M.  and Meder, B.  and Katus, H. A.  and Ludwig, N.  and Fischer, U.  and Meese, E. ",
   Title="{{I}dentification of novel {S}{N}{P}s in glioblastoma using targeted resequencing}",
   Journal="PLoS ONE",
   Year="2011",
   Volume="6",
   Number="6",
   Pages="e18158"
}

@Article{pmid21592396,
   Author="Schuler, M.  and Keller, A.  and Backes, C.  and Philippar, K.  and Lenhof, H. P.  and Bauer, P. ",
   Title="{{T}ranscriptome analysis by {G}ene{T}rail revealed regulation of functional categories in response to alterations of iron homeostasis in {A}rabidopsis thaliana}",
   Journal="BMC Plant Biol.",
   Year="2011",
   Volume="11",
   Pages="87"
}

@Article{pmid21558792,
   Author="Keller, A.  and Leidinger, P.  and Gislefoss, R.  and Haugen, A.  and Langseth, H.  and Staehler, P.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{S}table serum mi{R}{N}{A} profiles as potential tool for non-invasive lung cancer diagnosis}",
   Journal="RNA Biol.",
   Year="2011",
   Volume="8",
   Number="3",
   Pages="506--516"
}

@Article{pmid21503945,
   Author="Ehrhardt, M.  and Leidinger, P.  and Keller, A.  and Baumert, T.  and Diez, J.  and Meese, E.  and Meyerhans, A. ",
   Title="{{P}rofound differences of micro{R}{N}{A} expression patterns in hepatocytes and hepatoma cell lines commonly used in hepatitis {C} virus studies}",
   Journal="Hepatology",
   Year="2011",
   Volume="54",
   Number="3",
   Pages="1112--1113",
   Month="Sep"
}

@Article{pmid21388703,
   Author="Leidinger, P.  and Keller, A.  and Borries, A.  and Huwer, H.  and Rohling, M.  and Huebers, J.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{S}pecific peripheral mi{R}{N}{A} profiles for distinguishing lung cancer from {C}{O}{P}{D}}",
   Journal="Lung Cancer",
   Year="2011",
   Volume="74",
   Number="1",
   Pages="41--47",
   Month="Oct"
}

@Article{pmid21289491,
   Author="Shah, A. A.  and Leidinger, P.  and Keller, A.  and Wendschlag, A.  and Backes, C.  and Baus-Loncar, M.  and Meese, E.  and Blin, N. ",
   Title="{{T}he intestinal factor {T}ff3 and a mi{R}{N}{A} network regulate murine caloric metabolism}",
   Journal="RNA Biol.",
   Year="2011",
   Volume="8",
   Number="1",
   Pages="77--81"
}

@Article{pmid20506373,
   Author="Ludwig, N.  and Keller, A.  and Heisel, S.  and Leidinger, P.  and Rheinheimer, S.  and Andres, C.  and Stephan, B.  and Steudel, W. I.  and Donauer, E.  and Graf, N.  and Burgeth, B.  and Weickert, J.  and Lenhof, H. P.  and Meese, E. ",
   Journal="Int. J. Cancer",
   title="Novel immunogenic antigens increase classification accuracy in meningioma to 93.84%",
   Year="2011",
   Volume="128",
   Number="6",
   Pages="1493--1501",
   Month="Mar"
}

@Article{pmid22303398,
   Author="Leidinger, P.  and Keller, A.  and Meese, E. ",
   Title="{{M}icro{R}{N}{A}s - {I}mportant {M}olecules in {L}ung {C}ancer {R}esearch}",
   Journal="Front. Genet.",
   Year="2011",
   Volume="2",
   Pages="104"
}

@Article{pmid21726451,
   Author="Backes, C.  and Ludwig, N.  and Leidinger, P.  and Harz, C.  and Hoffmann, J.  and Keller, A.  and Meese, E.  and Lenhof, H. P. ",
   Title="{{I}mmunogenicity of autoantigens}",
   Journal="BMC Genomics",
   Year="2011",
   Volume="12",
   Pages="340"
}

@Article{Roth2011,
  author          = {Roth, Patrick and Wischhusen, Jörg and Happold, Caroline and Chandran, P Anoop and Hofer, Silvia and Eisele, Günter and Weller, Michael and Keller, Andreas},
  title           = {A specific miRNA signature in the peripheral blood of glioblastoma patients.},
  journal         = {Journal of neurochemistry},
  year            = {2011},
  volume          = {118},
  pages           = {449--457},
  month           = aug,
  issn            = {1471-4159},
  abstract        = {The prognosis of patients afflicted by glioblastoma remains poor. Biomarkers for the disease would be desirable in order to allow for an early detection of tumor progression or to indicate rapidly growing tumor subtypes requiring more intensive therapy. In this study, we investigated whether a blood-derived specific miRNA fingerprint can be defined in patients with glioblastoma. To this end, miRNA profiles from the blood of 20 patients with glioblastoma and 20 age- and sex-matched healthy controls were compared. Of 1158 tested miRNAs, 52 were significantly deregulated, as assessed by unadjusted Student's t-test at an alpha level of 0.05. Of these, two candidates, miR-128 (up-regulated) and miR-342-3p (down-regulated), remained significant after correcting for multiple testing by Benjamini-Hochberg adjustment with a p-value of 0.025. The altered expression of these two biomarkers was confirmed in a second cohort of glioblastoma patients and healthy controls by real-time PCR and validated for patients who had received neither radio- nor chemotherapy and for patients who had their glioblastomas resected more than 6 months ago. Moreover, using machine learning, a comprehensive miRNA signature was obtained that allowed for the discrimination between blood samples of glioblastoma patients and healthy controls with an accuracy of 81% [95% confidence interval (CI) 78-84%], specificity of 79% (95% CI 75-83%) and sensitivity of 83% (95% CI 71-85%). In summary, our proof-of-concept study demonstrates that blood-derived glioblastoma-associated characteristic miRNA fingerprints may be suitable biomarkers and warrant further exploration.},
  chemicals       = {Biomarkers, Tumor, MIRN128 microRNA, human, MIRN342 microRNA, human, MicroRNAs},
  citation-subset = {IM},
  completed       = {2011-09-13},
  country         = {England},
  doi             = {10.1111/j.1471-4159.2011.07307.x},
  issn-linking    = {0022-3042},
  issue           = {3},
  keywords        = {Adult; Aged; Aged, 80 and over; Biomarkers, Tumor, blood; Brain Neoplasms, blood, pathology; Data Interpretation, Statistical; Disease Progression; Female; Glioblastoma, blood, pathology; Humans; Male; MicroRNAs, blood; Microarray Analysis; Middle Aged; Reverse Transcriptase Polymerase Chain Reaction},
  nlm-id          = {2985190R},
  owner           = {NLM},
  pmid            = {21561454},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2015-11-19},
}

The prognosis of patients afflicted by glioblastoma remains poor. Biomarkers for the disease would be desirable in order to allow for an early detection of tumor progression or to indicate rapidly growing tumor subtypes requiring more intensive therapy. In this study, we investigated whether a blood-derived specific miRNA fingerprint can be defined in patients with glioblastoma. To this end, miRNA profiles from the blood of 20 patients with glioblastoma and 20 age- and sex-matched healthy controls were compared. Of 1158 tested miRNAs, 52 were significantly deregulated, as assessed by unadjusted Student's t-test at an alpha level of 0.05. Of these, two candidates, miR-128 (up-regulated) and miR-342-3p (down-regulated), remained significant after correcting for multiple testing by Benjamini-Hochberg adjustment with a p-value of 0.025. The altered expression of these two biomarkers was confirmed in a second cohort of glioblastoma patients and healthy controls by real-time PCR and validated for patients who had received neither radio- nor chemotherapy and for patients who had their glioblastomas resected more than 6 months ago. Moreover, using machine learning, a comprehensive miRNA signature was obtained that allowed for the discrimination between blood samples of glioblastoma patients and healthy controls with an accuracy of 81% [95% confidence interval (CI) 78-84%], specificity of 79% (95% CI 75-83%) and sensitivity of 83% (95% CI 71-85%). In summary, our proof-of-concept study demonstrates that blood-derived glioblastoma-associated characteristic miRNA fingerprints may be suitable biomarkers and warrant further exploration.

@Article{Keller2011,
  author          = {Keller, Andreas and Leidinger, Petra and Bauer, Andrea and Elsharawy, Abdou and Haas, Jan and Backes, Christina and Wendschlag, Anke and Giese, Nathalia and Tjaden, Christine and Ott, Katja and Werner, Jens and Hackert, Thilo and Ruprecht, Klemens and Huwer, Hanno and Huebers, Junko and Jacobs, Gunnar and Rosenstiel, Philip and Dommisch, Henrik and Schaefer, Arne and Müller-Quernheim, Joachim and Wullich, Bernd and Keck, Bastian and Graf, Norbert and Reichrath, Joerg and Vogel, Britta and Nebel, Almut and Jager, Sven U and Staehler, Peer and Amarantos, Ioannis and Boisguerin, Valesca and Staehler, Cord and Beier, Markus and Scheffler, Matthias and Büchler, Markus W and Wischhusen, Joerg and Haeusler, Sebastian F M and Dietl, Johannes and Hofmann, Sylvia and Lenhof, Hans-Peter and Schreiber, Stefan and Katus, Hugo A and Rottbauer, Wolfgang and Meder, Benjamin and Hoheisel, Joerg D and Franke, Andre and Meese, Eckart},
  title           = {Toward the blood-borne miRNome of human diseases.},
  journal         = {Nature methods},
  year            = {2011},
  volume          = {8},
  pages           = {841--843},
  month           = sep,
  issn            = {1548-7105},
  abstract        = {In a multicenter study, we determined the expression profiles of 863 microRNAs by array analysis of 454 blood samples from human individuals with different cancers or noncancer diseases, and validated this 'miRNome' by quantitative real-time PCR. We detected consistently deregulated profiles for all tested diseases; pathway analysis confirmed disease association of the respective microRNAs. We observed significant correlations (P = 0.004) between the genomic location of disease-associated genetic variants and deregulated microRNAs.},
  chemicals       = {MicroRNAs},
  citation-subset = {IM},
  completed       = {2011-12-23},
  country         = {United States},
  doi             = {10.1038/nmeth.1682},
  issn-linking    = {1548-7091},
  issue           = {10},
  keywords        = {Disease, genetics; Gene Expression Profiling; Genetic Variation, genetics; Humans; MicroRNAs, blood, genetics; Oligonucleotide Array Sequence Analysis; Reverse Transcriptase Polymerase Chain Reaction},
  nlm-id          = {101215604},
  owner           = {NLM},
  pii             = {nmeth.1682},
  pmid            = {21892151},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2017-02-20},
}

In a multicenter study, we determined the expression profiles of 863 microRNAs by array analysis of 454 blood samples from human individuals with different cancers or noncancer diseases, and validated this 'miRNome' by quantitative real-time PCR. We detected consistently deregulated profiles for all tested diseases; pathway analysis confirmed disease association of the respective microRNAs. We observed significant correlations (P = 0.004) between the genomic location of disease-associated genetic variants and deregulated microRNAs.

@Article{Meder2011,
  author          = {Meder, Benjamin and Keller, Andreas and Vogel, Britta and Haas, Jan and Sedaghat-Hamedani, Farbod and Kayvanpour, Elham and Just, Steffen and Borries, Anne and Rudloff, Jessica and Leidinger, Petra and Meese, Eckart and Katus, Hugo A and Rottbauer, Wolfgang},
  title           = {MicroRNA signatures in total peripheral blood as novel biomarkers for acute myocardial infarction.},
  journal         = {Basic research in cardiology},
  year            = {2011},
  volume          = {106},
  pages           = {13--23},
  month           = jan,
  issn            = {1435-1803},
  abstract        = {MicroRNAs (miRNAs) are important regulators of adaptive and maladaptive responses in cardiovascular diseases and hence are considered to be potential therapeutical targets. However, their role as novel biomarkers for the diagnosis of cardiovascular diseases still needs to be systematically evaluated. We assessed here for the first time whole-genome miRNA expression in peripheral total blood samples of patients with acute myocardial infarction (AMI). We identified 121 miRNAs, which are significantly dysregulated in AMI patients in comparison to healthy controls. Among these, miR-1291 and miR-663b show the highest sensitivity and specificity for the discrimination of cases from controls. Using a novel self-learning pattern recognition algorithm, we identified a unique signature of 20 miRNAs that predicts AMI with even higher power (specificity 96%, sensitivity 90%, and accuracy 93%). In addition, we show that miR-30c and miR-145 levels correlate with infarct sizes estimated by Troponin T release. The here presented study shows that single miRNAs and especially miRNA signatures derived from peripheral blood, could be valuable novel biomarkers for cardiovascular diseases.},
  chemicals       = {Biomarkers, MicroRNAs, Troponin T},
  citation-subset = {IM},
  completed       = {2011-04-18},
  country         = {Germany},
  doi             = {10.1007/s00395-010-0123-2},
  issn-linking    = {0300-8428},
  issue           = {1},
  keywords        = {Aged; Biomarkers, blood; Case-Control Studies; Female; Genome, Human; Genomics; Humans; Male; MicroRNAs, blood; Middle Aged; Myocardial Infarction, blood, diagnosis, etiology; Sensitivity and Specificity; Troponin T, blood},
  nlm-id          = {0360342},
  owner           = {NLM},
  pmid            = {20886220},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2015-11-19},
}

MicroRNAs (miRNAs) are important regulators of adaptive and maladaptive responses in cardiovascular diseases and hence are considered to be potential therapeutical targets. However, their role as novel biomarkers for the diagnosis of cardiovascular diseases still needs to be systematically evaluated. We assessed here for the first time whole-genome miRNA expression in peripheral total blood samples of patients with acute myocardial infarction (AMI). We identified 121 miRNAs, which are significantly dysregulated in AMI patients in comparison to healthy controls. Among these, miR-1291 and miR-663b show the highest sensitivity and specificity for the discrimination of cases from controls. Using a novel self-learning pattern recognition algorithm, we identified a unique signature of 20 miRNAs that predicts AMI with even higher power (specificity 96%, sensitivity 90%, and accuracy 93%). In addition, we show that miR-30c and miR-145 levels correlate with infarct sizes estimated by Troponin T release. The here presented study shows that single miRNAs and especially miRNA signatures derived from peripheral blood, could be valuable novel biomarkers for cardiovascular diseases.

@Article{Meder2011a,
  author          = {Meder, Benjamin and Haas, Jan and Keller, Andreas and Heid, Christiane and Just, Steffen and Borries, Anne and Boisguerin, Valesca and Scharfenberger-Schmeer, Maren and Stähler, Peer and Beier, Markus and Weichenhan, Dieter and Strom, Tim M and Pfeufer, Arne and Korn, Bernhard and Katus, Hugo A and Rottbauer, Wolfgang},
  title           = {Targeted next-generation sequencing for the molecular genetic diagnostics of cardiomyopathies.},
  journal         = {Circulation. Cardiovascular genetics},
  year            = {2011},
  volume          = {4},
  pages           = {110--122},
  month           = apr,
  issn            = {1942-3268},
  abstract        = {Today, mutations in more than 30 different genes have been found to cause inherited cardiomyopathies, some associated with very poor prognosis. However, because of the genetic heterogeneity and limitations in throughput and scalability of current diagnostic tools up until now, it is hardly possible to genetically characterize patients with cardiomyopathy in a fast, comprehensive, and cost-efficient manner. We established an array-based subgenomic enrichment followed by next-generation sequencing to detect mutations in patients with hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). With this approach, we show that the genomic region of interest can be enriched by a mean factor of 2169 compared with the coverage of the whole genome, resulting in high sequence coverage of selected disease genes and allowing us to define the genetic pathogenesis of cardiomyopathies in a single sequencing run. In 6 patients, we detected disease-causing mutations, 2 microdeletions, and 4 point mutations. Furthermore, we identified several novel nonsynonymous variants, which are predicted to be harmful, and hence, might be potential disease mutations or modifiers for DCM or HCM. The approach presented here allows for the first time a comprehensive genetic screening in patients with hereditary DCM or HCM in a fast and cost-efficient manner.},
  chemicals       = {Carrier Proteins, Codon, Nonsense, MYH7 protein, human, myosin-binding protein C, integrin-linked kinase, Protein-Serine-Threonine Kinases, Cardiac Myosins, Myosin Heavy Chains},
  citation-subset = {IM},
  completed       = {2011-08-10},
  country         = {United States},
  doi             = {10.1161/CIRCGENETICS.110.958322},
  issn-linking    = {1942-3268},
  issue           = {2},
  keywords        = {Adult; Base Sequence; Cardiac Myosins, genetics; Cardiomyopathy, Dilated, diagnosis, genetics; Cardiomyopathy, Hypertrophic, diagnosis, genetics; Carrier Proteins, genetics; Child; Codon, Nonsense; Female; Frameshift Mutation; Gene Deletion; Genetic Heterogeneity; Humans; Male; Middle Aged; Mutation, Missense; Myosin Heavy Chains, genetics; Point Mutation; Protein-Serine-Threonine Kinases, genetics; Sequence Analysis, DNA, methods},
  nlm-id          = {101489144},
  owner           = {NLM},
  pii             = {CIRCGENETICS.110.958322},
  pmid            = {21252143},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2013-11-21},
}

Today, mutations in more than 30 different genes have been found to cause inherited cardiomyopathies, some associated with very poor prognosis. However, because of the genetic heterogeneity and limitations in throughput and scalability of current diagnostic tools up until now, it is hardly possible to genetically characterize patients with cardiomyopathy in a fast, comprehensive, and cost-efficient manner. We established an array-based subgenomic enrichment followed by next-generation sequencing to detect mutations in patients with hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM). With this approach, we show that the genomic region of interest can be enriched by a mean factor of 2169 compared with the coverage of the whole genome, resulting in high sequence coverage of selected disease genes and allowing us to define the genetic pathogenesis of cardiomyopathies in a single sequencing run. In 6 patients, we detected disease-causing mutations, 2 microdeletions, and 4 point mutations. Furthermore, we identified several novel nonsynonymous variants, which are predicted to be harmful, and hence, might be potential disease mutations or modifiers for DCM or HCM. The approach presented here allows for the first time a comprehensive genetic screening in patients with hereditary DCM or HCM in a fast and cost-efficient manner.

@Article{pmid21113166,
   Author="Matzas, M.  and Staehler, P. F.  and Kefer, N.  and Siebelt, N.  and Boisguerin, V.  and Leonard, J. T.  and Keller, A.  and Stahler, C. F.  and Haberle, P.  and Gharizadeh, B.  and Babrzadeh, F.  and Church, G. M. ",
   Title="{{H}igh-fidelity gene synthesis by retrieval of sequence-verified {D}{N}{A} identified using high-throughput pyrosequencing}",
   Journal="Nat. Biotechnol.",
   Year="2010",
   Volume="28",
   Number="12",
   Pages="1291--1294",
   Month="Dec"
}

@Article{pmid20810122,
   Author="Melchior, K.  and Tholey, A.  and Heisel, S.  and Keller, A.  and Lenhof, H. P.  and Meese, E.  and Huber, C. G. ",
   Title="{{P}rotein- versus peptide fractionation in the first dimension of two-dimensional high-performance liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry for qualitative proteome analysis of tissue samples}",
   Journal="J. Chromatogr. A",
   Year="2010",
   Volume="1217",
   Number="40",
   Pages="6159--6168",
   Month="Oct"
}

@Article{pmid20683447,
   Author="Hausler, S. F.  and Keller, A.  and Chandran, P. A.  and Ziegler, K.  and Zipp, K.  and Heuer, S.  and Krockenberger, M.  and Engel, J. B.  and Honig, A.  and Scheffler, M.  and Dietl, J.  and Wischhusen, J. ",
   Title="{{W}hole blood-derived mi{R}{N}{A} profiles as potential new tools for ovarian cancer screening}",
   Journal="Br. J. Cancer",
   Year="2010",
   Volume="103",
   Number="5",
   Pages="693--700",
   Month="Aug"
}

@Article{pmid20529253,
   Author="Leidinger, P.  and Keller, A.  and Borries, A.  and Reichrath, J.  and Rass, K.  and Jager, S. U.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{H}igh-throughput mi{R}{N}{A} profiling of human melanoma blood samples}",
   Journal="BMC Cancer",
   Year="2010",
   Volume="10",
   Pages="262"
}

@Article{pmid20433717,
   Author="Sharbati, S.  and Friedlander, M. R.  and Sharbati, J.  and Hoeke, L.  and Chen, W.  and Keller, A.  and Stahler, P. F.  and Rajewsky, N.  and Einspanier, R. ",
   Title="{{D}eciphering the porcine intestinal micro{R}{N}{A} transcriptome}",
   Journal="BMC Genomics",
   Year="2010",
   Volume="11",
   Pages="275"
}

@Article{pmid20385225,
   Author="Heidbrink, C.  and Hausler, S. F.  and Buttmann, M.  and Ossadnik, M.  and Strik, H. M.  and Keller, A.  and Buck, D.  and Verbraak, E.  and van Meurs, M.  and Krockenberger, M.  and Mehling, M.  and Mittelbronn, M.  and Laman, J. D.  and Wiendl, H.  and Wischhusen, J. ",
   Title="{{R}educed cortisol levels in cerebrospinal fluid and differential distribution of 11beta-hydroxysteroid dehydrogenases in multiple sclerosis: implications for lesion pathogenesis}",
   Journal="Brain Behav. Immun.",
   Year="2010",
   Volume="24",
   Number="6",
   Pages="975--984",
   Month="Aug"
}

@Article{pmid20146812,
   Author="Leidinger, P.  and Keller, A.  and Heisel, S.  and Ludwig, N.  and Rheinheimer, S.  and Klein, V.  and Andres, C.  and Staratschek-Jox, A.  and Wolf, J.  and Stoelben, E.  and Stephan, B.  and Stehle, I.  and Hamacher, J.  and Huwer, H.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{I}dentification of lung cancer with high sensitivity and specificity by blood testing}",
   Journal="Respir. Res.",
   Year="2010",
   Volume="11",
   Pages="18"
}

@Article{Backes2010,
  author          = {Backes, Christina and Meese, Eckart and Lenhof, Hans-Peter and Keller, Andreas},
  title           = {A dictionary on microRNAs and their putative target pathways.},
  journal         = {Nucleic acids research},
  year            = {2010},
  volume          = {38},
  pages           = {4476--4486},
  month           = jul,
  issn            = {1362-4962},
  abstract        = {While in the last decade mRNA expression profiling was among the most popular research areas, over the past years the study of non-coding RNAs, especially microRNAs (miRNAs), has gained increasing interest. For almost 900 known human miRNAs hundreds of pretended targets are known. However, there is only limited knowledge about putative systemic effects of changes in the expression of miRNAs and their regulatory influence. We determined for each known miRNA the biochemical pathways in the KEGG and TRANSPATH database and the Gene Ontology categories that are enriched with respect to its target genes. We refer to these pathways and categories as target pathways of the corresponding miRNA. Investigating target pathways of miRNAs we found a strong relation to disease-related regulatory pathways, including mitogen-activated protein kinase (MAPK) signaling cascade, Transforming growth factor (TGF)-beta signaling pathway or the p53 network. Performing a sophisticated analysis of differentially expressed genes of 13 cancer data sets extracted from gene expression omnibus (GEO) showed that targets of specific miRNAs were significantly deregulated in these sets. The respective miRNA target analysis is also a novel part of our gene set analysis pipeline GeneTrail. Our study represents a comprehensive theoretical analysis of the relationship between miRNAs and their predicted target pathways. Our target pathways analysis provides a 'miRNA-target pathway' dictionary, which enables researchers to identify target pathways of differentially regulated miRNAs.},
  chemicals       = {MicroRNAs, RNA, Messenger},
  citation-subset = {IM},
  completed       = {2010-08-24},
  country         = {England},
  doi             = {10.1093/nar/gkq167},
  issn-linking    = {0305-1048},
  issue           = {13},
  keywords        = {Cluster Analysis; Dictionaries as Topic; Gene Expression Regulation; Gene Expression Regulation, Neoplastic; Gene Regulatory Networks; MicroRNAs, metabolism; Neoplasms, genetics; RNA, Messenger, metabolism},
  nlm-id          = {0411011},
  owner           = {NLM},
  pii             = {gkq167},
  pmc             = {PMC2910047},
  pmid            = {20299343},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-02-20},
}

While in the last decade mRNA expression profiling was among the most popular research areas, over the past years the study of non-coding RNAs, especially microRNAs (miRNAs), has gained increasing interest. For almost 900 known human miRNAs hundreds of pretended targets are known. However, there is only limited knowledge about putative systemic effects of changes in the expression of miRNAs and their regulatory influence. We determined for each known miRNA the biochemical pathways in the KEGG and TRANSPATH database and the Gene Ontology categories that are enriched with respect to its target genes. We refer to these pathways and categories as target pathways of the corresponding miRNA. Investigating target pathways of miRNAs we found a strong relation to disease-related regulatory pathways, including mitogen-activated protein kinase (MAPK) signaling cascade, Transforming growth factor (TGF)-beta signaling pathway or the p53 network. Performing a sophisticated analysis of differentially expressed genes of 13 cancer data sets extracted from gene expression omnibus (GEO) showed that targets of specific miRNAs were significantly deregulated in these sets. The respective miRNA target analysis is also a novel part of our gene set analysis pipeline GeneTrail. Our study represents a comprehensive theoretical analysis of the relationship between miRNAs and their predicted target pathways. Our target pathways analysis provides a 'miRNA-target pathway' dictionary, which enables researchers to identify target pathways of differentially regulated miRNAs.

@Article{Fischer2010,
  author          = {Fischer, Ulrike and Leidinger, Petra and Keller, Andreas and Folarin, Amos and Ketter, Ralf and Graf, Norbert and Lenhof, Hans-Peter and Meese, Eckart},
  title           = {Amplicons on chromosome 12q13-21 in glioblastoma recurrences.},
  journal         = {International journal of cancer},
  year            = {2010},
  volume          = {126},
  pages           = {2594--2602},
  month           = jun,
  issn            = {1097-0215},
  abstract        = {There is limited knowledge on the in vivo behavior of amplified regions in human tumors. First evidence indicates that amplicon structures are largely maintained in recurrent tumors. Here, we investigated the fate of amplified regions in several independent cases of recurrent glioblastoma and the possible association of 12q13-21 amplifications and survival. We analyzed 12q13-21 amplicon numbers and sizes in glioblastoma and their recurrences by array-CGH. The majority of the 12q13-21 amplicons found in the original tumor are lost in the subsequent recurrence. Likewise, the majority of the amplicons found in the first recurrence are lost in the second recurrence. The remaining amplicons of recurrences often expanded or were maintained in size. Because of re-emergences and de novo appearances of amplicons, however, the overall number of amplicons did not decrease in the recurrences. Understanding genetic changes including gene amplifications in the development of tumor recurrences will contribute to rational therapeutic strategies for an improved patient survival. We recognized a significant longer survival time in glioblastoma patients that lack amplifications of either CDK4, CYP27B1, XRCC6BP1 (KUB3), or MDM2.},
  citation-subset = {IM},
  completed       = {2010-04-23},
  country         = {United States},
  doi             = {10.1002/ijc.24971},
  issn-linking    = {0020-7136},
  issue           = {11},
  keywords        = {Adult; Aged; Biopsy; Chromosome Mapping; Chromosomes, Human, Pair 12, genetics; Comparative Genomic Hybridization, methods; Female; Gene Amplification, genetics; Glioblastoma, genetics, mortality, pathology, radiotherapy; Humans; Male; Middle Aged; Oligonucleotide Array Sequence Analysis; Recurrence; Survivors},
  nlm-id          = {0042124},
  owner           = {NLM},
  pmid            = {19839052},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2016-03-03},
}

There is limited knowledge on the in vivo behavior of amplified regions in human tumors. First evidence indicates that amplicon structures are largely maintained in recurrent tumors. Here, we investigated the fate of amplified regions in several independent cases of recurrent glioblastoma and the possible association of 12q13-21 amplifications and survival. We analyzed 12q13-21 amplicon numbers and sizes in glioblastoma and their recurrences by array-CGH. The majority of the 12q13-21 amplicons found in the original tumor are lost in the subsequent recurrence. Likewise, the majority of the amplicons found in the first recurrence are lost in the second recurrence. The remaining amplicons of recurrences often expanded or were maintained in size. Because of re-emergences and de novo appearances of amplicons, however, the overall number of amplicons did not decrease in the recurrences. Understanding genetic changes including gene amplifications in the development of tumor recurrences will contribute to rational therapeutic strategies for an improved patient survival. We recognized a significant longer survival time in glioblastoma patients that lack amplifications of either CDK4, CYP27B1, XRCC6BP1 (KUB3), or MDM2.

@Article{pmid20019846,
   Author="Ludwig, N.  and Keller, A.  and Heisel, S.  and Leidinger, P.  and Klein, V.  and Rheinheimer, S.  and Andres, C. U.  and Stephan, B.  and Steudel, W. I.  and Graf, N. M.  and Burgeth, B.  and Weickert, J.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{I}mproving seroreactivity-based detection of glioma}",
   Journal="Neoplasia",
   Year="2009",
   Volume="11",
   Number="12",
   Pages="1383--1389",
   Month="Dec"
}

@Article{pmid19823682,
   Author="Keller, A.  and Leidinger, P.  and Lange, J.  and Borries, A.  and Schroers, H.  and Scheffler, M.  and Lenhof, H. P.  and Ruprecht, K.  and Meese, E. ",
   Title="{{M}ultiple sclerosis: micro{R}{N}{A} expression profiles accurately differentiate patients with relapsing-remitting disease from healthy controls}",
   Journal="PLoS ONE",
   Year="2009",
   Volume="4",
   Number="10",
   Pages="e7440"
}

@Article{pmid19807914,
   Author="Keller, A.  and Leidinger, P.  and Borries, A.  and Wendschlag, A.  and Wucherpfennig, F.  and Scheffler, M.  and Huwer, H.  and Lenhof, H. P.  and Meese, E. ",
   Title="{mi{R}{N}{A}s in lung cancer - studying complex fingerprints in patient's blood cells by microarray experiments}",
   Journal="BMC Cancer",
   Year="2009",
   Volume="9",
   Pages="353"
}

@Article{pmid19673542,
   Author="Melchior, K.  and Tholey, A.  and Heisel, S.  and Keller, A.  and Lenhof, H. P.  and Meese, E.  and Huber, C. G. ",
   Title="{{P}roteomic study of human glioblastoma multiforme tissue employing complementary two-dimensional liquid chromatography- and mass spectrometry-based approaches}",
   Journal="J. Proteome Res.",
   Year="2009",
   Volume="8",
   Number="10",
   Pages="4604--4614",
   Month="Oct"
}

@Article{pmid19284601,
   Author="Leidinger, P.  and Keller, A.  and Heisel, S.  and Ludwig, N.  and Rheinheimer, S.  and Klein, V.  and Andres, C.  and Hamacher, J.  and Huwer, H.  and Stephan, B.  and Stehle, I.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{N}ovel autoantigens immunogenic in {C}{O}{P}{D} patients}",
   Journal="Respir. Res.",
   Year="2009",
   Volume="10",
   Pages="20"
}

@Article{pmid19253280,
   Author="Chatterjee, I.  and Schmitt, S.  and Batzilla, C. F.  and Engelmann, S.  and Keller, A.  and Ring, M. W.  and Kautenburger, R.  and Ziebuhr, W.  and Hecker, M.  and Preissner, K. T.  and Bischoff, M.  and Proctor, R. A.  and Beck, H. P.  and Lenhof, H. P.  and Somerville, G. A.  and Herrmann, M. ",
   Title="{{S}taphylococcus aureus {C}lp{C} {A}{T}{P}ase is a late growth phase effector of metabolism and persistence}",
   Journal="Proteomics",
   Year="2009",
   Volume="9",
   Number="5",
   Pages="1152--1176",
   Month="Mar"
}

@Article{pmid19003955,
   Author="Keller, A.  and Ludwig, N.  and Backes, C.  and Romeike, B. F.  and Comtesse, N.  and Henn, W.  and Steudel, W. I.  and Mawrin, C.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{G}enome wide expression profiling identifies specific deregulated pathways in meningioma}",
   Journal="Int. J. Cancer",
   Year="2009",
   Volume="124",
   Number="2",
   Pages="346--351",
   Month="Jan"
}

@Article{pmid18701916,
   Author="Keller, A.  and Ludwig, N.  and Comtesse, N.  and Henn, W.  and Steudel, W. I.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{C}ombining gene expression signatures and autoantibody profiles in human meningioma}",
   Journal="Gene Ther.",
   Year="2009",
   Volume="16",
   Number="2",
   Pages="184--189",
   Month="Feb"
}

@Article{Keller2009a,
  author    = {Keller, Andreas and Ludwig, Nicole and Heisel, Sabrina and Leidinger, Petra and Andres, Claudia and Steudel, Wolf-Ingo and Huwer, Hanno and Burgeth, Bernhard and Hein, Matthias and Weickert, Joachim and Meese, Eckart and Lenhof, Hans-Peter},
  title     = {Large-scale antibody profiling of human blood sera: The future of molecular diagnosis},
  journal   = {Informatik-Spektrum},
  year      = {2009},
  volume    = {32},
  number    = {4},
  pages     = {332-338},
  issn      = {0170-6012},
  doi       = {10.1007/s00287-009-0354-5},
  language  = {German},
  publisher = {Springer-Verlag},
  url       = {http://dx.doi.org/10.1007/s00287-009-0354-5},
}

@Article{Keller2009,
  author          = {Keller, Andreas and Backes, Christina and Gerasch, Andreas and Kaufmann, Michael and Kohlbacher, Oliver and Meese, Eckart and Lenhof, Hans-Peter},
  title           = {A novel algorithm for detecting differentially regulated paths based on gene set enrichment analysis.},
  journal         = {Bioinformatics (Oxford, England)},
  year            = {2009},
  volume          = {25},
  pages           = {2787--2794},
  month           = nov,
  issn            = {1367-4811},
  abstract        = {Deregulated signaling cascades are known to play a crucial role in many pathogenic processes, among them are tumor initiation and progression. In the recent past, modern experimental techniques that allow for measuring the amount of mRNA transcripts of almost all known human genes in a tissue or even in a single cell have opened new avenues for studying the activity of the signaling cascades and for understanding the information flow in the networks. We present a novel dynamic programming algorithm for detecting deregulated signaling cascades. The so-called FiDePa (Finding Deregulated Paths) algorithm interprets differences in the expression profiles of tumor and normal tissues. It relies on the well-known gene set enrichment analysis (GSEA) and efficiently detects all paths in a given regulatory or signaling network that are significantly enriched with differentially expressed genes or proteins. Since our algorithm allows for comparing a single tumor expression profile with the control group, it facilitates the detection of specific regulatory features of a tumor that may help to optimize tumor therapy. To demonstrate the capabilities of our algorithm, we analyzed a glioma expression dataset with respect to a directed graph that combined the regulatory networks of the KEGG and TRANSPATH database. The resulting glioma consensus network that encompasses all detected deregulated paths contained many genes and pathways that are known to be key players in glioma or cancer-related pathogenic processes. Moreover, we were able to correlate clinically relevant features like necrosis or metastasis with the detected paths. C++ source code is freely available, BiNA can be downloaded from http://www.bnplusplus.org/. ack@bioinf.uni-sb.de Supplementary data are available at Bioinformatics online.},
  chemicals       = {RNA, Messenger},
  citation-subset = {IM},
  completed       = {2010-01-26},
  country         = {England},
  doi             = {10.1093/bioinformatics/btp510},
  issn-linking    = {1367-4803},
  issue           = {21},
  keywords        = {Algorithms; Computational Biology, methods; Databases, Genetic; Gene Expression Profiling, methods; Gene Regulatory Networks; RNA, Messenger, metabolism},
  nlm-id          = {9808944},
  owner           = {NLM},
  pii             = {btp510},
  pmc             = {PMC2781748},
  pmid            = {19713416},
  pubmodel        = {Print-Electronic},
  pubstatus       = {ppublish},
  revised         = {2017-02-20},
}

Deregulated signaling cascades are known to play a crucial role in many pathogenic processes, among them are tumor initiation and progression. In the recent past, modern experimental techniques that allow for measuring the amount of mRNA transcripts of almost all known human genes in a tissue or even in a single cell have opened new avenues for studying the activity of the signaling cascades and for understanding the information flow in the networks. We present a novel dynamic programming algorithm for detecting deregulated signaling cascades. The so-called FiDePa (Finding Deregulated Paths) algorithm interprets differences in the expression profiles of tumor and normal tissues. It relies on the well-known gene set enrichment analysis (GSEA) and efficiently detects all paths in a given regulatory or signaling network that are significantly enriched with differentially expressed genes or proteins. Since our algorithm allows for comparing a single tumor expression profile with the control group, it facilitates the detection of specific regulatory features of a tumor that may help to optimize tumor therapy. To demonstrate the capabilities of our algorithm, we analyzed a glioma expression dataset with respect to a directed graph that combined the regulatory networks of the KEGG and TRANSPATH database. The resulting glioma consensus network that encompasses all detected deregulated paths contained many genes and pathways that are known to be key players in glioma or cancer-related pathogenic processes. Moreover, we were able to correlate clinically relevant features like necrosis or metastasis with the detected paths. C++ source code is freely available, BiNA can be downloaded from http://www.bnplusplus.org/. ack@bioinf.uni-sb.de Supplementary data are available at Bioinformatics online.

@Article{pmid19099609,
   Author="Keller, A.  and Backes, C.  and Al-Awadhi, M.  and Gerasch, A.  and Kuntzer, J.  and Kohlbacher, O.  and Kaufmann, M.  and Lenhof, H. P. ",
   Title="{{G}ene{T}rail{E}xpress: a web-based pipeline for the statistical evaluation of microarray experiments}",
   Journal="BMC Bioinformatics",
   Year="2008",
   Volume="9",
   Pages="552"
}

@Article{pmid18676746,
   Author="Ludwig, N.  and Keller, A.  and Comtesse, N.  and Rheinheimer, S.  and Pallasch, C.  and Fischer, U.  and Fassbender, K.  and Steudel, W. I.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{P}attern of serum autoantibodies allows accurate distinction between a tumor and pathologies of the same organ}",
   Journal="Clin. Cancer Res.",
   Year="2008",
   Volume="14",
   Number="15",
   Pages="4767--4774",
   Month="Aug"
}

@Article{pmid18649359,
   Author="Leidinger, P.  and Keller, A.  and Ludwig, N.  and Rheinheimer, S.  and Hamacher, J.  and Huwer, H.  and Stehle, I.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{T}oward an early diagnosis of lung cancer: an autoantibody signature for squamous cell lung carcinoma}",
   Journal="Int. J. Cancer",
   Year="2008",
   Volume="123",
   Number="7",
   Pages="1631--1636",
   Month="Oct"
}

@Article{pmid18478111,
   Author="Heisel, S. M.  and Ketter, R.  and Keller, A.  and Klein, V.  and Pallasch, C. P.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{I}ncreased seroreactivity to glioma-expressed antigen 2 in brain tumor patients under radiation}",
   Journal="PLoS ONE",
   Year="2008",
   Volume="3",
   Number="5",
   Pages="e2164"
}

@Article{Fischer2008,
  author          = {Fischer, Ulrike and Keller, Andreas and Leidinger, Petra and Deutscher, Stephanie and Heisel, Sabrina and Urbschat, Steffi and Lenhof, Hans-Peter and Meese, Eckart},
  title           = {A different view on DNA amplifications indicates frequent, highly complex, and stable amplicons on 12q13-21 in glioma.},
  journal         = {Molecular cancer research : MCR},
  year            = {2008},
  volume          = {6},
  pages           = {576--584},
  month           = apr,
  issn            = {1541-7786},
  abstract        = {To further understand the biological significance of amplifications for glioma development and recurrencies, we characterized amplicon frequency and size in low-grade glioma and amplicon stability in vivo in recurring glioblastoma. We developed a 12q13-21 amplicon-specific genomic microarray and a bioinformatics amplification prediction tool to analyze amplicon frequency, size, and maintenance in 40 glioma samples including 16 glioblastoma, 10 anaplastic astrocytoma, 7 astrocytoma WHO grade 2, and 7 pilocytic astrocytoma. Whereas previous studies reported two amplified subregions, we found a more complex situation with many amplified subregions. Analyzing 40 glioma, we found that all analyzed glioblastoma and the majority of pilocytic astrocytoma, grade 2 astrocytoma, and anaplastic astrocytoma showed at least one amplified subregion, indicating a much higher amplification frequency than previously suggested. Amplifications in low-grade glioma were smaller in size and displayed clearly different distribution patterns than amplifications in glioblastoma. One glioblastoma and its recurrencies revealed an amplified subregion of 5 Mb that was stable for 6 years. Expression analysis of the amplified region revealed 10 overexpressed genes (i.e., KUB3, CTDSP2, CDK4, OS-9, DCTN2, RAB3IP, FRS2, GAS41, MDM2, and RAP1B) that were consistently overexpressed in all cases that carried this amplification. Our data indicate that amplifications on 12q13-21 (a) are more frequent than previously thought and present in low-grade tumors and (b) are maintained as extended regions over long periods of time.},
  chemicals       = {Carbocyanines, DNA, Neoplasm, cyanine dye 3, cyanine dye 5},
  citation-subset = {IM},
  completed       = {2008-07-07},
  country         = {United States},
  doi             = {10.1158/1541-7786.MCR-07-0283},
  issn-linking    = {1541-7786},
  issue           = {4},
  keywords        = {Adult; Aged; Blotting, Southern; Carbocyanines; Child; Child, Preschool; Chromosomes, Artificial, Bacterial; Chromosomes, Human, Pair 12, genetics; Computational Biology; Cosmids; DNA, Neoplasm, genetics; Female; Gene Amplification; Gene Expression Regulation, Neoplastic; Genes, Neoplasm; Glioma, genetics; Humans; In Situ Hybridization, Fluorescence; Male; Middle Aged; Oligonucleotide Array Sequence Analysis},
  nlm-id          = {101150042},
  owner           = {NLM},
  pii             = {6/4/576},
  pmid            = {18403636},
  pubmodel        = {Print},
  pubstatus       = {ppublish},
  revised         = {2008-04-11},
}

To further understand the biological significance of amplifications for glioma development and recurrencies, we characterized amplicon frequency and size in low-grade glioma and amplicon stability in vivo in recurring glioblastoma. We developed a 12q13-21 amplicon-specific genomic microarray and a bioinformatics amplification prediction tool to analyze amplicon frequency, size, and maintenance in 40 glioma samples including 16 glioblastoma, 10 anaplastic astrocytoma, 7 astrocytoma WHO grade 2, and 7 pilocytic astrocytoma. Whereas previous studies reported two amplified subregions, we found a more complex situation with many amplified subregions. Analyzing 40 glioma, we found that all analyzed glioblastoma and the majority of pilocytic astrocytoma, grade 2 astrocytoma, and anaplastic astrocytoma showed at least one amplified subregion, indicating a much higher amplification frequency than previously suggested. Amplifications in low-grade glioma were smaller in size and displayed clearly different distribution patterns than amplifications in glioblastoma. One glioblastoma and its recurrencies revealed an amplified subregion of 5 Mb that was stable for 6 years. Expression analysis of the amplified region revealed 10 overexpressed genes (i.e., KUB3, CTDSP2, CDK4, OS-9, DCTN2, RAB3IP, FRS2, GAS41, MDM2, and RAP1B) that were consistently overexpressed in all cases that carried this amplification. Our data indicate that amplifications on 12q13-21 (a) are more frequent than previously thought and present in low-grade tumors and (b) are maintained as extended regions over long periods of time.

@Article{pmid17683603,
   Author="Keller, A.  and Backes, C.  and Lenhof, H. P. ",
   Title="{{C}omputation of significance scores of unweighted {G}ene {S}et {E}nrichment {A}nalyses}",
   Journal="BMC Bioinformatics",
   Year="2007",
   Volume="8",
   Pages="290"
}

@Article{pmid17592829,
   Author="Elnakady, Y. A.  and Rohde, M.  and Sasse, F.  and Backes, C.  and Keller, A.  and Lenhof, H. P.  and Weissman, K. J.  and Mueller, R. ",
   Title="{{E}vidence for the mode of action of the highly cytotoxic {S}treptomyces polyketide kendomycin}",
   Journal="Chembiochem",
   Year="2007",
   Volume="8",
   Number="11",
   Pages="1261--1272",
   Month="Jul"
}

@Article{pmid17526521,
   Author="Backes, C.  and Keller, A.  and Kuentzer, J.  and Kneissl, B.  and Comtesse, N.  and Elnakady, Y. A.  and Mueller, R.  and Meese, E.  and Lenhof, H. P. ",
   Title="{{G}ene{T}rail--advanced gene set enrichment analysis}",
   Journal="Nucleic Acids Res.",
   Year="2007",
   Volume="35",
   Pages="W186--192",
   Month="Jul"
}

@Article{pmid17478503,
   Author="Keller, A.  and Comtesse, N.  and Ludwig, N.  and Meese, E.  and Lenhof, H. P. ",
   Title="{{S}e{P}a{C}{S}--a web-based application for classification of seroreactivity profiles}",
   Journal="Nucleic Acids Res.",
   Year="2007",
   Volume="35",
   Pages="W683--687",
   Month="Jul"
}

@Article{pmid17290396,
   Author="Comtesse, N.  and Keller, A.  and Diesinger, I.  and Bauer, C.  and Kayser, K.  and Huwer, H.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{F}requent overexpression of the genes {F}{X}{R}1, {C}{L}{A}{P}{M}1 and {E}{I}{F}4{G} located on amplicon 3q26-27 in squamous cell carcinoma of the lung}",
   Journal="Int. J. Cancer",
   Year="2007",
   Volume="120",
   Number="12",
   Pages="2538--2544",
   Month="Jun"
}

@Article{Keller2006,
  author          = {Keller, Andreas and Ludwig, Nicole and Comtesse, Nicole and Hildebrandt, Andreas and Meese, Eckart and Lenhof, Hans-Peter},
  title           = {A minimally invasive multiple marker approach allows highly efficient detection of meningioma tumors.},
  journal         = {BMC bioinformatics},
  year            = {2006},
  volume          = {7},
  pages           = {539},
  month           = dec,
  issn            = {1471-2105},
  abstract        = {The development of effective frameworks that permit an accurate diagnosis of tumors, especially in their early stages, remains a grand challenge in the field of bioinformatics. Our approach uses statistical learning techniques applied to multiple antigen tumor antigen markers utilizing the immune system as a very sensitive marker of molecular pathological processes. For validation purposes we choose the intracranial meningioma tumors as model system since they occur very frequently, are mostly benign, and are genetically stable. A total of 183 blood samples from 93 meningioma patients (WHO stages I-III) and 90 healthy controls were screened for seroreactivity with a set of 57 meningioma-associated antigens. We tested several established statistical learning methods on the resulting reactivity patterns using 10-fold cross validation. The best performance was achieved by Naïve Bayes Classifiers. With this classification method, our framework, called Minimally Invasive Multiple Marker (MIMM) approach, yielded a specificity of 96.2%, a sensitivity of 84.5%, and an accuracy of 90.3%, the respective area under the ROC curve was 0.957. Detailed analysis revealed that prediction performs particularly well on low-grade (WHO I) tumors, consistent with our goal of early stage tumor detection. For these tumors the best classification result with a specificity of 97.5%, a sensitivity of 91.3%, an accuracy of 95.6%, and an area under the ROC curve of 0.971 was achieved using a set of 12 antigen markers only. This antigen set was detected by a subset selection method based on Mutual Information. Remarkably, our study proves that the inclusion of non-specific antigens, detected not only in tumor but also in normal sera, increases the performance significantly, since non-specific antigens contribute additional diagnostic information. Our approach offers the possibility to screen members of risk groups as a matter of routine such that tumors hopefully can be diagnosed immediately after their genesis. The early detection will finally result in a higher cure- and lower morbidity-rate.},
  chemicals       = {Antigens, Neoplasm, Biomarkers, Tumor},
  citation-subset = {IM},
  completed       = {2007-02-06},
  country         = {England},
  doi             = {10.1186/1471-2105-7-539},
  issn-linking    = {1471-2105},
  keywords        = {Algorithms; Antigens, Neoplasm, analysis; Biomarkers, Tumor, analysis; Diagnosis, Computer-Assisted, methods; Gene Expression Profiling, methods; Humans; Immunoassay, methods; Meningeal Neoplasms, diagnosis, immunology; Meningioma, diagnosis, immunology; Pattern Recognition, Automated, methods; Reproducibility of Results; Sensitivity and Specificity},
  nlm-id          = {100965194},
  owner           = {NLM},
  pii             = {1471-2105-7-539},
  pmc             = {PMC1769403},
  pmid            = {17184519},
  pubmodel        = {Electronic},
  pubstatus       = {epublish},
  revised         = {2015-11-19},
}

The development of effective frameworks that permit an accurate diagnosis of tumors, especially in their early stages, remains a grand challenge in the field of bioinformatics. Our approach uses statistical learning techniques applied to multiple antigen tumor antigen markers utilizing the immune system as a very sensitive marker of molecular pathological processes. For validation purposes we choose the intracranial meningioma tumors as model system since they occur very frequently, are mostly benign, and are genetically stable. A total of 183 blood samples from 93 meningioma patients (WHO stages I-III) and 90 healthy controls were screened for seroreactivity with a set of 57 meningioma-associated antigens. We tested several established statistical learning methods on the resulting reactivity patterns using 10-fold cross validation. The best performance was achieved by Naïve Bayes Classifiers. With this classification method, our framework, called Minimally Invasive Multiple Marker (MIMM) approach, yielded a specificity of 96.2%, a sensitivity of 84.5%, and an accuracy of 90.3%, the respective area under the ROC curve was 0.957. Detailed analysis revealed that prediction performs particularly well on low-grade (WHO I) tumors, consistent with our goal of early stage tumor detection. For these tumors the best classification result with a specificity of 97.5%, a sensitivity of 91.3%, an accuracy of 95.6%, and an area under the ROC curve of 0.971 was achieved using a set of 12 antigen markers only. This antigen set was detected by a subset selection method based on Mutual Information. Remarkably, our study proves that the inclusion of non-specific antigens, detected not only in tumor but also in normal sera, increases the performance significantly, since non-specific antigens contribute additional diagnostic information. Our approach offers the possibility to screen members of risk groups as a matter of routine such that tumors hopefully can be diagnosed immediately after their genesis. The early detection will finally result in a higher cure- and lower morbidity-rate.

@Article{pmid15983380,
   Author="Comtesse, N.  and Zippel, A.  and Walle, S.  and Monz, D.  and Backes, C.  and Fischer, U.  and Mayer, J.  and Ludwig, N.  and Hildebrandt, A.  and Keller, A.  and Steudel, W. I.  and Lenhof, H. P.  and Meese, E. ",
   Title="{{C}omplex humoral immune response against a benign tumor: frequent antibody response against specific antigens as diagnostic targets}",
   Journal="Proc. Natl. Acad. Sci. U.S.A.",
   Year="2005",
   Volume="102",
   Number="27",
   Pages="9601--9606",
   Month="Jul"
}