@article {Hirsch2023.09.18.558305,
	author = {Pascal Hirsch and Azat Tagirdzhanov and Aleksandra Kushnareva and Ilia Olkhovskii and Simon Graf and Georges P. Schmartz and Julian Hegemann and Kenan Bozh{\"u}y{\"u}k and M{\"u}ller Rolf and Andreas Keller and Alexey Gurevich},
	title = {ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome},
	elocation-id = {2023.09.18.558305},
	year = {2023},
	doi = {10.1101/2023.09.18.558305},
	publisher = {Cold Spring Harbor Laboratory},
	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/.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2023/10/21/2023.09.18.558305},
	eprint = {https://www.biorxiv.org/content/early/2023/10/21/2023.09.18.558305.full.pdf},
	journal = {bioRxiv}
}

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/.Competing Interest StatementThe authors have declared no competing interest.

@article {Rosch2023.03.06.531264,
	author = {Michael E. G. Rosch and Jacqueline Rehner and Georges P. Schmartz and Sascha K. Manier and Uta Becker and Rolf M{\"u}ller and Markus R. Meyer and Andreas Keller and S{\"o}ren L. Becker and Verena Keller},
	title = {Time series of chicken stool metagenomics and egg metabolomics in changing production systems},
	elocation-id = {2023.03.06.531264},
	year = {2023},
	doi = {10.1101/2023.03.06.531264},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Different production systems of livestock animals influence various factors, including the gut microbiota. We investigated whether changing the conditions from barns to free-range impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment. Over the six time points, 12 taxa - mostly lactobacilli - changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken.Our data suggest that the gut microbiota can change over time following a change in production systems. This change also influences the metabolites in the eggs. We understand the study as a proof-of-concept that justifies larger scale observations with more individual chicken and longer observation periods.Competing Interest StatementGPS, RM, and AK are co-founders of MooH GmbH, a company developing metagenomic based oral health testing. UB is head of microbiology and diagnostics at MIP Pharma GmbH, Sankt Ingbert, Germany. All other authors have no conflict of interest.},
	URL = {https://www.biorxiv.org/content/early/2023/03/08/2023.03.06.531264},
	eprint = {https://www.biorxiv.org/content/early/2023/03/08/2023.03.06.531264.full.pdf},
	journal = {bioRxiv}
}

Different production systems of livestock animals influence various factors, including the gut microbiota. We investigated whether changing the conditions from barns to free-range impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment. Over the six time points, 12 taxa - mostly lactobacilli - changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken.Our data suggest that the gut microbiota can change over time following a change in production systems. This change also influences the metabolites in the eggs. We understand the study as a proof-of-concept that justifies larger scale observations with more individual chicken and longer observation periods.Competing Interest StatementGPS, RM, and AK are co-founders of MooH GmbH, a company developing metagenomic based oral health testing. UB is head of microbiology and diagnostics at MIP Pharma GmbH, Sankt Ingbert, Germany. All other authors have no conflict of interest.

@article {Hahn2022.09.18.508419,
	author = {Oliver Hahn and Aulden G Foltz and Micaiah Atkins and Blen Kedir and Patricia Moran-Losada and Ian H Guldner and Christy Munson and Fabian Kern and R{\'o}bert P{\'a}lovics and Nannan Lu and Hui Zhang and Achint Kaur and Jacob Hull and John R Huguenard and Sebastian Gr{\"o}nke and Benoit Lehallier and Linda Partridge and Andreas Keller and Tony Wyss-Coray},
	title = {A spatiotemporal map of the aging mouse brain reveals white matter tracts as vulnerable foci},
	elocation-id = {2022.09.18.508419},
	year = {2023},
	doi = {10.1101/2022.09.18.508419},
	publisher = {Cold Spring Harbor Laboratory},
	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-seq 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 glia aging was particularly accelerated in white matter compared to cortical regions, while 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.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2023/04/17/2022.09.18.508419},
	eprint = {https://www.biorxiv.org/content/early/2023/04/17/2022.09.18.508419.full.pdf},
	journal = {bioRxiv}
}

Aging is the key risk factor for cognitive decline, yet the molecular changes underlying brain aging remain poorly understood. Here, we conducted spatiotemporal RNA-seq 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 glia aging was particularly accelerated in white matter compared to cortical regions, while 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.Competing Interest StatementThe authors have declared no competing interest.

@article {Hirsch2023.09.18.558305,
	author = {Pascal Hirsch and Azat Tagirdzhanov and Aleksandra Kushnareva and Ilia Olkhovskii and Simon Graf and Georges P. Schmartz and Julian Hegemann and Kenan Bozh{\"u}y{\"u}k and M{\"u}ller Rolf and Andreas Keller and Alexey Gurevich},
	title = {ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome},
	elocation-id = {2023.09.18.558305},
	year = {2023},
	doi = {10.1101/2023.09.18.558305},
	publisher = {Cold Spring Harbor Laboratory},
	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/.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2023/10/21/2023.09.18.558305},
	eprint = {https://www.biorxiv.org/content/early/2023/10/21/2023.09.18.558305.full.pdf},
	journal = {bioRxiv}
}

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/.Competing Interest StatementThe authors have declared no competing interest.

@article {Yu2023.11.06.565829,
	author = {Zheng Yu and Varun Sasidharan-Nair and Agnes Bonifacius and Fawad Khan and Thalea Buchta and Michael Beckstette and Jana Niemz and Philipp Hilgendorf and Beate Pietzsch and Philip Mausberg and Andreas Keller and Christine Falk and Dirk Busch and Melanie M. Brinkmann and Kilian Schober and Luka Cicin-Sain and Fabian M{\"u}ller and Britta Eiz-Vesper and Stefan Floess and Jochen Huehn},
	title = {DNA methylation profiling identifies TBKBP1 as potent amplifier of cytotoxic activity in CMV-specific human CD8+ T cells},
	elocation-id = {2023.11.06.565829},
	year = {2023},
	doi = {10.1101/2023.11.06.565829},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Epigenetic mechanisms stabilize gene expression patterns during CD8+ T cell differentiation. However, although adoptive transfer of virus-specific T cells is clinically applied to reduce the risk of virus infection or reactivation in immunocompromised individuals, the DNA methylation pattern of virus-specific CD8+ T cells is largely unknown. Hence, we here performed whole-genome bisulfite sequencing of cytomegalovirus-specific human CD8+ T cells and found that they display a unique DNA methylation pattern consisting of 79 differentially methylated regions when compared to bulk memory CD8+ T cells. Among them was TBKBP1, coding for TBK-binding protein 1 that can interact with TANK-binding kinase 1 (TBK1) and mediate pro-inflammatory responses in innate immune cells downstream of intracellular virus sensing. Since TBKBP1 has not yet been reported in T cells, we aimed to unravel its role in virus-specific CD8+ T cells. TBKBP1 demethylation in terminal effector CD8+ T cells correlated with TBKBP1 expression and was stable upon long-term in vitro culture. TBKBP1 overexpression resulted in enhanced TBK1 phosphorylation upon stimulation of CD8+ T cells and significantly improved their virus neutralization capacity. Collectively, our data demonstrate that TBKBP1 modulates virus-specific CD8+ T cell responses and could be exploited as therapeutic target to improve adoptive T cell therapies.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2023/11/06/2023.11.06.565829},
	eprint = {https://www.biorxiv.org/content/early/2023/11/06/2023.11.06.565829.full.pdf},
	journal = {bioRxiv}
}

Epigenetic mechanisms stabilize gene expression patterns during CD8+ T cell differentiation. However, although adoptive transfer of virus-specific T cells is clinically applied to reduce the risk of virus infection or reactivation in immunocompromised individuals, the DNA methylation pattern of virus-specific CD8+ T cells is largely unknown. Hence, we here performed whole-genome bisulfite sequencing of cytomegalovirus-specific human CD8+ T cells and found that they display a unique DNA methylation pattern consisting of 79 differentially methylated regions when compared to bulk memory CD8+ T cells. Among them was TBKBP1, coding for TBK-binding protein 1 that can interact with TANK-binding kinase 1 (TBK1) and mediate pro-inflammatory responses in innate immune cells downstream of intracellular virus sensing. Since TBKBP1 has not yet been reported in T cells, we aimed to unravel its role in virus-specific CD8+ T cells. TBKBP1 demethylation in terminal effector CD8+ T cells correlated with TBKBP1 expression and was stable upon long-term in vitro culture. TBKBP1 overexpression resulted in enhanced TBK1 phosphorylation upon stimulation of CD8+ T cells and significantly improved their virus neutralization capacity. Collectively, our data demonstrate that TBKBP1 modulates virus-specific CD8+ T cell responses and could be exploited as therapeutic target to improve adoptive T cell therapies.Competing Interest StatementThe authors have declared no competing interest.

@article {Henn2022.03.14.484360,
	author = {Henn, Dominic and Zhao, Dehua and Chen, Kellen and Trotsyuk, Artem and Bonham, Clark Andrew and Fischer, Katharina S. and Kehl, Tim and Fehlmann, Tobias and Sivaraj, Dharshan and Greco, Autumn H. and Moortgat Illouz, Sylvia E. and Padmanabhan, Jagannath and Barrera, Janos A. and Kneser, Ulrich and Lenhof, Hans-Peter and Januszyk, Michael and Levi, Benjamin and Keller, Andreas and Longaker, Michael T. and Qi, Lei S. and Gurtner, Geoffrey C.},
	title = {Cas9-Mediated Knockout of Ndrg2 Enhances the Regenerative Potential of Dendritic Cells for Wound Healing},
	elocation-id = {2022.03.14.484360},
	year = {2022},
	doi = {10.1101/2022.03.14.484360},
	publisher = {Cold Spring Harbor Laboratory},
	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 achieved widespread adoption into clinical practice. Here, we developed a novel CRISPR/Cas9 approach to precisely edit dendritic cells (DCs) to enhance their therapeutic potential for healing chronic wounds. Using single-cell RNA sequencing (scRNA-seq) of tolerogenic DCs, we discover N-myc downregulated gene 2 (Ndrg2), which marks a specific population of DC progenitors, as a promising target for CRISPR knockout (KO). Ndrg2-KO alters the transcriptomic profile of DCs and preserves an immature cell state with a strong, pro-angiogenic and regenerative capacity. We then incorporated our CRISPR-based cell engineering within a hydrogel technology for in vivo cell delivery and developed a highly effective translational approach for DC 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 DCs for treating various types of chronic wounds.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2022/03/15/2022.03.14.484360},
	eprint = {https://www.biorxiv.org/content/early/2022/03/15/2022.03.14.484360.full.pdf},
	journal = {bioRxiv}
}

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 achieved widespread adoption into clinical practice. Here, we developed a novel CRISPR/Cas9 approach to precisely edit dendritic cells (DCs) to enhance their therapeutic potential for healing chronic wounds. Using single-cell RNA sequencing (scRNA-seq) of tolerogenic DCs, we discover N-myc downregulated gene 2 (Ndrg2), which marks a specific population of DC progenitors, as a promising target for CRISPR knockout (KO). Ndrg2-KO alters the transcriptomic profile of DCs and preserves an immature cell state with a strong, pro-angiogenic and regenerative capacity. We then incorporated our CRISPR-based cell engineering within a hydrogel technology for in vivo cell delivery and developed a highly effective translational approach for DC 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 DCs for treating various types of chronic wounds.Competing Interest StatementThe authors have declared no competing interest.

@article {Herr2021.05.04.21256497,
	author = {Herr, Christian and Mang, Sebastian and Mozafari, Bahareh and G{\"u}nther, Katharina and Speer, Thimoteus and Seibert, Martina and Srikakulam, Sanjay Kumar and Beisswenger, Christoph and Ritzmann, Felix and Keller, Andreas and M{\"u}ller, Rolf and Smola, Sigrun and Eisinger, Dominic and Zemlin, Michael and Danziger, Guy and Volk, Thomas and H{\"o}rsch, 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 Sch{\"a}fer, Harald and Eltges, Kai and Lepper, Philipp M. and Bals, Robert and CORSAAR study group},
	title = {Distinct patterns of blood cytokines beyond a cytokine storm predict mortality in COVID-19},
	elocation-id = {2021.05.04.21256497},
	year = {2021},
	doi = {10.1101/2021.05.04.21256497},
	publisher = {Cold Spring Harbor Laboratory Press},
	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.Findings 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.Interpretation Several newly identified blood markers were increased in patients with severe COVID-19 (AAT, EN-RAGE, ICAM-1, myoglobin, SAP, TIMP-1, vWF, decorin, HGF, MMP7, PECAM-1) or in patients that died (FRTN, SCF, TIMP-1, CA-9, CEA, decorin, HGF). The use of established assay technologies allows for rapid translation into clinical practice.Funding No role of the funding source.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThe funders of the study had no role in study design, data collection, data interpretation, or writing of the report. The corresponding author had full access to all data in the study and had final responsibility for the decision to submit for publication. This work was supported by grants of the Rolf M. Schwiete Stiftung (2020-013), the Saarland University, and The State of Saarland. Protein biomarker assays have been performed in collaboration with Myriad RBM.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The studies have been approved by the ethics committee of the Aerztekammer des Saarlandes, and all patients or their legal representatives gave their informed consent.All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll data concerning this manuscript is available within the manuscript or its supplement.},
	URL = {https://www.medrxiv.org/content/early/2021/05/04/2021.05.04.21256497},
	eprint = {https://www.medrxiv.org/content/early/2021/05/04/2021.05.04.21256497.full.pdf},
	journal = {medRxiv}
}

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.Findings 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.Interpretation Several newly identified blood markers were increased in patients with severe COVID-19 (AAT, EN-RAGE, ICAM-1, myoglobin, SAP, TIMP-1, vWF, decorin, HGF, MMP7, PECAM-1) or in patients that died (FRTN, SCF, TIMP-1, CA-9, CEA, decorin, HGF). The use of established assay technologies allows for rapid translation into clinical practice.Funding No role of the funding source.Competing Interest StatementThe authors have declared no competing interest.Funding StatementThe funders of the study had no role in study design, data collection, data interpretation, or writing of the report. The corresponding author had full access to all data in the study and had final responsibility for the decision to submit for publication. This work was supported by grants of the Rolf M. Schwiete Stiftung (2020-013), the Saarland University, and The State of Saarland. Protein biomarker assays have been performed in collaboration with Myriad RBM.Author DeclarationsI confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained.YesThe details of the IRB/oversight body that provided approval or exemption for the research described are given below:The studies have been approved by the ethics committee of the Aerztekammer des Saarlandes, and all patients or their legal representatives gave their informed consent.All necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived.YesI understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance).YesI have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable.YesAll data concerning this manuscript is available within the manuscript or its supplement.

@article {Yang2021.04.26.441262,
	author = {Yang, Andrew C. and Vest, Ryan T. and Kern, Fabian and Lee, Davis P. and Maat, Christina A. and Losada, Patricia M. and Chen, Michelle B. and Agam, Maayan and Schaum, Nicholas and Khoury, Nathalie and Calcuttawala, Kruti and P{\'a}lovics, R{\'o}bert and Shin, Andrew and Wang, Elizabeth Y. and Luo, Jian and Gate, David and Siegenthaler, Julie A. and McNerney, M. Windy and Keller, Andreas and Wyss-Coray, Tony},
	title = {A human brain vascular atlas reveals diverse cell mediators of Alzheimer's disease risk},
	elocation-id = {2021.04.26.441262},
	year = {2021},
	doi = {10.1101/2021.04.26.441262},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {The human brain vasculature is of vast medical importance: its dysfunction causes disability and death, and the specialized structure it forms{\textemdash}the blood-brain barrier{\textemdash}impedes treatment of nearly all brain disorders. Yet, no molecular atlas of the human brain vasculature exists. Here, we develop Vessel Isolation and Nuclei Extraction for Sequencing (VINE-seq) to profile the major human brain vascular and perivascular cell types through 143,793 single-nucleus transcriptomes from 25 hippocampus and cortex samples of 17 control and Alzheimer's disease (AD) patients. We identify brain region-enriched pathways and genes divergent between humans and mice, including those involved in disease. We describe the principles of human arteriovenous organization, recapitulating a gradual endothelial and punctuated mural cell continuum; but discover that many zonation and cell-type markers differ between species. We discover two subtypes of human pericytes, marked by solute transport and extracellular matrix (ECM) organization; and define perivascular versus meningeal fibroblast specialization. In AD, we observe a selective vulnerability of ECM-maintaining pericytes and gene expression patterns implicating dysregulated blood flow. With an expanded survey of brain cell types, we find that 30 of the top 45 AD GWAS genes are expressed in the human brain vasculature, confirmed in situ. Vascular GWAS genes map to endothelial protein transport, adaptive immune, and ECM pathways. Many are microglia-specific in mice, suggesting an evolutionary transfer of AD risk to human vascular cells. Our work unravels the molecular basis of the human brain vasculature, informing our understanding of overall brain health, disease, and therapy.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2021/04/27/2021.04.26.441262},
	eprint = {https://www.biorxiv.org/content/early/2021/04/27/2021.04.26.441262.full.pdf},
	journal = {bioRxiv}
}

The human brain vasculature is of vast medical importance: its dysfunction causes disability and death, and the specialized structure it forms—the blood-brain barrier—impedes treatment of nearly all brain disorders. Yet, no molecular atlas of the human brain vasculature exists. Here, we develop Vessel Isolation and Nuclei Extraction for Sequencing (VINE-seq) to profile the major human brain vascular and perivascular cell types through 143,793 single-nucleus transcriptomes from 25 hippocampus and cortex samples of 17 control and Alzheimer's disease (AD) patients. We identify brain region-enriched pathways and genes divergent between humans and mice, including those involved in disease. We describe the principles of human arteriovenous organization, recapitulating a gradual endothelial and punctuated mural cell continuum; but discover that many zonation and cell-type markers differ between species. We discover two subtypes of human pericytes, marked by solute transport and extracellular matrix (ECM) organization; and define perivascular versus meningeal fibroblast specialization. In AD, we observe a selective vulnerability of ECM-maintaining pericytes and gene expression patterns implicating dysregulated blood flow. With an expanded survey of brain cell types, we find that 30 of the top 45 AD GWAS genes are expressed in the human brain vasculature, confirmed in situ. Vascular GWAS genes map to endothelial protein transport, adaptive immune, and ECM pathways. Many are microglia-specific in mice, suggesting an evolutionary transfer of AD risk to human vascular cells. Our work unravels the molecular basis of the human brain vasculature, informing our understanding of overall brain health, disease, and therapy.Competing Interest StatementThe authors have declared no competing interest.

@article {Kern2021.05.07.443093,
	author = {Kern, Fabian and Kuhn, Thomas and Ludwig, Nicole and Simon, Martin and Gr{\"o}ger, Laura and Fabis, Natalie and Salhab, Abdulrahman and Fehlmann, Tobias and Hahn, Oliver and Engel, Annika and Koch, Marcus and Koehler, Jana and Winek, Katarzyna and Soreq, Hermona and Fuhrmann, Gregor and Wyss-Coray, Tony and Meese, Eckart and Laschke, Matthias W. and Keller, Andreas},
	title = {Vesicle-bound regulatory RNAs are associated with tissue aging},
	elocation-id = {2021.05.07.443093},
	year = {2021},
	doi = {10.1101/2021.05.07.443093},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Previous work on murine models and human demonstrated global as well as tissue-specific molecular aging trajectories in solid tissues and body fluids1{\textendash}8. Extracellular vesicles like exosomes play a crucial role in communication and information exchange in between such systemic factors and solid tissues9,10. We sequenced freely circulating and vesicle-bound small regulatory RNAs in mice at five time points across the average life span from 2 to 18 months. Intriguingly, each small RNA class exhibits unique aging patterns, which showed differential signatures between vesicle-bound and freely circulating molecules. In particular, tRNA fragments showed overall highest correlation with aging which also matched well between sample types, facilitating age prediction with non-negative matrix factorization (86\% accuracy). Interestingly, rRNAs exhibited inverse correlation trajectories between vesicles and plasma while vesicle-bound microRNAs (miRNAs) were exceptionally strong associated with aging. Affected miRNAs regulate the inflammatory response and transcriptional processes, and adipose tissues show considerable effects in associated gene regulatory modules. Finally, nanoparticle tracking and electron microscopy suggest a shift from overall many small to fewer but larger vesicles in aged plasma, potentially contributing to systemic aging trajectories and affecting the molecular aging of organs.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2021/05/08/2021.05.07.443093},
	eprint = {https://www.biorxiv.org/content/early/2021/05/08/2021.05.07.443093.full.pdf},
	journal = {bioRxiv}
}

Previous work on murine models and human demonstrated global as well as tissue-specific molecular aging trajectories in solid tissues and body fluids1–8. Extracellular vesicles like exosomes play a crucial role in communication and information exchange in between such systemic factors and solid tissues9,10. We sequenced freely circulating and vesicle-bound small regulatory RNAs in mice at five time points across the average life span from 2 to 18 months. Intriguingly, each small RNA class exhibits unique aging patterns, which showed differential signatures between vesicle-bound and freely circulating molecules. In particular, tRNA fragments showed overall highest correlation with aging which also matched well between sample types, facilitating age prediction with non-negative matrix factorization (86% accuracy). Interestingly, rRNAs exhibited inverse correlation trajectories between vesicles and plasma while vesicle-bound microRNAs (miRNAs) were exceptionally strong associated with aging. Affected miRNAs regulate the inflammatory response and transcriptional processes, and adipose tissues show considerable effects in associated gene regulatory modules. Finally, nanoparticle tracking and electron microscopy suggest a shift from overall many small to fewer but larger vesicles in aged plasma, potentially contributing to systemic aging trajectories and affecting the molecular aging of organs.Competing Interest StatementThe authors have declared no competing interest.

@article {henn211,
author = {Henn, Dominic and Chen, Kellen and Fehlmann, Tobias and Sivaraj, Dharshan and Maan, Zeshaan and Bonham, Clark and Barrera, Janos and Mays, Chyna and Greco, Autumn and Illouz, Sylvia and Lin, John and Foster, Deshka and Padmanabhan, Jagannath and Momeni, Arash and Nguyen, Dung and Wan, Derrick and Kneser, Ulrich and Januszyk, Michael and Keller, Andreas and Gurtner, Geoffrey},
year = {2021},
month = {02},
title = {Xenogeneic Skin Transplantation Promotes Angiogenesis and Tissue Regeneration Through Vitamin D-Activated Trem2+ Macrophages},
doi = {10.1101/2021.02.26.432991},
	abstract = {Skin allo- and xenotransplantation are the standard treatment for major burns when donor sites for autografts are not available and have been shown to significantly accelerate wound healing. Although the cellular elements of foreign grafts are rejected, the extracellular matrix components integrate into the wound and may underlie their beneficial effects on wound healing. The molecular mechanisms defining the relationship between the immune response to foreign grafts and their impact on wound healing have not been fully elucidated. Here, we investigated changes in collagen architecture after xenogeneic implantation of clinically available human biologic scaffolds. We show that collagen deposition in response to the implantation of human split-thickness skin grafts (hSTSG) containing live cells recapitulates normal skin architecture, whereas human acellular dermal matrix (ADM) grafts led to highly aligned collagen deposition, characteristic of fibrosis and scar. Using single-cell RNA-sequencing, we show that macrophage differentiation in response to hSTSG is driven by vitamin D (VD) signaling toward Trem2+ subpopulations with an enrichment of pro-angiogenic and anti-fibrotic transcriptomic programs. We subsequently induced this regenerative subpopulation in vitro by treating bone marrow-derived cells with vitamin D3 and found that hydrogel delivery of Trem2+ macrophages significantly accelerated wound closure in a human-like murine excisional wound model. Our study identifies the preclinical therapeutic potential of Trem2+ macrophages to mitigate fibrosis and promote wound healing and provides a novel effective strategy to develop advanced cell therapies for complex wounds.},
	URL = {https://www.biorxiv.org/content/10.1101/2021.02.26.432991v1},
}

Skin allo- and xenotransplantation are the standard treatment for major burns when donor sites for autografts are not available and have been shown to significantly accelerate wound healing. Although the cellular elements of foreign grafts are rejected, the extracellular matrix components integrate into the wound and may underlie their beneficial effects on wound healing. The molecular mechanisms defining the relationship between the immune response to foreign grafts and their impact on wound healing have not been fully elucidated. Here, we investigated changes in collagen architecture after xenogeneic implantation of clinically available human biologic scaffolds. We show that collagen deposition in response to the implantation of human split-thickness skin grafts (hSTSG) containing live cells recapitulates normal skin architecture, whereas human acellular dermal matrix (ADM) grafts led to highly aligned collagen deposition, characteristic of fibrosis and scar. Using single-cell RNA-sequencing, we show that macrophage differentiation in response to hSTSG is driven by vitamin D (VD) signaling toward Trem2+ subpopulations with an enrichment of pro-angiogenic and anti-fibrotic transcriptomic programs. We subsequently induced this regenerative subpopulation in vitro by treating bone marrow-derived cells with vitamin D3 and found that hydrogel delivery of Trem2+ macrophages significantly accelerated wound closure in a human-like murine excisional wound model. Our study identifies the preclinical therapeutic potential of Trem2+ macrophages to mitigate fibrosis and promote wound healing and provides a novel effective strategy to develop advanced cell therapies for complex wounds.

@article {becker1,
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, Joerg and Wagenpfeil, Gudrun and Fassbender, Klaus and Keller, Andreas and Unger, Marcus},
year = {2021},
month = {02},
pages = {},
title = {Effects of Resistant Starch on Symptoms, Fecal Markers and Gut Microbiota in Parkinson′s Disease — The RESISTA-PD Trial},
doi = {10.1101/2021.02.07.21251098},
	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 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 receiving RS (PD + RS), 30 control subjects receiving RS, and 25 PD patients receiving 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 calls for long-term studies, also investigating whether RS is able to modify the clinical course of PD.},
	URL = {https://www.medrxiv.org/content/10.1101/2021.02.07.21251098v1},
}

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 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 receiving RS (PD + RS), 30 control subjects receiving RS, and 25 PD patients receiving 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 calls for long-term studies, also investigating whether RS is able to modify the clinical course of PD.

@article {Palovics2020.11.06.367078,
	author = {Palovics, Robert and Keller, Andreas and Schaum, Nicholas and Tan, Weilun and Fehlmann, Tobias and Borja, Michael and Webber, James and McGeever, Aaron and Bonanno, Liana and , and Pisco, Angela Oliveira and Karkanias, Jim and Neff, Norma F. and Darmanis, Spyros and Quake, Stephen R. and Wyss-Coray, Tony},
	title = {Molecular hallmarks of heterochronic parabiosis at single cell resolution},
	elocation-id = {2020.11.06.367078},
	year = {2020},
	doi = {10.1101/2020.11.06.367078},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Slowing or reversing biological ageing would have major implications for mitigating disease risk and maintaining vitality. While an increasing number of interventions show promise for rejuvenation, the effectiveness on disparate cell types across the body and the molecular pathways susceptible to rejuvenation remain largely unexplored. We performed single-cell RNA-sequencing on 13 organs to reveal cell type specific responses to young or aged blood in heterochronic parabiosis. Adipose mesenchymal stromal cells, hematopoietic stem cells, hepatocytes, and endothelial cells from multiple tissues appear especially responsive. On the pathway level, young blood invokes novel 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. Intriguingly, 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. Altogether, these data lay the groundwork for a systemic understanding of the interplay between blood-borne factors and cellular integrity.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2020/11/08/2020.11.06.367078},
	eprint = {https://www.biorxiv.org/content/early/2020/11/08/2020.11.06.367078.full.pdf},
	journal = {bioRxiv}
}

Slowing or reversing biological ageing would have major implications for mitigating disease risk and maintaining vitality. While an increasing number of interventions show promise for rejuvenation, the effectiveness on disparate cell types across the body and the molecular pathways susceptible to rejuvenation remain largely unexplored. We performed single-cell RNA-sequencing on 13 organs to reveal cell type specific responses to young or aged blood in heterochronic parabiosis. Adipose mesenchymal stromal cells, hematopoietic stem cells, hepatocytes, and endothelial cells from multiple tissues appear especially responsive. On the pathway level, young blood invokes novel 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. Intriguingly, 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. Altogether, these data lay the groundwork for a systemic understanding of the interplay between blood-borne factors and cellular integrity.Competing Interest StatementThe authors have declared no competing interest.

@article {Yang2020.10.22.349415,
	author = {Yang, Andrew Chris and Kern, Fabian and Losada, Patricia M and Maat, Christina A and Schmartz, Georges and Fehlmann, Tobias and Schaum, Nicholas and Lee, Davis P and Calcuttawala, Kruti and Vest, Ryan T and Gate, David and Berdnik, Daniela and McNerney, M. Windy and Channappa, Divya and Cobos, Inma and Ludwig, Nicole and Schulz-Schaeffer, Walter J. and Keller, Andreas and Wyss-Coray, Tony},
	title = {Broad transcriptional dysregulation of brain and choroid plexus cell types with COVID-19},
	elocation-id = {2020.10.22.349415},
	year = {2020},
	doi = {10.1101/2020.10.22.349415},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Though SARS-CoV-2 primarily targets the respiratory system, it is increasingly appreciated that patients may suffer neurological symptoms of varied severity. However, an unbiased understanding of the molecular processes across brain cell types that could contribute to these symptoms in COVID-19 patients is still missing. Here, we profile 47,678 droplet-based single-nucleus transcriptomes from the frontal cortex and choroid plexus across 10 non-viral, 4 COVID-19, and 1 influenza patient. We complement transcriptomic data with immunohistochemical staining for the presence of SARS-CoV-2. We find that all major cortex parenchymal and choroid plexus cell types are affected transcriptionally with COVID-19. This arises, in part, from SARS-CoV-2 infection of the cortical brain vasculature, meninges, and choroid plexus, stimulating increased inflammatory signaling into the brain. In parallel, peripheral immune cells infiltrate the brain, microglia activate programs mediating the phagocytosis of live neurons, and astrocytes dysregulate genes involved in neurotransmitter homeostasis. Among neurons, layer 2/3 excitatory neurons--evolutionarily expanded in humans--show a specific downregulation of genes encoding major SNARE and synaptic vesicle components, predicting compromised synaptic transmission. These perturbations are not observed in terminal influenza. Many COVID-19 gene expression changes are shared with those in chronic brain disorders and reside in genetic variants associated with cognitive function, schizophrenia, and depression. Our findings and public dataset provide a molecular framework and new opportunities to understand COVID-19 related neurological disease.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2020/10/22/2020.10.22.349415},
	eprint = {https://www.biorxiv.org/content/early/2020/10/22/2020.10.22.349415.full.pdf},
	journal = {bioRxiv}
}

Though SARS-CoV-2 primarily targets the respiratory system, it is increasingly appreciated that patients may suffer neurological symptoms of varied severity. However, an unbiased understanding of the molecular processes across brain cell types that could contribute to these symptoms in COVID-19 patients is still missing. Here, we profile 47,678 droplet-based single-nucleus transcriptomes from the frontal cortex and choroid plexus across 10 non-viral, 4 COVID-19, and 1 influenza patient. We complement transcriptomic data with immunohistochemical staining for the presence of SARS-CoV-2. We find that all major cortex parenchymal and choroid plexus cell types are affected transcriptionally with COVID-19. This arises, in part, from SARS-CoV-2 infection of the cortical brain vasculature, meninges, and choroid plexus, stimulating increased inflammatory signaling into the brain. In parallel, peripheral immune cells infiltrate the brain, microglia activate programs mediating the phagocytosis of live neurons, and astrocytes dysregulate genes involved in neurotransmitter homeostasis. Among neurons, layer 2/3 excitatory neurons–evolutionarily expanded in humans–show a specific downregulation of genes encoding major SNARE and synaptic vesicle components, predicting compromised synaptic transmission. These perturbations are not observed in terminal influenza. Many COVID-19 gene expression changes are shared with those in chronic brain disorders and reside in genetic variants associated with cognitive function, schizophrenia, and depression. Our findings and public dataset provide a molecular framework and new opportunities to understand COVID-19 related neurological disease.Competing Interest StatementThe authors have declared no competing interest.

@article {Keller2020.03.26.009597,
	author = {Keller, Andreas and Fehlmann, Tobias and Backes, Christina and Kern, Fabian and Gislefoss, Randi and Langseth, Hilde and Rounge, Trine B. and Ludwig, Nicole and Meese, Eckart},
	title = {Competitive learning suggests circulating miRNA profiles for cancers decades prior to diagnosis},
	elocation-id = {2020.03.26.009597},
	year = {2020},
	doi = {10.1101/2020.03.26.009597},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Small non-coding RNAs such as microRNAs are master regulators of gene expression. One of the most promising applications of miRNAs is the use as liquid biopsy. Especially early diagnosis is an effective means to increase patients overall survival. E.g. in oncology a tumor is detected at best prior to its clinical manifestation. We generated genome-wide miRNA profiles from serum of patients and controls from the population-based Janus Serum Bank (JSB) and analyzed them by bioinformatics and artificial intelligence approaches. JSB contains sera from 318,628 originally healthy persons, more than 96,000 of whom later developed cancer. We selected 210 serum samples of patients with lung, colon or breast cancer at three time points prior to diagnosis, after cancer diagnosis and controls. The controls were matched with regard to age of the blood donor and to the time points of blood drawing, which were 27, 32, or 38 years prior to diagnosis. 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 had adjusted p-values\<10-10). Further, 91miRNAs were differently expressed in pre-diagnostic samples as compared to controls (nominal p\<0.05). Unsupervised competitive learning by self-organized maps indicated larges effects in lung cancer samples while breast cancer samples showed the least pronounced changes. Self-organized maps also highlighted 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. Our results indicate that tumors may be indicated by serum miRNAs decades prior the clinical manifestation.},
	URL = {https://www.biorxiv.org/content/early/2020/03/29/2020.03.26.009597},
	eprint = {https://www.biorxiv.org/content/early/2020/03/29/2020.03.26.009597.full.pdf},
	journal = {bioRxiv}
}

Small non-coding RNAs such as microRNAs are master regulators of gene expression. One of the most promising applications of miRNAs is the use as liquid biopsy. Especially early diagnosis is an effective means to increase patients overall survival. E.g. in oncology a tumor is detected at best prior to its clinical manifestation. We generated genome-wide miRNA profiles from serum of patients and controls from the population-based Janus Serum Bank (JSB) and analyzed them by bioinformatics and artificial intelligence approaches. JSB contains sera from 318,628 originally healthy persons, more than 96,000 of whom later developed cancer. We selected 210 serum samples of patients with lung, colon or breast cancer at three time points prior to diagnosis, after cancer diagnosis and controls. The controls were matched with regard to age of the blood donor and to the time points of blood drawing, which were 27, 32, or 38 years prior to diagnosis. 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 had adjusted p-values<10-10). Further, 91miRNAs were differently expressed in pre-diagnostic samples as compared to controls (nominal p<0.05). Unsupervised competitive learning by self-organized maps indicated larges effects in lung cancer samples while breast cancer samples showed the least pronounced changes. Self-organized maps also highlighted 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. Our results indicate that tumors may be indicated by serum miRNAs decades prior the clinical manifestation.

@article {Kern2020.03.05.978890,
	author = {Kern, Fabian and Fehlmann, Tobias and Solomon, Jeffrey and Schwed, Louisa and Backes, Christina and Meese, Eckart and Keller, Andreas},
	title = {miEAA 2.0: Integrating multi-species microRNA enrichment analysis and workflow management systems},
	elocation-id = {2020.03.05.978890},
	year = {2020},
	doi = {10.1101/2020.03.05.978890},
	publisher = {Cold Spring Harbor Laboratory},
	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 Homo sapiens, Mus musculus, and Rattus norvegicus. 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 miR-Base 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 visualisations such as heatmaps and running sum curves with background distributions. Lastly, additional methods to correct for multiple hypothesis testing were implemented. We demonstrate the new features using case studies for human kidney cancer and mouse samples. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.},
	URL = {https://www.biorxiv.org/content/early/2020/03/06/2020.03.05.978890},
	eprint = {https://www.biorxiv.org/content/early/2020/03/06/2020.03.05.978890.full.pdf},
	journal = {bioRxiv}
}

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 Homo sapiens, Mus musculus, and Rattus norvegicus. 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 miR-Base 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 visualisations such as heatmaps and running sum curves with background distributions. Lastly, additional methods to correct for multiple hypothesis testing were implemented. We demonstrate the new features using case studies for human kidney cancer and mouse samples. The tool is freely accessible at: https://www.ccb.uni-saarland.de/mieaa2.

@article {Isakova430561,
	author = {Isakova, Alina and Fehlmann, Tobias and Keller, Andreas and Quake, Stephen R.},
	title = {A mouse tissue atlas of small non-coding RNA},
	elocation-id = {430561},
	year = {2020},
	doi = {10.1101/430561},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Small non-coding 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 (miRNA, snoRNA, snRNA, scaRNA and tRNA fragments) across eleven mouse tissues by deep sequencing. Using fourteen biological replicates spanning both sexes, we identified that ~ 30\% of small ncRNAs are distributed across the body in a tissue-specific manner with some are also being sexually dimorphic. We found that 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 eleven 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 for the first time in this study. Furthermore, by combining these findings with single-cell ATAC-seq data, we were able to connect identified brain-specific ncRNA 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 this data will be a resource for the further identification of ncRNAs involved in tissue-function in health and dysfunction in disease.HIGHLIGHTS- An atlas of tissue levels of multiple small ncRNA classes generated from 14 biological replicates of both sexes across 11 tissues- Distinct distribution patterns of miRNA arms and tRNA fragments across tissues suggest the existence of tissue-specific mechanisms of ncRNA cleavage and retention- miRNA expression is sex specific in healthy tissues- Small RNA-seq and scATAC-seq data integration produce a detailed map of cell-type specific ncRNA profiles in the mouse brain},
	URL = {https://www.biorxiv.org/content/early/2020/01/30/430561},
	eprint = {https://www.biorxiv.org/content/early/2020/01/30/430561.full.pdf},
	journal = {bioRxiv}
}

Small non-coding 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 (miRNA, snoRNA, snRNA, scaRNA and tRNA fragments) across eleven mouse tissues by deep sequencing. Using fourteen biological replicates spanning both sexes, we identified that   30% of small ncRNAs are distributed across the body in a tissue-specific manner with some are also being sexually dimorphic. We found that 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 eleven 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 for the first time in this study. Furthermore, by combining these findings with single-cell ATAC-seq data, we were able to connect identified brain-specific ncRNA 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 this data will be a resource for the further identification of ncRNAs involved in tissue-function in health and dysfunction in disease.HIGHLIGHTS- An atlas of tissue levels of multiple small ncRNA classes generated from 14 biological replicates of both sexes across 11 tissues- Distinct distribution patterns of miRNA arms and tRNA fragments across tissues suggest the existence of tissue-specific mechanisms of ncRNA cleavage and retention- miRNA expression is sex specific in healthy tissues- Small RNA-seq and scATAC-seq data integration produce a detailed map of cell-type specific ncRNA profiles in the mouse brain

@article {Kern2020.06.01.127092,
	author = {Kern, Fabian and Fehlmann, Tobias and Violich, Ivo and Alsop, Eric and Hutchins, Elizabeth and Kahraman, Mustafa and Grammes, Nadja Liddy and Guimaraes, Pedro and Backes, Christina and Poston, Kathleen and Casey, Bradford and Balling, Rudi and Geffers, Lars and Krueger, Rejko and Galasko, Douglas and Mollenhauer, Brit and Meese, Eckart and Wyss-Coray, Tony and Craig, David Wesley and Van Keuren-Jensen, Kendall and Keller, Andreas},
	title = {Deep sncRNA-seq of the PPMI cohort to study Parkinsons disease progression},
	elocation-id = {2020.06.01.127092},
	year = {2020},
	doi = {10.1101/2020.06.01.127092},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Coding and non-coding RNAs have diagnostic and prognostic importance in Parkinsons diseases (PD). We studied circulating small non-coding RNAs (sncRNAs) in 7,003 samples from two longitudinal PD cohorts (Parkinsons Progression Marker Initiative (PPMI) and Luxembourg Parkinsons Study (NCER-PD)) and modelled their influence on the transcriptome. First, we sequenced sncRNAs in 5,450 blood samples of 1,614 individuals in PPMI. The majority of 323 billion reads (59 million reads per sample) mapped to miRNAs. Other covered RNA classes include piRNAs, rRNAs, snoRNAs, tRNAs, scaRNAs, and snRNAs. De-regulated miRNAs were associated with the disease and disease progression and occur in two distinct waves in the third and seventh decade of live. Originating mostly from a characteristic set of immune cells they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. By profiling 1,553 samples from 1,024 individuals in the NCER-PD cohort using an independent technology, we validate relevant findings from the sequencing study. Finally, network analysis of sncRNAs and transcriptome sequencing of the original cohort identified regulatory modules emerging in progressing PD patients.Competing Interest StatementThe authors have declared no competing interest.},
	URL = {https://www.biorxiv.org/content/early/2020/06/01/2020.06.01.127092},
	eprint = {https://www.biorxiv.org/content/early/2020/06/01/2020.06.01.127092.full.pdf},
	journal = {bioRxiv}
}

Coding and non-coding RNAs have diagnostic and prognostic importance in Parkinsons diseases (PD). We studied circulating small non-coding RNAs (sncRNAs) in 7,003 samples from two longitudinal PD cohorts (Parkinsons Progression Marker Initiative (PPMI) and Luxembourg Parkinsons Study (NCER-PD)) and modelled their influence on the transcriptome. First, we sequenced sncRNAs in 5,450 blood samples of 1,614 individuals in PPMI. The majority of 323 billion reads (59 million reads per sample) mapped to miRNAs. Other covered RNA classes include piRNAs, rRNAs, snoRNAs, tRNAs, scaRNAs, and snRNAs. De-regulated miRNAs were associated with the disease and disease progression and occur in two distinct waves in the third and seventh decade of live. Originating mostly from a characteristic set of immune cells they resemble a systemic inflammation response and mitochondrial dysfunction, two hallmarks of PD. By profiling 1,553 samples from 1,024 individuals in the NCER-PD cohort using an independent technology, we validate relevant findings from the sequencing study. Finally, network analysis of sncRNAs and transcriptome sequencing of the original cohort identified regulatory modules emerging in progressing PD patients.Competing Interest StatementThe authors have declared no competing interest.

@article {Kern2020.03.25.007351,
	author = {Kern, Fabian Michael 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},
	elocation-id = {2020.03.25.007351},
	year = {2020},
	doi = {10.1101/2020.03.25.007351},
	publisher = {Cold Spring Harbor Laboratory},
	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{\textquoteright}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 customised arm switch analyses along with comprehensive visualisations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.},
	URL = {https://www.biorxiv.org/content/early/2020/03/25/2020.03.25.007351},
	eprint = {https://www.biorxiv.org/content/early/2020/03/25/2020.03.25.007351.full.pdf},
	journal = {bioRxiv}
}

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\textquoterights disease biomarker data set and from a comparison of tissues in Homo sapiens and Mus musculus. In summary, miRSwitch offers a broad range of customised arm switch analyses along with comprehensive visualisations, and is freely available at: https://www.ccb.uni-saarland.de/mirswitch/.

@article {Hickl793950,
	author = {Hickl, D. and Drews, F. and Girke, C. and Zimmer, D. and Mühlhaus, T. and Hauth, J. and Nordström, K. and Trentmann, O. and Neuhaus, H.E. and Fehlmann, T. and Keller, A. and Simon, M. and Möhlmann, T.},
	title = {Differential degradation of RNA species by autophagy related pathways in plants},
	elocation-id = {793950},
	year = {2019},
	doi = {10.1101/793950},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {An important function of the plant vacuole is the recycling of the delivered proteins and RNA by autophagy. We provide the first plant vacuolar small RNome by isolation of intact vacuoles from Barley and Arabidopsis, subsequent RNA purification and Next Generation Sequencing. In these vacuolar sRNomes, all types of cellular RNAs were found including those of chloroplast origin, suggesting a bulk-type of RNA transfer to, and breakdown in vacuoles. ATG5 is a major representative of autophagy genes and the vacuolar RNA composition in corresponding knockout plants differed clearly from controls as most chloroplast derived RNA species were missing. Moreover, the read length distribution of RNAs found in ATG5 mutants differed to control samples, indicating altered RNA processing. In contrast, vacuolar RNA length and composition of plants lacking the vacuolar RNase2 (rns2-2), involved in cellular RNA homeostasis, showed minor alterations, only. Our data therefore suggests that mainly autophagy components are responsible for selective transport and targeting of different RNA species into the vacuole for degradation. In addition, mature miRNAs were detected in all vacuolar preparations, however in ATG5 mutants at much lower frequency, indicating a new biological role for vacuolar miRNAs apart from becoming degraded.},
	URL = {https://www.biorxiv.org/content/early/2019/10/17/793950},
	eprint = {https://www.biorxiv.org/content/early/2019/10/17/793950.full.pdf},
	journal = {bioRxiv}
}

An important function of the plant vacuole is the recycling of the delivered proteins and RNA by autophagy. We provide the first plant vacuolar small RNome by isolation of intact vacuoles from Barley and Arabidopsis, subsequent RNA purification and Next Generation Sequencing. In these vacuolar sRNomes, all types of cellular RNAs were found including those of chloroplast origin, suggesting a bulk-type of RNA transfer to, and breakdown in vacuoles. ATG5 is a major representative of autophagy genes and the vacuolar RNA composition in corresponding knockout plants differed clearly from controls as most chloroplast derived RNA species were missing. Moreover, the read length distribution of RNAs found in ATG5 mutants differed to control samples, indicating altered RNA processing. In contrast, vacuolar RNA length and composition of plants lacking the vacuolar RNase2 (rns2-2), involved in cellular RNA homeostasis, showed minor alterations, only. Our data therefore suggests that mainly autophagy components are responsible for selective transport and targeting of different RNA species into the vacuole for degradation. In addition, mature miRNAs were detected in all vacuolar preparations, however in ATG5 mutants at much lower frequency, indicating a new biological role for vacuolar miRNAs apart from becoming degraded.

@article {Lehallier751115,
	author = {Lehallier, Benoit and Gate, David and Schaum, Nicholas and Nanasi, Tibor and Lee, Song Eun and Yousef, Hanadie and Losada, Patricia Moran and Berdnik, Daniela and Keller, Andreas and Verghese, Joe and Sathyan, Sanish and Franceschi, Claudio and Milman, Sofiya and Barzilai, Nir and Wyss-Coray, Tony},
	title = {Undulating changes in human plasma proteome across lifespan are linked to disease},
	elocation-id = {751115},
	year = {2019},
	doi = {10.1101/751115},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Aging is the predominant risk factor for numerous chronic diseases that limit healthspan. Mechanisms of aging are thus increasingly recognized as therapeutic targets. Blood from young mice reverses aspects of aging and disease across multiple tissues, pointing to the intriguing possibility that age-related molecular changes in blood can provide novel insight into disease biology. We measured 2,925 plasma proteins from 4,331 young adults to nonagenarians and developed a novel bioinformatics approach which uncovered profound 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 of aging and disease and offers potential pathways for aging interventions.},
	URL = {https://www.biorxiv.org/content/early/2019/09/01/751115},
	eprint = {https://www.biorxiv.org/content/early/2019/09/01/751115.full.pdf},
	journal = {bioRxiv}
}

Aging is the predominant risk factor for numerous chronic diseases that limit healthspan. Mechanisms of aging are thus increasingly recognized as therapeutic targets. Blood from young mice reverses aspects of aging and disease across multiple tissues, pointing to the intriguing possibility that age-related molecular changes in blood can provide novel insight into disease biology. We measured 2,925 plasma proteins from 4,331 young adults to nonagenarians and developed a novel bioinformatics approach which uncovered profound 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 of aging and disease and offers potential pathways for aging interventions.

@article {Kern721928,
	author = {Kern, Fabian and Ludwig, Nicole and Backes, Christina and Maldener, Esther and Fehlmann, Tobias and Suleymanov, Artur and Meese, Eckart and Hecksteden, Anne and Keller, Andreas and Meyer, Tim},
	title = {Systematic assessment of blood-borne microRNAs highlights molecular profiles of endurance sport and carbohydrate uptake},
	elocation-id = {721928},
	year = {2019},
	doi = {10.1101/721928},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Multiple studies endorsed the positive effect of regular exercising 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 2, 549 miRNAs in whole-blood samples from 23 healthy and untrained adult participants of a cross-over study, consisting of 8 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, 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 (VO2 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 demon-strate 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 VO2 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 miRNAs expression can be altered due to regular endurance training, independent of the carbohydrate availability in the timeframe around training. 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.VO2max Maximal aerobic capacitymiRNAmicroRNACHOCarbohydrates},
	URL = {https://www.biorxiv.org/content/early/2019/08/01/721928},
	eprint = {https://www.biorxiv.org/content/early/2019/08/01/721928.full.pdf},
	journal = {bioRxiv}
}

Multiple studies endorsed the positive effect of regular exercising 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 2, 549 miRNAs in whole-blood samples from 23 healthy and untrained adult participants of a cross-over study, consisting of 8 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, 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 (VO2 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 demon-strate 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 VO2 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 miRNAs expression can be altered due to regular endurance training, independent of the carbohydrate availability in the timeframe around training. 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.VO2max Maximal aerobic capacitymiRNAmicroRNACHOCarbohydrates

@article {Schaum662254,
	author = {Schaum, Nicholas and Lehallier, Benoit and Hahn, Oliver and Hosseinzadeh, Shayan and Lee, Song E. and Sit, Rene and Lee, Davis P. and Losada, Patricia Mor{\'a}n and Zardeneta, Macy E. and P{\'a}lovics, R{\'o}bert and Fehlmann, Tobias and Webber, James and McGeever, Aaron and Zhang, Hui and Berdnik, Daniela and Tan, Weilun and Zee, Alexander and Tan, Michelle and , and Pisco, Angela and Karkanias, Jim and Neff, Norma F. and Keller, Andreas and Darmanis, Spyros and Quake, Stephen R. and Wyss-Coray, Tony},
	title = {The murine transcriptome reveals global aging nodes with organ-specific phase and amplitude},
	elocation-id = {662254},
	year = {2019},
	doi = {10.1101/662254},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Aging is the single greatest cause of disease and death worldwide, and so understanding the associated processes could vastly improve quality of life. While the field has identified major categories of aging damage such as altered intercellular communication, loss of proteostasis, and eroded mitochondrial function1, these deleterious processes interact with extraordinary complexity within and between organs. Yet, a comprehensive analysis of aging dynamics organism-wide is lacking. Here we performed RNA-sequencing of 17 organs and plasma proteomics at 10 ages across the mouse lifespan. We uncover previously unknown linear and non-linear expression shifts during aging, which cluster in strikingly consistent trajectory groups with coherent biological functions, including extracellular matrix regulation, unfolded protein binding, mitochondrial function, and inflammatory and immune response. Remarkably, these gene sets are expressed similarly across tissues, differing merely in age of onset and amplitude. Especially pronounced is widespread immune cell activation, detectable first in white adipose depots in middle age. Single-cell RNA-sequencing confirms the accumulation of adipose T and B cells, including immunoglobulin J-expressing plasma cells, which also accrue concurrently across diverse organs. Finally, we show how expression shifts in distinct tissues are highly correlated with corresponding protein levels in plasma, thus potentially contributing to aging of the systemic circulation. Together, these data demonstrate a similar yet asynchronous inter- and intra-organ progression of aging, thereby providing a foundation to track systemic sources of declining health at old age.},
	URL = {https://www.biorxiv.org/content/early/2019/06/07/662254},
	eprint = {https://www.biorxiv.org/content/early/2019/06/07/662254.full.pdf},
	journal = {bioRxiv}
}

Aging is the single greatest cause of disease and death worldwide, and so understanding the associated processes could vastly improve quality of life. While the field has identified major categories of aging damage such as altered intercellular communication, loss of proteostasis, and eroded mitochondrial function1, these deleterious processes interact with extraordinary complexity within and between organs. Yet, a comprehensive analysis of aging dynamics organism-wide is lacking. Here we performed RNA-sequencing of 17 organs and plasma proteomics at 10 ages across the mouse lifespan. We uncover previously unknown linear and non-linear expression shifts during aging, which cluster in strikingly consistent trajectory groups with coherent biological functions, including extracellular matrix regulation, unfolded protein binding, mitochondrial function, and inflammatory and immune response. Remarkably, these gene sets are expressed similarly across tissues, differing merely in age of onset and amplitude. Especially pronounced is widespread immune cell activation, detectable first in white adipose depots in middle age. Single-cell RNA-sequencing confirms the accumulation of adipose T and B cells, including immunoglobulin J-expressing plasma cells, which also accrue concurrently across diverse organs. Finally, we show how expression shifts in distinct tissues are highly correlated with corresponding protein levels in plasma, thus potentially contributing to aging of the systemic circulation. Together, these data demonstrate a similar yet asynchronous inter- and intra-organ progression of aging, thereby providing a foundation to track systemic sources of declining health at old age.

@article {Ludwig638213,
	author = {Ludwig, Nicole and Fehlmann, Tobias and Gogol, Manfred and Maetzler, Walter and Deutscher, Stephanie and Gurlit, Simone and Schulte, Claudia and von Thaler, Anna-Katharina and Deuschle, Christian and Metzger, Florian and Berg, Daniela and Suenkel, Ulrike and Keller, Verena and Backes, Christina and Lenhof, Hans-Peter and Meese, Eckart and Keller, Andreas},
	title = {Machine learning to detect Alzheimer{\textquoteright}s disease from circulating non-coding RNAs},
	elocation-id = {638213},
	year = {2019},
	doi = {10.1101/638213},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Background To develop therapeutics for Alzheimer{\textquoteright}s disease, early detection of patients awakes new hope. Circulating small non-coding RNAs are among the prominent candidates for a blood-based diagnosis, requiring however growing cohort sizes.Methods We determined abundance levels of 21 known circulating microRNAs in 465 individuals encompassing Alzheimer{\textquoteright}s patients and controls recruited in US and Germany. We computed models to assess the relation between microRNA-expression and phenotypes, gender, age and disease severity (Mini-Mental State Examination MMSE).Results 20 of 21 miRNAs were consistently dys-regulated in the US and Germany. 18 were significantly correlated to neurodegeneration (adjusted p\<0.05) with highest significance for miR-532-5p (adjusted p=4.8{\texttimes}10-30). Ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted p=0.0002). Machine learning models reached an AUC value of 87.6\% in differentiating AD patients from controls.Conclusions Our data provide strong evidence for the relevance of circulating non-coding RNAs to detect Alzheimer{\textquoteright}s from a blood sample.},
	URL = {https://www.biorxiv.org/content/early/2019/05/14/638213},
	eprint = {https://www.biorxiv.org/content/early/2019/05/14/638213.full.pdf},
	journal = {bioRxiv}
}

Background To develop therapeutics for Alzheimer\textquoterights disease, early detection of patients awakes new hope. Circulating small non-coding RNAs are among the prominent candidates for a blood-based diagnosis, requiring however growing cohort sizes.Methods We determined abundance levels of 21 known circulating microRNAs in 465 individuals encompassing Alzheimer\textquoterights patients and controls recruited in US and Germany. We computed models to assess the relation between microRNA-expression and phenotypes, gender, age and disease severity (Mini-Mental State Examination MMSE).Results 20 of 21 miRNAs were consistently dys-regulated in the US and Germany. 18 were significantly correlated to neurodegeneration (adjusted p<0.05) with highest significance for miR-532-5p (adjusted p=4.8×10-30). Ten miRNAs were significantly correlated with MMSE, in particular miR-26a/26b-5p (adjusted p=0.0002). Machine learning models reached an AUC value of 87.6% in differentiating AD patients from controls.Conclusions Our data provide strong evidence for the relevance of circulating non-coding RNAs to detect Alzheimer\textquoterights from a blood sample.

@article {Galata463901,
	author = {Galata, Valentina and Laczny, C{\'e}dric C. and Backes, Christina and Hemmrich-Stanisak, Georg and Schmolke, Susanne and Franke, Andre and Meese, Eckart and Herrmann, Mathias and M{\"u}ller, Lutz von and Plum, Achim and M{\"u}ller, Rolf and St{\"a}hler, Cord and Posch, Andreas E. and Keller, Andreas},
	title = {Integrating Culture-based Antibiotic Resistance Profiles with Whole-genome Sequencing Data for 11,087 Clinical Isolates},
	elocation-id = {463901},
	year = {2018},
	doi = {10.1101/463901},
	publisher = {Cold Spring Harbor Laboratory},
	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 of 11,087 isolates were 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 could be observed including increasing 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 such as 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 a resource, GEAR-base, available for academic research use free of charge at https://gear-base.com.},
	URL = {https://www.biorxiv.org/content/early/2018/11/07/463901},
	eprint = {https://www.biorxiv.org/content/early/2018/11/07/463901.full.pdf},
	journal = {bioRxiv}
}

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 of 11,087 isolates were 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 could be observed including increasing 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 such as 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 a resource, GEAR-base, available for academic research use free of charge at https://gear-base.com.

@article {Rounge247155,
	author = {Rounge, Trine B and Umu, Sinan U and Keller, Andreas and Meese, Eckart and Ursin, Giske and Tretli, Steinar and Lyle, Robert and Langseth, Hilde},
	title = {Circulating small non-coding RNAs associated with age, sex, smoking, body mass and physical activity},
	elocation-id = {247155},
	year = {2018},
	doi = {10.1101/247155},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Non-coding RNAs (ncRNA) are regulators of cell functions and circulating ncRNAs from the majority of RNA classes, such as miRNA, tRNA, piRNAs, lncRNA, snoRNA, snRNA and miscRNAs, are potential non-invasive biomarkers. Understanding how non-disease traits influence ncRNA expression is essential for assessing their biomarker potential.We studied associations of common traits (sex, age, smoking, body mass, physical activity, and technical factors such as sample storage and processing) with serum ncRNAs. We used RNAseq data from 526 donors from the Janus Serum Bank and traits from health examination surveys. We identified associations between all RNA classes and traits. Ageing showed the strongest association with ncRNA expression, both in terms of statistical significance and number of RNAs, regardless of RNA class. Serum processing modifications and storage times significantly altered expression levels of a number of ncRNAs. Interestingly, smoking cessation generally restored RNA expression to non-smoking levels, although for some isomiRs, mRNA fragments and tRNAs smoking-related expression levels persisted.Our results show that common traits influence circulating ncRNA expression. Therefore it is clear that ncRNA biomarker analyses should be adjusted for age and sex. In addition, for specific ncRNAs identified in our study, analyses should also be adjusted for body mass, smoking, physical activity and serum processing and storage.},
	URL = {https://www.biorxiv.org/content/early/2018/01/12/247155},
	eprint = {https://www.biorxiv.org/content/early/2018/01/12/247155.full.pdf},
	journal = {bioRxiv}
}

Non-coding RNAs (ncRNA) are regulators of cell functions and circulating ncRNAs from the majority of RNA classes, such as miRNA, tRNA, piRNAs, lncRNA, snoRNA, snRNA and miscRNAs, are potential non-invasive biomarkers. Understanding how non-disease traits influence ncRNA expression is essential for assessing their biomarker potential.We studied associations of common traits (sex, age, smoking, body mass, physical activity, and technical factors such as sample storage and processing) with serum ncRNAs. We used RNAseq data from 526 donors from the Janus Serum Bank and traits from health examination surveys. We identified associations between all RNA classes and traits. Ageing showed the strongest association with ncRNA expression, both in terms of statistical significance and number of RNAs, regardless of RNA class. Serum processing modifications and storage times significantly altered expression levels of a number of ncRNAs. Interestingly, smoking cessation generally restored RNA expression to non-smoking levels, although for some isomiRs, mRNA fragments and tRNAs smoking-related expression levels persisted.Our results show that common traits influence circulating ncRNA expression. Therefore it is clear that ncRNA biomarker analyses should be adjusted for age and sex. In addition, for specific ncRNAs identified in our study, analyses should also be adjusted for body mass, smoking, physical activity and serum processing and storage.

@article {Umu186320,
	author = {Umu, Sinan U{\u g}ur and Langseth, Hilde and Bucher-Jonannessen, Cecilie and Fromm, Bastian and Keller, Andreas and Meese, Eckart and Lauritzen, Marianne and Leithaug, Magnus and Lyle, Robert and Rounge, Trine},
	title = {A comprehensive profile of circulating RNAs in human serum},
	elocation-id = {186320},
	year = {2017},
	doi = {10.1101/186320},
	publisher = {Cold Spring Harbor Laboratory},
	abstract = {Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion lllumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA). We also investigated biological and technical variation in expression, and the results suggest that many RNA molecules identified in serum contain signs of biological variation. They are therefore unlikely to be random degradation by-products. In addition, the presence of specific fragments of tRNA, snoRNA, Vault RNA and Y_RNA indicates protection from degradation. Our results suggest that many circulating RNAs in serum can be potential biomarkers.},
	URL = {https://www.biorxiv.org/content/early/2017/09/08/186320},
	eprint = {https://www.biorxiv.org/content/early/2017/09/08/186320.full.pdf},
	journal = {bioRxiv}
}

Non-coding RNA (ncRNA) molecules have fundamental roles in cells and many are also stable in body fluids as extracellular RNAs. In this study, we used RNA sequencing (RNA-seq) to investigate the profile of small non-coding RNA (sncRNA) in human serum. We analyzed 10 billion lllumina reads from 477 serum samples, included in the Norwegian population-based Janus Serum Bank (JSB). We found that the core serum RNA repertoire includes 258 micro RNAs (miRNA), 441 piwi-interacting RNAs (piRNA), 411 transfer RNAs (tRNA), 24 small nucleolar RNAs (snoRNA), 125 small nuclear RNAs (snRNA) and 123 miscellaneous RNAs (misc-RNA). We also investigated biological and technical variation in expression, and the results suggest that many RNA molecules identified in serum contain signs of biological variation. They are therefore unlikely to be random degradation by-products. In addition, the presence of specific fragments of tRNA, snoRNA, Vault RNA and Y_RNA indicates protection from degradation. Our results suggest that many circulating RNAs in serum can be potential biomarkers.