@article{Roy2018,
abstract = {Mycobacterium tuberculosis (Mtb) infection reveals complex and dynamic host-pathogen interactions, leading to host protection or pathogenesis. Using a unique transcriptome technology (CAGE), we investigated the promoter-based transcriptional landscape of IFN$\gamma$ (M1) or IL-4/IL-13 (M2) stimulated macrophages during Mtb infection in a time-kinetic manner. Mtb infection widely and drastically altered macrophage-specific gene expression, which is far larger than that of M1 or M2 activations. Gene Ontology enrichment analysis for Mtb-induced differentially expressed genes revealed various terms, related to host-protection and inflammation, enriched in up-regulated genes. On the other hand, terms related to dis-regulation of cellular functions were enriched in down-regulated genes. Differential expression analysis revealed known as well as novel transcription factor genes in Mtb infection, many of them significantly down-regulated. IFN$\gamma$ or IL-4/IL-13 pre-stimulation induce additional differentially expressed genes in Mtb-infected macrophages. Cluster analysis uncovered significant numbers, prolonging their expressional changes. Furthermore, Mtb infection augmented cytokine-mediated M1 and M2 pre-activations. In addition, we identified unique transcriptional features of Mtb-mediated differentially expressed lncRNAs. In summary we provide a comprehensive in depth gene expression/regulation profile in Mtb-infected macrophages, an important step forward for a better understanding of host-pathogen interaction dynamics in Mtb infection.},
author = {Roy, Sugata and Schmeier, Sebastian and Kaczkowski, Bogumil and Arner, Erik and Alam, Tanvir and Ozturk, Mumin and Tamgue, Ousman and Parihar, Suraj P. and Kawaji, Hideya and Itoh, Masayoshi and Lassmann, Timo and Carninci, Piero and Hayashizaki, Yoshihide and Forrest, Alistair R.R. and Guler, Reto and Bajic, Vladimir B. and Brombacher, Frank and Suzuki, Harukazu},
doi = {10.1038/s41598-018-24509-6},
file = {:C$\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Roy et al. - 2018 - Transcriptional landscape of iMycobacterium tuberculosisi infection in macrophages.pdf:pdf},
issn = {20452322},
journal = {Scientific Reports},
keywords = {OA,fund{\_}ack,original},
mendeley-tags = {OA,fund{\_}ack,original},
month = {dec},
number = {1},
pages = {6758},
pmid = {29712924},
publisher = {Nature Publishing Group},
title = {{Transcriptional landscape of \textit{Mycobacterium tuberculosis} infection in macrophages}},
volume = {8},
year = {2018}
}

{"_id":"A3T8Q7m3mHi4hpm4y","bibbaseid":"roy-schmeier-kaczkowski-arner-alam-ozturk-tamgue-parihar-etal-transcriptionallandscapeofimycobacteriumtuberculosisiinfectioninmacrophages-2018","author_short":["Roy, S.","Schmeier, S.","Kaczkowski, B.","Arner, E.","Alam, T.","Ozturk, M.","Tamgue, O.","Parihar, S. P.","Kawaji, H.","Itoh, M.","Lassmann, T.","Carninci, P.","Hayashizaki, Y.","Forrest, A. R.","Guler, R.","Bajic, V. B.","Brombacher, F.","Suzuki, H."],"bibdata":{"bibtype":"article","type":"article","abstract":"Mycobacterium tuberculosis (Mtb) infection reveals complex and dynamic host-pathogen interactions, leading to host protection or pathogenesis. Using a unique transcriptome technology (CAGE), we investigated the promoter-based transcriptional landscape of IFN$γ$ (M1) or IL-4/IL-13 (M2) stimulated macrophages during Mtb infection in a time-kinetic manner. Mtb infection widely and drastically altered macrophage-specific gene expression, which is far larger than that of M1 or M2 activations. Gene Ontology enrichment analysis for Mtb-induced differentially expressed genes revealed various terms, related to host-protection and inflammation, enriched in up-regulated genes. On the other hand, terms related to dis-regulation of cellular functions were enriched in down-regulated genes. Differential expression analysis revealed known as well as novel transcription factor genes in Mtb infection, many of them significantly down-regulated. IFN$γ$ or IL-4/IL-13 pre-stimulation induce additional differentially expressed genes in Mtb-infected macrophages. Cluster analysis uncovered significant numbers, prolonging their expressional changes. Furthermore, Mtb infection augmented cytokine-mediated M1 and M2 pre-activations. In addition, we identified unique transcriptional features of Mtb-mediated differentially expressed lncRNAs. In summary we provide a comprehensive in depth gene expression/regulation profile in Mtb-infected macrophages, an important step forward for a better understanding of host-pathogen interaction dynamics in Mtb infection.","author":[{"propositions":[],"lastnames":["Roy"],"firstnames":["Sugata"],"suffixes":[]},{"propositions":[],"lastnames":["Schmeier"],"firstnames":["Sebastian"],"suffixes":[]},{"propositions":[],"lastnames":["Kaczkowski"],"firstnames":["Bogumil"],"suffixes":[]},{"propositions":[],"lastnames":["Arner"],"firstnames":["Erik"],"suffixes":[]},{"propositions":[],"lastnames":["Alam"],"firstnames":["Tanvir"],"suffixes":[]},{"propositions":[],"lastnames":["Ozturk"],"firstnames":["Mumin"],"suffixes":[]},{"propositions":[],"lastnames":["Tamgue"],"firstnames":["Ousman"],"suffixes":[]},{"propositions":[],"lastnames":["Parihar"],"firstnames":["Suraj","P."],"suffixes":[]},{"propositions":[],"lastnames":["Kawaji"],"firstnames":["Hideya"],"suffixes":[]},{"propositions":[],"lastnames":["Itoh"],"firstnames":["Masayoshi"],"suffixes":[]},{"propositions":[],"lastnames":["Lassmann"],"firstnames":["Timo"],"suffixes":[]},{"propositions":[],"lastnames":["Carninci"],"firstnames":["Piero"],"suffixes":[]},{"propositions":[],"lastnames":["Hayashizaki"],"firstnames":["Yoshihide"],"suffixes":[]},{"propositions":[],"lastnames":["Forrest"],"firstnames":["Alistair","R.R."],"suffixes":[]},{"propositions":[],"lastnames":["Guler"],"firstnames":["Reto"],"suffixes":[]},{"propositions":[],"lastnames":["Bajic"],"firstnames":["Vladimir","B."],"suffixes":[]},{"propositions":[],"lastnames":["Brombacher"],"firstnames":["Frank"],"suffixes":[]},{"propositions":[],"lastnames":["Suzuki"],"firstnames":["Harukazu"],"suffixes":[]}],"doi":"10.1038/s41598-018-24509-6","file":":C$\\$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Roy et al. - 2018 - Transcriptional landscape of iMycobacterium tuberculosisi infection in macrophages.pdf:pdf","issn":"20452322","journal":"Scientific Reports","keywords":"OA,fund_ack,original","mendeley-tags":"OA,fund_ack,original","month":"dec","number":"1","pages":"6758","pmid":"29712924","publisher":"Nature Publishing Group","title":"Transcriptional landscape of <i>Mycobacterium tuberculosis</i> infection in macrophages","volume":"8","year":"2018","bibtex":"@article{Roy2018,\r\nabstract = {Mycobacterium tuberculosis (Mtb) infection reveals complex and dynamic host-pathogen interactions, leading to host protection or pathogenesis. Using a unique transcriptome technology (CAGE), we investigated the promoter-based transcriptional landscape of IFN$\\gamma$ (M1) or IL-4/IL-13 (M2) stimulated macrophages during Mtb infection in a time-kinetic manner. Mtb infection widely and drastically altered macrophage-specific gene expression, which is far larger than that of M1 or M2 activations. Gene Ontology enrichment analysis for Mtb-induced differentially expressed genes revealed various terms, related to host-protection and inflammation, enriched in up-regulated genes. On the other hand, terms related to dis-regulation of cellular functions were enriched in down-regulated genes. Differential expression analysis revealed known as well as novel transcription factor genes in Mtb infection, many of them significantly down-regulated. IFN$\\gamma$ or IL-4/IL-13 pre-stimulation induce additional differentially expressed genes in Mtb-infected macrophages. Cluster analysis uncovered significant numbers, prolonging their expressional changes. Furthermore, Mtb infection augmented cytokine-mediated M1 and M2 pre-activations. In addition, we identified unique transcriptional features of Mtb-mediated differentially expressed lncRNAs. In summary we provide a comprehensive in depth gene expression/regulation profile in Mtb-infected macrophages, an important step forward for a better understanding of host-pathogen interaction dynamics in Mtb infection.},\r\nauthor = {Roy, Sugata and Schmeier, Sebastian and Kaczkowski, Bogumil and Arner, Erik and Alam, Tanvir and Ozturk, Mumin and Tamgue, Ousman and Parihar, Suraj P. and Kawaji, Hideya and Itoh, Masayoshi and Lassmann, Timo and Carninci, Piero and Hayashizaki, Yoshihide and Forrest, Alistair R.R. and Guler, Reto and Bajic, Vladimir B. and Brombacher, Frank and Suzuki, Harukazu},\r\ndoi = {10.1038/s41598-018-24509-6},\r\nfile = {:C$\\backslash$:/Users/01462563/AppData/Local/Mendeley Ltd./Mendeley Desktop/Downloaded/Roy et al. - 2018 - Transcriptional landscape of iMycobacterium tuberculosisi infection in macrophages.pdf:pdf},\r\nissn = {20452322},\r\njournal = {Scientific Reports},\r\nkeywords = {OA,fund{\\_}ack,original},\r\nmendeley-tags = {OA,fund{\\_}ack,original},\r\nmonth = {dec},\r\nnumber = {1},\r\npages = {6758},\r\npmid = {29712924},\r\npublisher = {Nature Publishing Group},\r\ntitle = {{Transcriptional landscape of \\textit{Mycobacterium tuberculosis} infection in macrophages}},\r\nvolume = {8},\r\nyear = {2018}\r\n}\r\n","author_short":["Roy, S.","Schmeier, S.","Kaczkowski, B.","Arner, E.","Alam, T.","Ozturk, M.","Tamgue, O.","Parihar, S. P.","Kawaji, H.","Itoh, M.","Lassmann, T.","Carninci, P.","Hayashizaki, Y.","Forrest, A. R.","Guler, R.","Bajic, V. B.","Brombacher, F.","Suzuki, H."],"key":"Roy2018","id":"Roy2018","bibbaseid":"roy-schmeier-kaczkowski-arner-alam-ozturk-tamgue-parihar-etal-transcriptionallandscapeofimycobacteriumtuberculosisiinfectioninmacrophages-2018","role":"author","urls":{},"keyword":["OA","fund_ack","original"],"metadata":{"authorlinks":{}}},"bibtype":"article","biburl":"https://drive.google.com/uc?export=download&id=1-JLqZ7RwZ3VC2d6ErLGHAtOeMRS_7GCz","dataSources":["Krmt6gt9ktB2s6ARh"],"keywords":["oa","fund_ack","original"],"search_terms":["transcriptional","landscape","mycobacterium","tuberculosis","infection","macrophages","roy","schmeier","kaczkowski","arner","alam","ozturk","tamgue","parihar","kawaji","itoh","lassmann","carninci","hayashizaki","forrest","guler","bajic","brombacher","suzuki"],"title":"Transcriptional landscape of <i>Mycobacterium tuberculosis</i> infection in macrophages","year":2018}