An IL-27-Driven Transcriptional Network Identifies Regulators of IL-10 Expression across T Helper Cell Subsets

[1]  R. Xavier,et al.  Pathway paradigms revealed from the genetics of inflammatory bowel disease , 2020, Nature.

[2]  A. Regev,et al.  Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses. , 2019, Immunity.

[3]  V. Kuchroo,et al.  Epigenetic and transcriptional mechanisms for the regulation of IL-10. , 2019, Seminars in immunology.

[4]  Aviv Regev,et al.  Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis , 2019, Cell.

[5]  W. Shi,et al.  c-Maf-dependent Treg cell control of intestinal TH17 cells and IgA establishes host–microbiota homeostasis , 2019, Nature Immunology.

[6]  Ricardo J. Miragaia,et al.  Genome-wide CRISPR Screens in T Helper Cells Reveal Pervasive Crosstalk between Activation and Differentiation , 2017, Cell.

[7]  R. Rad,et al.  Blimp1 Prevents Methylation of Foxp3 and Loss of Regulatory T Cell Identity at Sites of Inflammation , 2019, Cell reports.

[8]  E. Deutsch,et al.  CCR2-Dependent Recruitment of Tregs and Monocytes Following Radiotherapy Is Associated with TNFα-Mediated Resistance , 2019, Cancer Immunology Research.

[9]  C. Hunter,et al.  IL-27 and TCR Stimulation Promote T Cell Expression of Multiple Inhibitory Receptors , 2019, ImmunoHorizons.

[10]  Jung Ok Shim,et al.  Recent Advance in Very Early Onset Inflammatory Bowel Disease , 2019, Pediatric gastroenterology, hepatology & nutrition.

[11]  V. Kuchroo,et al.  Multilayer regulation of CD4 T cell subset differentiation in the era of single cell genomics. , 2019, Advances in immunology.

[12]  J. Gustafsson,et al.  Molecular and functional heterogeneity of IL-10-producing CD4+ T cells , 2018, Nature Communications.

[13]  Chihiro Ogawa,et al.  Blimp-1 Functions as a Molecular Switch to Prevent Inflammatory Activity in Foxp3+RORγt+ Regulatory T Cells , 2018, Cell reports.

[14]  Yan Zhou,et al.  Transcription factor c‐Maf is essential for IL‐10 gene expression in B cells , 2018, Scandinavian journal of immunology.

[15]  Chih-Chung Lin,et al.  Bhlhe40 is an essential repressor of IL-10 during Mycobacterium tuberculosis infection , 2018, The Journal of experimental medicine.

[16]  Keji Zhao,et al.  The transcription factor Bhlhe40 is a switch of inflammatory versus antiinflammatory Th1 cell fate determination , 2017, The Journal of experimental medicine.

[17]  Aviv Regev,et al.  Induction and transcriptional regulation of the co-inhibitory gene module in T cells , 2018, Nature.

[18]  M. Schmitz,et al.  The Crosstalk of Endoplasmic Reticulum (ER) Stress Pathways with NF-κB: Complex Mechanisms Relevant for Cancer, Inflammation and Infection , 2018, Biomedicines.

[19]  N. Luscombe,et al.  c-Maf controls immune responses by regulating disease-specific gene networks and repressing IL-2 in CD4+ T cells , 2018, Nature Immunology.

[20]  Paul Hoffman,et al.  Integrating single-cell transcriptomic data across different conditions, technologies, and species , 2018, Nature Biotechnology.

[21]  Richard Bonneau,et al.  c-Maf-dependent regulatory T cells mediate immunological tolerance to a gut pathobiont , 2018, Nature.

[22]  James T. Robinson,et al.  Variant Review with the Integrative Genomics Viewer. , 2017, Cancer research.

[23]  S. McColl,et al.  Eomesodermin promotes the development of type 1 regulatory T (TR1) cells , 2017, Science Immunology.

[24]  Xiuli Liu,et al.  IL-10 and IL-10 Receptor Mutations in Very Early Onset Inflammatory Bowel Disease , 2017, Gastroenterology research.

[25]  Richard Bonneau,et al.  Critical role of IRF1 and BATF in forming chromatin landscape during type 1 regulatory cell differentiation , 2017, Nature Immunology.

[26]  M. Krummel,et al.  CCR2 Influences T Regulatory Cell Migration to Tumors and Serves as a Biomarker of Cyclophosphamide Sensitivity. , 2016, Cancer research.

[27]  Howard Y. Chang,et al.  Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution , 2016, Nature Genetics.

[28]  Charles H. Yoon,et al.  Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq , 2016, Science.

[29]  W. Leonard,et al.  IL-21 Signaling in Immunity , 2016, F1000Research.

[30]  R. Kumar,et al.  Blimp-1-Dependent IL-10 Production by Tr1 Cells Regulates TNF-Mediated Tissue Pathology , 2016, PLoS pathogens.

[31]  A. ten Brinke,et al.  IL-10/IFNγ co-expressing CD4(+) T cells induced by IL-10 DC display a regulatory gene profile and downmodulate T cell responses. , 2016, Clinical immunology.

[32]  Konstantinos Biliouris,et al.  Regulation of bifurcating B cell trajectories by mutual antagonism between transcription factors IRF4 and IRF8 , 2015, Nature Immunology.

[33]  A. Regev,et al.  CD5L/AIM Regulates Lipid Biosynthesis and Restrains Th17 Cell Pathogenicity , 2015, Cell.

[34]  B. Bernstein,et al.  Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation , 2015, Nature.

[35]  P. Linsley,et al.  MAST: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data , 2015, Genome Biology.

[36]  C. Clish,et al.  Metabolic control of type 1 regulatory T cell differentiation by AHR and HIF1-α , 2015, Nature Medicine.

[37]  C. Hunter,et al.  The immunobiology of interleukin-27. , 2015, Annual review of immunology.

[38]  R. Ahmed,et al.  An IL-27/NFIL3 signaling axis drives Tim-3 and IL-10 expression and T cell dysfunction , 2015, Nature Communications.

[39]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[40]  J. Gough,et al.  Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy , 2014, Nature Communications.

[41]  S. Rutz,et al.  Role of Blimp-1 in programing Th effector cells into IL-10 producers , 2014, The Journal of experimental medicine.

[42]  L. Harrington,et al.  T-bet controls intestinal chronic inflammation via regulation of IL-10 production by CD4 T cells (MUC8P.806) , 2014 .

[43]  R. Taneja,et al.  Bhlhe40 controls cytokine production by T cells and is essential for pathogenicity in autoimmune neuroinflammation , 2014, Nature Communications.

[44]  Mark S. Sundrud,et al.  Small-molecule RORγt antagonists inhibit T helper 17 cell transcriptional network by divergent mechanisms. , 2014, Immunity.

[45]  N. Mukaida,et al.  Ag and IL‐2 immune complexes efficiently expand Ag‐specific Treg cells that migrate in response to chemokines and reduce localized immune responses , 2014, European journal of immunology.

[46]  A. O’Garra,et al.  The regulation of IL-10 expression. , 2014, Current topics in microbiology and immunology.

[47]  E. Latz,et al.  High density lipoprotein mediates anti-inflammatory transcriptional reprogramming of macrophages via the transcriptional repressor ATF3 , 2013, Nature Immunology.

[48]  B. Diamond,et al.  Transcriptional and functional profiling of human intestinal dendritic cells reveals conserved specialization and a role for Bcl-6 and Blimp-1 in terminal subset differentiation , 2013, Nature Immunology.

[49]  Nadezhda T. Doncheva,et al.  Association between variants of PRDM1 and NDP52 and Crohn's disease, based on exome sequencing and functional studies. , 2013, Gastroenterology.

[50]  yang-xin fu,et al.  Lymphotoxin signalling in immune homeostasis and the control of microorganisms , 2013, Nature Reviews Immunology.

[51]  A. Regev,et al.  Dynamic regulatory network controlling Th17 cell differentiation , 2013, Nature.

[52]  S. Nutt,et al.  CD8α+ DCs can be induced in the absence of transcription factors Id2, Nfil3, and Batf3. , 2013, Blood.

[53]  A. Regev,et al.  Induction of pathogenic Th17 cells by inducible salt sensing kinase SGK1 , 2013, Nature.

[54]  S. Hasnain,et al.  IL-10 promotes production of intestinal mucus by suppressing protein misfolding and endoplasmic reticulum stress in goblet cells. , 2013, Gastroenterology.

[55]  S. Kneitz,et al.  Sequential Induction of Effector Function, Tissue Migration and Cell Death during Polyclonal Activation of Mouse Regulatory T-Cells , 2012, PloS one.

[56]  Richard Bonneau,et al.  A Validated Regulatory Network for Th17 Cell Specification , 2012, Cell.

[57]  David C. Wilson,et al.  Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease , 2012, Nature.

[58]  D. Roos,et al.  The cytokines interleukin 27 and interferon-γ promote distinct Treg cell populations required to limit infection-induced pathology. , 2012, Immunity.

[59]  Nir Friedman,et al.  A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. , 2012, Molecular cell.

[60]  Y. Maehara,et al.  Key role of ATF3 in p53-dependent DR5 induction upon DNA damage of human colon cancer cells , 2012, Oncogene.

[61]  C. Birchmeier,et al.  The Transcription Factor c-Maf Controls Touch Receptor Development and Function , 2012, Science.

[62]  H. So,et al.  Interaction of Ets-1 with HDAC1 Represses IL-10 Expression in Th1 Cells , 2012, The Journal of Immunology.

[63]  S. Iyer,et al.  Role of interleukin 10 transcriptional regulation in inflammation and autoimmune disease. , 2012, Critical reviews in immunology.

[64]  J. O’Shea,et al.  Early Th1 cell differentiation is marked by a Tfh cell-like transition. , 2011, Immunity.

[65]  B. Diamond,et al.  Tolerogenic function of Blimp-1 in dendritic cells , 2011, The Journal of Experimental Medicine.

[66]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[67]  Changyou Wu,et al.  IL-27 induces the differentiation of Tr1-like cells from human naive CD4+ T cells via the phosphorylation of STAT1 and STAT3. , 2011, Immunology letters.

[68]  Francis J. Huber,et al.  Th17 cells express interleukin-10 receptor and are controlled by Foxp3⁻ and Foxp3+ regulatory CD4+ T cells in an interleukin-10-dependent manner. , 2011, Immunity.

[69]  W. Shi,et al.  The transcription factors Blimp-1 and IRF4 jointly control the differentiation and function of effector regulatory T cells , 2011, Nature Immunology.

[70]  S. Rutz,et al.  Regulation and functions of the IL-10 family of cytokines in inflammation and disease. , 2011, Annual review of immunology.

[71]  Jingxian Zhao,et al.  Highly Activated Cytotoxic CD8 T Cells Express Protective IL-10 at the Peak of Coronavirus-Induced Encephalitis , 2011, The Journal of Immunology.

[72]  Chen-feng Qi,et al.  IFN Regulatory Factor 8 Restricts the Size of the Marginal Zone and Follicular B Cell Pools , 2011, The Journal of Immunology.

[73]  H. Weiner,et al.  The Aryl hydrocarbon Receptor (AhR) interacts with c-Maf to promote the differentiation of IL-27-induced regulatory type 1 (TR1) cells , 2010, Nature Immunology.

[74]  W. Huber,et al.  which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2011 .

[75]  J. Bream,et al.  Cell type-specific regulation of IL-10 expression in inflammation and disease , 2010, Immunologic research.

[76]  Mark Coles,et al.  The basic leucine zipper transcription factor E4BP4 is essential for natural killer cell development , 2009, Nature Immunology.

[77]  V. Kuchroo,et al.  Cutting Edge: IL-27 Induces the Transcription Factor c-Maf, Cytokine IL-21, and the Costimulatory Receptor ICOS that Coordinately Act Together to Promote Differentiation of IL-10-Producing Tr1 Cells1 , 2009, The Journal of Immunology.

[78]  Gary D. Stormo,et al.  The AP-1 transcription factor Batf controls TH17 differentiation , 2009, Nature.

[79]  R. Jessberger,et al.  Regulatory T cells sequentially migrate from inflamed tissues to draining lymph nodes to suppress the alloimmune response. , 2009, Immunity.

[80]  Lior Pachter,et al.  Sequence Analysis , 2020, Definitions.

[81]  Gal Chechik,et al.  Timing of Gene Expression Responses to Environmental Changes , 2009, J. Comput. Biol..

[82]  T. Matsuyama,et al.  A distal cis-regulatory element, CNS-9, controls NFAT1 and IRF4-mediated IL-10 gene activation in T helper cells. , 2009, Molecular immunology.

[83]  Yuka Kanno,et al.  Global mapping of H3K4me3 and H3K27me3 reveals specificity and plasticity in lineage fate determination of differentiating CD4+ T cells. , 2009, Immunity.

[84]  E. Unanue,et al.  Batf3 Deficiency Reveals a Critical Role for CD8α+ Dendritic Cells in Cytotoxic T Cell Immunity , 2008, Science.

[85]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[86]  S. Rutz,et al.  Notch regulates IL-10 production by T helper 1 cells , 2008, Proceedings of the National Academy of Sciences.

[87]  M. Batten,et al.  Cutting Edge: IL-27 Is a Potent Inducer of IL-10 but Not FoxP3 in Murine T Cells , 2008, The Journal of Immunology.

[88]  Yang Du,et al.  BHLHB2 Controls Bdnf Promoter 4 Activity and Neuronal Excitability , 2008, The Journal of Neuroscience.

[89]  H. Weiner,et al.  A dominant function for interleukin 27 in generating interleukin 10–producing anti-inflammatory T cells , 2007, Nature Immunology.

[90]  Christopher A Hunter,et al.  Interleukins 27 and 6 induce STAT3-mediated T cell production of interleukin 10 , 2007, Nature Immunology.

[91]  Mohamed El-behi,et al.  Suppression of autoimmune inflammation of the central nervous system by interleukin 10 secreted by interleukin 27–stimulated T cells , 2007, Nature Immunology.

[92]  A. Rudensky,et al.  Regulatory T cells expressing interleukin 10 develop from Foxp3+ and Foxp3− precursor cells in the absence of interleukin 10 , 2007, Nature Immunology.

[93]  R. Flavell,et al.  Role of STAT3 in liver regeneration: survival, DNA synthesis, inflammatory reaction and liver mass recovery , 2007, Laboratory Investigation.

[94]  G. Rogler,et al.  Interleukin 10 blocked endoplasmic reticulum stress in intestinal epithelial cells: impact on chronic inflammation , 2007, Gastroenterology.

[95]  Ashok Kumar,et al.  Haplotype-Independent Costimulation of IL-10 Secretion by SDF-1/CXCL12 Proceeds via AP-1 Binding to the Human IL-10 Promoter1 , 2007, The Journal of Immunology.

[96]  F. Sutterwala,et al.  Expression of interleukin-10 in intestinal lymphocytes detected by an interleukin-10 reporter knockin tiger mouse. , 2006, Immunity.

[97]  L. Hennighausen,et al.  Interleukin 27 negatively regulates the development of interleukin 17–producing T helper cells during chronic inflammation of the central nervous system , 2006, Nature Immunology.

[98]  D. Danilenko,et al.  Interleukin 27 limits autoimmune encephalomyelitis by suppressing the development of interleukin 17–producing T cells , 2006, Nature Immunology.

[99]  Michal Linial,et al.  Novel Unsupervised Feature Filtering of Biological Data , 2006, ISMB.

[100]  Qiong Shen,et al.  Transcription factor IRF4 controls plasma cell differentiation and class-switch recombination , 2006, Nature Immunology.

[101]  P. Möller,et al.  Foxp3-expressing CD103+ regulatory T cells accumulate in dendritic cell aggregates of the colonic mucosa in murine transfer colitis. , 2006, The American journal of pathology.

[102]  H. Weiner,et al.  Reciprocal developmental pathways for the generation of pathogenic effector TH17 and regulatory T cells , 2006, Nature.

[103]  Kathleen A. Kennedy,et al.  Systems biology approaches identify ATF3 as a negative regulator of Toll-like receptor 4 , 2006, Nature.

[104]  J. Woodgett,et al.  IFN-gamma suppresses IL-10 production and synergizes with TLR2 by regulating GSK3 and CREB/AP-1 proteins. , 2006, Immunity.

[105]  J. Mesirov,et al.  GenePattern 2.0 , 2006, Nature Genetics.

[106]  K. Calame,et al.  Transcriptional repressor Blimp-1 regulates T cell homeostasis and function , 2006, Nature Immunology.

[107]  A. O’Garra,et al.  GATA-3 Directly Remodels the IL-10 Locus Independently of IL-4 in CD4+ T Cells , 2006, The Journal of Immunology.

[108]  J. Jorcano,et al.  Conditional ablation of C/EBPβ demonstrates its keratinocyte-specific requirement for cell survival and mouse skin tumorigenesis , 2006, Oncogene.

[109]  Jeffrey T. Leek,et al.  Gene expression EDGE : extraction and analysis of differential gene expression , 2006 .

[110]  R. Kastelein,et al.  IL-27 Limits IL-2 Production during Th1 Differentiation1 , 2006, The Journal of Immunology.

[111]  John D. Storey,et al.  Significance analysis of time course microarray experiments. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[112]  Lihua Song,et al.  The Protooncogene c-Maf Is an Essential Transcription Factor for IL-10 Gene Expression in Macrophages1 , 2005, Journal of Immunology.

[113]  E. Wagner,et al.  The AP1 transcription factor Fra2 is required for efficient cartilage development , 2004, Development.

[114]  G. Wu,et al.  The IL-27 Receptor (WSX-1) Is an Inhibitor of Innate and Adaptive Elements of Type 2 Immunity1 , 2004, The Journal of Immunology.

[115]  Hao Shen,et al.  Control of Effector CD8+ T Cell Function by the Transcription Factor Eomesodermin , 2003, Science.

[116]  T. Mak,et al.  The IL-27R (WSX-1) is required to suppress T cell hyperactivity during infection. , 2003, Immunity.

[117]  K. Calame,et al.  Blimp-1 is required for the formation of immunoglobulin secreting plasma cells and pre-plasma memory B cells. , 2003, Immunity.

[118]  Lei-Chin Chen,et al.  Functional Cooperation of Simian Virus 40 Promoter Factor 1 and CCAAT/Enhancer-Binding Protein β and δ in Lipopolysaccharide-Induced Gene Activation of IL-10 in Mouse Macrophages1 , 2003, The Journal of Immunology.

[119]  L. Chodosh,et al.  Hlx is induced by and genetically interacts with T-bet to promote heritable TH1 gene induction , 2002, Nature Immunology.

[120]  S. Szabo,et al.  The Transcription Factor T-bet Regulates Mucosal T Cell Activation in Experimental Colitis and Crohn's Disease , 2002, The Journal of experimental medicine.

[121]  S. Szabo,et al.  Development of Spontaneous Airway Changes Consistent with Human Asthma in Mice Lacking T-bet , 2002, Science.

[122]  N. Killeen,et al.  Homeostatic Competition Among T Cells Revealed by Conditional Inactivation of the Mouse Cd4 Gene , 2001, The Journal of experimental medicine.

[123]  W. M. Weaver,et al.  A critical role for Dnmt1 and DNA methylation in T cell development, function, and survival. , 2001, Immunity.

[124]  J. M. Arbeit,et al.  Hypoxia-inducible Factor-1α Is a Positive Factor in Solid Tumor Growth , 2000 .

[125]  J. M. Arbeit,et al.  Hypoxia-inducible factor-1alpha is a positive factor in solid tumor growth. , 2000, Cancer research.

[126]  Susan D. Spencer,et al.  The Orphan Receptor CRF2-4 Is an Essential Subunit of the Interleukin 10 Receptor , 1998, The Journal of experimental medicine.

[127]  C. Fathman,et al.  CD45RBhigh CD4+ T cells from IFN-γ knockout mice do not induce wasting disease , 1997 .

[128]  G. Martin,et al.  Analysis of Fgf8 gene function in vertebrate development. , 1997, Cold Spring Harbor symposia on quantitative biology.

[129]  Y. Kan,et al.  NRF2, a member of the NFE2 family of transcription factors, is not essential for murine erythropoiesis, growth, and development. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[130]  M. Kaplan,et al.  Impaired IL-12 responses and enhanced development of Th2 cells in Stat4-deficient mice , 1996, Nature.

[131]  J. Reddy,et al.  Characterization of a murine Ahr null allele: involvement of the Ah receptor in hepatic growth and development. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[132]  T. Lints,et al.  Hlx homeo box gene is essential for an inductive tissue interaction that drives expansion of embryonic liver and gut. , 1996, Genes & development.

[133]  L. Tabak,et al.  T-cell-specific deletion of a polypeptide N-acetylgalactosaminyl-transferase gene by site-directed recombination. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[134]  N. Muthusamy,et al.  Defective activation and survival of T cells lacking the Ets-1 transcription factor , 1995, Nature.

[135]  K. Rajewsky,et al.  Interleukin-10-deficient mice develop chronic enterocolitis , 1993, Cell.

[136]  T. Taniguchi,et al.  Targeted disruption of IRF-1 or IRF-2 results in abnormal type I IFN gene induction and aberrant lymphocyte development , 1993, Cell.

[137]  J. D. de Vries,et al.  Autoreactive T cell clones specific for class I and class II HLA antigens isolated from a human chimera , 1988, The Journal of experimental medicine.