Inflammation-induced IgA+ cells dismantle anti-liver cancer immunity

[1]  M. Kudo,et al.  Nivolumab in patients with advanced hepatocellular carcinoma (CheckMate 040): an open-label, non-comparative, phase 1/2 dose escalation and expansion trial , 2017, The Lancet.

[2]  Jose A Navas-Molina,et al.  Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns , 2017, mSystems.

[3]  P. Vogel,et al.  IL-33 regulates the IgA-microbiota axis to restrain IL-1α-dependent colitis and tumorigenesis. , 2016, The Journal of clinical investigation.

[4]  Jianguo Xia,et al.  Using MetaboAnalyst 3.0 for Comprehensive Metabolomics Data Analysis , 2016, Current protocols in bioinformatics.

[5]  R. Spang,et al.  Comparison of Gene Expression Patterns Between Mouse Models of Nonalcoholic Fatty Liver Disease and Liver Tissues From Patients. , 2016, Gastroenterology.

[6]  K. Reinert,et al.  OpenMS: a flexible open-source software platform for mass spectrometry data analysis , 2016, Nature Methods.

[7]  D. Kleiner,et al.  Histology of Nonalcoholic Fatty Liver Disease and Nonalcoholic Steatohepatitis in Adults and Children. , 2016, Clinics in liver disease.

[8]  Vanessa M. Hubbard-Lucey,et al.  De-Risking Immunotherapy: Report of a Consensus Workshop of the Cancer Immunotherapy Consortium of the Cancer Research Institute , 2016, Cancer Immunology Research.

[9]  Ji Luo,et al.  NAFLD causes selective CD4+ T lymphocyte loss and promotes hepatocarcinogenesis , 2016, Nature.

[10]  Gwendolyn M. Jang,et al.  Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding. , 2015, Cell host & microbe.

[11]  A. Dhanda,et al.  Immune dysfunction in acute alcoholic hepatitis. , 2015, World journal of gastroenterology.

[12]  Amit G Singal,et al.  Hepatocellular Carcinoma From Epidemiology to Prevention: Translating Knowledge into Practice. , 2015, Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association.

[13]  M. Karin,et al.  Immunity, inflammation, and cancer: an eternal fight between good and evil. , 2015, The Journal of clinical investigation.

[14]  K. Deisseroth,et al.  Hybrid Periportal Hepatocytes Regenerate the Injured Liver without Giving Rise to Cancer , 2015, Cell.

[15]  M. Menon,et al.  The expanding family of regulatory B cells , 2015, International immunology.

[16]  Rob Knight,et al.  Analysis of composition of microbiomes: a novel method for studying microbial composition , 2015, Microbial ecology in health and disease.

[17]  S. Rosenberg,et al.  Adoptive cell transfer as personalized immunotherapy for human cancer , 2015, Science.

[18]  Jessica Zucman-Rossi,et al.  Exome sequencing of hepatocellular carcinomas identifies new mutational signatures and potential therapeutic targets , 2015, Nature Genetics.

[19]  Christopher J. Kane,et al.  Immunosuppressive plasma cells impede T cell-dependent immunogenic chemotherapy , 2015, Nature.

[20]  Hiromi Nakamura,et al.  Trans-ancestry mutational landscape of hepatocellular carcinoma genomes , 2014, Nature Genetics.

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

[22]  H. Moch,et al.  Metabolic activation of intrahepatic CD8+ T cells and NKT cells causes nonalcoholic steatohepatitis and liver cancer via cross-talk with hepatocytes. , 2014, Cancer cell.

[23]  M. Karin,et al.  ER stress cooperates with hypernutrition to trigger TNF-dependent spontaneous HCC development. , 2014, Cancer cell.

[24]  Alexandre Corthay,et al.  Does the Immune System Naturally Protect Against Cancer? , 2014, Front. Immunol..

[25]  A. Burt,et al.  Serum immunoglobulin levels predict fibrosis in patients with non-alcoholic fatty liver disease. , 2014, Journal of hepatology.

[26]  Deepak Mittal,et al.  New insights into cancer immunoediting and its three component phases--elimination, equilibrium and escape. , 2014, Current opinion in immunology.

[27]  Rob Knight,et al.  EMPeror: a tool for visualizing high-throughput microbial community data , 2013, GigaScience.

[28]  Kristen Jepsen,et al.  Identification of Liver Cancer Progenitors Whose Malignant Progression Depends on Autocrine IL-6 Signaling , 2013, Cell.

[29]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[30]  P. Brandtzaeg.  Secretory IgA: Designed for Anti-Microbial Defense , 2013, Front. Immunol..

[31]  Kenji Suzuki,et al.  A murine model for non-alcoholic steatohepatitis showing evidence of association between diabetes and hepatocellular carcinoma , 2013, Medical Molecular Morphology.

[32]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[33]  Hollis G. Potter,et al.  Author Manuscript , 2013 .

[34]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[35]  K. Iwaisako,et al.  Interleukin-17 signaling in inflammatory, Kupffer cells, and hepatic stellate cells exacerbates liver fibrosis in mice. , 2012, Gastroenterology.

[36]  Andreas Wilke,et al.  The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome , 2012, GigaScience.

[37]  Raul Rabadan,et al.  Promotion of hepatocellular carcinoma by the intestinal microbiota and TLR4. , 2012, Cancer cell.

[38]  Pablo Cingolani,et al.  © 2012 Landes Bioscience. Do not distribute. , 2022 .

[39]  William A. Walters,et al.  Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms , 2012, The ISME Journal.

[40]  Eric P. Nawrocki,et al.  An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea , 2011, The ISME Journal.

[41]  Tandy J. Warnow,et al.  SEPP: SATe -Enabled Phylogenetic Placement , 2011, Pacific Symposium on Biocomputing.

[42]  T. Luedde,et al.  Senescence surveillance of pre-malignant hepatocytes limits liver cancer development , 2011, Nature.

[43]  J. Wolchok,et al.  Novel cancer immunotherapy agents with survival benefit: recent successes and next steps , 2011, Nature Reviews Cancer.

[44]  Thomas M. Keane,et al.  Mouse genomic variation and its effect on phenotypes and gene regulation , 2011, Nature.

[45]  T. Luedde,et al.  NF-κB in the liver—linking injury, fibrosis and hepatocellular carcinoma , 2011, Nature Reviews Gastroenterology &Hepatology.

[46]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[47]  Richard A. Flavell,et al.  The polarization of immune cells in the tumour environment by TGFβ , 2010, Nature Reviews Immunology.

[48]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[49]  William A. Walters,et al.  QIIME allows analysis of high-throughput community sequencing data , 2010, Nature Methods.

[50]  Lieping Chen,et al.  PD-1 regulates germinal center B cell survival and the formation and affinity of long-lived plasma cells , 2010, Nature Immunology.

[51]  R. Ahmed,et al.  Features of responding T cells in cancer and chronic infection. , 2010, Current opinion in immunology.

[52]  M. Karin,et al.  Hepatocyte IKKbeta/NF-kappaB inhibits tumor promotion and progression by preventing oxidative stress-driven STAT3 activation. , 2010, Cancer cell.

[53]  Jun Hee Lee,et al.  Dietary and Genetic Obesity Promote Liver Inflammation and Tumorigenesis by Enhancing IL-6 and TNF Expression , 2010, Cell.

[54]  M. Karin,et al.  Hepatocyte IKK β / NF-κ B inhibits tumor promotion and progression by preventing oxidative stress driven STAT 3 activation , 2010 .

[55]  A. Waisman,et al.  Nonredundant Roles for B Cell-Derived IL-10 in Immune Counter-Regulation1 , 2009, The Journal of Immunology.

[56]  Richard Durbin,et al.  Sequence analysis Fast and accurate short read alignment with Burrows – Wheeler transform , 2009 .

[57]  A. Cerutti.  The regulation of IgA class switching , 2008, Nature Reviews Immunology.

[58]  Yosuke Osawa,et al.  TLR4 enhances TGF-β signaling and hepatic fibrosis , 2007, Nature Medicine.

[59]  R. Knight,et al.  UniFrac: a New Phylogenetic Method for Comparing Microbial Communities , 2005, Applied and Environmental Microbiology.

[60]  Pablo Tamayo,et al.  Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[61]  T. Phan,et al.  Altered Migration, Recruitment, and Somatic Hypermutation in the Early Response of Marginal Zone B Cells to T Cell-Dependent Antigen1 , 2005, The Journal of Immunology.

[62]  Brian Bierie,et al.  Effect of conditional knockout of the type II TGF-beta receptor gene in mammary epithelia on mammary gland development and polyomavirus middle T antigen induced tumor formation and metastasis. , 2005, Cancer research.

[63]  Alok J. Saldanha,et al.  Java Treeview - extensible visualization of microarray data , 2004, Bioinform..

[64]  S Miyano,et al.  Open source clustering software. , 2004, Bioinformatics.

[65]  M. Daly,et al.  PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes , 2003, Nature Genetics.

[66]  Jhagvaral Hasbold,et al.  B Cell Receptor–independent Stimuli Trigger Immunoglobulin (Ig) Class Switch Recombination and Production of IgG Autoantibodies by Anergic Self-Reactive B Cells , 2003, The Journal of experimental medicine.

[67]  R. Tisch,et al.  The preferential ability of B lymphocytes to act as diabetogenic APC in NOD mice depends on expression of self‐antigen‐specific immunoglobulin receptors , 2002, European journal of immunology.

[68]  Y. Tsuruta,et al.  A new method for quantitative analysis of the mouse T-cell receptor V region repertoires: comparison of repertoires among strains , 2001, Immunogenetics.

[69]  Y. Iwakura,et al.  Generation of polymeric immunoglobulin receptor-deficient mouse with marked reduction of secretory IgA. , 1999, Journal of immunology.

[70]  A. Bradley,et al.  Targeted deletion of the IgA constant region in mice leads to IgA deficiency with alterations in expression of other Ig isotypes. , 1999, Journal of immunology.

[71]  F. Chisari,et al.  Immune Pathogenesis of Hepatocellular Carcinoma , 1998, The Journal of experimental medicine.

[72]  A. Benedetti,et al.  Interferon gamma decreases hepatic stellate cell activation and extracellular matrix deposition in rat liver fibrosis , 1996, Hepatology.

[73]  Kristin A. Hogquist,et al.  T cell receptor antagonist peptides induce positive selection , 1994, Cell.

[74]  F. Alt,et al.  Immunoglobulin gene rearrangement in B cell deficient mice generated by targeted deletion of the JH locus. , 1993, International immunology.

[75]  T. Mak,et al.  Less Mortality but More Relapses in Experimental Allergic Encephalomyelitis in CD8-/- Mice , 1992, Science.

[76]  Susumu Tonegawa,et al.  RAG-1-deficient mice have no mature B and T lymphocytes , 1992, Cell.

[77]  D. Faith.  Conservation evaluation and phylogenetic diversity , 1992 .

[78]  Klaus Rajewsky,et al.  A B cell-deficient mouse by targeted disruption of the membrane exon of the immunoglobulin μ chain gene , 1991, Nature.