{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,28]],"date-time":"2026-09-28T21:16:16Z","timestamp":1790630176488,"version":"4.1.0"},"reference-count":132,"publisher":"Rockefeller University Press","issue":"12","license":[{"start":{"date-parts":[[2020,9,3]],"date-time":"2020-09-03T00:00:00Z","timestamp":1599091200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/www.rupress.org\/terms\/"},{"start":{"date-parts":[[2021,6,7]],"date-time":"2021-06-07T00:00:00Z","timestamp":1623024000000},"content-version":"vor","delay-in-days":277,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc-sa\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI081923"],"award-info":[{"award-number":["AI081923"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI113923"],"award-info":[{"award-number":["AI113923"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["AI132122"],"award-info":[{"award-number":["AI132122"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007911","name":"Center for Microbiome Innovation at UCSD","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007911","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01DK61931"],"award-info":[{"award-number":["R01DK61931"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["R01DK068271"],"award-info":[{"award-number":["R01DK068271"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000062","name":"National Institute of Diabetes and Digestive and Kidney Diseases","doi-asserted-by":"publisher","award":["P30DK034854"],"award-info":[{"award-number":["P30DK034854"]}],"id":[{"id":"10.13039\/100000062","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["rupress.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2020,12,7]]},"abstract":"<jats:p>Intestinal barrier leakage constitutes a potential therapeutic target for many inflammatory diseases and represents a disease progression marker during chronic viral infections. However, the causes of altered gut barrier remain mostly unknown. Using murine infection with lymphocytic choriomeningitis virus, we demonstrate that, in contrast to an acute viral strain, a persistent viral isolate leads to long-term viral replication in hematopoietic and mesenchymal cells, but not epithelial cells (IECs), in the intestine. Viral persistence drove sustained intestinal epithelial barrier leakage, which was characterized by increased paracellular flux of small molecules and was associated with enhanced colitis susceptibility. Type I IFN signaling caused tight junction dysregulation in IECs, promoted gut microbiome shifts and enhanced intestinal CD8 T cell responses. Notably, both type I IFN receptor blockade and CD8 T cell depletion prevented infection-induced barrier leakage. Our study demonstrates that infection with a virus that persistently replicates in the intestinal mucosa increases epithelial barrier permeability and reveals type I IFNs and CD8 T cells as causative factors of intestinal leakage during chronic infections.<\/jats:p>","DOI":"10.1084\/jem.20192276","type":"journal-article","created":{"date-parts":[[2020,9,3]],"date-time":"2020-09-03T13:30:46Z","timestamp":1599139846000},"update-policy":"https:\/\/doi.org\/10.1084\/jem.crossmarkpolicy","source":"Crossref","is-referenced-by-count":49,"title":["Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection"],"prefix":"10.1084","volume":"217","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1812-6704","authenticated-orcid":true,"given":"Lara","family":"Labarta-Bajo","sequence":"first","affiliation":[{"name":"Division of Biological Sciences, University of California, San Diego, La Jolla, CA 1"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0310-8186","authenticated-orcid":true,"given":"Steven P.","family":"Nilsen","sequence":"additional","affiliation":[{"name":"Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 2"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3930-1663","authenticated-orcid":true,"given":"Gregory","family":"Humphrey","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California, San Diego, La Jolla, CA 3"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4453-9465","authenticated-orcid":true,"given":"Tara","family":"Schwartz","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California, San Diego, La Jolla, CA 3"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6793-5770","authenticated-orcid":true,"given":"Karenina","family":"Sanders","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California, San Diego, La Jolla, CA 3"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5655-8300","authenticated-orcid":true,"given":"Austin","family":"Swafford","sequence":"additional","affiliation":[{"name":"Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 4"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0975-9019","authenticated-orcid":true,"given":"Rob","family":"Knight","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, University of California, San Diego, La Jolla, CA 3"},{"name":"Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA 4"},{"name":"Department of Bioengineering, University of California, San Diego, La Jolla, CA 5"},{"name":"Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 6"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0627-9455","authenticated-orcid":true,"given":"Jerrold R.","family":"Turner","sequence":"additional","affiliation":[{"name":"Laboratory of Mucosal Barrier Pathobiology, Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 2"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8699-1623","authenticated-orcid":true,"given":"Elina I.","family":"Z\u00fa\u00f1iga","sequence":"additional","affiliation":[{"name":"Division of Biological Sciences, University of California, San Diego, La Jolla, CA 1"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"291","published-online":{"date-parts":[[2020,9,3]]},"reference":[{"key":"2023072801164148200_bib1","doi-asserted-by":"publisher","first-page":"17022","DOI":"10.1073\/pnas.0708469104","article-title":"Conventional dendritic cells regulate the outcome of colonic inflammation independently of T cells","volume":"104","author":"Abe","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023072801164148200_bib2","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1016\/j.immuni.2012.04.011","article-title":"Commensal bacteria calibrate the activation threshold of innate antiviral immunity","volume":"37","author":"Abt","year":"2012","journal-title":"Immunity"},{"key":"2023072801164148200_bib3","doi-asserted-by":"publisher","first-page":"1719","DOI":"10.1084\/jem.167.5.1719","article-title":"Organ-specific selection of viral variants during chronic infection","volume":"167","author":"Ahmed","year":"1988","journal-title":"J. Exp. Med"},{"key":"2023072801164148200_bib4","doi-asserted-by":"publisher","first-page":"521","DOI":"10.1084\/jem.160.2.521","article-title":"Selection of genetic variants of lymphocytic choriomeningitis virus in spleens of persistently infected mice. Role in suppression of cytotoxic T lymphocyte response and viral persistence","volume":"160","author":"Ahmed","year":"1984","journal-title":"J. Exp. Med"},{"key":"2023072801164148200_bib5","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1038\/mi.2015.58","article-title":"The effect of timing of antiretroviral therapy on CD4+ T-cell reconstitution in the intestine of HIV-infected patients","volume":"9","author":"Allers","year":"2016","journal-title":"Mucosal Immunol"},{"key":"2023072801164148200_bib6","doi-asserted-by":"publisher","first-page":"481","DOI":"10.4049\/jimmunol.1601278","article-title":"Distribution and Activation of CD8+ T Cells in the Duodenal Mucosa before and after HIV Seroconversion","volume":"198","author":"Allers","year":"2017","journal-title":"J. Immunol"},{"key":"2023072801164148200_bib7","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00191-16","article-title":"Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns","volume":"2","author":"Amir","year":"2017","journal-title":"mSystems"},{"key":"2023072801164148200_bib8","doi-asserted-by":"publisher","first-page":"8161","DOI":"10.1128\/JVI.00889-12","article-title":"Progressive loss of memory T cell potential and commitment to exhaustion during chronic viral infection","volume":"86","author":"Angelosanto","year":"2012","journal-title":"J. Virol"},{"key":"2023072801164148200_bib9","doi-asserted-by":"publisher","first-page":"682","DOI":"10.1038\/nature04444","article-title":"Restoring function in exhausted CD8 T cells during chronic viral infection","volume":"439","author":"Barber","year":"2006","journal-title":"Nature"},{"key":"2023072801164148200_bib10","doi-asserted-by":"publisher","first-page":"562","DOI":"10.1016\/j.immuni.2017.04.008","article-title":"Homeostatic Immunity and the Microbiota","volume":"46","author":"Belkaid","year":"2017","journal-title":"Immunity"},{"key":"2023072801164148200_bib11","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1189\/jlb.1HI0314-154R","article-title":"Lymphocytic choriomeningitis virus persistence promotes effector-like memory differentiation and enhances mucosal T cell distribution","volume":"97","author":"Beura","year":"2015","journal-title":"J. Leukoc. Biol"},{"key":"2023072801164148200_bib12","doi-asserted-by":"publisher","first-page":"18224","DOI":"10.18632\/oncotarget.24804","article-title":"Increased gut permeability in cancer cachexia: mechanisms and clinical relevance","volume":"9","author":"Bindels","year":"2018","journal-title":"Oncotarget"},{"key":"2023072801164148200_bib13","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s40168-018-0470-z","article-title":"Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2\u2019s q2-feature-classifier plugin","volume":"6","author":"Bokulich","year":"2018","journal-title":"Microbiome"},{"key":"2023072801164148200_bib14","first-page":"3556","article-title":"Global genomic analysis reveals rapid control of a robust innate response in SIV-infected sooty mangabeys","volume":"119","author":"Bosinger","year":"2009","journal-title":"J. Clin. Invest"},{"key":"2023072801164148200_bib15","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1002\/cpim.34","article-title":"The Mouse Model of Infection with Citrobacter rodentium","volume":"119","author":"Bouladoux","year":"2017","journal-title":"Curr. Protoc. Immunol"},{"key":"2023072801164148200_bib16","doi-asserted-by":"publisher","first-page":"1365","DOI":"10.1038\/nm1511","article-title":"Microbial translocation is a cause of systemic immune activation in chronic HIV infection","volume":"12","author":"Brenchley","year":"2006","journal-title":"Nat. Med"},{"key":"2023072801164148200_bib17","doi-asserted-by":"publisher","DOI":"10.1101\/cshperspect.a029314","article-title":"Cell Biology of Tight Junction Barrier Regulation and Mucosal Disease","volume":"10","author":"Buckley","year":"2018","journal-title":"Cold Spring Harb. Perspect. Biol"},{"key":"2023072801164148200_bib18","doi-asserted-by":"publisher","first-page":"820","DOI":"10.1038\/mi.2017.88","article-title":"The cytosolic sensor STING is required for intestinal homeostasis and control of inflammation","volume":"11","author":"Canesso","year":"2018","journal-title":"Mucosal Immunol"},{"key":"2023072801164148200_bib19","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"2023072801164148200_bib20","doi-asserted-by":"publisher","first-page":"1621","DOI":"10.1038\/ismej.2012.8","article-title":"Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms","volume":"6","author":"Caporaso","year":"2012","journal-title":"ISME J"},{"key":"2023072801164148200_bib21","doi-asserted-by":"publisher","first-page":"1337","DOI":"10.2147\/CMAR.S188192","article-title":"Claudin gene expression profiles and clinical value in colorectal tumors classified according to their molecular subtype","volume":"11","author":"Cherradi","year":"2019","journal-title":"Cancer Manag. Res"},{"key":"2023072801164148200_bib22","doi-asserted-by":"publisher","first-page":"G735","DOI":"10.1152\/ajpgi.90551.2008","article-title":"Vasoactive intestinal peptide ameliorates intestinal barrier disruption associated with Citrobacter rodentium-induced colitis","volume":"297","author":"Conlin","year":"2009","journal-title":"Am. J. Physiol. Gastrointest. Liver Physiol"},{"key":"2023072801164148200_bib23","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1038\/ncb0804-699","article-title":"Cytoplasmic intermediate filaments revealed as dynamic and multipurpose scaffolds","volume":"6","author":"Coulombe","year":"2004","journal-title":"Nat. Cell Biol"},{"key":"2023072801164148200_bib24","doi-asserted-by":"publisher","first-page":"2956","DOI":"10.1016\/S0002-9270(99)00500-6","article-title":"Intestinal permeability test as a predictor of clinical course in Crohn\u2019s disease","volume":"94","author":"D\u2019Inc\u00e0","year":"1999","journal-title":"Am. J. Gastroenterol"},{"key":"2023072801164148200_bib25","doi-asserted-by":"publisher","first-page":"1339","DOI":"10.1016\/j.cell.2016.10.043","article-title":"A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility","volume":"167","author":"Desai","year":"2016","journal-title":"Cell"},{"key":"2023072801164148200_bib26","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","volume":"72","author":"DeSantis","year":"2006","journal-title":"Appl. Environ. Microbiol"},{"key":"2023072801164148200_bib27","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.3720","article-title":"Atropos: specific, sensitive, and speedy trimming of sequencing reads","volume":"5","author":"Didion","year":"2017","journal-title":"PeerJ"},{"key":"2023072801164148200_bib28","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics"},{"key":"2023072801164148200_bib29","doi-asserted-by":"publisher","first-page":"2380","DOI":"10.1002\/eji.201344219","article-title":"Type I IFN signaling triggers immunopathology in tuberculosis-susceptible mice by modulating lung phagocyte dynamics","volume":"44","author":"Dorhoi","year":"2014","journal-title":"Eur. J. Immunol"},{"key":"2023072801164148200_bib30","doi-asserted-by":"publisher","first-page":"6016","DOI":"10.3748\/wjg.v23.i33.6016","article-title":"Dextran sodium sulfate colitis murine model: An indispensable tool for advancing our understanding of inflammatory bowel diseases pathogenesis","volume":"23","author":"Eichele","year":"2017","journal-title":"World J. Gastroenterol"},{"key":"2023072801164148200_bib31","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1001052","article-title":"Damaged intestinal epithelial integrity linked to microbial translocation in pathogenic simian immunodeficiency virus infections","volume":"6","author":"Estes","year":"2010","journal-title":"PLoS Pathog"},{"key":"2023072801164148200_bib32","doi-asserted-by":"publisher","first-page":"D649","DOI":"10.1093\/nar\/gkx1132","article-title":"The Reactome Pathway Knowledgebase","volume":"46","author":"Fabregat","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2023072801164148200_bib33","doi-asserted-by":"publisher","first-page":"1383","DOI":"10.1084\/jem.187.9.1383","article-title":"Induction and exhaustion of lymphocytic choriomeningitis virus-specific cytotoxic T lymphocytes visualized using soluble tetrameric major histocompatibility complex class I-peptide complexes","volume":"187","author":"Gallimore","year":"1998","journal-title":"J. Exp. Med"},{"key":"2023072801164148200_bib34","doi-asserted-by":"publisher","first-page":"69","DOI":"10.1186\/s12915-014-0069-1","article-title":"The Earth Microbiome project: successes and aspirations","volume":"12","author":"Gilbert","year":"2014","journal-title":"BMC Biol"},{"key":"2023072801164148200_bib35","doi-asserted-by":"publisher","first-page":"796","DOI":"10.1038\/s41592-018-0141-9","article-title":"Qiita: rapid, web-enabled microbiome meta-analysis","volume":"15","author":"Gonzalez","year":"2018","journal-title":"Nat. Methods"},{"key":"2023072801164148200_bib36","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1046\/j.1461-0248.2001.00230.x","article-title":"Quantifying biodiversity: procedures and pitfalls in the measurement and comparison of species richness","volume":"4","author":"Gotelli","year":"2001","journal-title":"Ecol. Lett"},{"key":"2023072801164148200_bib37","doi-asserted-by":"publisher","first-page":"690","DOI":"10.1038\/s41591-019-0393-7","article-title":"Intracellular MLCK1 diversion reverses barrier loss to restore mucosal homeostasis","volume":"25","author":"Graham","year":"2019","journal-title":"Nat. Med"},{"key":"2023072801164148200_bib38","doi-asserted-by":"publisher","first-page":"620","DOI":"10.1016\/j.yexcr.2010.12.017","article-title":"CXCR3 in T cell function","volume":"317","author":"Groom","year":"2011","journal-title":"Exp. Cell Res"},{"key":"2023072801164148200_bib39","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0074957","article-title":"Bacterial community mapping of the mouse gastrointestinal tract","volume":"8","author":"Gu","year":"2013","journal-title":"PLoS One"},{"key":"2023072801164148200_bib40","first-page":"574","article-title":"Gut microbiome dysbiosis and increased intestinal permeability in children with islet autoimmunity and type 1 diabetes: A prospective cohort study","volume":"20","author":"Harbison","year":"2019","journal-title":"Pediatr. Diabetes"},{"key":"2023072801164148200_bib41","doi-asserted-by":"publisher","first-page":"7886","DOI":"10.1128\/JVI.02612-09","article-title":"Downregulation of robust acute type I interferon responses distinguishes nonpathogenic simian immunodeficiency virus (SIV) infection of natural hosts from pathogenic SIV infection of rhesus macaques","volume":"84","author":"Harris","year":"2010","journal-title":"J. Virol"},{"key":"2023072801164148200_bib42","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1146\/annurev-med-012017-043208","article-title":"CD8 T Cell Exhaustion in Chronic Infection and Cancer: Opportunities for Interventions","volume":"69","author":"Hashimoto","year":"2018","journal-title":"Annu. Rev. Med"},{"key":"2023072801164148200_bib43","doi-asserted-by":"publisher","first-page":"1578","DOI":"10.1136\/gutjnl-2013-306226","article-title":"Altered intestinal microbiota and blood T cell phenotype are shared by patients with Crohn\u2019s disease and their unaffected siblings","volume":"63","author":"Hedin","year":"2014","journal-title":"Gut"},{"key":"2023072801164148200_bib44","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00069-18","article-title":"Evaluating the Information Content of Shallow Shotgun Metagenomics","volume":"3","author":"Hillmann","year":"2018","journal-title":"mSystems"},{"key":"2023072801164148200_bib45","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1016\/j.virol.2006.12.025","article-title":"Mapping and restriction of a dominant viral CD4+ T cell core epitope by both MHC class I and MHC class II","volume":"363","author":"Homann","year":"2007","journal-title":"Virology"},{"key":"2023072801164148200_bib46","doi-asserted-by":"publisher","first-page":"1043","DOI":"10.1016\/j.immuni.2019.11.002","article-title":"Proliferating Transitory T Cells with an Effector-like Transcriptional Signature Emerge from PD-1+ Stem-like CD8+ T Cells during Chronic Infection","volume":"51","author":"Hudson","year":"2019","journal-title":"Immunity"},{"key":"2023072801164148200_bib47","doi-asserted-by":"publisher","first-page":"417","DOI":"10.1038\/nature19330","article-title":"Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy","volume":"537","author":"Im","year":"2016","journal-title":"Nature"},{"key":"2023072801164148200_bib48","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1038\/nature11582","article-title":"Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease","volume":"491","author":"Jostins","year":"2012","journal-title":"Nature"},{"key":"2023072801164148200_bib49","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1093\/nar\/28.1.27","article-title":"KEGG: kyoto encyclopedia of genes and genomes","volume":"28","author":"Kanehisa","year":"2000","journal-title":"Nucleic Acids Res"},{"key":"2023072801164148200_bib50","doi-asserted-by":"publisher","first-page":"637","DOI":"10.1084\/jem.20050821","article-title":"Type I interferons act directly on CD8 T cells to allow clonal expansion and memory formation in response to viral infection","volume":"202","author":"Kolumam","year":"2005","journal-title":"J. Exp. Med"},{"key":"2023072801164148200_bib51","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"2023072801164148200_bib52","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/j.ydbio.2012.07.005","article-title":"EpCAM contributes to formation of functional tight junction in the intestinal epithelium by recruiting claudin proteins","volume":"371","author":"Lei","year":"2012","journal-title":"Dev. Biol"},{"key":"2023072801164148200_bib53","doi-asserted-by":"publisher","first-page":"1726","DOI":"10.1126\/science.1168676","article-title":"Visualizing antigen-specific and infected cells in situ predicts outcomes in early viral infection","volume":"323","author":"Li","year":"2009","journal-title":"Science"},{"key":"2023072801164148200_bib54","doi-asserted-by":"publisher","first-page":"6456","DOI":"10.1074\/jbc.270.12.6456","article-title":"Human intestinal H+\/peptide cotransporter. Cloning, functional expression, and chromosomal localization","volume":"270","author":"Liang","year":"1995","journal-title":"J. Biol. Chem"},{"key":"2023072801164148200_bib55","doi-asserted-by":"publisher","first-page":"1739","DOI":"10.1093\/bioinformatics\/btr260","article-title":"Molecular signatures database (MSigDB) 3.0","volume":"27","author":"Liberzon","year":"2011","journal-title":"Bioinformatics"},{"key":"2023072801164148200_bib56","doi-asserted-by":"publisher","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol"},{"key":"2023072801164148200_bib57","doi-asserted-by":"publisher","first-page":"441","DOI":"10.1146\/annurev-cellbio-092910-154237","article-title":"Aerobic glycolysis: meeting the metabolic requirements of cell proliferation","volume":"27","author":"Lunt","year":"2011","journal-title":"Annu. Rev. Cell Dev. Biol"},{"key":"2023072801164148200_bib58","doi-asserted-by":"publisher","first-page":"617","DOI":"10.1016\/j.chom.2012.04.017","article-title":"Plasmacytoid dendritic cells are productively infected and activated through TLR-7 early after arenavirus infection","volume":"11","author":"Macal","year":"2012","journal-title":"Cell Host Microbe"},{"key":"2023072801164148200_bib59","doi-asserted-by":"publisher","first-page":"1275","DOI":"10.1136\/gutjnl-2013-304833","article-title":"A decrease of the butyrate-producing species Roseburia hominis and Faecalibacterium prausnitzii defines dysbiosis in patients with ulcerative colitis","volume":"63","author":"Machiels","year":"2014","journal-title":"Gut"},{"key":"2023072801164148200_bib60","doi-asserted-by":"publisher","first-page":"2797","DOI":"10.4049\/jimmunol.170.6.2797","article-title":"Cutting edge: impairment of dendritic cells and adaptive immunity by Ebola and Lassa viruses","volume":"170","author":"Mahanty","year":"2003","journal-title":"J. Immunol"},{"key":"2023072801164148200_bib61","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1093\/femsec\/fix153","article-title":"Identification of universal gut microbial biomarkers of common human intestinal diseases by meta-analysis","volume":"93","author":"Mancabelli","year":"2017","journal-title":"FEMS Microbiol. Ecol"},{"key":"2023072801164148200_bib62","doi-asserted-by":"publisher","first-page":"2035","DOI":"10.1097\/QAD.0b013e3283112d29","article-title":"Microbial translocation is associated with sustained failure in CD4+ T-cell reconstitution in HIV-infected patients on long-term highly active antiretroviral therapy","volume":"22","author":"Marchetti","year":"2008","journal-title":"AIDS"},{"key":"2023072801164148200_bib63","doi-asserted-by":"publisher","first-page":"290","DOI":"10.2144\/000114559","article-title":"DNA extraction for streamlined metagenomics of diverse environmental samples","volume":"62","author":"Marotz","year":"2017","journal-title":"Biotechniques"},{"key":"2023072801164148200_bib64","doi-asserted-by":"publisher","first-page":"116","DOI":"10.1136\/gutjnl-2012-304119","article-title":"Western diet induces dysbiosis with increased E coli in CEABAC10 mice, alters host barrier function favouring AIEC colonisation","volume":"63","author":"Martinez-Medina","year":"2014","journal-title":"Gut"},{"key":"2023072801164148200_bib65","doi-asserted-by":"publisher","first-page":"7340","DOI":"10.1128\/JVI.67.12.7340-7349.1993","article-title":"Molecular determinants of macrophage tropism and viral persistence: importance of single amino acid changes in the polymerase and glycoprotein of lymphocytic choriomeningitis virus","volume":"67","author":"Matloubian","year":"1993","journal-title":"J. Virol"},{"key":"2023072801164148200_bib66","doi-asserted-by":"publisher","first-page":"34844","DOI":"10.1074\/jbc.M112.399998","article-title":"The bactericidal activity of the C-type lectin RegIII\u03b2 against Gram-negative bacteria involves binding to lipid A","volume":"287","author":"Miki","year":"2012","journal-title":"J. Biol. Chem"},{"key":"2023072801164148200_bib67","doi-asserted-by":"publisher","first-page":"1005","DOI":"10.1016\/j.immuni.2015.06.006","article-title":"Interleukin-33 in Tissue Homeostasis, Injury, and Inflammation","volume":"42","author":"Molofsky","year":"2015","journal-title":"Immunity"},{"key":"2023072801164148200_bib68","doi-asserted-by":"publisher","first-page":"2719","DOI":"10.1038\/s41467-019-10656-5","article-title":"Establishing microbial composition measurement standards with reference frames","volume":"10","author":"Morton","year":"2019","journal-title":"Nat. Commun"},{"key":"2023072801164148200_bib69","doi-asserted-by":"publisher","first-page":"15430","DOI":"10.1073\/pnas.0702579104","article-title":"Viral targeting of fibroblastic reticular cells contributes to immunosuppression and persistence during chronic infection","volume":"104","author":"Mueller","year":"2007","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023072801164148200_bib70","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1038\/nature12729","article-title":"Antibacterial membrane attack by a pore-forming intestinal C-type lectin","volume":"505","author":"Mukherjee","year":"2014","journal-title":"Nature"},{"key":"2023072801164148200_bib71","doi-asserted-by":"publisher","first-page":"701","DOI":"10.1038\/s41579-019-0252-z","article-title":"Citrobacter rodentium-host-microbiota interactions: immunity, bioenergetics and metabolism","volume":"17","author":"Mullineaux-Sanders","year":"2019","journal-title":"Nat. Rev. Microbiol"},{"key":"2023072801164148200_bib72","doi-asserted-by":"publisher","first-page":"1737","DOI":"10.1038\/s41564-019-0470-1","article-title":"IFN-I and IL-22 mediate protective effects of intestinal viral infection","volume":"4","author":"Neil","year":"2019","journal-title":"Nat. Microbiol"},{"key":"2023072801164148200_bib73","doi-asserted-by":"publisher","first-page":"2063","DOI":"10.1126\/science.1074900","article-title":"Critical role for STAT4 activation by type 1 interferons in the interferon-gamma response to viral infection","volume":"297","author":"Nguyen","year":"2002","journal-title":"Science"},{"key":"2023072801164148200_bib74","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.1016\/j.cgh.2013.07.001","article-title":"Intestinal permeability defects: is it time to treat?","volume":"11","author":"Odenwald","year":"2013","journal-title":"Clin. Gastroenterol. Hepatol"},{"key":"2023072801164148200_bib75","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/nrgastro.2016.169","article-title":"The intestinal epithelial barrier: a therapeutic target?","volume":"14","author":"Odenwald","year":"2017","journal-title":"Nat. Rev. Gastroenterol. Hepatol"},{"key":"2023072801164148200_bib76","doi-asserted-by":"publisher","first-page":"694","DOI":"10.1016\/0016-5085(90)90290-H","article-title":"A novel method in the induction of reliable experimental acute and chronic ulcerative colitis in mice","volume":"98","author":"Okayasu","year":"1990","journal-title":"Gastroenterology"},{"key":"2023072801164148200_bib77","doi-asserted-by":"publisher","first-page":"3402","DOI":"10.1002\/eji.1830251230","article-title":"Presentation of endogenous viral proteins in association with major histocompatibility complex class II: on the role of intracellular compartmentalization, invariant chain and the TAP transporter system","volume":"25","author":"Oxenius","year":"1995","journal-title":"Eur. J. Immunol"},{"key":"2023072801164148200_bib78","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1016\/j.ajpath.2011.10.025","article-title":"Probiotic bacteria induce maturation of intestinal claudin 3 expression and barrier function","volume":"180","author":"Patel","year":"2012","journal-title":"Am. J. Pathol"},{"key":"2023072801164148200_bib79","doi-asserted-by":"publisher","first-page":"261","DOI":"10.1006\/geno.1996.0045","article-title":"Mouse chromosomal location of four Na\/H exchanger isoform genes","volume":"31","author":"Pathak","year":"1996","journal-title":"Genomics"},{"key":"2023072801164148200_bib80","doi-asserted-by":"publisher","first-page":"290","DOI":"10.1038\/nbt.3122","article-title":"StringTie enables improved reconstruction of a transcriptome from RNA-seq reads","volume":"33","author":"Pertea","year":"2015","journal-title":"Nat. Biotechnol"},{"key":"2023072801164148200_bib81","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1038\/nri3608","article-title":"Intestinal epithelial cells: regulators of barrier function and immune homeostasis","volume":"14","author":"Peterson","year":"2014","journal-title":"Nat. Rev. Immunol"},{"key":"2023072801164148200_bib82","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1007\/s11894-010-0135-y","article-title":"Intestinal mesenchymal cells","volume":"12","author":"Pinchuk","year":"2010","journal-title":"Curr. Gastroenterol. Rep"},{"key":"2023072801164148200_bib83","doi-asserted-by":"publisher","first-page":"40","DOI":"10.1016\/j.ebiom.2016.01.028","article-title":"Reversing Gut Damage in HIV Infection: Using Non-Human Primate Models to Instruct Clinical Research","volume":"4","author":"Ponte","year":"2016","journal-title":"EBioMedicine"},{"key":"2023072801164148200_bib84","doi-asserted-by":"publisher","first-page":"1601","DOI":"10.1016\/j.bbadis.2011.08.010","article-title":"Gut barrier dysfunction in the Apc(Min\/+) mouse model of colon cancer cachexia","volume":"1812","author":"Puppa","year":"2011","journal-title":"Biochim. Biophys. Acta"},{"key":"2023072801164148200_bib85","doi-asserted-by":"publisher","first-page":"C1669","DOI":"10.1152\/ajpcell.00202.2007","article-title":"Rodent intestinal folate transporters (SLC46A1): secondary structure, functional properties, and response to dietary folate restriction","volume":"293","author":"Qiu","year":"2007","journal-title":"Am. J. Physiol. Cell Physiol"},{"key":"2023072801164148200_bib86","doi-asserted-by":"publisher","first-page":"341","DOI":"10.1038\/nri.2016.42","article-title":"Gut microbiota, metabolites and host immunity","volume":"16","author":"Rooks","year":"2016","journal-title":"Nat. Rev. Immunol"},{"key":"2023072801164148200_bib87","doi-asserted-by":"publisher","first-page":"7206","DOI":"10.1073\/pnas.121183498","article-title":"Identification and characterization of a lysosomal transporter for small neutral amino acids","volume":"98","author":"Sagn\u00e9","year":"2001","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023072801164148200_bib88","doi-asserted-by":"publisher","first-page":"2064","DOI":"10.1128\/JCM.33.8.2064-2068.1995","article-title":"Genetic and biochemical characterization of Citrobacter rodentium sp. nov","volume":"33","author":"Schauer","year":"1995","journal-title":"J. Clin. Microbiol"},{"key":"2023072801164148200_bib89","doi-asserted-by":"publisher","first-page":"3757","DOI":"10.1182\/blood.V98.13.3757","article-title":"Simian immunodeficiency virus (SIV)-specific cytotoxic T lymphocytes in gastrointestinal tissues of chronically SIV-infected rhesus monkeys","volume":"98","author":"Schmitz","year":"2001","journal-title":"Blood"},{"key":"2023072801164148200_bib90","doi-asserted-by":"publisher","first-page":"1249","DOI":"10.1084\/jem.192.9.1249","article-title":"Immunosuppression and resultant viral persistence by specific viral targeting of dendritic cells","volume":"192","author":"Sevilla","year":"2000","journal-title":"J. Exp. Med"},{"key":"2023072801164148200_bib91","doi-asserted-by":"publisher","first-page":"5621","DOI":"10.1128\/JVI.77.10.5621-5631.2003","article-title":"Trafficking of human immunodeficiency virus type 1-specific CD8+ T cells to gut-associated lymphoid tissue during chronic infection","volume":"77","author":"Shacklett","year":"2003","journal-title":"J. Virol"},{"key":"2023072801164148200_bib92","doi-asserted-by":"publisher","first-page":"1910","DOI":"10.1172\/JCI35412","article-title":"Type I IFNs mediate development of postinfluenza bacterial pneumonia in mice","volume":"119","author":"Shahangian","year":"2009","journal-title":"J. Clin. Invest"},{"key":"2023072801164148200_bib93","first-page":"306","article-title":"The mathematical theory of communication. 1963","volume":"14","author":"Shannon","year":"1997","journal-title":"MD Comput"},{"key":"2023072801164148200_bib94","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1146\/annurev-physiol-012110-142150","article-title":"Tight junction pore and leak pathways: a dynamic duo","volume":"73","author":"Shen","year":"2011","journal-title":"Annu. Rev. Physiol"},{"key":"2023072801164148200_bib95","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1083\/jcb.200408064","article-title":"PATJ regulates tight junction formation and polarity in mammalian epithelial cells","volume":"168","author":"Shin","year":"2005","journal-title":"J. Cell Biol"},{"key":"2023072801164148200_bib96","doi-asserted-by":"publisher","first-page":"1425","DOI":"10.1093\/carcin\/20.8.1425","article-title":"Increased tight junctional permeability is associated with the development of colon cancer","volume":"20","author":"Soler","year":"1999","journal-title":"Carcinogenesis"},{"key":"2023072801164148200_bib97","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1038\/274168a0","article-title":"Induction of macrophage production and proliferation by a purified colony stimulating factor","volume":"274","author":"Stanley","year":"1978","journal-title":"Nature"},{"key":"2023072801164148200_bib98","doi-asserted-by":"publisher","first-page":"458","DOI":"10.1016\/j.chom.2012.10.001","article-title":"Chronic bystander infections and immunity to unrelated antigens","volume":"12","author":"Stelekati","year":"2012","journal-title":"Cell Host Microbe"},{"key":"2023072801164148200_bib99","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1111\/nyas.13343","article-title":"Zonulin transgenic mice show altered gut permeability and increased morbidity\/mortality in the DSS colitis model","volume":"1397","author":"Sturgeon","year":"2017","journal-title":"Ann. N. Y. Acad. Sci"},{"key":"2023072801164148200_bib100","doi-asserted-by":"publisher","first-page":"407","DOI":"10.1053\/j.gastro.2013.04.011","article-title":"TNFR2 activates MLCK-dependent tight junction dysregulation to cause apoptosis-mediated barrier loss and experimental colitis","volume":"145","author":"Su","year":"2013","journal-title":"Gastroenterology"},{"key":"2023072801164148200_bib101","doi-asserted-by":"publisher","first-page":"15545","DOI":"10.1073\/pnas.0506580102","article-title":"Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles","volume":"102","author":"Subramanian","year":"2005","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2023072801164148200_bib102","doi-asserted-by":"publisher","first-page":"905","DOI":"10.1038\/mi.2013.106","article-title":"Transmigrated neutrophils in the intestinal lumen engage ICAM-1 to regulate the epithelial barrier and neutrophil recruitment","volume":"7","author":"Sumagin","year":"2014","journal-title":"Mucosal Immunol"},{"key":"2023072801164148200_bib103","doi-asserted-by":"publisher","first-page":"85","DOI":"10.1016\/j.chom.2014.11.004","article-title":"Type I interferons link viral infection to enhanced epithelial turnover and repair","volume":"17","author":"Sun","year":"2015","journal-title":"Cell Host Microbe"},{"key":"2023072801164148200_bib104","doi-asserted-by":"publisher","first-page":"250","DOI":"10.1111\/j.1600-0609.1998.tb01710.x","article-title":"Intestinal permeability in patients with acute myeloid leukemia","volume":"61","author":"Sundstr\u00f6m","year":"1998","journal-title":"Eur. J. Haematol"},{"key":"2023072801164148200_bib105","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1016\/j.coviro.2011.10.026","article-title":"Type I interferons: diversity of sources, production pathways and effects on immune responses","volume":"1","author":"Swiecki","year":"2011","journal-title":"Curr. Opin. Virol"},{"key":"2023072801164148200_bib106","doi-asserted-by":"publisher","first-page":"391","DOI":"10.3389\/fmicb.2017.00391","article-title":"Metaproteogenomics Reveals Taxonomic and Functional Changes between Cecal and Fecal Microbiota in Mouse","volume":"8","author":"Tanca","year":"2017","journal-title":"Front. Microbiol"},{"key":"2023072801164148200_bib107","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1126\/science.1235214","article-title":"Persistent LCMV infection is controlled by blockade of type I interferon signaling","volume":"340","author":"Teijaro","year":"2013","journal-title":"Science"},{"key":"2023072801164148200_bib108","doi-asserted-by":"publisher","first-page":"1376","DOI":"10.1126\/science.aar3318","article-title":"Hyperglycemia drives intestinal barrier dysfunction and risk for enteric infection","volume":"359","author":"Thaiss","year":"2018","journal-title":"Science"},{"key":"2023072801164148200_bib109","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1053\/gast.2000.8523","article-title":"Surrogate markers of intestinal inflammation are predictive of relapse in patients with inflammatory bowel disease","volume":"119","author":"Tibble","year":"2000","journal-title":"Gastroenterology"},{"key":"2023072801164148200_bib110","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s12981-016-0103-1","article-title":"Gut barrier structure, mucosal immunity and intestinal microbiota in the pathogenesis and treatment of HIV infection","volume":"13","author":"Tincati","year":"2016","journal-title":"AIDS Res. Ther"},{"key":"2023072801164148200_bib111","doi-asserted-by":"publisher","first-page":"145","DOI":"10.1016\/j.immuni.2009.06.015","article-title":"Cell-intrinsic transforming growth factor-beta signaling mediates virus-specific CD8+ T cell deletion and viral persistence in vivo","volume":"31","author":"Tinoco","year":"2009","journal-title":"Immunity"},{"key":"2023072801164148200_bib112","doi-asserted-by":"publisher","first-page":"386","DOI":"10.2353\/ajpath.2007.070152","article-title":"Epithelial cell adhesion molecule: more than a carcinoma marker and adhesion molecule","volume":"171","author":"Trzpis","year":"2007","journal-title":"Am. J. Pathol"},{"key":"2023072801164148200_bib113","doi-asserted-by":"publisher","first-page":"671","DOI":"10.1016\/j.chom.2017.05.009","article-title":"IL-22\u00a0Upregulates Epithelial Claudin-2 to Drive Diarrhea and Enteric Pathogen Clearance","volume":"21","author":"Tsai","year":"2017","journal-title":"Cell Host Microbe"},{"key":"2023072801164148200_bib114","doi-asserted-by":"publisher","first-page":"799","DOI":"10.1038\/nri2653","article-title":"Intestinal mucosal barrier function in health and disease","volume":"9","author":"Turner","year":"2009","journal-title":"Nat. Rev. Immunol"},{"key":"2023072801164148200_bib115","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1016\/j.immuni.2016.07.021","article-title":"T Cell Factor 1-Expressing Memory-like CD8(+) T Cells Sustain the Immune Response to Chronic Viral Infections","volume":"45","author":"Utzschneider","year":"2016","journal-title":"Immunity"},{"key":"2023072801164148200_bib116","doi-asserted-by":"publisher","first-page":"427","DOI":"10.1126\/science.280.5362.427","article-title":"Gastrointestinal tract as a major site of CD4+ T cell depletion and viral replication in SIV infection","volume":"280","author":"Veazey","year":"1998","journal-title":"Science"},{"key":"2023072801164148200_bib117","doi-asserted-by":"publisher","first-page":"296","DOI":"10.1016\/j.immuni.2014.06.014","article-title":"Symbiotic bacterial metabolites regulate gastrointestinal barrier function via the xenobiotic sensor PXR and Toll-like receptor 4","volume":"41","author":"Venkatesh","year":"2014","journal-title":"Immunity"},{"key":"2023072801164148200_bib118","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1016\/j.cell.2009.06.036","article-title":"Redefining chronic viral infection","volume":"138","author":"Virgin","year":"2009","journal-title":"Cell"},{"key":"2023072801164148200_bib119","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1007\/s10620-015-3935-y","article-title":"Assessment of the Intestinal Barrier with Five Different Permeability Tests in Healthy C57BL\/6J and BALB\/cJ Mice","volume":"61","author":"Volynets","year":"2016","journal-title":"Dig. Dis. Sci"},{"key":"2023072801164148200_bib120","doi-asserted-by":"publisher","first-page":"75","DOI":"10.3390\/v10020075","article-title":"Mammarenaviral Infection Is Dependent on Directional Exposure to and Release from Polarized Intestinal Epithelia","volume":"10","author":"Warner","year":"2018","journal-title":"Viruses"},{"key":"2023072801164148200_bib121","doi-asserted-by":"publisher","first-page":"12037","DOI":"10.1074\/jbc.M109.064808","article-title":"Epithelial myosin light chain kinase activation induces mucosal interleukin-13 expression to alter tight junction ion selectivity","volume":"285","author":"Weber","year":"2010","journal-title":"J. Biol. Chem"},{"key":"2023072801164148200_bib122","doi-asserted-by":"publisher","first-page":"503","DOI":"10.1146\/annurev.ph.47.030185.002443","article-title":"The glucose transporter of mammalian cells","volume":"47","author":"Wheeler","year":"1985","journal-title":"Annu. Rev. Physiol"},{"key":"2023072801164148200_bib123","doi-asserted-by":"publisher","first-page":"4911","DOI":"10.1128\/JVI.77.8.4911-4927.2003","article-title":"Viral persistence alters CD8 T-cell immunodominance and tissue distribution and results in distinct stages of functional impairment","volume":"77","author":"Wherry","year":"2003","journal-title":"J. Virol"},{"key":"2023072801164148200_bib124","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1016\/j.immuni.2007.09.006","article-title":"Molecular signature of CD8+ T cell exhaustion during chronic viral infection","volume":"27","author":"Wherry","year":"2007","journal-title":"Immunity"},{"key":"2023072801164148200_bib125","doi-asserted-by":"publisher","first-page":"430","DOI":"10.1093\/clinids\/24.3.430","article-title":"Increased gastrointestinal permeability in patients with Plasmodium falciparum malaria","volume":"24","author":"Wilairatana","year":"1997","journal-title":"Clin. Infect. Dis"},{"key":"2023072801164148200_bib126","doi-asserted-by":"publisher","first-page":"202","DOI":"10.1126\/science.1235208","article-title":"Blockade of chronic type I interferon signaling to control persistent LCMV infection","volume":"340","author":"Wilson","year":"2013","journal-title":"Science"},{"key":"2023072801164148200_bib127","doi-asserted-by":"publisher","DOI":"10.1126\/sciimmunol.aai8593","article-title":"The TCF1-Bcl6 axis counteracts type I interferon to repress exhaustion and maintain T cell stemness","volume":"1","author":"Wu","year":"2016","journal-title":"Sci. Immunol"},{"key":"2023072801164148200_bib128","doi-asserted-by":"publisher","first-page":"1437","DOI":"10.1016\/0140-6736(93)90882-H","article-title":"Intestinal permeability and the prediction of relapse in Crohn\u2019s disease","volume":"341","author":"Wyatt","year":"1993","journal-title":"Lancet"},{"key":"2023072801164148200_bib129","doi-asserted-by":"publisher","first-page":"17350","DOI":"10.1074\/jbc.M213286200","article-title":"Claudin-8 expression in Madin-Darby canine kidney cells augments the paracellular barrier to cation permeation","volume":"278","author":"Yu","year":"2003","journal-title":"J. Biol. Chem"},{"key":"2023072801164148200_bib130","doi-asserted-by":"publisher","first-page":"2205","DOI":"10.1084\/jem.188.12.2205","article-title":"Viral immune evasion due to persistence of activated T cells without effector function","volume":"188","author":"Zajac","year":"1998","journal-title":"J. Exp. Med"},{"key":"2023072801164148200_bib131","doi-asserted-by":"publisher","first-page":"1028","DOI":"10.1016\/j.immuni.2019.10.009","article-title":"CD4","volume":"51","author":"Zander","year":"2019","journal-title":"Immunity"},{"key":"2023072801164148200_bib132","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1146\/annurev-virology-100114-055226","article-title":"Innate and Adaptive Immune Regulation During Chronic Viral Infections","volume":"2","author":"Zuniga","year":"2015","journal-title":"Annu. Rev. Virol"}],"container-title":["Journal of Experimental Medicine"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/rupress.org\/jem\/article-pdf\/doi\/10.1084\/jem.20192276\/1822896\/jem_20192276.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/rupress.org\/jem\/article-pdf\/doi\/10.1084\/jem.20192276\/1822896\/jem_20192276.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,7,28]],"date-time":"2023-07-28T01:21:38Z","timestamp":1690507298000},"score":1,"resource":{"primary":{"URL":"https:\/\/rupress.org\/jem\/article\/217\/12\/e20192276\/152069\/Type-I-IFNs-and-CD8-T-cells-increase-intestinal"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,9,3]]},"references-count":132,"journal-issue":{"issue":"12","published-print":{"date-parts":[[2020,12,7]]}},"URL":"https:\/\/doi.org\/10.1084\/jem.20192276","relation":{},"ISSN":["0022-1007","1540-9538"],"issn-type":[{"value":"0022-1007","type":"print"},{"value":"1540-9538","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,9,3]]},"article-number":"e20192276"}}