{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T03:49:33Z","timestamp":1790480973865,"version":"4.1.0"},"reference-count":68,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T00:00:00Z","timestamp":1646092800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/pages\/standard-publication-reuse-rights"}],"funder":[{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["U19AI111143"],"award-info":[{"award-number":["U19AI111143"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["K08AI132739"],"award-info":[{"award-number":["K08AI132739"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"HHS | NIH | National Cancer Institute","doi-asserted-by":"publisher","award":["P30CA008748"],"award-info":[{"award-number":["P30CA008748"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"HHS | NIH | National Cancer Institute","doi-asserted-by":"publisher","award":["U54CA209975"],"award-info":[{"award-number":["U54CA209975"]}],"id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100009729","name":"Ludwig Institute for Cancer Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100009729","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100017922","name":"Potts Memorial Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100017922","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Mucosal-associated invariant T (MAIT) cells are innate-like lymphocytes that recognize microbial vitamin B metabolites and have emerging roles in infectious disease, autoimmunity, and cancer. Although MAIT cells are identified by a semi-invariant TCR, their phenotypic and functional heterogeneity is not well understood. Here we present an integrated single cell transcriptomic analysis of over 76,000 human MAIT cells during early and prolonged Ag-specific activation with the MR1 ligand 5-OP-RU and nonspecific TCR stimulation. We show that MAIT cells span a broad range of homeostatic, effector, helper, tissue-infiltrating, regulatory, and exhausted phenotypes, with distinct gene expression programs associated with CD4+ or CD8+ coexpression. During early activation, MAIT cells rapidly adopt a cytotoxic phenotype characterized by high expression of GZMB, IFNG and TNF. In contrast, prolonged stimulation induces heterogeneous states defined by proliferation, cytotoxicity, immune modulation, and exhaustion. We further demonstrate a FOXP3 expressing MAIT cell subset that phenotypically resembles conventional regulatory T cells. Moreover, scRNAseq-defined MAIT cell subpopulations were also detected in individuals recently exposed to Mycobacterium tuberculosis, confirming their presence during human infection. To our knowledge, our study provides the first comprehensive atlas of human MAIT cells in activation conditions and defines substantial functional heterogeneity, suggesting complex roles in health and disease.<\/jats:p>","DOI":"10.4049\/jimmunol.2100522","type":"journal-article","created":{"date-parts":[[2022,2,11]],"date-time":"2022-02-11T12:30:36Z","timestamp":1644582636000},"page":"1042-1056","source":"Crossref","is-referenced-by-count":58,"title":["Single-Cell Transcriptional Profiling Reveals Signatures of Helper, Effector, and Regulatory MAIT Cells during Homeostasis and Activation"],"prefix":"10.1093","volume":"208","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4952-7041","authenticated-orcid":false,"given":"Charles Kyriakos","family":"Vorkas","sequence":"first","affiliation":[{"name":"Division of Infectious Diseases, Weill Cornell Medicine, Cornell University , New York, NY"},{"name":"Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chirag","family":"Krishna","sequence":"additional","affiliation":[{"name":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8630-2928","authenticated-orcid":false,"given":"Kelin","family":"Li","sequence":"additional","affiliation":[{"name":"Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1049-5767","authenticated-orcid":false,"given":"Jeffrey","family":"Aub\u00e9","sequence":"additional","affiliation":[{"name":"Division of Chemical Biology and Medicinal Chemistry, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill , Chapel Hill, NC"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel W","family":"Fitzgerald","sequence":"additional","affiliation":[{"name":"Division of Infectious Diseases, Weill Cornell Medicine, Cornell University , New York, NY"},{"name":"Center for Global Health, Weill Cornell Medicine, Cornell University , New York, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5552-6427","authenticated-orcid":false,"given":"Linas","family":"Mazutis","sequence":"additional","affiliation":[{"name":"Single Cell Research Initiative, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina S","family":"Leslie","sequence":"additional","affiliation":[{"name":"Computational and Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7918-5164","authenticated-orcid":false,"given":"Michael S","family":"Glickman","sequence":"additional","affiliation":[{"name":"Immunology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center , New York, NY"},{"name":"Division of Infectious Diseases, Memorial Sloan Kettering Cancer Center , New York, NY"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,3,1]]},"reference":[{"key":"2025021008563217100_r1","doi-asserted-by":"crossref","first-page":"1110","DOI":"10.1038\/s41590-019-0444-8","article-title":"The biology and functional importance of MAIT cells","volume":"20","author":"Godfrey","year":"2019","journal-title":"Nat. Immunol."},{"key":"2025021008563217100_r2","doi-asserted-by":"crossref","first-page":"e0191837","DOI":"10.1371\/journal.pone.0191837","article-title":"Synthesis, stabilization, and characterization of the MR1 ligand precursor 5-amino-6-d-ribitylaminouracil (5-A-RU)","volume":"13","author":"Li","year":"2018","journal-title":"PLoS One"},{"key":"2025021008563217100_r3","doi-asserted-by":"crossref","first-page":"e121899","DOI":"10.1172\/jci.insight.121899","article-title":"Mucosal-associated invariant and \u03b3\u03b4 T cell subsets respond to initial Mycobacterium tuberculosis infection","volume":"3","author":"Vorkas","year":"2018","journal-title":"JCI Insight"},{"key":"2025021008563217100_r4","doi-asserted-by":"crossref","first-page":"eaao2556","DOI":"10.1126\/sciimmunol.aao2556","article-title":"MR1 displays the microbial metabolome driving selective MR1-restricted T cell receptor usage","volume":"3","author":"Harriff","year":"2018","journal-title":"Sci. Immunol."},{"key":"2025021008563217100_r5","doi-asserted-by":"crossref","first-page":"164","DOI":"10.1038\/nature01433","article-title":"Selection of evolutionarily conserved mucosal-associated invariant T cells by MR1. [Published erratum appears in 2003 Nature 423: 1018.]","volume":"422","author":"Treiner","year":"2003","journal-title":"Nature"},{"key":"2025021008563217100_r6","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1038\/gene.2016.41","article-title":"A polymorphism in human MR1 is associated with mRNA expression and susceptibility to tuberculosis","volume":"18","author":"Seshadri","year":"2017","journal-title":"Genes Immun."},{"key":"2025021008563217100_r7","doi-asserted-by":"crossref","first-page":"494","DOI":"10.1126\/science.aaw2719","article-title":"Microbial metabolites control the thymic development of mucosal-associated invariant T cells","volume":"366","author":"Legoux","year":"2019","journal-title":"Science"},{"key":"2025021008563217100_r8","doi-asserted-by":"crossref","first-page":"415","DOI":"10.1038\/87720","article-title":"Memory CD8+ T cell differentiation: initial antigen encounter triggers a developmental program in na\u00efve cells","volume":"2","author":"Kaech","year":"2001","journal-title":"Nat. Immunol."},{"key":"2025021008563217100_r9","doi-asserted-by":"crossref","first-page":"E5434","DOI":"10.1073\/pnas.1705759114","article-title":"Multiple layers of heterogeneity and subset diversity in human MAIT cell responses to distinct microorganisms and to innate cytokines","volume":"114","author":"Dias","year":"2017","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2025021008563217100_r10","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.1002\/eji.201747312","article-title":"Human MAIT cells are rapidly activated by Aspergillus spp. in an APC-dependent manner","volume":"48","author":"Jahreis","year":"2018","journal-title":"Eur. J. Immunol."},{"key":"2025021008563217100_r11","doi-asserted-by":"crossref","first-page":"e2001930","DOI":"10.1371\/journal.pbio.2001930","article-title":"MAIT cells launch a rapid, robust and distinct hyperinflammatory response to bacterial superantigens and quickly acquire an anergic phenotype that impedes their cognate antimicrobial function: defining a novel mechanism of superantigen-induced immunopathology and immunosuppression","volume":"15","author":"Shaler","year":"2017","journal-title":"PLoS Biol."},{"key":"2025021008563217100_r12","doi-asserted-by":"crossref","first-page":"3061","DOI":"10.1016\/j.celrep.2019.08.054","article-title":"TCR- or cytokine-activated CD8+ mucosal-associated invariant T cells are rapid polyfunctional effectors that can coordinate immune responses","volume":"28","author":"Lamichhane","year":"2019","journal-title":"Cell Rep."},{"key":"2025021008563217100_r13","doi-asserted-by":"crossref","first-page":"3077","DOI":"10.1016\/j.celrep.2019.08.050","article-title":"TCR and inflammatory signals tune human MAIT cells to exert specific tissue repair and effector functions","volume":"28","author":"Leng","year":"2019","journal-title":"Cell Rep."},{"key":"2025021008563217100_r14","doi-asserted-by":"crossref","first-page":"11653","DOI":"10.1038\/ncomms11653","article-title":"MAIT cells are activated during human viral infections","volume":"7","author":"van Wilgenburg","year":"2016","journal-title":"Nat. Commun."},{"key":"2025021008563217100_r15","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1111\/imcb.12021","article-title":"Human blood MAIT cell subsets defined using MR1 tetramers","volume":"96","author":"Gherardin","year":"2018","journal-title":"Immunol. Cell Biol."},{"key":"2025021008563217100_r16","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.3389\/fimmu.2017.01031","article-title":"Shared and distinct phenotypes and functions of human CD161++ V\u03b17.2+ T cell subsets","volume":"8","author":"Kurioka","year":"2017","journal-title":"Front. Immunol."},{"key":"2025021008563217100_r17","doi-asserted-by":"crossref","first-page":"E11513","DOI":"10.1073\/pnas.1812273115","article-title":"The CD4\u2212CD8\u2212 MAIT cell subpopulation is a functionally distinct subset developmentally related to the main CD8+ MAIT cell pool","volume":"115","author":"Dias","year":"2018","journal-title":"Proc. Natl. Acad. Sci. 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Blood Marrow Transplant."},{"key":"2025021008563217100_r33","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1038\/ni.3854","article-title":"Cytotoxic and regulatory roles of mucosal-associated invariant T cells in type 1 diabetes. [Published erratum appears in 2018 Nat. Immunol. 19: 1035.]","volume":"18","author":"Rouxel","year":"2017","journal-title":"Nat. Immunol."},{"key":"2025021008563217100_r34","doi-asserted-by":"crossref","first-page":"8987","DOI":"10.1073\/pnas.90.19.8987","article-title":"Activation and differentiation requirements of primary T cells in vitro","volume":"90","author":"Sagerstr\u00f6m","year":"1993","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"2025021008563217100_r35","doi-asserted-by":"crossref","first-page":"2477","DOI":"10.1016\/j.molcel.2021.03.045","article-title":"A unified atlas of CD8 T cell dysfunctional states in cancer and infection","volume":"81","author":"Pritykin","year":"2021","journal-title":"Mol. 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