{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,30]],"date-time":"2026-10-30T00:12:08Z","timestamp":1793319128009,"version":"4.5.0"},"reference-count":98,"publisher":"American Association for the Advancement of Science (AAAS)","issue":"798","content-domain":{"domain":["www.science.org"],"crossmark-restriction":true},"short-container-title":["Sci. Transl. Med."],"published-print":{"date-parts":[[2025,5,14]]},"abstract":"<jats:p>\n            Intestinal inflammation continues in a subset of patients with celiac disease despite a gluten-free diet. Here, by applying multi-omic single-cell analysis to duodenal biopsies, we found that low-grade malignancies with lymphoma driver mutations in patients with refractory celiac disease type 2 (RCD2) are comprised by surface CD3-negative (sCD3\n            <jats:sup>\u2212<\/jats:sup>\n            ) lymphocytes stalled at an innate lymphoid cell (ILC)\u2013progenitor T cell stage undergoing extensive\n            <jats:italic toggle=\"yes\">TRA<\/jats:italic>\n            ,\n            <jats:italic toggle=\"yes\">TRB<\/jats:italic>\n            , and\n            <jats:italic toggle=\"yes\">TRD<\/jats:italic>\n            TCR recombination. In people with refractory celiac disease type 1 (RCD1), a disease currently lacking explanation, we identified sCD3\n            <jats:sup>+<\/jats:sup>\n            T cells with lymphoma driver mutations in 6 of 10 individuals with RCD1 and in one of the patients with active, recently diagnosed celiac disease. Furthermore, the mutant T cells formed large TCR\u03b1\u03b2 clones and displayed inflammatory and cytotoxic molecular profiles. Thus, accumulation of lymphoma driver\u2013mutated T cells and sCD3\n            <jats:sup>\u2212<\/jats:sup>\n            progenitors may contribute to chronic, nonresponsive celiac disease.\n          <\/jats:p>","DOI":"10.1126\/scitranslmed.adp6812","type":"journal-article","created":{"date-parts":[[2025,5,14]],"date-time":"2025-05-14T17:58:37Z","timestamp":1747245517000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark","source":"Crossref","is-referenced-by-count":17,"title":["Expanded T cell clones with lymphoma driver somatic mutations accumulate in refractory celiac disease"],"prefix":"10.1126","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6998-3805","authenticated-orcid":true,"given":"Mandeep","family":"Singh","sequence":"first","affiliation":[{"name":"Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia."},{"name":"School of Clinical Medicine, Faculty of Medicine &amp; Health, UNSW Sydney, Sydney, NSW 2052, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Raymond H. Y.","family":"Louie","sequence":"additional","affiliation":[{"name":"School of Computer Science and Engineering, UNSW Sydney, Sydney, NSW 2052, Australia."},{"name":"School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6557-9373","authenticated-orcid":true,"given":"Jerome","family":"Samir","sequence":"additional","affiliation":[{"name":"School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0788-6513","authenticated-orcid":true,"given":"Matthew A.","family":"Field","sequence":"additional","affiliation":[{"name":"Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia."},{"name":"Australian Institute of Tropical Health and Medicine and Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Smithfield, QLD 4878, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4836-7154","authenticated-orcid":true,"given":"Claire","family":"Milthorpe","sequence":"additional","affiliation":[{"name":"Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thiruni","family":"Adikari","sequence":"additional","affiliation":[{"name":"School of Medical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6571-4560","authenticated-orcid":true,"given":"Joseph","family":"Mackie","sequence":"additional","affiliation":[{"name":"Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia."},{"name":"School of Clinical Medicine, Faculty of Medicine &amp; Health, UNSW Sydney, Sydney, NSW 2052, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3788-7568","authenticated-orcid":true,"given":"Ellise","family":"Roper","sequence":"additional","affiliation":[{"name":"Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Megan","family":"Faulks","sequence":"additional","affiliation":[{"name":"Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia."}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9952-7069","authenticated-orcid":true,"given":"Katherine J. 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