{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,4,16]],"date-time":"2026-04-16T05:43:31Z","timestamp":1776318211685,"version":"3.50.1"},"posted":{"date-parts":[[2025,1,17]]},"group-title":"Immunology","reference-count":33,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2025,1,17]],"date-time":"2025-01-17T00:00:00Z","timestamp":1737072000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.biorxiv.org\/about\/FAQ#license"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,1,17]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Ulcerative Colitis (UC) is characterized by chronic, relapsing and remitting inflammation in the colon and rectum. Pathogenic T cell activity is thought to play a major role in this process. T cell effector function is determined by the T cell receptor (TCR) and the antigen it recognizes. Examining the TCR repertoire can provide key insights into the adaptive immune response.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Objective<\/jats:title>\n                  <jats:p>To characterize the longitudinal TCR repertoire of patients with UC across disease activity to determine if recurrent antigen(s) are responsible for active inflammation.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Design<\/jats:title>\n                  <jats:p>Bulk TCR V\u03b2 sequencing was done on colon tissue of 20 patients with UC across multiple time points of disease. Corresponding clinical metadata was also obtained over the same time period for each patient to map their clinical disease course. The top ten most highly abundant clones from each time point were longitudinally tracked and correlated with disease phenotype.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Seventy-five percent of patients did not have overlapping abundant TCR clones across multiple time points of disease. The remaining 25% of patients had one to five TCR clones present in high abundance in their tissue during every time point analyzed.<\/jats:p>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Conclusion<\/jats:title>\n                  <jats:p>These results demonstrate that most patients with UC do not share a similar TCR repertoire over time, indicating that times of inflammation are associated with unique antigen exposures. A smaller group of patients have persistent, private TCR clones with high abundance, 60% of whom had more unremitting, active disease.<\/jats:p>\n                <\/jats:sec>","DOI":"10.1101\/2025.01.13.632427","type":"posted-content","created":{"date-parts":[[2025,1,17]],"date-time":"2025-01-17T09:35:13Z","timestamp":1737106513000},"source":"Crossref","is-referenced-by-count":2,"title":["Longitudinal T cell repertoire analysis reveals dynamic clonal T cell populations in Ulcerative Colitis"],"prefix":"10.64898","author":[{"given":"Kristi C.","family":"Briggs","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica S.","family":"Lin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lara","family":"Chaaban","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alyssa","family":"Parian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Lazarev","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florin","family":"Selaru","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Franck","family":"Housseau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kellie N.","family":"Smith","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joanna M. P.","family":"Melia","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"54368","reference":[{"key":"2025012021301346000_2025.01.13.632427v1.1","doi-asserted-by":"publisher","DOI":"10.1001\/jama.2023.15389"},{"issue":"6","key":"2025012021301346000_2025.01.13.632427v1.2","first-page":"969","article-title":"Outcome of Ulcerative Colitis 20 Years after Diagnosis in a Prospective Population-based Inception Cohort from South-Eastern Norway, the IBSEN Study","volume":"15","year":"2020","journal-title":"Journal of Crohn\u2019s and colitis"},{"key":"2025012021301346000_2025.01.13.632427v1.3","doi-asserted-by":"publisher","DOI":"10.1038\/nri1132"},{"key":"2025012021301346000_2025.01.13.632427v1.4","doi-asserted-by":"publisher","DOI":"10.1016\/S0923-2494(98)80151-X"},{"issue":"4","key":"2025012021301346000_2025.01.13.632427v1.5","first-page":"38","article-title":"T cell receptor sequencing in autoimmunity","volume":"2","year":"2020","journal-title":"JoLS, Journal of Life Sciences"},{"issue":"5","key":"2025012021301346000_2025.01.13.632427v1.6","first-page":"1320","article-title":"Circulating and Tissue-Resident CD4+ T Cells With Reactivity to Intestinal Microbiota Are Abundant in Healthy Individuals and Function Is Altered During Inflammation","volume":"153","year":"2017","journal-title":"Gastroenterology (New York, N.Y. 1943)"},{"key":"2025012021301346000_2025.01.13.632427v1.7","doi-asserted-by":"crossref","first-page":"100373","DOI":"10.1016\/j.iotech.2023.100373","article-title":"TCR sequencing: applications in immuno-oncology research","volume":"17","year":"2023","journal-title":"Immuno-oncology technology"},{"key":"2025012021301346000_2025.01.13.632427v1.8","doi-asserted-by":"publisher","DOI":"10.1002\/art.33488"},{"key":"2025012021301346000_2025.01.13.632427v1.9","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1502967112"},{"key":"2025012021301346000_2025.01.13.632427v1.10","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1101526"},{"key":"2025012021301346000_2025.01.13.632427v1.11","doi-asserted-by":"publisher","DOI":"10.1038\/s41591-023-02613-z"},{"key":"2025012021301346000_2025.01.13.632427v1.12","doi-asserted-by":"publisher","DOI":"10.1080\/00365520802600961"},{"key":"2025012021301346000_2025.01.13.632427v1.13","doi-asserted-by":"publisher","DOI":"10.1172\/JCI118921"},{"key":"2025012021301346000_2025.01.13.632427v1.14","doi-asserted-by":"publisher","DOI":"10.1016\/0198-8859(96)00079-1"},{"key":"2025012021301346000_2025.01.13.632427v1.15","doi-asserted-by":"publisher","DOI":"10.1093\/ecco-jcc\/jjx012"},{"key":"2025012021301346000_2025.01.13.632427v1.16","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.156.8.3024"},{"key":"2025012021301346000_2025.01.13.632427v1.17","doi-asserted-by":"publisher","DOI":"10.1111\/j.1600-065X.2006.00480.x"},{"key":"2025012021301346000_2025.01.13.632427v1.18","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2022.932373"},{"key":"2025012021301346000_2025.01.13.632427v1.19","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.157.7.3183"},{"issue":"4","key":"2025012021301346000_2025.01.13.632427v1.20","first-page":"301","article-title":"Evidence for an Altered T-Cell Receptor Repertoire in Crohn\u2019s Disease","volume":"17","year":"1994","journal-title":"Autoimmunity (Chur, Switzerland)"},{"key":"2025012021301346000_2025.01.13.632427v1.21","doi-asserted-by":"publisher","DOI":"10.1172\/JCI114634"},{"key":"2025012021301346000_2025.01.13.632427v1.22","doi-asserted-by":"publisher","DOI":"10.1023\/A:1011007922707"},{"key":"2025012021301346000_2025.01.13.632427v1.23","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-023-06431-8"},{"key":"2025012021301346000_2025.01.13.632427v1.24","unstructured":"Elisa Rosati . The T-cell receptor repertoire in inflammatory bowel diseasesKiel University; 2020."},{"issue":"1","key":"2025012021301346000_2025.01.13.632427v1.25","first-page":"119","article-title":"T Cell Repertoire Homogeneity and Blood-Gut Overlap in Patients With Inflammatory Bowel Disease","volume":"17","year":"2024","journal-title":"CMGH"},{"key":"2025012021301346000_2025.01.13.632427v1.26","doi-asserted-by":"publisher","DOI":"10.1038\/mi.2013.51"},{"key":"2025012021301346000_2025.01.13.632427v1.27","doi-asserted-by":"publisher","DOI":"10.1097\/MIB.0000000000000752"},{"key":"2025012021301346000_2025.01.13.632427v1.28","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx286"},{"key":"2025012021301346000_2025.01.13.632427v1.29","doi-asserted-by":"crossref","unstructured":"Rosati E , Pogorelyy MV , Dowds CM , et al. Identification of Disease-associated Traits and Clonotypes in the T Cell Receptor Repertoire of Monozygotic Twins Affected by Inflammatory Bowel Diseases. Journal of Crohn\u2019s and colitis 2020 May 1;.","DOI":"10.1093\/ecco-jcc\/jjz210"},{"key":"2025012021301346000_2025.01.13.632427v1.30","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.adk3060"},{"key":"2025012021301346000_2025.01.13.632427v1.31","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-50932-4"},{"issue":"7","key":"2025012021301346000_2025.01.13.632427v1.32","doi-asserted-by":"crossref","first-page":"e002642","DOI":"10.1136\/jitc-2021-002642","article-title":"Evaluating T-cell cross-reactivity between tumors and immune-related adverse events with TCR sequencing: pitfalls in interpretations of functional relevance","volume":"9","year":"2021","journal-title":"Journal for immunotherapy of cancer"},{"key":"2025012021301346000_2025.01.13.632427v1.33","unstructured":"immunarch: An R Package for Painless Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires.;."}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2025.01.13.632427","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,1,15]],"date-time":"2026-01-15T07:52:33Z","timestamp":1768463553000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2025.01.13.632427"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,1,17]]},"references-count":33,"URL":"https:\/\/doi.org\/10.1101\/2025.01.13.632427","relation":{},"subject":[],"published":{"date-parts":[[2025,1,17]]},"subtype":"preprint"}}