{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,9,26]],"date-time":"2026-09-26T16:58:39Z","timestamp":1790441919556,"version":"4.1.0"},"posted":{"date-parts":[[2026,9,23]]},"group-title":"Immunology","reference-count":64,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T00:00:00Z","timestamp":1790121600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"award":["grant no. 2021091"],"award-info":[{"award-number":["grant no. 2021091"]}],"id":[{"id":"https:\/\/ror.org\/04n65rp89","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/00knt4f32","id-type":"ROR","asserted-by":"publisher"}]},{"award":["NIDDK LRP Award (2L30 DK126220)"],"award-info":[{"award-number":["NIDDK LRP Award (2L30 DK126220)"]}],"id":[{"id":"https:\/\/ror.org\/01cwqze88","id-type":"ROR","asserted-by":"publisher"}]},{"id":[{"id":"https:\/\/ror.org\/00yt0ea73","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Stanford Translational Research and Applied Medicine (TRAM) Scholar Award"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,9,23]]},"abstract":"<jats:title>SUMMARY<\/jats:title>\n                <jats:p>Single-cell studies have defined immune states in inflammatory bowel disease (IBD), but how adaptive receptor histories organize circulating immunity remains unclear. We generated a single-cell transcriptomic atlas of peripheral blood from 249 participants with Crohn\u2019s disease, ulcerative colitis, or non-IBD control status, including 182 with productive TCR and BCR recovery. Expanded TCR clonotypes marked inflammatory-memory and cytotoxic states, while distinct but similar paired TCRs shared inflammatory programs across participants. BCR lineage maturation linked IgA-associated mucosal and plasma B cell programs to somatic mutation and class switching, distinguishing maturation-associated biology from clonal expansion. Helper, regulatory, and cytotoxic T-cell programs covaried with B-cell states, and inferred interactions nominated reciprocal antigen-presentation and helper pathways. Repertoire-based machine learning distinguished diagnosis, inflammation, and contemporaneous six-month treatment-response status. Together, this atlas connects receptor architecture to coordinated systemic immune remodeling, establishes a foundation for repertoire-informed patient stratification, and prioritizes candidate mechanisms of IBD pathogenesis.<\/jats:p>\n                <jats:sec>\n                  <jats:title>GRAPHICAL ABSTRACT<\/jats:title>\n                  <jats:fig id=\"ufig1\" position=\"float\" fig-type=\"figure\" orientation=\"portrait\">\n                    <jats:graphic xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"753043v1_ufig1\" position=\"float\" orientation=\"portrait\"\/>\n                  <\/jats:fig>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>Highlights<\/jats:title>\n                  <jats:list list-type=\"bullet\">\n                    <jats:list-item>\n                      <jats:p>Paired single-cell receptors map circulating adaptive immune states across IBD<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>TCR expansion and paired-chain convergence identify inflammatory programs<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>BCR lineage maturation links plasma programs to mutation and class switching<\/jats:p>\n                    <\/jats:list-item>\n                    <jats:list-item>\n                      <jats:p>Repertoire features benchmark diagnosis and clinical-state classification<\/jats:p>\n                    <\/jats:list-item>\n                  <\/jats:list>\n                <\/jats:sec>\n                <jats:sec>\n                  <jats:title>In Brief<\/jats:title>\n                  <jats:p>\n                    Gubatan\n                    <jats:italic>et al.<\/jats:italic>\n                    present a peripheral blood single-cell transcriptome and paired immune-receptor atlas across IBD and controls. Clone-aware analyses connect TCR expansion and sequence similarity to inflammatory programs, distinguish B-cell phenotype from lineage maturation, and link participant-level T\u2013B covariation to an inferred ligand\u2013 receptor interactome. Machine learning models with repertoire features classify diagnosis, inflammatory status, and contemporaneous six-month treatment-response status.\n                  <\/jats:p>\n                <\/jats:sec>","DOI":"10.64898\/2026.09.20.753043","type":"posted-content","created":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T18:35:14Z","timestamp":1790188514000},"source":"Crossref","is-referenced-by-count":0,"title":["Single-cell immune repertoire atlas maps coordinated circulating adaptive immune states in inflammatory bowel disease"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6037-2883","authenticated-orcid":false,"given":"John","family":"Gubatan","sequence":"first","affiliation":[{"name":"Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA"},{"name":"Division of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, 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