{
  "abstract": "SUMMARY 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’s 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. GRAPHICAL ABSTRACT Highlights Paired single-cell receptors map circulating adaptive immune states across IBD TCR expansion and paired-chain convergence identify inflammatory programs BCR lineage maturation links plasma programs to mutation and class switching Repertoire features benchmark diagnosis and clinical-state classification In Brief Gubatan et al. 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–B covariation to an inferred ligand– receptor interactome. Machine learning models with repertoire features classify diagnosis, inflammatory status, and contemporaneous six-month treatment-response status.",
  "abstract_shown": true,
  "affiliations": [
    "Mayo Clinic"
  ],
  "article_type": "New results",
  "arxiv": null,
  "author_total": 20,
  "authors": [
    {
      "affs": [
        0
      ],
      "name": "J. Gubatan"
    },
    {
      "name": "J. Ye"
    },
    {
      "name": "C. Lund-Andersen"
    },
    {
      "name": "J. Canas"
    },
    {
      "name": "Y. Zhou"
    },
    {
      "name": "T. Boye"
    },
    {
      "name": "J. Hoang"
    },
    {
      "name": "R. Sojwal"
    },
    {
      "name": "T. Fardeen"
    },
    {
      "name": "T. Tran"
    },
    {
      "name": "P. Sokzini"
    },
    {
      "name": "A. H. Koh"
    },
    {
      "name": "M. Gibson"
    },
    {
      "name": "Y. Huang"
    },
    {
      "name": "K. Peterson"
    },
    {
      "name": "S. Sinha"
    },
    {
      "name": "S. Rogalla"
    },
    {
      "name": "O. H. Nielsen"
    },
    {
      "name": "M. J. Rosen"
    },
    {
      "name": "G. K. Sandve"
    }
  ],
  "bibtex": "https://research.draconitic.com/paper/31yh8n13cx3vc.bib",
  "cited_by": 0,
  "doi": "10.64898/2026.09.20.753043",
  "fulltext_url": "https://www.biorxiv.org/content/10.64898/2026.09.20.753043v1.full",
  "id": "31yh8n13cx3vc",
  "issns": [],
  "landing_url": "https://www.biorxiv.org/content/10.64898/2026.09.20.753043v1",
  "language": null,
  "licence": "PDM-1.0",
  "licence_label": "Public domain",
  "licence_source": "journal",
  "licence_url": "https://creativecommons.org/publicdomain/mark/1.0/",
  "metadata_licence": null,
  "native_subjects": [
    [
      "biorxiv",
      "immunology"
    ],
    [
      "openalex",
      "1311|Inflammatory Bowel Disease"
    ]
  ],
  "openalex": "W7214095792",
  "pdf_url": "https://www.biorxiv.org/content/10.64898/2026.09.20.753043v1.full.pdf",
  "pmcid": null,
  "pmid": null,
  "published": "2026-09-20",
  "publisher": null,
  "ris": "https://research.draconitic.com/paper/31yh8n13cx3vc.ris",
  "sources": [
    {
      "first_seen": "2026-10-30T12:24:08Z",
      "native_id": "10.64898/2026.09.20.753043",
      "source": "biorxiv",
      "url": "https://www.biorxiv.org/content/10.64898/2026.09.20.753043v1"
    }
  ],
  "subjects": [
    {
      "field": "biology",
      "origin": "biorxiv:immunology",
      "subfield": "immunology"
    }
  ],
  "title": "Single-cell immune repertoire atlas maps coordinated circulating adaptive immune states in inflammatory bowel disease",
  "title_text": "Single-cell immune repertoire atlas maps coordinated circulating adaptive immune states in inflammatory bowel disease",
  "type": "preprint",
  "updated_at": "2026-10-30T12:24:08Z",
  "url": "https://research.draconitic.com/paper/31yh8n13cx3vc",
  "venue": "bioRxiv",
  "versions": []
}