Evidence map›Paper›PMID 42817982›Full record

ArticlebioRxiv : the preprint server for biology2026

Single-cell immune repertoire atlas maps coordinated circulating adaptive immune states in inflammatory bowel disease.

John Gubatan, Jiayu Ye, Christin Lund-Andersen, Jorge Canas, Yuxi Zhou, Theresa Boye, Jacqueline Hoang, Raoul S Sojwal, Touran Fardeen, Tracy Tran and 10 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

20 authors.

John GubatanDivision of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA.ORCID 0000-0001-6037-2883
Jiayu YeDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.
Christin Lund-AndersenScientific Computing and Machine Learning Group, Department of Informatics, University of Oslo, Oslo, Norway.
Jorge CanasDivision of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA.
Yuxi ZhouDivision of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA.
Theresa BoyeDepartment of Gastroenterology, Herlev Hospital, University of Copenhagen, Denmark.
Jacqueline HoangDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.
Raoul S SojwalDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.
Touran FardeenDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.
Tracy TranDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Stanford University School of Medicine, Stanford, CA, USA.
Peacha SokziniDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.
Ally Hamin KohDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.
Marielle GibsonDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.
Yuting HuangDivision of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA.
Kathryn PetersonDivision of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL, USA.
Sidhartha R SinhaDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.
Stephan RogallaDivision of Gastroenterology and Hepatology, Stanford University School of Medicine, Stanford, CA, USA.
Ole Haagen NielsenDepartment of Gastroenterology, Herlev Hospital, University of Copenhagen, Denmark.
Michael J RosenDivision of Pediatric Gastroenterology, Hepatology, and Nutrition, Stanford University School of Medicine, Stanford, CA, USA.
Geir Kjetil SandveScientific Computing and Machine Learning Group, Department of Informatics, University of Oslo, Oslo, Norway.

Funding

NIDDK NIH HHS L30 DK126220
6 · The paper itself

Abstract

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.

Indexed as

B cell receptorcirculating adaptive immunityclass switchingclonotypeCrohn’s diseaseimmune organizationimmune repertoireInflammatory bowel diseasemachine learningresourcesingle-cell atlassomatic hypermutationT cell receptorulcerative colitis

Identifiers

PMID42817982
PMCPMC13622131

What OpenQuestion holds

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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.