Evidence map›Paper›PMID 42587037›Full record

ArticleNature immunology2026

Epigenetic modulation of stromal cell states underpins pathological tissue niches in Crohn's disease.

Simon Koplev, Osheen Sharma, Simon Woelfel, Ni Huang, Mathilde Pohin, Adrian Feile, Maria Warschinke, Mikel Rezola Artero, Sharujan Suthakaran, Ioannis Sarropoulos and 35 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature immunology, 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

45 authors.

Simon KoplevCambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-8586-5614
Osheen SharmaTranslational Gastroenterology and Liver Unit, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-9051-3664
Simon WoelfelTranslational Gastroenterology and Liver Unit, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0003-2528-0582
Ni HuangWellcome Sanger Institute, Cambridge, UK.
Mathilde PohinImmunoConcept University of Bordeaux, Immunology and Immunogenetic Unit University Hospital of Bordeaux, Bordeaux, France.
Adrian FeileInstitute of Biochemistry II, Jena University Hospital, Jena, Germany.ORCID http://orcid.org/0000-0003-0216-1409
Maria WarschinkeInstitute of Biochemistry II, Jena University Hospital, Jena, Germany.
Mikel Rezola ArteroKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Sharujan SuthakaranTranslational Gastroenterology and Liver Unit, University of Oxford, Oxford, UK.ORCID http://orcid.org/0009-0008-7000-0811
Ioannis SarropoulosCambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-2242-0562
J Patrick PettCambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-5249-444X
Julia NymanDepartment of Gene Technology, KTH Royal Institute of Technology, Science for Life Laboratory, Stockholm, Sweden.ORCID http://orcid.org/0009-0000-3285-6602
Tom ThomasKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Duy PhamWellcome Sanger Institute, Cambridge, UK.
Bin LiBig Data Institute/Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
Moustafa AttarKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0003-4116-1276
Julia PakpoorKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Kate Milosevic-HuttonTranslational Gastroenterology and Liver Unit, University of Oxford, Oxford, UK.
Alistair EastonDepartment of Oncology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-8148-5406
Matt ButlerUCB Pharma, Slough, UK.
James DunfordBotnar Institute, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-9932-4042
Martin PhilpottBotnar Institute, University of Oxford, Oxford, UK.
Mark ColesKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-8079-9358
Christopher D BuckleyKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-6924-6402
Calliope DendrouKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0003-1179-4021
Khalid ShamiyahTranslational Gastroenterology and Liver Unit, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-3392-2621
Lorenz KretschmerCambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.ORCID http://orcid.org/0000-0003-0987-8429
Lisa DratvaCambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-2873-6787
Fadi IssaNuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-8279-7732
Joanna HesterNuffield Department of Surgical Sciences, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-7466-3849
Jens RittscherBig Data Institute/Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK.
Alissa WalshTranslational Gastroenterology and Liver Unit, University of Oxford, Oxford, UK.
Simon P TravisKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-2690-4361
Fränze ProgatzkyKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Lukas W UngerDepartment of Colorectal Surgery, Oxford University Hospitals, Oxford, UK.
Mark BignellDepartment of Colorectal Surgery, Oxford University Hospitals, Oxford, UK.
Katherine BakerDepartment of Colorectal Surgery, Oxford University Hospitals, Oxford, UK.
Bruce GeorgeDepartment of Colorectal Surgery, Oxford University Hospitals, Oxford, UK.
Hussein Al-MossawiNuffield Department of Orthopedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
Paul KlenermanTranslational Gastroenterology and Liver Unit, University of Oxford, Oxford, UK.
Alexander S MosigInstitute of Biochemistry II, Jena University Hospital, Jena, Germany.ORCID http://orcid.org/0000-0002-5687-2444
Udo OppermannBotnar Institute, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-9984-5342
Sarah A Teichmann *Cambridge Stem Cell Institute, Jeffrey Cheah Biomedical Centre, Cambridge Biomedical Campus, Cambridge, UK.ORCID http://orcid.org/0000-0002-6294-6366
Fiona M Powrie *Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0003-3312-5929
Matthias Friedrich *Translational Gastroenterology and Liver Unit, University of Oxford, Oxford, UK. matthias.friedrich@ndm.ox.ac.uk.ORCID http://orcid.org/0000-0002-7551-4853

Funding

Wellcome Trust
6 · The paper itself

Abstract

Stromal cell states are altered in active Crohn's disease (CD), but their origin and phenotypic stability are unknown. Using single-cell spatial transcriptomics, RNA sequencing and ATAC sequencing of ~2,500,000 cells, we map 18 distinct stromal cell states within their cellular and cytokine signaling environments in human full-thickness CD bowel. Inflammatory fibroblasts (IFs) reside in immune cell-rich mucosal ulcers and are induced through combinatorial cytokine exposure suppressing submucosal universal fibroblast programs. The IF state is stabilized through transcription factor (TF) activity of GLI3, TWIST1, ETV4, PRDM1 and RELB, and does not spontaneously revert; however, histone deacetylase inhibition destabilizes the IF state, preventing IF secretome-induced epithelial transmigration and activation of neutrophils. The IF open chromatin configuration is distinct from that of fibrotic contractile stroma, which populate adjoining immune-depleted submucosal fibrotic niches. These findings show that microenvironments in pathological tissue niches shape open chromatin configuration of stromal states that are amenable to modulation by epigenetic modifiers.

Indexed as

Crohn DiseaseEpigenesis, GeneticFibroblastsIntestinal MucosaStromal CellsAnimalsCellular MicroenvironmentChromatinCytokinesHumansTranscription FactorsChromatinCytokinesTranscription Factors

Identifiers

PMID42587037
PMCPMC13506348

What OpenQuestion holds

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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.