Evidence map›Paper›PMID 39438660›Full record

ArticleNature immunology2024

A longitudinal single-cell atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease.

Tom Thomas, Matthias Friedrich, Charlotte Rich-Griffin, Mathilde Pohin, Devika Agarwal, Julia Pakpoor, Carl Lee, Ruchi Tandon, Aniko Rendek, Dominik Aschenbrenner and 39 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature immunology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
68citing papers in PubMed, 1 pooled it
–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

68 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  20. Local and circulating cytotoxic CD4medRxiv : the preprint server for health sciences · 2026
    Article

8 more citing papers are in PubMed but not listed here.

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

49 authors.

Tom ThomasKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Matthias Friedrich *Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Charlotte Rich-Griffin *Centre for Human Genetics, University of Oxford, Oxford, UK.
Mathilde Pohin *Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Devika Agarwal *Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Julia PakpoorKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Carl LeeKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Ruchi TandonUniversity College London Hospitals NHS Foundation Trust, London, UK.
Aniko RendekOxford University Hospitals NHS Foundation Trust, Oxford, UK.
Dominik AschenbrennerTranslational Gastroenterology & Liver Unit, John Radcliffe Hospital, Headington, Oxford, UK.
Ashwin JainarayananKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Alexandru VodaKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Jacqueline H Y SiuKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Raphael Sanches-PeresKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Eloise NeeKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Dharshan SathananthanUniversity of Adelaide, Adelaide, Australia.
Dylan KotliarBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Peter ToddCentre for Human Genetics, University of Oxford, Oxford, UK.
Maria KiourlappouCentre for Human Genetics, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0003-1792-9206
Lisa GartnerTranslational Gastroenterology & Liver Unit, John Radcliffe Hospital, Headington, Oxford, UK.ORCID http://orcid.org/0000-0002-3273-651X
Nicholas IlottKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-8432-8622
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
Jason TurnerRheumatology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK.ORCID http://orcid.org/0000-0002-5423-5302
Saba NayarRheumatology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK.ORCID http://orcid.org/0000-0002-4350-110X
Jonas MackerodtKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
Fan ZhangBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Anna JonssonBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Michael BrennerBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6202-8445
Soumya RaychaudhuriBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-1901-8265
Ruth KulickeCelsius Therapeutics, Cambridge, MA, USA.
Danielle RamsdellCelsius Therapeutics, Cambridge, MA, USA.
Nicolas StranskyCelsius Therapeutics, Cambridge, MA, USA.
Ray PagliariniCelsius Therapeutics, Cambridge, MA, USA.
Piotr BieleckiCelsius Therapeutics, Cambridge, MA, USA.
Noah SpiesCelsius Therapeutics, Cambridge, MA, USA.
Brian MarsdenCentre for Human Genetics, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-1937-4091
Stephen TaylorCentre for Human Genetics, University of Oxford, Oxford, UK.
Allon WagnerDepartment of Electrical Engineering and Computer Science, University of California, Berkeley, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-5095-6009
Paul KlenermanTranslational Gastroenterology & Liver Unit, John Radcliffe Hospital, Headington, Oxford, UK.
Alissa WalshTranslational Gastroenterology & Liver Unit, John Radcliffe Hospital, Headington, Oxford, UK.
Mark ColesKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0001-8079-9358
Luke Jostins-DeanKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0002-2475-3969
Fiona M PowrieKennedy Institute of Rheumatology, University of Oxford, Oxford, UK.ORCID http://orcid.org/0000-0003-3312-5929
Andrew FilerRheumatology Research Group, Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK.ORCID http://orcid.org/0000-0001-8164-6249
Simon TravisKennedy Institute of Rheumatology, University of Oxford, Oxford, UK. simon.travis@kennedy.ox.ac.uk.ORCID http://orcid.org/0000-0002-2690-4361
Holm H UhligTranslational Gastroenterology & Liver Unit, John Radcliffe Hospital, Headington, Oxford, UK. holm.uhlig@ndm.ox.ac.uk.ORCID http://orcid.org/0000-0002-6111-7355
Calliope A DendrouKennedy Institute of Rheumatology, University of Oxford, Oxford, UK. calliope.dendrou@kennedy.ox.ac.uk.ORCID http://orcid.org/0000-0003-1179-4021
Christopher D BuckleyKennedy Institute of Rheumatology, University of Oxford, Oxford, UK. christopher.buckley@kennedy.ox.ac.uk.ORCID http://orcid.org/0000-0001-6924-6402

Funding

Wellcome Trust
6 · The paper itself

Abstract

Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires a cellular understanding of treatment response. We describe a therapeutic atlas for Crohn's disease (CD) and ulcerative colitis (UC) following adalimumab, an anti-tumour necrosis factor (anti-TNF) treatment. We generated ~1 million single-cell transcriptomes, organised into 109 cell states, from 216 gut biopsies (41 subjects), revealing disease-specific differences. A systems biology-spatial analysis identified granuloma signatures in CD and interferon (IFN)-response signatures localising to T cell aggregates and epithelial damage in CD and UC. Pretreatment differences in epithelial and myeloid compartments were associated with remission outcomes in both diseases. Longitudinal comparisons demonstrated disease progression in nonremission: myeloid and T cell perturbations in CD and increased multi-cellular IFN signalling in UC. IFN signalling was also observed in rheumatoid arthritis (RA) synovium with a lymphoid pathotype. Our therapeutic atlas represents the largest cellular census of perturbation with the most common biologic treatment, anti-TNF, across multiple inflammatory diseases.

Indexed as

AdalimumabSingle-Cell AnalysisAdultArthritis, RheumatoidColitis, UlcerativeCrohn DiseaseFemaleHumansInflammatory Bowel DiseasesInterferonsLongitudinal StudiesMaleSignal TransductionTranscriptomeTumor Necrosis Factor-alphaAdalimumabInterferonsTumor Necrosis Factor-alpha

Identifiers

PMID39438660
PMCPMC11519010

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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.