Evidence map›Paper›PMID 40562913›Full record

ArticleNature genetics2025

Single-cell and spatial transcriptomics of stricturing Crohn's disease highlights a fibrosis-associated network.

Lingjia Kong, Sathish Subramanian, Åsa Segerstolpe, Vy Tran, Angela R Shih, Grace T Carter, Hiroko Kunitake, Shaina W Twardus, Jasmine Li, Shivam Gandhi and 14 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.

0numbers the graph read from it
0cells of the map it votes in
33citing 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

33 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Review
  6. Article
  7. Article
  8. Review
  9. Article
  10. Local and circulating cytotoxic CD4medRxiv : the preprint server for health sciences · 2026
    Article
  11. Review
  12. Article
  13. Article
  14. Hidden immune memory niches in inflammatory skin diseases.bioRxiv : the preprint server for biology · 2026
    Article
  15. IL1βJournal of translational medicine · 2026
    Article
  16. Fibroblast diversity within human gut-associated lymphoid tissues.The Journal of experimental medicine · 2026
    Article
  17. Article
  18. Article
  19. Review
  20. Article
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

24 authors.

Lingjia KongBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Sathish SubramanianBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Åsa SegerstolpeBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Vy TranCenter for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Angela R ShihDepartment of Pathology and Laboratory Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.ORCID http://orcid.org/0000-0002-8945-5997
Grace T CarterBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-5514-4237
Hiroko KunitakeDepartment of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Shaina W TwardusCenter for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Jasmine LiBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Shivam GandhiCenter for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Marco E KaperCenter for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Christy CauleyDepartment of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Eric J ChenBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Caroline B M PorterBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Toni M DeloreyBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-6614-3803
Liliana BordeianouDepartment of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Rocco RicciardiDepartment of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Ashwin N AnanthakrishnanDivision of Gastroenterology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Helena LauBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Daniel B GrahamBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0002-8403-8115
Richard HodinDepartment of Surgery, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
Jacques DeguineBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-9218-3040
Christopher S SmillieBroad Institute of MIT and Harvard, Cambridge, MA, USA. csmillie@mgh.harvard.edu.ORCID http://orcid.org/0000-0002-7606-3433
Ramnik J XavierBroad Institute of MIT and Harvard, Cambridge, MA, USA. xavier@molbio.mgh.harvard.edu.ORCID http://orcid.org/0000-0002-5630-5167

Funding

Pilot & Feasibility ProgramP30DK043351 · NIDDK · MASSACHUSETTS GENERAL HOSPITAL · PI RAYMOND T CHUNG · 1991 to 2026
$35.3M
Spatial and temporal resolution to dissect cellular circuits controlling intestinal physiology, immunity, and inflammatory pathologiesRC2DK135492 · NIDDK · BROAD INSTITUTE, INC. · PI Caroline Uhler, Ramnik J Xavier · 2023 to 2026
$7.9M
NIDDK NIH HHS P30 DK043351NIDDK NIH HHS RC2 DK135492
6 · The paper itself

Abstract

Fibrosis is a major complication of Crohn's disease (CD) marked by excess deposition of extracellular matrix, leading to stricturing and functional impairment. As mechanistic characterization and therapeutic options are lacking, we paired single-cell and spatial transcriptomics in 61 samples from 21 patients with CD and 10 patients without inflammatory bowel disease (IBD). Intestinal strictures were characterized by increased immune cells, including IgG

Indexed as

Crohn DiseaseTranscriptomeAdultCD4-Positive T-LymphocytesFemaleFibroblastsFibrosisGene Expression ProfilingHumansMaleMiddle AgedSingle-Cell Analysis

Identifiers

PMID40562913
PMCPMC12709777

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.