single-cell RNA sequencing of healthy control, ulcerative colitis, and primary sclerosing cholangitis concomitant with ulcerative colitis colonic mucosa

Dataset overview

Participants 22

Samples None

Reuse readiness 6.3/10 evidence-backed score

Primary sclerosing cholangitis displays distinct colonic mucosa topography yet a shared mast cell state with ulcerative colitis.

Tearle JL, Sviriaeva E, Zhang F, Jackson KJ, Kaye J, Tavakoli P, Koentgen S, Warren J, et al. · Nature communications · 2026

Abstract

Primary sclerosing cholangitis (PSC) is a chronic, progressing cholestatic disease that often co-occurs with inflammatory bowel disease (PSC-IBD). PSC-IBD affecting the colon (PSC-ulcerative colitis or PSC-UC) resembles clinical UC, but is characterised by less severe disease flares, right-colon predominance, and a greater lifetime risk of colorectal cancer than UC alone. To elucidate differences in the underlying biology between PSC-UC and UC, here we combine single-cell mRNA and antigen receptor sequencing, 16S ribosomal RNA gene analysis and spatial transcriptomics on biopsies from four colon regions of patients with PSC-UC and UC during endoscopic remission or at the time of relapse. We show that the PSC-UC colon, compared to healthy control (HC) or UC colon, harbours distinct and region-specific mucosal-adherent microbial communities and an enrichment of activated CD8 T and γδ T cells at the right colon, even in the absence of histological inflammation. By contrast, a TMEM176B<sup>+</sup> mast cell population that may be pro-tumourigenic is enriched in the colon during disease relapse in both PSC-UC and UC colon. These results highlight that the PSC-UC and UC colonic mucosa are fundamentally different while sharing similar cell programmes during active disease. Our data thus provide insights to guide tailored clinical management and precision therapies.

doi:10.1038/s41467-026-75231-1 ↗ PMID 42414303 ↗

Study facts

Organism: Homo sapiens
Platform: 10x Genomics
Age group: adult
Disease groups: —
Anatomical sites: ascending colon, descending colon, rectum, transverse colon

Data availability

Processed matrix

File types H5AD

5bd4d642-ff0e-4104-ab5b-e6238ceda7cf.h5ad ↗

Strengths & limitations for reuse

Strengths

Processed matrices are advertised
Cell metadata are advertised
Participant counts are documented

Limitations

Not documented: raw counts are advertised

Extraction evidence & provenance

Each extracted field is shown with the source excerpt and location used to resolve it.

Assay

Field	Value	Evidence
`assay.assay_type`	10x 5' v2 from source	assay=10x 5' v2 Section `structured repository metadata`, offset —
`assay.library_chemistry`	10x 5' v2 and 10x 5' v3	"assay": [{"label": "10x 5' v2", "ontology_term_id": "EFO:0009900"}, {"label": "10x 5' v3", "ontology_term_id": "EFO:0022605"}] Section `dataset-authority`, offset —
`assay.platform`	10x Genomics inferred	"assay": [{"label": "10x 5' v2" Section `dataset-authority`, offset —
`assay.sequencing_type`	scrna_seq from source	sequencing_type=scrna_seq Section `structured repository metadata`, offset —

Cohort

Field Value Evidence

Field	Value	Evidence
`cohort.age_group`	adult inferred	"development_stage": [{"label": "21-year-old stage" Section `dataset-authority`, offset —
`cohort.disease_activity_metadata_available`	True	patients with PSC-UC and UC during endoscopic remission or at the time of relapse Section `abstract`, offset —
`cohort.total_participants`	22 inferred	"donor_id": ["PSC-1", "PSC-2", "PSC-3", "UC-1", "UC-2", "UC-3", "UC-4", "PSC-4", "UC-7", "PSC-5", "UC-8", "PSC-6", "UC-10", "HC-1", "PSC-7", "UC-9", "411c", "414c", "417c", "432c", "440c", "HC-2"] Section `dataset-authority`, offset —

cohort.age_group

adult inferred

"development_stage": [{"label": "21-year-old stage"

Section dataset-authority, offset —

cohort.disease_activity_metadata_available

True

patients with PSC-UC and UC during endoscopic remission or at the time of relapse

Section abstract, offset —

cohort.total_participants

22 inferred

"donor_id": ["PSC-1", "PSC-2", "PSC-3", "UC-1", "UC-2", "UC-3", "UC-4", "PSC-4", "UC-7", "PSC-5", "UC-8", "PSC-6", "UC-10", "HC-1", "PSC-7", "UC-9", "411c", "414c", "417c", "432c", "440c", "HC-2"]