Foundry120 atlas

← IBD single-cell transcriptomics

Gene expression at single cell level of stromal cells from the distal colon of normal sites of colorectal cancer and inflamed sites of ulcerative colitis.

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Dataset overview

Participants None
Samples 13
Reuse readiness 4.1/10 evidence-backed score

OTUD3 prevents ulcerative colitis by inhibiting microbiota-mediated STING activation.

Li B, Sakaguchi T, Tani H, Ito T, Murakami M, Okumura R, Kobayashi M, Okuzaki D, et al. · Science immunology · 2025

Abstract

Ulcerative colitis (UC) develops through a complicated interaction between the host and microbiota. Intestinal fibroblasts are believed to play crucial roles in the pathogenesis of UC, but the influence of the host-microbiota interaction on the pathophysiology of intestinal fibroblasts remains poorly understood. Here, we demonstrate that OTU deubiquitinase 3 (OTUD3) suppresses pathologic activation of fibroblasts exposed to microbial cyclic GMP-AMP (3'3'-cGAMP) in the colon by deubiquitinating stimulator of interferon genes (STING). Mice harboring a UC risk missense variant in the <i>Otud3</i> gene showed pathological features of UC in the colon after transplantation of a fecal microbiota with the potential to produce excessive cGAMP from patients with UC. Collectively, these results highlight a mechanism of the interaction between OTUD3 in host fibroblasts and STING-activating microbiota in UC development.

doi:10.1126/sciimmunol.adm6843 ↗ PMID 40680146 ↗

Study facts

Organism
Homo sapiens
Platform
DNBSEQ-G400
Age group
—
Disease groups
—
Anatomical sites
distal colon

Data availability

  • Processed matrix

File types TAR

Strengths & limitations for reuse

Strengths

  • Processed matrices are advertised

Limitations

  • Not documented: raw counts are advertised
  • Not documented: cell metadata are advertised
  • Not documented: participant counts are documented
Extraction evidence & provenance

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

Assay

FieldValueEvidence
assay.platform DNBSEQ-G400
"instrument_model": "DNBSEQ-G400"

Section samples, offset —
assay.reference_genome hg38
Assembly: hg38

Section samples, offset —
assay.sequencing_type scrna_seq
We used single cell RNA sequencing (scRNA-seq) to analyze the diversity of stromal cells in the lamina propria of colon.

Section series, offset —

Data_Assets

FieldValueEvidence
data_assets.open_access True
Public on May 13 2025

Section series, offset —
data_assets.processed_matrix True
Supplementary files format and content: Filtered matrix and cell barcode files in tar.gz

Section samples, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['distal colon']
Gene expression at single cell level of stromal cells from the distal colon of normal sites of colorectal cancer and inflamed sites of ulcerative colitis.

Section —, offset —
specimens.inflamed_status_available True
Live CD90+CD45-CD31-EpCAM- stromal cells from human lamina propria mononuclear cells (LPMCs) of colorectal cancer and ulcerative colitis (UC) were isolated by Fluorescence activated cell sorting (FACS) and analysed using scRNA-seq.

Section series, offset —
specimens.number_of_samples 13
"n_samples": 13

Section —, offset —