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Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Visium]

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Dataset overview

Participants None
Samples 2
Reuse readiness 5.7/10 evidence-backed score

Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn's disease strictures.

Bauer-Rowe KE, Pham B, Griffin M, Liang NE, Kim A, Lu JM, Januszyk M, Guo JL, et al. · Cell · 2025

Abstract

A significant complication of Crohn's disease (CD) is intestinal fibrosis, which narrows the bowel lumen to form a stricture. Creeping fat (CF) is the wrapping of mesenteric adipose tissue around diseased bowel, of which the role in CD stricture progression is unclear. By constructing a human single-cell CD fibroblast atlas, we identified CF-derived, CTHRC1+ fibroblasts enriched for Yes-associated protein (YAP)/transcriptional co-activator with PDZ-binding motif (TAZ) signatures and localized to a fibrotic CF-bowel wall interface within the stricture. We further showed that analogous Cthrc1+ mouse fibroblasts derive from mesenteric adipose tissue stromal cells, infiltrate fibrotic bowel, and deposit extracellular matrix in a YAP/TAZ-dependent manner in a mouse model of intestinal fibrosis. Our findings identify CF as a key source of pro-fibrotic fibroblasts and raise the possibility of improving future clinical management of stricture progression by targeting not only the bowel but also CF.

doi:10.1016/j.cell.2025.08.029 ↗ PMID 40967215 ↗ PMC12453597 ↗

Study facts

Organism
Homo sapiens
Platform
10x Genomics Visium
Age group
paediatric
Disease groups
—
Anatomical sites
Intestinal Stricture

Data availability

  • Raw counts
  • Processed matrix
  • Spatial coordinates
  • Histology images
  • Analysis code

File types CSVH5JSONMTXPNGTSV

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Processed matrices are advertised
  • Spatial coordinates are advertised
  • Histology images are advertised
  • Analysis code is available

Limitations

  • 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 10x Genomics Visium
Spatial transcriptomics ... using the 10X Genomics platform.

Section series_overall_design, offset —
assay.reference_genome mm10
genome alignment against the Cell Ranger mm10 reference genome. Assembly: mm10

Section samples.data_processing, offset —
assay.resolution spot
tissue_position_list.csv.gz: list of spatial barcodes and the coordinates specifying spots

Section samples.data_processing, offset —
assay.sequencing_based True from source
GEO assay type/library strategy: OTHER

Section GEO family SOFT, offset —

Cohort

FieldValueEvidence
cohort.age_group paediatric
By performing scRNA-seq and Visium on pediatric CD strictures

Section series_summary, offset —

Data_Assets

FieldValueEvidence
data_assets.analysis_code True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8471nnn/GSM8471388/suppl/GSM8471388_InnerBowel_barcodes.tsv.gz

Section GEO family SOFT, offset —
data_assets.file_manifest True from source
Supplementary files enumerated in family SOFT (ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8471nnn/GSM8471388/suppl/GSM8471388_InnerBowel_barcodes.tsv.gz, ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8471nnn/GSM8471388/suppl/GSM8471388_InnerBowel_raw_feature_bc_matrix.h5, ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8471nnn/GSM8471388/suppl/GSM8471388_InnerBowel_tissue_hires_image.png.gz, ftp://ftp.ncbi.n

Section GEO family SOFT, offset —
data_assets.histology_images True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8471nnn/GSM8471388/suppl/GSM8471388_InnerBowel_tissue_hires_image.png.gz

Section GEO family SOFT, offset —
data_assets.open_access True
Public on Aug 23 2025

Section series_status, offset —
data_assets.processed_matrix True from source
GEO deposit evidence: H5 in GEO suppfile types

Section GEO record summary, offset —
data_assets.raw_counts True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8471nnn/GSM8471388/suppl/GSM8471388_InnerBowel_raw_feature_bc_matrix.h5

Section GEO family SOFT, offset —
data_assets.spatial_coordinates True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM8471nnn/GSM8471388/suppl/GSM8471388_InnerBowel_tissue_positions_list.csv.gz

Section GEO family SOFT, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['Intestinal Stricture'] from source
GEO sample source names: Intestinal Stricture

Section GEO family SOFT, offset —
specimens.number_of_samples 2 computed
2 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.number_of_tissue_sections 2
we harvested a 1cm-thick wedge from an intestinal stricture and divided it into two sections

Section samples.extract_protocol, offset —
specimens.preservation_method Flash frozen in OCT; cryosectioned at -20C
we flash froze tissue samples in OCT using a Thermo Scientific Thermo-Flask container filled with liquid nitrogen... Tissues were cyrosectioned at -20C

Section samples.extract_protocol, offset —