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

Dataset overview

Participants None

Samples 8

Reuse readiness 5.0/10 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 Xenium
Age group: paediatric
Disease groups: —
Anatomical sites: Intestinal Stricture, Normal Bowel

Data availability

Processed matrix
Histology images

File types H5PARQUETTIFF

Small Intestine8

Accession	Sample	Tissue	Molecule
`GSM8968701`	Region_1_0038414_Stricture	Small Intestine	other
`GSM8968702`	Region_2_0038414_Uninvolved	Small Intestine	other
`GSM8968703`	Region_1_0038438_Stricture	Small Intestine	other
`GSM8968704`	Region_2_0038438_Uninvolved	Small Intestine	other
`GSM8968705`	Region_1_0038555_Stricture	Small Intestine	other
`GSM8968706`	Region_2_0038555_Stricture	Small Intestine	other
`GSM8968707`	Region_1_0038556_Stricture	Small Intestine	other
`GSM8968708`	Region_2_0038556_Uninvolved	Small Intestine	other

Strengths & limitations for reuse

Strengths

Processed matrices are advertised
Histology images are advertised

Limitations

Not documented: raw counts are advertised
Not documented: spatial coordinates 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

Field	Value	Evidence
`assay.panel_size`	470	with 470 custom gene probes Section `series_overall_design`, offset —
`assay.platform`	10x Genomics Xenium	Spatial transcriptomics of human bowel and mesenteric adipose tissue using the 10X Genomics Xenium platform Section `series_overall_design`, offset —
`assay.resolution`	cellular	imaging to identify the RNA within each cell of a tissue Section `data_processing`, offset —
`assay.segmentation_method`	Cell segmentation after staining	Custom gene probes were added to tissue samples to hybridize with target RNA and then stained to perform cell segmentation. Section `data_processing`, offset —
`assay.sequencing_based`	False inferred	Samples are then run on a Xenium Analyzer with performs fluorescent probe hybridization and imaging Section `data_processing`, offset —
`assay.whole_transcriptome`	False	using the 10X Genomics Xenium platform with 470 custom gene probes Section `series_overall_design`, offset —

Cohort

Field Value Evidence

Field	Value	Evidence
`cohort.age_group`	paediatric	By performing scRNA-seq, Visium and Xenium on pediatric CD strictures Section `series_summary`, offset —

cohort.age_group

paediatric

By performing scRNA-seq, Visium and Xenium on pediatric CD strictures

Section series_summary, offset —

Data_Assets

Field	Value	Evidence
`data_assets.file_manifest`	True	filelist.txt Section `filelist.txt`, offset —
`data_assets.histology_images`	True from source	GEO deposit evidence: TIFF in GEO suppfile types Section `GEO record summary`, offset —
`data_assets.open_access`	True	Public on Sep 17 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 —

Specimens

Field	Value	Evidence
`specimens.anatomical_sites`	['Intestinal Stricture', 'Normal Bowel'] from source	GEO sample source names: Intestinal Stricture; Normal Bowel Section `GEO family SOFT`, offset —
`specimens.inflamed_status_available`	True	Region_1_0038414_Stricture ... source_name: Intestinal Stricture; Region_2_0038414_Uninvolved ... source_name: Normal Bowel Section `samples`, offset —
`specimens.number_of_samples`	8 computed	8 GSM records parsed from GEO family SOFT Section `GEO family SOFT`, offset —
`specimens.preservation_method`	Flash-frozen in OCT; cryosectioned at -20°C	we flash froze tissue samples in OCT ... Tissues were cyrosectioned at -20C onto Xenium slide Section `extract_protocol`, offset —