Foundry120 atlas

← IBD spatial transcriptomics

Genetic profiles of small intestinal and colonic metaplastic Paneth cells by spatial transcriptomics

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Dataset overview

Participants 2
Samples 2
Reuse readiness 7.4/10 evidence-backed score

IL-22 induces Paneth cell metaplasia in the colonic epithelium of ulcerative colitis, promoting wound healing via REG3A.

Muto T, Ito G, Katsuda H, Hiraguri Y, Fujii S, Yamamoto K, Bernardes JP, Hinrichsen F, et al. · Nature communications · 2026

Abstract

Paneth cell metaplasia (PCM) is a phenomenon in which Paneth cells, typically found in the small intestine, appear in the colonic epithelium of patients with ulcerative colitis (UC). Our study demonstrates that the PCM occurrence correlates with disease duration and active inflammation. Furthermore, we identified IL-22, an inflammation-associated cytokine, as a key regulator that promotes PCM formation in the colonic epithelium through suppression of Notch signaling and induces REG3A expression within metaplastic niches. In vitro, we show that Reg3a directly enhances cell proliferation and promotes wound healing using mouse colonic organoids. In vivo, Reg3a<sup>ΔIEC</sup> mice in both acute and chronic DSS-induced colitis models exhibit delayed wound healing. Additionally, studies conducted with patient-derived human colonic organoids revealed that REG3A administration stimulates cell proliferation and accelerates wound healing. Together, these findings support a protective role of PCM-associated REG3A in the colonic epithelium of patients with UC.

doi:10.1038/s41467-026-71136-1 ↗ PMID 41904124 ↗ PMC13195176 ↗

Study facts

Organism
Homo sapiens
Platform
10x Genomics Visium HD
Age group
adult
Disease groups
Ulcerative colitis
Anatomical sites
terminal ileum, colon

Data availability

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

File types JSONMTXPARQUETPNGTIFFTSVTXT

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
  • Participant-to-sample mapping is available
  • 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 HD
mounted on Visium HD slides (10x Genomics)

Section extract_protocol, offset —
assay.platform_version Space Ranger v3.0.0 from source
Space Ranger v3.0.0

Section GEO family SOFT, offset —
assay.reference_genome GRCh38 from source
GRCh38

Section GEO family SOFT, offset —
assay.resolution cellular
spatial transcriptomics, with near single-cell resolution

Section Results—Spatial transcriptomic landscape, offset —
assay.sequencing_based True from source
GEO assay type/library strategy: OTHER

Section GEO family SOFT, offset —
assay.whole_transcriptome True inferred
Released mRNA molecules hybridized to spatially barcoded capture oligonucleotides on the slide surface.

Section Spatial transcriptomic analysis—Library preparation, offset —

Cohort

FieldValueEvidence
cohort.age_group adult
Human intestinal biopsy samples and ESD specimens were obtained from adult patients of both sexes

Section Methods—Ethics approval, offset —
cohort.study_design cross_sectional inferred
biopsies were obtained from two ulcerative colitis patients during endoscopy.

Section series_overall_design, offset —
cohort.total_participants 2
Paired terminal ileum and colon biopsies were obtained from two ulcerative colitis patients during endoscopy.

Section series_overall_design, offset —
cohort.ulcerative_colitis_participants 2
Paired terminal ileum and colon biopsies were obtained from two ulcerative colitis patients during endoscopy.

Section series_overall_design, offset —

Data_Assets

FieldValueEvidence
data_assets.analysis_code True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM9198nnn/GSM9198042/suppl/GSM9198042_B21_07755_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/GSM9198nnn/GSM9198042/suppl/GSM9198042_B21_07755_barcodes.tsv.gz, ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM9198nnn/GSM9198042/suppl/GSM9198042_B21_07755_tissue_hires_image.png.gz, ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM9198nnn/GSM9198042/suppl/GSM9198042_B21_07755_tissue_positions.parquet.gz)

Section GEO family SOFT, offset —
data_assets.histology_images True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM9198nnn/GSM9198042/suppl/GSM9198042_B21_07755_tissue_hires_image.png.gz

Section GEO family SOFT, offset —
data_assets.open_access True
Public on Jan 26 2026

Section series_status, offset —
data_assets.processed_matrix True
matrix.mtx.gz : gene expressin count data in Matrix Market Exchange Format

Section data_processing, offset —
data_assets.raw_counts True from source
GEO deposit evidence: MTX in GEO suppfile types

Section GEO record summary, offset —
data_assets.spatial_coordinates True from source
GEO deposit evidence: ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM9198nnn/GSM9198042/suppl/GSM9198042_B21_07755_tissue_positions.parquet.gz

Section GEO family SOFT, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['terminal ileum, colon'] from source
GEO sample source names: terminal ileum, colon

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.participant_to_sample_mapping_available True
Ulcerative colitis patient 1

Section sample titles, offset —
specimens.participant_to_section_mapping_available True
Paired terminal ileum and colon biopsies were obtained from two ulcerative colitis patients

Section series_overall_design, offset —
specimens.preservation_method formalin-fixed paraffin-embedded (FFPE)
Formalin-fixed paraffin-embedded (FFPE) tissue sections were cut at a thickness of 5 µm

Section Spatial transcriptomic analysis—Tissue preparation and H&E staining, offset —
specimens.specimen_type biopsy
terminal ileum biopsy, and sigmoid colon biopsy

Section sample titles, offset —