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Ulcerative colitis Xenium In Situ Spatial Gene Expression

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Dataset overview

Participants 1
Samples 2
Reuse readiness 5.6/10 evidence-backed score

A microbiome-reactive TMIGD2<sup>hi</sup> Th17 subset is spatially enriched at the intestinal epithelium and expanded in inflammatory bowel disease.

Pedersen TK, Jain T, Segerstolpe Å, Lin C, Shih AR, Yuan L, Ashenberg O, Kaper ME, et al. · Immunity · 2026

Abstract

Subsets of intestinal CD4<sup>+</sup> T cells directly recognize commensal bacteria and coordinate tolerance versus protective immunity. Our limited understanding of CD4<sup>+</sup> T cell specificities and corresponding functional phenotypes has created a barrier to deciphering the mechanisms of mucosal homeostasis and inflammation mediated by the adaptive immune system. To address this, we leveraged an immunodominant Bacteroidetes epitope in SusC to perform single-cell profiling of the SusC-specific and total CD4<sup>+</sup> T cell landscapes in intestinal tissues of patients with inflammatory bowel disease (IBD). By analyzing phenotypes and T cell receptor specificities in parallel, we uncovered phenotypic diversification of T helper 17 (Th17) cells in IBD and identified an epithelial-localized, SusC-reactive Th17 subset that is BACH2<sup>lo</sup>, GZMA<sup>hi</sup>, and expresses the costimulatory receptor TMIGD2. Together, our results highlight the utility of tracking commensal-specific T cell responses to define specialized subsets of Th17 cells associated with loss of tolerance to the microbiome.

doi:10.1016/j.immuni.2026.09.026 ↗ PMID 42933395 ↗

Study facts

Organism
Homo sapiens
Platform
Xenium In Situ Spatial Gene Expression (10x Genomics)
Age group
—
Disease groups
Ulcerative colitis
Anatomical sites
Colon

Data availability

  • Processed matrix
  • Histology images

File types H5PARQUETTIFF

Strengths & limitations for reuse

Strengths

  • Processed matrices are advertised
  • Histology images are advertised
  • Participant counts are documented

Limitations

  • Not documented: raw counts are advertised
  • Not documented: spatial coordinates are advertised
Extraction evidence & provenance

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

Assay

FieldValueEvidence
assay.panel_size 5000
Xenium Prime Pan-Human 5,000-plex probe panel

Section series_overall_design, offset 1050
assay.platform Xenium In Situ Spatial Gene Expression (10x Genomics)
performed spatial transcriptomics (Xenium, 10x Genomics)

Section title/summary, offset 2500
assay.platform_version Xenium Prime Pan-Human
Xenium Prime Pan-Human 5,000-plex probe panel

Section series_overall_design, offset 1050
assay.resolution cellular inferred
To investigate the spatial localization of CD4 T cells we performed spatial transcriptomics (Xenium, 10x Genomics)

Section summary, offset 2900
assay.sequencing_based False inferred
hybridization using the Xenium Prime Pan-Human 5,000-plex probe panel

Section series_overall_design, offset 1050
assay.whole_transcriptome False
Xenium Prime Pan-Human 5,000-plex probe panel

Section series_overall_design, offset 1050

Cohort

FieldValueEvidence
cohort.total_participants 1
from one patient with UC.

Section summary, offset 3000
cohort.ulcerative_colitis_participants 1
In patients with Ulcerative colitis (UC)

Section summary, offset 2960

Data_Assets

FieldValueEvidence
data_assets.file_manifest True
filelist.txt

Section file listing, 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 Oct 15 2026

Section series_status, offset 180
data_assets.processed_matrix True from source
GEO deposit evidence: H5 in GEO suppfile types

Section GEO record summary, offset —

Specimens

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

Section GEO family SOFT, offset —
specimens.inflamed_status_available True
histopathologically confirmed inflamed (most affected) and less inflamed (least affected) resected tissue

Section series_overall_design, offset 850
specimens.number_of_samples 2 computed
2 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.preservation_method FFPE
"tissue preservation method": {"FFPE": 2}

Section sample_values_with_sample_counts.characteristics, offset 1480
specimens.specimen_type resection
less inflamed (least affected) resected tissue from one patient with UC

Section series_overall_design, offset 910