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← IBD spatial transcriptomics

Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [CosMx]

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Dataset overview

Participants None
Samples 60
Reuse readiness 5.0/10 evidence-backed score

Spatial transcriptomics atlas of inflammatory bowel disease to guide implementation in research consortiums and clinical trials.

Li Y, Wei C, Yang W, Wang H, Robinson A, Peshek I, Yu T, Park J, et al. · Nature communications · 2026

Abstract

Using over 100 intestinal tissue sections from non-diseased controls and patients with ulcerative colitis or Crohn's disease across multiple inflammatory bowel disease consortia, we construct a spatially resolved atlas containing over three million cells and systematically evaluate two imaging-based spatial transcriptomics platforms. Here we show that CosMx tends to achieve higher detection efficiency than Xenium across commercially available panels in both ulcerative colitis and Crohn's disease, whereas Xenium shows reduced performance associated with tissue type, block quality, and panel size. CosMx identifies regulatory T cell associated biology in both disease subtypes, which we validate using independent laboratory experiments and multi-plex spatial multi-omics. CosMx's data quality remains stable across variation in fixation time and sectioning procedures, supporting its operational feasibility for multi-center studies. This study establishes a technical and biological benchmark for the application of single-cell-resolved spatial transcriptomics in gastrointestinal tissue, enabling more reliable application of spatial technologies in translational inflammatory bowel disease research.

doi:10.1038/s41467-026-72482-w ↗ PMID 42049732 ↗ PMC13328602 ↗

Study facts

Organism
Homo sapiens
Platform
CosMx
Age group
—
Disease groups
—
Anatomical sites
human Ileum, human rectum, human colon

Data availability

  • Analysis code

Strengths & limitations for reuse

Strengths

  • Analysis code is available

Limitations

  • Not documented: raw counts are advertised
  • Not documented: processed matrices 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

FieldValueEvidence
assay.platform CosMx
Performance differences in spatial transcriptomics platforms identify Treg biology in human inflammatory bowel disease [CosMx]

Section geo_record_summary, offset —
assay.platform_version CosMx 1.0 and CosMx 2.0
re-running samples on a recently upgraded CosMx platform (CosMx 2.0)

Section Future directions: power calculations, offset 52000
assay.resolution cellular
We present a comprehensive data resource of over 1.5 million spatially profiled intestinal cells

Section series.series_summary, offset 1200
assay.sequencing_based False
we systematically compared two imaging based spatial transcriptomics platforms (CosMx and Xenium)

Section series.series_summary, offset 1100
assay.whole_transcriptome False
The CosMx multi-tissue panel (950 genes)

Section Results: CosMx multi-tissue panel versus Xenium multi-tissue panel, offset 3300

Cohort

FieldValueEvidence
cohort.disease_activity_metadata_available True
Using intestinal biopsies (n = 40) from patients with inflammatory bowel disease (IBD) of varying disease states and disease locations and non-diseased controls

Section series.series_summary, offset 7000
cohort.study_design cross_sectional
All human tissue samples analyzed in this study were collected in a cross-sectional manner, and no post-intervention samples were included.

Section Methods, offset 63700

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
Custom scripts for data processing and quality evaluation are available at https://zenodo.org/records/19006691

Section Code availability, offset 75600
data_assets.open_access True
Public on Mar 13 2026

Section series.series_status, offset —
data_assets.sample_metadata True
"characteristics": {"tissue": "Ileum"}

Section samples, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['human Ileum', 'human rectum', 'human colon'] from source
GEO sample source names: human Ileum; human rectum; human colon

Section GEO family SOFT, offset —
specimens.inflamed_status_available True
Ileum_CD_Inflamed: 5, Ileum_CD_NonInflamed: 5, Ileum_UC_NonInflamed: 2, Rectum_CD_Noninflamed: 2, Rectum_CD_inflamed: 2

Section series.series_overall_design, offset 400
specimens.number_of_samples 60 computed
60 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.preservation_method formalin-fixed, paraffin-embedded (FFPE)
Formalin-fixed, paraffin-embedded blocks were cut into sections on positively charged slides

Section samples.extract_protocol, offset —
specimens.specimen_type biopsy
Using intestinal biopsies (n = 40) from patients with inflammatory bowel disease

Section series.series_summary, offset 650