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Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Merscope]

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Dataset overview

Participants None
Samples 1
Reuse readiness 6.4/10 evidence-backed score

Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks.

Mennillo E, Lotstein ML, Lee G, Hou JH, Johri V, Leet DE, Ekstrand CA, Tsui J, et al. · The Journal of clinical investigation · 2026

Abstract

Imaging-based, single-cell, spatial transcriptomics (iSCST) of FFPE tissue enables comprehensive analysis of archived specimens while preserving spatial context, critical to an understanding of ulcerative colitis (UC) pathology. Here, we deployed a robust framework for applying iSCST to clinical FFPE mucosal biopsies from patients with UC or immune checkpoint inhibitor-induced colitis, as well as patients serving as healthy controls. iSCST using custom Xenium gene panels enabled precise detection of diverse cell subsets and disease-specific genes. We mapped transcriptionally distinct fibroblast subsets within mucosal niches, including inflammation-associated fibroblasts (IAFs), and identified colitis-specific neighborhoods formed by IAFs, monocytes, and neutrophils. Transcriptional signatures and spatial neighborhoods uncovered through iSCST were associated with vedolizumab (VDZ) response, with nonresponders exhibiting either an innate IAF-monocyte-neutrophil signature or adaptive gut-associated lymphoid tissue signature, while responders showed enrichment of an epithelial cellular neighborhood. These signatures were validated in an internal and an external dataset, supporting the existence of 2 distinct archetypes of treatment resistance to VDZ in UC. This iSCST framework provides a powerful approach for analyzing FFPE tissues, offering insights into colitis-associated cellular networks and identifying biomarkers to enhance patient risk stratification in routine clinical workflows.

doi:10.1172/jci202488 ↗ PMID 42262875 ↗ PMC13367960 ↗

Study facts

Organism
Homo sapiens
Platform
MERSCOPE
Age group
—
Disease groups
—
Anatomical sites
Non-IBD controls and patients with ulcerative colitis (UC)

Data availability

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

File types CSV

Strengths & limitations for reuse

Strengths

  • Raw counts are advertised
  • Processed matrices are advertised
  • Spatial coordinates 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.panel_size 280
280 gene custom panel

Section samples[0].characteristics, offset 500
assay.platform MERSCOPE
Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Merscope]

Section series.series_title, offset —
assay.resolution subcellular
3 commercially available, FFPE-compatible platforms with subcellular resolution

Section Results: iSCST approaches, offset —
assay.sequencing_based False
Imaging-based single-cell spatial transcriptomics (iSCST)

Section series, offset —
assay.whole_transcriptome False
280 gene custom panel

Section samples[0].characteristics, offset —

Data_Assets

FieldValueEvidence
data_assets.analysis_code True
All code necessary for recreating the reported analyses and figures is available

Section Data availability, offset —
data_assets.file_manifest True from source
filelist.txt

Section filelist.txt, offset —
data_assets.molecule_coordinates True
cell and transcript location information file

Section samples[0].data_processing, offset —
data_assets.open_access True from source
Public on May 21 2026

Section series_status, offset —
data_assets.processed_matrix True
loading the cell-feature matrix file (cell_by_gene.csv)

Section samples[0].data_processing, offset —
data_assets.raw_counts True
loading the cell-feature matrix file (cell_by_gene.csv)

Section samples[0].data_processing, offset —
data_assets.sample_metadata True
"characteristics": {"panel": "280 gene custom panel", "tissue": "FFPE mucosal biopsies"}

Section samples[0], offset —
data_assets.spatial_coordinates True
cell and transcript location information file (micron_to_mosaic_pixel_transform.csv)

Section samples[0].data_processing, offset —

Specimens

FieldValueEvidence
specimens.anatomical_sites ['Non-IBD controls and patients with ulcerative colitis (UC)'] from source
GEO sample source names: Non-IBD controls and patients with ulcerative colitis (UC)

Section GEO family SOFT, offset —
specimens.number_of_samples 1 computed
1 GSM records parsed from GEO family SOFT

Section GEO family SOFT, offset —
specimens.preservation_method formalin-fixed, paraffin-embedded (FFPE)
FFPE mucosal biopsies

Section samples[0].characteristics, offset 650
specimens.specimen_type biopsy
Tissue microarrays (TMAs) were constructed from FFPE blocks, using 1.1-1.5 mm cores.

Section samples[0].extract_protocol, offset 1050