GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE282nnn/GSE282124/primaryOK200OtherHomo sapiensOtherhttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE282124GEOGSEfalseSingle-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks [Merscope]Imaging-based single-cell spatial transcriptomics (iSCST) on formalin-fixed, paraffin-embedded (FFPE) tissue enables comprehensive analysis of archived specimens while preserving spatial context, critical to an understanding of ulcerative colitis (UC) pathology. Here, we developed, benchmarked, and applied a robust framework for applying iSCST to clinical FFPE mucosal biopsies from patients with UC, immune checkpoint inhibitor-induced (ICI) colitis and 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 uncovered through iSCST were associated with vedolizumab (VDZ) response, with non-responders exhibiting either an IAF-monocyte signature or adaptive gut-associated lymphoid tissue (GALT) signature, while responders showed enrichment of epithelial gene expression. These signatures were validated in both internal and publicly-available external datasets. 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.2026/05/21GSE282124GSM863648533762282124Homo sapiens