Single-cell spatial transcriptomics of formalin-fixed, paraffin-embedded biopsies reveals colitis-associated cell networks
Spatial maps of intestinal biopsies predict which ulcerative colitis patients won't respond to specific therapy, enabling earlier treatment switches.
Using Xenium-based imaging spatial transcriptomics on archived FFPE mucosal biopsies from UC patients, this JCI study identifies two mechanistically distinct non-responder archetypes to vedolizumab — enabling potential precision patient stratification for IBD therapy. The framework is validated in an independent dataset and is directly applicable to routine clinical FFPE material.
What the study was
- Study design
- Translational study (iSCST on clinical FFPE biopsies + external validation dataset)
- Population
- Patients with ulcerative colitis (UC), ICI-induced colitis, and healthy controls; clinical FFPE mucosal biopsies
- Category
- Diagnostics
- Maturity
- Exploratory
- Journal
- Journal of Clinical Investigation
Why it surfaced
Technically innovative spatial transcriptomics in routine FFPE (not fresh-frozen) tissue is a major practical advance; IBD is not a primary watchlist topic but precision stratification of treatment resistance is high-value. JCI publication with independent validation lends credibility. Watchlist relevance via immunotherapy resistance mechanisms.
A plain-language summary of published research — not medical advice. Talk to a clinician about your own care.