Spatial Transcriptomics to Study Tissue-Specific Pathways Linked to Secondary Anti-TNF Resistance in Crohn’s Disease 2307998

Introduction Crohn’s disease is a chronic inflammatory disorder of the gastrointestinal tract affecting millions worldwide. TNF-α—blocking antibodies are widely used to control inflammation and induce remission; however, more than half of patients either fail to respond initially or develop secondary loss of response. While anti-drug antibodies (ADA) account for a subset of cases, some patients develop treatment resistance through mechanisms that remain poorly understood and cannot be overcome by dose escalation. Methods To investigate these mechanisms, we assembled a cohort of archival intestinal biopsies from patients with either ADA-negative secondary loss of response or sustained response to TNF-α inhibitors. Samples were incorporated into tissue microarrays and analyzed using Xenium spatial transcriptomics with a customized panel of intestinal and inflammation-associated genes. The same tissue sections were subsequently profiled by high-plex immunofluorescence using PhenoCycler staining with a panel of over 20 markers. Results Integrated spatial transcriptomic and proteomic analyses identified inflammation-associated cell populations and molecular pathways linked to secondary loss of response in the ileum and colon. Conclusion These signatures suggest pharmacodynamic mechanisms underlying ADA-negative treatment failure and highlight candidate prognostic biomarkers for future loss of response. Funding Source The Leona M. and Harry B.