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

Abstract 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. Helmsley Charitable Trust Topic Categories Mucosal and Regional Immunology (MUC)