Mucosal ecosystems of the ileum and colon shape the therapeutic response in Crohn's Disease

Many Crohn's disease patients fail to respond to biologic therapies targeting canonical immune pathways, and the mechanisms underlying treatment non-response remain poorly understood. Integrating single-cell and spatial transcriptomics, we generated a comprehensive mucosal atlas of 380,000 cells spanning the terminal ileum and ascending colon of healthy donors and Crohn's disease patients receiving biologics. We revealed site-specific programs centered on TNF-expressing macrophages embedded within epithelial-stromal networks: follicle-associated enterocytes dictated immune activation in the ileum, while FAP-expressing stromal cells served this role in the colon. Co-expression network analysis further identified lineage-specific programs associating non-response, including a novel epithelial marker BPIFB1 independent of known genetic risk loci. Co-expression marker Z-scores significantly differed between responders and non-responders in published datasets. Together, these findings define a non-responder-specific epithelial-stromal-immune ecosystem that sustains chronic inflammation, providing a framework for stratifying treatment resistance and informing therapeutic strategies in Crohn's disease and other barrier organ disorders.