Predicting Pouchitis in Inflammatory Bowel Disease Through Immune-Epithelial Profiling

About This Grant

PROJECT SUMMARY AND ABSTRACT Patients with inflammatory bowel disease (IBD) often require a restorative proctocolectomy and ileal pouch- anal anastomosis (IPAA) for medically refractory ulcerative colitis (UC) or colonic Crohn’s disease (CD), which involves removal of the entire colon and rectum while preserving the anal sphincter with the creation of a pouch organ by looping healthy ileum into a J-shape that serves as an internal pelvic reservoir. While an IPAA preserves continence and avoids the requirement for a permanent ileostomy, approximately 50% of patients develop pouchitis— a de novo inflammatory condition of the ileal reservoir—resulting in substantial morbidity. The pathogenesis of pouchitis remains poorly understood. Our preliminary data using ExCITE-seq, a multi- modal single-cell sequencing platform, revealed that patients who later develop pouchitis exhibit a distinct immune-epithelial signature in the pre-IPAA ileum, including enrichment of Th17 cells, epithelial remodeling, and persistent clonal T cell expansion. Additionally, stem cells derived from inflamed pouch tissue demonstrated epigenetic alterations associated with impaired viability and secretory lineage differentiation. We hypothesize that pre-existing Th17-driven immune dysregulation and aberrant epithelial responses contribute to the development of pouchitis. To test this hypothesis, in Aim 1, we will evaluate the relationship between the immune microenvironment in the pre-IPAA ileum and subsequent pouchitis. In an existing cohort of patients with longitudinal follow-up we will assess pre-IPAA ileal tissue for Th17-associated immune infiltration, epithelial apoptosis, and spatial transcriptomic profiles, and associating these findings with clinical pouch outcomes. Aim 2 will define how pouchitis-associated immune dysregulation impacts epithelial biology. We will determine the impact of Th17-mediated cytokines on epithelial cell fate and viability using organoid models derived from pre-IPAA ileum and investigate the role of the microbiome in modulating this immune-epithelial axis through integrated metagenomic analyses of pre-IPAA ileostomy stool. Collectively, this work will identify predictive immune, epithelial, and microbial biomarkers and mechanisms of pouchitis, with the potential to inform IPAA eligibility and guide preventive therapeutic strategies in pouchitis.