Genetic regulation of epithlial injury in ulcerative colitis

ABSTRACT Ulcerative colitis (UC) affects nearly one million US adults. Refractory disease is still common, and the current trial-and-error treatment approach causes delays in identifying optimal therapy for individual patients. Anti-TNF remains a commonly prescribed biologic for UC, but approximately one-third of patients fail to respond and about one-third lose response over time. Understanding the role of IBD-associated genes in intestinal epithelial cell (IEC) injury, especially in determining therapy response or resistance, is a critical unmet need for aligning patients with effective treatment options. Our long-term goal is to develop cytoprotective strategies and identify formalin-fixed, paraffin embedded (FFPE) tissue signatures that correlate with therapy response. The objective of this proposal is to elucidate IEC injury pathways that govern anti-TNF therapy effectiveness, and to discover predictive biomarkers in FFPE biopsies indicative of anti-TNF treatment outcome. Our rationale is that TNF- dependent and independent mechanisms of IEC injury dictate anti-TNF therapy response or resistance. Our novel approach employs an innovative mouse model, A20/Abin-1T-ΔIEC, exhibiting severe colitis that mirrors anti-TNF refractory UC. This model is instrumental in identifying TNF-independent pathways of intestinal injury. Complementing this mouse model, we will apply pioneering spatial transcriptomics assays to analyze archived FFPE patient biopsies, revealing treatment response signatures in routinely collected samples. Predictive biomarkers in FFPE biopsies would integrate best with current clinical workflows, since nearly all IBD patients have archived FFPE biopsies. Additionally, we leverage well-characterized colonic organoids derived from healthy controls and UC patients for mechanistic in vitro assays to characterize primary IEC responses to death stimuli. The specific aims include: 1. Delineating TNF-independent (anti-TNF refractory) mechanisms of IEC death via the A20/Abin-1T-ΔIEC mouse model, hypothesizing that IL-1B signaling is a crucial driver of mucosal injury. 2. Validating IEC injury pathways correlated with anti-TNF treatment response and non-response in FFPE specimens, using a customized gene panel for detailed spatial transcriptomics. 3. Assessing differential sensitivities of UC-derived IEC organoids to death stimuli and cytoprotective factors, hypothesizing a distinct response pattern in UC-derived organoids compared to controls. This proposal integrates a novel mouse model, advanced spatial transcriptomics, and patient-derived organoid cultures to pinpoint critical mechanisms of IEC injury and develop biomarkers indicative of anti-TNF treatment response. By advancing this research, we aim to significantly impact precision medicine for UC, aligning medications to individual patient epithelial biology, while identifying new therapeutic targets.