STOOL EXFOLIOME RNA SEQUENCING ENABLES NON-INVASIVE DETECTION OF MUCOSAL DAMAGE IN IBD

Abstract The ability to monitor mucosal injury and inflammatory status in a non-invasive and data-rich manner remains a critical unmet need in inflammatory bowel disease (IBD). Endoscopy, the current gold standard for assessing mucosal damage, is invasive, costly, and poorly suited for frequent monitoring in either clinical practice or drug development trials. Commonly used biomarkers, such as fecal calprotectin or blood-based assays, provide only limited information and cannot capture the full complexity of mucosal pathology or therapeutic response. Here, we present Foli-seq, a non-invasive exfoliome RNA sequencing approach that directly profiles intestinal transcriptomes shed into stool. This approach leverages the natural exfoliation of gut epithelial and immune cells and captures a wide spectrum of host-derived RNA signals despite the overwhelming microbial and dietary background. Through optimized RNA capture chemistry and unbiased amplification, Foli-seq achieves robust and sensitive quantification of human RNA transcripts from stool, providing insight into pathways related to epithelial barrier function, immune activation, and tissue repair. In our mucosal damage monitoring program, we demonstrate that stool exfoliome profiles can: 1. Differentiate between remission, mild, and moderate-to-severe disease activity. 2. Detect transcriptomic signatures consistent with endoscopic evidence of mucosal injury. 3. Provide early indicators of treatment response, offering potential for predicting therapeutic outcomes. This work establishes Foli-seq as a transformative tool for non-invasive mucosal damage assessment in IBD. By enabling frequent, patient-friendly sampling and multidimensional molecular readouts, Foli-seq has the potential to accelerate clinical decision-making, improve patient stratification in trials, and reduce dependence on invasive procedures. Figure 1: