UC severity shapes mucosal cellular landscape Raw sequence reads

Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease that disrupts the lives of millions worldwide. While previous studies have investigated the cellular composition of inflamed mucosa, how cell types and molecular circuits are altered across macroscopic lesions of varying severity remains unexplored. Here, we mapped the cellular heterogeneity and signaling networks shaping these lesions. We performed single-cell RNA sequencing (scRNA-seq) on biopsies from UC patients and healthy donors, stratifying lesions by endoscopic Mayo subscore (EMS). The microbiome composition was assessed via 16S rRNA sequencing, and histological features were extracted from corresponding hematoxylin and eosin (H&E) staining using a text-vision multi-modal model. Key findings were validated using RNA in situ hybridization. Profiling 59 biopsy regions from 12 UC patients and 7 controls, we found that among tested clinical metrics, the binary EMS (inactive: EMS <= 1; active: EMS >= 2) best captured the observed cellular and microbial diversity. Active lesions were marked by the appearance of inflammatory and antigen-presenting epithelial stem cells and an expansion of DEFA5+ DEFA6+ Paneth-like cells, normally absent in healthy mucosa. The frequencies of blood endothelial cells, regulatory T cells, and TOX+ exhausted T cells also increased with disease severity. Paneth-like cells interacted with many mucosal cell types via their expressed ligands PRSS2 and PLA2G2A while global ligand-receptor analysis highlighted arterial and vein-derived endothelial subtypes as central signaling hubs within inflamed mucosa. Our single-cell atlas reveals dynamic, severity-linked cellular remodeling and signaling networks across UC lesions, providing new insights into disease pathogenesis and highlighting potential therapeutic entry points. Sequencing was performed at the Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna under the project ID JMF-2404-06.