Current Bioinformatics Seminar
Time: 11AM Tuesdays.
Venue: Davis Auditorium and Online
16 June 2026
Mapping excess epithelial cell death in inflammatory bowel disease through spatial transcriptomics and digital pathology AI
Yunzhuo (Emily) ZhouWEHI
Inflammatory bowel disease (IBD) is characterised by altered cytokine signalling, maladaptive immunity, dysbiosis and intestinal barrier dysfunction. Although many patients achieve clinical remission after therapy, relapse remains common, suggesting that disease-associated mechanisms can persist even when clinically apparent inflammation is reduced. The broader study identifies aberrant epithelial cell death signalling as an early and persistent feature of IBD, involving inflammatory reprogramming of epithelial cells and downstream apoptotic and necroptotic pathways. In this seminar, I will focus on the spatial transcriptomics component of the study. Using Xenium spatial profiling of intestinal biopsies across non-IBD, quiescent and active disease states, we mapped epithelial, immune and stromal cell populations in tissue context and examined how disease-associated epithelial programs are spatially organised. I will present our analysis of inflammatory epithelial states, including NOS2-associated absorptive colonocyte populations, and how these cells relate to neighbouring immune and stromal compartments across disease activity. These spatial analyses provide a tissue-level view of disease-associated epithelial states, highlighting where they emerge and how they are embedded within the local mucosal environment. I will also introduce our preliminary digital pathology AI workflow, which links Xenium-derived cell-type annotations with aligned H&E images to explore whether histological morphology can predict local cellular composition and inflammatory epithelial patterns in IBD tissue.