MULTI-MODAL ANALYSIS OF INFLAMMATORY BOWEL DISEASE TISSUE FOR BIOMARKER DISCOVERY

Abstract Though Inflammatory Bowel Disease (IBD) prevalence continues to increase, treatment remains challenging due to the complex etiology spanning genetic and tissue pathology. Despite significant progress, the relationship between gene expression, histopathology, and clinical outcomes remains incomplete. To provide insights into the heterogeneous nature of IBD, we created balanced cross-sectional retrospective multi-modal datasets. We analyzed multi-modal data from patients diagnosed with IBD to evaluate the relationship between histopathological features, genomic and spatial profiling data to delineate multi-modal signatures that correlate to clinical outcomes and potentially subclassify IBD patients. Sections from diagnostic gastrointestinal FFPE tissue blocks were used to measure gene expression from ribosome-depleted RNA that correlated to levels of inflammation. Case matched sections from tissue with no histological evidence of inflammation served as intra- patient RNA expression controls and provided Whole Genome Sequence (WGS) data to evaluate germline IBD risk profiles. Histopathological annotation of H&E stained gastrointestinal tissue scans from diagnosis provided insights into tissue architecture, inflammation, and spatial distribution of cells associated with IBD. To further characterize cellular composition of the gastrointestinal layers with respect to inflammation hallmarks and disease-state progression, tissues were labeled with a precise number of antibodies to assess tissue architecture, GLP-1 related markers, and immune cell infiltration by Imaging Mass Cytometry (IMC). Comparing representative IBD cases of diagnosed low, moderate, and severe levels of inflammation, we illustrate the complex nature of the relationship between WGS, differential gene expression, and spatial analyses of cell neighborhoods using molecular markers and cellular content within the tissues. Such multi-modal biomarkers may represent comprehensively the mechanism(s) of disease to serve as valuable therapeutic targets and informative diagnostic tests to better define molecular subgroupings of IBD to accommodate the variability observed in individual patients. Figure 1:A cross sectional image of H&E stained villi from the small intestineFigure 2:A cross sectional IMC image of villi from the small intestine, used for cellular neighborhood analyses