We aim to elucidate mechanisms of malignant transformation from inflammatory bowel disease (IBD) to cancer and identify biomarkers and drug targets for early diagnosis and treatment. We hypothesize that malignant transformation from IBD) to colorectal cancer (CRC) is driven by spatially coordinated molecular programs within specific multi-cellular disease modules (MCDMs), characterized by distinct epithelial plasticity and immune microenvironment remodeling. By integrating high-definition Visium spatial transcriptomics with cell-type–resolved signaling analysis, we can identify early-stage biomarkers and actionable upstream regulators (URs) which may prevent progression to dysplasia and cancer.