Organoid modeling to determine and reverse age-related epigenetic changes contributing to risk of colorectal cancer

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There is great need to develop systems in which the course for initiation and progression of cancer, and therapies directed at these steps can be studied directly in mouse and human cells, and over time courses relevant to real world tumorigenesis. While engineered mouse models are valuable, there is a need to develop complementary systems where meaningful, relatively rapid in-vitro work can yield substantial pre-clinical insights leading to final animal testing. In this regard, we have developed an organoid model which is yielding important data for studying the age-related risks for developing colorectal cancer (CRC). The studies build on extensive data, now just in press, derived from mouse organoids from normal proximal colon wherein we have modeled key steps in the initiation and progression of CRC. The key findings are that despite the organoids being genetically stable over time, they evolve an abnormal, gene promoter CpG island phenotype (CIMP) during long periods of growth. This pattern is very similar to changes seen with aging in normal human colon and which parallels the increasing CRC risk with age. CIMP involves repression of associated gene expression, and/or perhaps even more importantly affects inducibility of genes which otherwise normally function in a feedback fashion to blunt abnormal WNT and other stem pathway activation, prevent abnormal retention of cell renewal, and induce differentiation. In this context, induction of Braf mutations in the older versus younger organoids result in a much more rapid evolution of autonomous Wnt pathway activation, stem cell versus differentiation features and one-step transformation by oncogenic Braf. The resulting cancers have typical histologic features and the epigenetic abnormality of CIMP resembling oncogenic BRAF-driven human proximal colon CRCs. Critically, CRISPR- mediated simultaneous inactivation of multiple CIMP target genes in young organoids rapidly converts these to the old organoid phenotype, importantly resulting in rapid one-step transformation by oncogenic Braf. In the current proposal, we will determine the role of genes affected by age-related CIMP in driving human CRC in the context of KRAS, BRAF and APC mutations, thus addressing the epigenetic dependency of ~75% of CRC evolution. This includes extrapolating our studies to human colon organoids. Importantly, our unique models provide a novel setting to test whether epigenetic therapies can alter the above evolution of CIMP to suppress age-related changes, which may otherwise enhance CRC risk. Results from these studies may allow insights for strategies to prevent and/or intercept CRC evolution. All of the work in our proposal has potential to define management strategies for CRC prevention and interception, which could prove especially valuable for decreasing CRC risk in individuals harboring familial germ line predisposition to colon polyps and for patients with inflammatory bowel diseases.