Epigenetic dysregulation in APC-negative colorectal cancer

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The incidence of colorectal cancer (CRC) is higher in African Americans (AAs) compared with US whites (NHWs) overall, but the disparity is more extreme in persons with earlier age of onset. The median age of onset is 65 in AAs compared to 72 in NHWs, and early-onset CRC is more than twice as frequent in AAs than in NHWs. In addition, epidemiologic evidence suggests that younger age CRCs may have a more rapid progression through the steps of carcinogenesis. Yet, younger age CRC is not well characterized in any population, and we have no explanation for its higher incidence in AAs. In a recent genomic analysis of a series of Chicago African American CRC cases, we found an excess of CRCs lacking mutation in the tumor suppressor gene APC (APC mutation-negative CRCs). Microsatellite stable APC mutation-negative CRCs were associated with younger age of diagnosis, fewer numbers of somatic mutations, and microsatellite and chromosome stability. Importantly, we discovered that APC mutation-negative CRCs exhibited a novel methylation profile characterized by increased levels of methylation in key cancer driver genes including those in stem-cell maintenance and the WNT signaling pathway. Based on our preliminary data, we hypothesize that epigenetic dysregulation in APC mutation-negative CRCs drives specific DNA methylation changes and gene regulatory networks that maintain a stem-like cancer phenotype. The overall goal of the project is to characterize the molecular mechanisms that drive this novel subtype of CRCs. We have three aims. Aim 1. Identify and characterize significant differentially methylated regions in AA CRC. Hypothesis: Tumor- specific differentially methylated regions are associated with carcinogenesis in APC mutation-negative CRCs. APC mutation-negative CRCs will be associated with earlier age of onset and with distinct molecular and clinicopathological features. Aim 2. Identify and characterize differentially expressed genes and regulatory networks in AA CRCs. Hypothesis: Specific regulatory networks that maintain a stem-like cancer phenotype are associated with APC mutation-negative CRCs. Aim 3. Determine driver gene dependencies of AA CRCs in organoid cancer models. Hypothesis: Suppression of specific WNT signaling factors and epigenetic modulators will induce increased epithelial differentiation in APC mutation-negative organoids in comparison to APC mutation-positive organoids. The proposed studies will provide essential knowledge of the DNA methylation and gene expression changes underlying AA CRCs and will characterize cancer cell responses to chemical challenge. The new knowledge will provide translatable information, including diagnostic and predictive biomarkers and precision-medicine approaches, that could be used to treat a novel subtype of CRC that occurs in excess in AAs and is associated with earlier age of onset.