Abstract 721: Epigenetic intervention in the prevention of Lynch Syndrome Colorectal Cancer

Abstract Introduction: Lynch Syndrome (LS) is the most common cause of hereditary colorectal cancer (CRC) affecting >1 million Americans. LS is caused by germline mutations in one of four DNA mismatch repair (MMR) genes, generating several hundreds of mutations in microsatellite coding sequences. Although defects in the MMR machinery are the principal mechanism driving LS carcinogenesis, the role of the epigenome through histone and DNA methylation remains unexplored. Hypermethylation of MLH1 is detected in 15% of sporadic MMR-deficient CRC and also in LSCRC, indicating a pivotal role of DNA methylation in LSCRC. In this study, we investigated the landscape of DNA methylation and EZH2-mediated histone H3 lysine 27 methylation in LS tumor samples, and tested the preventive effects of GSK-503, on tumor formation using a novel LS mouse model. Methods: We profiled the somatic mutational, global DNA methylation landscape, and performed ChIP-seq in LS precancers and tumors. Patient-derived organoids (PDO) from colonic tissues treated with EZH2 and 5-AZA were used for gene expression analysis. LS mice (Villin-Cre;Msh2fl/fl;TgfβRII-KI) were treated for 9 weeks with EZH2 inhibitor GSK503 to assess the effect on polyp formation in vivo monitored through murine colonoscopy. Results: Our mutational profiling via whole-exome-seq and gene expression survey of 10 LSCRC and 33 pre-cancers showed accumulation of somatic mutations and aberrant expression patterns in key epigenetic regulators including EZH2 and DNMT3A, which suggests dysregulation of epigenetic control in LS. Global DNA methylation using RRBS in tumors of 3 LS patients showed that gene promoters were more hypermethylated when compared to matched normal samples. Immunohistochemistry data showed higher expression of EZH2 in tumors when compared to precancerous and normal colonic mucosa. ChIPseq analysis demonstrated high levels of H3K27me3 present in gene promoters of stem cell marker genes (WNT9A, LGR5, and ASCL2), and immune-related genes (CD4, CD8a, and HLA-E). Interestingly, 577 out of 2756 DNA hypermethylated genes from RRBS analysis displayed high levels of H3K27me3, thus indicating a central role of EZH2 in epigenetic programming of LS neoplasms. RNAseq data from PDOs treated with 5-AZA (DNMT inhibitor) and GSK503 (EZH2 inhibitor) showed that both epigenetic inhibitors led to the reactivation of silenced genes in colorectal carcinogenesis such as CDKN2A, RUNX3, IGFBP3, and immune genes, including CD40, CD4, SEMA3B, CXRC6/6, and ICAM1. Finally, a 9-week chemo-preventive treatment of a cohort of LS mice with GSK503 significantly decreased polyp formation when compared to control, and polyp reduction was associated with increased infiltration of cytotoxic CD8a+ Tcells and NK in the large intestine mucosa. Conclusions: These results demonstrate the chemopreventive potential of EZH2 inhibitors in prevention of LS-associated tumors through an immune modulation approach. Citation Format: Laura Reyes Uribe, Charles M Bowen, Kyera Evans, Hong Wu, Fahriye Duzagac, Krishna Sinha, Eduardo Vilar. Epigenetic intervention in the prevention of Lynch Syndrome Colorectal Cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 721.