Abstract B003: BRAFV600E is essential for maintenance of the CpG island methylator phenotype and DNA methylation of PRC2 target genes in colon cancer

Abstract In colon cancer, the BRAFV600E mutation is strongly associated with the CpG island methylator phenotype (CIMP). Here, we characterized the contribution of BRAFV600E to maintenance of aberrant DNA methylation. A reverse CRISPR gene editing approach was applied to revert the V600E mutation in BRAF back to wildtype (E600V) in organoids derived from a late-stage tumour. DNA methylation analyses identified 5187 differentially methylated CpGs within CpG islands, predominantly hypermethylated (82%) in BRAFV600E organoids, including genes associated with CIMP, as well as Polycomb Repressor Complex 2 (PRC2) target genes. RNA sequencing showed that expression of those genes was concordantly repressed. Furthermore, BRAFV600Einduced high expression of PRC2 core components (EZH2, SUZ12, EED), caused PRC2-induced H3K27 trimethylation in promoter regions, and maintained a PRC2-associated embryonic phenotype. This phenotype was lost following mutation correction or pharmacological inhibition of DNA methylation. These findings show that BRAFV600E maintains aberrant DNA and histone methylation patterns in advanced colon cancer, likely preserving the transformed phenotype by silencing of PRC2 target genes. Epigenetic therapies may have value in the treatment of BRAFV600E-mutant colon cancer. Citation Format: Layla El Bouazzaoui, Jeroen M Bugter, Emre Küçükköse, André Verheem, Jasmin B Post, Nicola Fenderico, Inne H.M Borel Rinkes, Hugo J.G Snippert, Madelon M Maurice, Onno Kranenburg. BRAFV600E is essential for maintenance of the CpG island methylator phenotype and DNA methylation of PRC2 target genes in colon cancer [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: DNA Methylation, Clonal Hematopoiesis, and Cancer; 2025 Feb 1-4; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2025;85(3 Suppl):Abstract nr B003.