BRAF(V600E) maintains the CpG island methylator phenotype, and DNA methylation of PRC2 targets genes in colon cancer.

In colon cancer, the BRAF(V600E) mutation is strongly associated with the CpG island methylator phenotype (CIMP). Here, we characterized the contribution of BRAF(V600E) to maintenance of aberrant DNA methylation using CRISPR-LbCpf1-corrected BRAF (V600E) organoids. DNA methylation analyses identified 5,187 differentially methylated CpGs within CpG islands-82% hypermethylated in BRAF(V600E) organoids-including CIMP-associated genes and polycomb repressor complex 2 (PRC2) target genes. RNA sequencing showed concordant repression of these genes. Furthermore, BRAF(V600E) organoids demonstrated high expression of PRC2 core components (EZH2, SUZ12, and EED), showed PRC2-induced H3K27 trimethylation in promoter regions, and maintained a PRC2-associated embryonic phenotype. This phenotype was lost following mutation correction or DNA methylation inhibition. These findings show that BRAF(V600E) maintains aberrant DNA and histone methylation patterns in advanced colon cancer, likely preserving the transformed phenotype. Silencing of PRC2 target genes may contribute to this phenomenon. Epigenetic therapies may have value in the treatment of BRAF(V600E)-mutant colon cancer.