# BRAFV600E maintains the CpG island methylator phenotype, and DNA methylation of PRC2 targets genes in colon cancer

## TL;DR

This study shows that the BRAFV600E mutation helps maintain abnormal DNA methylation in colon cancer, which could be targeted with epigenetic therapies.

## Contribution

The study reveals that BRAFV600E sustains DNA methylation and PRC2 gene silencing in colon cancer.

## Key findings

- BRAFV600E correction leads to demethylation and gene reactivation in colon cancer organoids.
- BRAFV600E maintains hypermethylation of PRC2 target genes in colorectal cancer.
- Epigenetic therapies may reverse the aggressive phenotype of BRAFV600E-mutant 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 using CRISPR-LbCpf1-corrected BRAF (V600E) organoids. DNA methylation analyses identified 5,187 differentially methylated CpGs within CpG islands—82% hypermethylated in BRAFV600E organoids—including CIMP-associated genes and polycomb repressor complex 2 (PRC2) target genes. RNA sequencing showed concordant repression of these genes. Furthermore, BRAFV600E 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 BRAFV600E 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 BRAFV600E-mutant colon cancer.

•Correction of BRAFV600E leads to demethylation and de-repression of CIMP-H genes•BRAFV600E maintains hypermethylation of PRC2 target genes in CRC•Epigenetic therapies may counteract the aggressive phenotype of BRAFV600E mutant CRC

Correction of BRAFV600E leads to demethylation and de-repression of CIMP-H genes

BRAFV600E maintains hypermethylation of PRC2 target genes in CRC

Epigenetic therapies may counteract the aggressive phenotype of BRAFV600E mutant CRC

Molecular Genetics; Epigenetics; Cancer; Transcriptomics