BRAFV600E maintains the CpG island methylator phenotype, and DNA methylation of PRC2 targets genes in colon cancer
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
Affiliations
Layla El Bouazzaoui
Division of Imaging and Cancer, Laboratory Translational Oncology, UMC Utrecht, Utrecht, the Netherlands; Oncode Institute and Center for Molecular Medicine, UMC Utrecht, Utrecht, the Netherlands; Utrecht Platform for Organoid Technology, Utrecht University, Utrecht, the Netherlands
Jeroen M. Bugter
Oncode Institute and Center for Molecular Medicine, UMC Utrecht, Utrecht, the Netherlands
Emre Küçükköse
Division of Imaging and Cancer, Laboratory Translational Oncology, UMC Utrecht, Utrecht, the Netherlands
André Verheem
Division of Imaging and Cancer, Laboratory Translational Oncology, UMC Utrecht, Utrecht, the Netherlands
Jasmin B. Post
Oncode Institute and Center for Molecular Medicine, UMC Utrecht, Utrecht, the Netherlands
Nicola Fenderico
Oncode Institute and Center for Molecular Medicine, UMC Utrecht, Utrecht, the Netherlands
Inne H.M. Borel Rinkes
Division of Imaging and Cancer, Laboratory Translational Oncology, UMC Utrecht, Utrecht, the Netherlands
Hugo J.G. Snippert
Oncode Institute and Center for Molecular Medicine, UMC Utrecht, Utrecht, the Netherlands
Madelon M. Maurice
Oncode Institute and Center for Molecular Medicine, UMC Utrecht, Utrecht, the Netherlands; Utrecht Platform for Organoid Technology, Utrecht University, Utrecht, the Netherlands; Corresponding author
Onno Kranenburg
Division of Imaging and Cancer, Laboratory Translational Oncology, UMC Utrecht, Utrecht, the Netherlands; Utrecht Platform for Organoid Technology, Utrecht University, Utrecht, the Netherlands; Corresponding author
Summary: 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.
