El Bouazzaoui Layla, Bugter Jeroen M, Küçükköse Emre, Verheem André, Post Jasmin B, Fenderico Nicola, Borel Rinkes Inne H M, Snippert Hugo J G, Maurice Madelon M, Kranenburg Onno
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.
iScience. 2025 Jun 14;28(7):112905. doi: 10.1016/j.isci.2025.112905. eCollection 2025 Jul 18.
In colon cancer, the BRAF mutation is strongly associated with the CpG island methylator phenotype (CIMP). Here, we characterized the contribution of BRAF to maintenance of aberrant DNA methylation using CRISPR-LbCpf1-corrected (V600E) organoids. DNA methylation analyses identified 5,187 differentially methylated CpGs within CpG islands-82% hypermethylated in BRAF organoids-including CIMP-associated genes and polycomb repressor complex 2 (PRC2) target genes. RNA sequencing showed concordant repression of these genes. Furthermore, BRAF 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 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-mutant colon cancer.
在结肠癌中，BRAF突变与CpG岛甲基化表型（CIMP）密切相关。在此，我们使用CRISPR-LbCpf1校正的（V600E）类器官来表征BRAF对维持异常DNA甲基化的作用。DNA甲基化分析在CpG岛内鉴定出5187个差异甲基化的CpG位点，其中82%在BRAF类器官中发生高甲基化，包括与CIMP相关的基因和多梳抑制复合物2（PRC2）的靶基因。RNA测序显示这些基因受到一致的抑制。此外，BRAF类器官显示出PRC2核心成分（EZH2、SUZ12和EED）的高表达，在启动子区域显示出PRC2诱导的H3K27三甲基化，并维持与PRC2相关的胚胎表型。在突变校正或DNA甲基化抑制后，这种表型消失。这些发现表明，BRAF在晚期结肠癌中维持异常的DNA和组蛋白甲基化模式，可能保留了转化表型。PRC2靶基因的沉默可能导致了这一现象。表观遗传疗法可能对BRAF突变型结肠癌的治疗具有价值。
