Center for Human and Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands.
Clin Epigenetics. 2013 Jan 16;5(1):2. doi: 10.1186/1868-7083-5-2.
Cancer-specific hypermethylation of (promoter) CpG islands is common during the tumorigenesis of colon cancer. Although associations between certain genetic aberrations, such as BRAF mutation and microsatellite instability, and the CpG island methylator phenotype (CIMP), have been found, the mechanisms by which these associations are established are still unclear. We studied genome-wide DNA methylation differences between colorectal tumors carrying a BRAF mutation and BRAF wildtype tumors.
Using differential methylation hybridization on oligonucleotide microarrays representing 32,171 CpG-rich regions, we identified 1,770 regions with differential methylation between colorectal tumor and paired normal colon. Next, we compared the tumor/normal methylation ratios between different groups of patients. Related to CIMP, we identified 749 differentially methylated regions, of which 86% had a higher tumor/normal methylation ratio in the CIMP-positive group. We identified 758 regions with a BRAF mutation-specific methylation change, of which 96% had a higher tumor/normal methylation ratio in the BRAF mutant group. Among the genes affected by BRAF mutation-specific methylation changes, we found enrichment of several cancer-related pathways, including the PI3 kinase and Wnt signaling pathways. To focus on genes that are silenced in a tumor-specific rather than a lineage-specific manner, we used information on the epigenetic silencing mark H3K27me3 in embryonic stem (ES) cells. Among the genes showing BRAF mutation-specific promoter methylation but no H3K27me3 mark in ES cells were forkhead box (FOX) transcription factors associated with the PI3 kinase pathway, as well as MLH1 and SMO. Repression of FOXD3 gene expression in tumors could be related to its promoter hypermethylation.
We identified new BRAF mutation-specific methylation changes in colorectal cancer. Epigenetic downregulation of these targets may contribute to mutationally active BRAF-driven tumorigenesis, explaining its association with aberrant DNA methylation.
在结肠癌的肿瘤发生过程中，（启动子）CpG 岛的癌症特异性高甲基化很常见。尽管已经发现了某些遗传异常（如 BRAF 突变和微卫星不稳定性）与 CpG 岛甲基化表型（CIMP）之间的关联，但这些关联建立的机制尚不清楚。我们研究了携带 BRAF 突变的结直肠肿瘤与 BRAF 野生型肿瘤之间全基因组 DNA 甲基化差异。
我们使用代表 32171 个富含 CpG 的区域的寡核苷酸微阵列进行差异甲基化杂交，鉴定出 1770 个在结直肠肿瘤与配对正常结肠之间存在差异甲基化的区域。接下来，我们比较了不同组患者之间的肿瘤/正常甲基化比值。与 CIMP 相关，我们鉴定出 749 个差异甲基化区域，其中 CIMP 阳性组中有 86%的区域肿瘤/正常甲基化比值较高。我们鉴定出 758 个具有 BRAF 突变特异性甲基化变化的区域，其中 BRAF 突变组中有 96%的区域肿瘤/正常甲基化比值较高。在受 BRAF 突变特异性甲基化变化影响的基因中，我们发现了几个癌症相关途径的富集，包括 PI3 激酶和 Wnt 信号通路。为了关注以肿瘤特异性而不是谱系特异性方式沉默的基因，我们使用了胚胎干细胞（ES）中表观遗传沉默标记 H3K27me3 的信息。在表现出 BRAF 突变特异性启动子甲基化但在 ES 细胞中没有 H3K27me3 标记的基因中，有与 PI3 激酶途径相关的 FOX 转录因子，以及 MLH1 和 SMO。肿瘤中 FOXD3 基因表达的抑制可能与其启动子过度甲基化有关。
我们在结直肠癌中发现了新的 BRAF 突变特异性甲基化变化。这些靶标的表观遗传下调可能有助于突变激活的 BRAF 驱动的肿瘤发生，解释了其与异常 DNA 甲基化的关联。
