Boot Arnoud, Oosting Jan, van Eendenburg Jaap D H, Kuppen Peter J K, Morreau Hans, van Wezel Tom
Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands.
Department of Surgery, Leiden University Medical Center, Leiden, The Netherlands.
PLoS One. 2017 Sep 20;12(9):e0184900. doi: 10.1371/journal.pone.0184900. eCollection 2017.
Genetic and epigenetic alterations mark colorectal cancer (CRC). Global hypomethylation is observed in nearly all CRC, but a distinct subset of CRC show the CpG Island Methylator Phenotype (CIMP). These tumors show DNA hypermethylation of a specific subset of CpG islands, resulting in transcriptional downregulation of nearby genes. Recently we reported the establishment of novel CRC cell lines derived from primary and metastatic CRC tissues. In this study we describe the DNA methylation profiling of these low passage CRC cell lines. We generated global DNA methylation profiles with Infinium HumanMethylation450 BeadChips and analysed them in conjunction with matching gene expression profiles. Multidimensional scaling of the DNA methylation and gene expression datasets showed that BRAF mutated cell lines form a distinct group. In this group we investigated the 706 loci which we have previously identified to be hypermethylated in BRAF mutant CRC. We validated the significant findings in the The Cancer Genome Atlas colon adenocarcinoma dataset. Our analysis identified ELOVL5, FAM127B, MTERF1, ZNF606 to be subject to transcriptional downregulation through DNA hypermethylation in CRC. We further investigated ELOVL5 with qPCR and immunohistochemical staining, validating our results, but did not find a clear relation between ELOVL5 expression and tumor stage or relapse free survival. ELOVL5, FAM127B, MTERF1, ZNF606 are involved in important cellular processes such as apoptosis, lipogenesis and the downstream transcriptional effect of the MAPK-pathway. We have identified a DNA methylation profile regulating key cellular processes in CRC, resulting in a growth advantage to the tumor cells.
基因和表观遗传改变是结直肠癌（CRC）的标志。几乎在所有的结直肠癌中都观察到全基因组低甲基化，但有一个独特的结直肠癌亚群表现出CpG岛甲基化表型（CIMP）。这些肿瘤显示出特定CpG岛亚群的DNA高甲基化，导致附近基因的转录下调。最近我们报道了从原发性和转移性结直肠癌组织中建立新型结直肠癌细胞系。在本研究中，我们描述了这些低传代数结直肠癌细胞系的DNA甲基化谱。我们使用Infinium HumanMethylation450 BeadChips生成了全基因组DNA甲基化谱，并结合匹配的基因表达谱对其进行分析。DNA甲基化和基因表达数据集的多维标度分析表明，BRAF突变的细胞系形成一个独特的组。在这个组中，我们研究了我们之前确定在BRAF突变型结直肠癌中高甲基化的706个位点。我们在癌症基因组图谱结肠腺癌数据集中验证了这些重要发现。我们的分析确定ELOVL5、FAM127B、MTERF1、ZNF606在结直肠癌中因DNA高甲基化而受到转录下调。我们进一步用qPCR和免疫组织化学染色研究了ELOVL5，验证了我们的结果，但未发现ELOVL5表达与肿瘤分期或无复发生存之间存在明确关系。ELOVL5、FAM127B、MTERF1、ZNF606参与重要的细胞过程，如细胞凋亡、脂肪生成和MAPK信号通路的下游转录效应。我们确定了一种调节结直肠癌关键细胞过程的DNA甲基化谱，从而赋予肿瘤细胞生长优势。
