Gao Fei, Xia Yudong, Wang Junwen, Lin Zhilong, Ou Ying, Liu Xing, Liu Weilong, Zhou Boping, Luo Huijuan, Zhou Baojin, Wen Bo, Zhang Xiuqing, Huang Jian
Genome Biol. 2014 Dec 3;15(12):533. doi: 10.1186/s13059-014-0533-9.
Differences in 5-hydroxymethylcytosine, 5hmC, distributions may complicate previous observations of abnormal cytosine methylation statuses that are used for the identification of new tumor suppressor gene candidates that are relevant to human hepatocarcinogenesis. The simultaneous detection of 5-methylcytosine and 5-hydroxymethylcytosine is likely to stimulate the discovery of aberrantly methylated genes with increased accuracy in human hepatocellular carcinoma.
Here, we performed ultra-performance liquid chromatography/tandem mass spectrometry and single-base high-throughput sequencing, Hydroxymethylation and Methylation Sensitive Tag sequencing, HMST-seq, to synchronously measure these two modifications in human hepatocellular carcinoma samples. After identification of differentially methylated and hydroxymethylated genes in human hepatocellular carcinoma, we integrate DNA copy-number alterations, as determined using array-based comparative genomic hybridization data, with gene expression to identify genes that are potentially silenced by promoter hypermethylation.
We report a high enrichment of genes with epigenetic aberrations in cancer signaling pathways. Six genes were selected as tumor suppressor gene candidates, among which, ECM1, ATF5 and EOMES are confirmed via siRNA experiments to have potential anti-cancer functions.
5-羟甲基胞嘧啶（5hmC）分布的差异可能会使先前关于异常胞嘧啶甲基化状态的观察结果变得复杂，这些观察结果用于识别与人类肝癌发生相关的新的肿瘤抑制基因候选物。同时检测5-甲基胞嘧啶和5-羟甲基胞嘧啶可能会促进在人类肝细胞癌中更准确地发现异常甲基化基因。
在此，我们进行了超高效液相色谱/串联质谱分析以及单碱基高通量测序，即羟甲基化和甲基化敏感标签测序（HMST-seq），以同步测量人类肝癌样本中的这两种修饰。在鉴定出人类肝癌中差异甲基化和羟甲基化的基因后，我们将基于阵列的比较基因组杂交数据确定的DNA拷贝数改变与基因表达相结合，以识别可能因启动子高甲基化而沉默的基因。
我们报告了癌症信号通路中具有表观遗传异常的基因高度富集。选择了六个基因作为肿瘤抑制基因候选物，其中，通过小干扰RNA实验证实ECM1、ATF5和EOMES具有潜在的抗癌功能。
