Methylation Profiles Reveal Distinct Subgroup of Hepatocellular Carcinoma Patients with Poor Prognosis

Hepatocellular Carcinoma (HCC) is one of the leading causes of cancer-associated mortality worldwide. However, the role of epigenetic changes such as aberrant DNA methylation in hepatocarcinogenesis remains largely unclear. In this study, we examined the methylation profiles of 59 HCC patients. Using consensus hierarchical clustering with feature selection, we identified three tumor subgroups based on their methylation profiles and correlated these subgroups with clinicopathological parameters. Interestingly, one tumor subgroup is different from the other 2 subgroups and the methylation profile of this subgroup is the most distinctly different from the non-tumorous liver tissues. Significantly, this subgroup of patients was found to be associated with poor overall as well as disease-free survival. To further understand the pathways modulated by the deregulation of methylation in HCC patients, we integrated data from both the methylation as well as the gene expression profiles of these 59 HCC patients. In these patients, while 4416 CpG sites were differentially methylated between the tumors compared to the adjacent non-tumorous tissues, only 536 of these CpG sites were associated with differences in the expression of their associated genes. Pathway analysis revealed that forty-four percent of the most significant upstream regulators of these 536 genes were involved in inflammation-related NFκB pathway. These data suggest that inflammation via the NFκB pathway play an important role in modulating gene expression of HCC patients through methylation. Overall, our analysis provides an understanding on aberrant methylation profile in HCC patients.

肝细胞癌（Hepatocellular Carcinoma, HCC）是全球范围内与癌症相关死亡的主要诱因之一。然而表观遗传改变（如异常DNA甲基化）在肝细胞癌变过程中所扮演的角色，目前仍未得到充分阐明。本研究针对59例肝细胞癌患者的甲基化谱展开分析：通过结合特征选择的一致性分层聚类（consensus hierarchical clustering）方法，基于患者的甲基化谱将肿瘤样本划分为三个亚组，并将这些亚组与临床病理参数进行关联分析。值得注意的是，其中一个肿瘤亚组与其余两个亚组存在显著差异，且该亚组的甲基化谱与非肿瘤肝组织的差异最为显著。更为重要的是，该亚组患者的总生存期与无病生存期均较差。为进一步阐明肝细胞癌患者中甲基化失调所调控的信号通路，本研究整合了这59例患者的甲基化谱与基因表达谱数据。在这些患者中，肿瘤组织与癌旁非肿瘤组织间共有4416个CpG位点（CpG sites）存在差异甲基化，但其中仅536个CpG位点与其关联基因的表达差异相关。通路富集分析显示，这536个基因的最显著上游调控因子中，有44%参与了炎症相关的NF-κB信号通路（NFκB pathway）。上述数据表明，通过NF-κB信号通路介导的炎症反应，可通过甲基化调控肝细胞癌患者的基因表达。综上，本研究的分析为阐明肝细胞癌患者的异常甲基化谱提供了新的认识。