通过 TCGA 数据库搜索鉴定出五个异常表达的基因，这些基因可能通过 DNA 甲基化改变参与肝癌的发生。
Identification by TCGA database search of five genes that are aberrantly expressed and involved in hepatocellular carcinoma potentially via DNA methylation changes.
机构信息
Center for Health and Environmental Risk Research, National Institute for Environmental Studies, Tsukuba, Japan.
Graduate School of Pharmaceutical Sciences, Tokyo University of Science, Noda, Japan.
出版信息
Environ Health Prev Med. 2020 Jul 23;25(1):31. doi: 10.1186/s12199-020-00871-8.
BACKGROUND
Various treatments for hepatocellular carcinoma (HCC) are utilized in clinical practice; however, the prognosis is still poor on account of high recurrence rates. DNA methylation levels of CpG islands around promoters (promoter CpGis) inversely regulate gene expression and closely involved in carcinogenesis. As a new strategy, several chemicals globally inhibiting DNA methylation have been developed aiming at reducing DNA methylation levels and maintaining the expression of tumor suppressor genes. On the other hand, since these drugs nonspecifically modify DNA methylation, they can cause serious adverse effects. In order to ameliorate the methods by targeting specific CpGs, information of cancer-related genes that are regulated by DNA methylation is required.
METHODS
We searched candidate genes whose expressions were regulated by DNA methylation of promoter CpGi and which are involved in HCC cases. To do so, we first identified genes whose expression were changed in HCC by comparing gene expressions of 371 HCC tissues and 41 non-tumor tissues using the Cancer Genome Atlas (TCGA) database. The genes were further selected for poor prognosis by log-rank test of Kaplan-Meier plot and for cancer relevance by Pubmed search. Expression profiles of upregulated genes in HCC tissues were assessed by Gene Ontology (GO) analysis. Finally, using DNA methylation data of TCGA database, we selected genes whose promoter DNA methylation levels were inversely correlated with gene expression.
RESULTS
We found 115 genes which were significantly up- or downregulated in HCC tissues and were associated with poor prognosis and cancer relevance. The upregulated genes were significantly enriched in cell division, cell cycle, and cell proliferation. Among the upregulated genes in HCC, we identified hypomethylation of CpGis around promoters of FANCB, KIF15, KIF4A, ERCC6L, and UBE2C. In addition, TCGA data showed that the tumor suppressor gene P16 is unexpectedly overexpressed in many types of cancers.
CONCLUSIONS
We identified five candidate genes whose expressions were regulated by DNA methylation of promoter CpGi and associate with cancer cases and poor prognosis in HCC. Modification of site-specific DNA methylation of these genes enables a different approach for HCC treatment with higher selectivity and lower adverse effects.
背景
在临床实践中，有多种治疗肝细胞癌（HCC）的方法，但由于高复发率，预后仍较差。启动子周围 CpG 岛的 DNA 甲基化水平（启动子 CpGis）可反向调节基因表达，与癌症的发生密切相关。作为一种新策略，全球已有几种化学物质被开发出来，旨在降低 DNA 甲基化水平并维持肿瘤抑制基因的表达，这些药物可抑制 DNA 甲基化。另一方面，由于这些药物非特异性地修饰 DNA 甲基化，它们可能会引起严重的不良反应。为了改善针对特定 CpG 的方法，需要了解受 DNA 甲基化调控的与癌症相关的基因信息。
方法
我们首先使用癌症基因组图谱（TCGA）数据库比较了 371 例 HCC 组织和 41 例非肿瘤组织的基因表达，以确定受启动子 CpGi DNA 甲基化调控且与 HCC 相关的候选基因。通过 Kaplan-Meier 图的对数秩检验选择预后不良的基因，通过 Pubmed 搜索选择与癌症相关的基因。采用基因本体论（GO）分析评估 HCC 组织中上调基因的表达谱。最后，我们使用 TCGA 数据库的 DNA 甲基化数据，选择与基因表达呈负相关的基因。
结果
我们发现 115 个基因在 HCC 组织中显著上调或下调，与预后不良和癌症相关。上调基因在细胞分裂、细胞周期和细胞增殖中显著富集。在 HCC 中上调的基因中，我们发现 FANCB、KIF15、KIF4A、ERCC6L 和 UBE2C 基因启动子 CpGis 的低甲基化。此外，TCGA 数据表明，肿瘤抑制基因 P16 在许多类型的癌症中出乎意料地过表达。
结论
我们鉴定了 5 个候选基因，这些基因的表达受启动子 CpGi 的 DNA 甲基化调控，并与 HCC 中的癌症病例和不良预后相关。这些基因的特定部位 DNA 甲基化的修饰为 HCC 治疗提供了一种更高选择性和更低不良反应的新方法。
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