Development of a novel approach, the epigenome-based outlier approach, to identify tumor-suppressor genes silenced by aberrant DNA methylation
Development of a novel approach, the epigenome-based outlier approach, to identify tumor-suppressor genes silenced by aberrant DNA methylation
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DOI：
10.1016/j.canlet.2012.03.016
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发表时间：
2012-09-28
期刊：
影响因子：
9.7
通讯作者：
Ushijima, Toshikazu
中科院分区：
文献类型：
--
作者：
Kikuyama, Mizuho;Takeshima, Hideyuki;Ushijima, Toshikazu
鉴定因启动子 CpG 岛 (CGI) 异常甲基化而沉默的肿瘤抑制基因 (TSG) 很重要，但由于大量甲基化基因作为致癌过程的乘客而受到阻碍。为了克服这个问题，我们利用了这样一个事实：在正常细胞中，绝大多数癌症中甲基化的基因缺乏 RNA 聚合酶 II (Pol II)，并且在其启动子 CGI 中具有组蛋白 H3 赖氨酸 27 (H3K27me3) 三甲基化。首先，我们证明了乳腺癌中六个已知 TSG 中的三个和结肠癌中三个已知 TSG 中的两个具有 Pol II，并且在正常细胞中缺乏 H3K27me3，这是一般规则的异常值。 BRCA1、HOXA5、MLH1 和 RASSF1A 具有较高的 Pol II，但在正常细胞中仅以低水平表达，并且不太可能根据其在正常细胞中的表达状态被识别为异常值。然后，利用正常细胞中的表观基因组状态（Pol II 结合和 H3K27me3），我们对乳腺癌中的异常值进行了全基因组搜索，并鉴定了 14 个异常启动子 CGI。其中，DZIP1、FBN2、HOXA5和HOXC9被证实在原发性乳腺癌样本中被甲基化。在乳腺癌细胞系中敲除 DZIP1 会导致其生长增加，表明它是一种新型 TSG。与表达微阵列数据识别的异常值相比，基于表观基因组状态的异常值包含独特的 TSG，包括 DZIP1。这些结果表明，与基于表达的异常值方法相比，基于表观基因组的异常值方法能够识别一组不同的 TSG。 (C) 2012 Elsevier Ireland Ltd. 保留所有权利。
Identification of tumor-suppressor genes (TSGs) silenced by aberrant methylation of promoter CpG islands (CGIs) is important, but hampered by a large number of genes methylated as passengers of carcinogenesis. To overcome this issue, we here took advantage of the fact that the vast majority of genes methylated in cancers lack, in normal cells, RNA polymerase II (Pol II) and have trimethylation of histone H3 lysine 27 (H3K27me3) in their promoter CGIs. First, we demonstrated that three of six known TSGs in breast cancer and two of three in colon cancer had Pol II and lacked H3K27me3 in normal cells, being outliers to the general rule. BRCA1, HOXA5, MLH1, and RASSF1A had high Pol II, but were expressed only at low levels in normal cells, and were unlikely to be identified as outliers by their expression statuses in normal cells. Then, using epigenome statuses (Pol II binding and H3K27me3) in normal cells, we made a genome-wide search for outliers in breast cancers, and identified 14 outlier promoter CGIs. Among these, DZIP1, FBN2, HOXA5, and HOXC9 were confirmed to be methylated in primary breast cancer samples. Knockdown of DZIP1 in breast cancer cell lines led to increases of their growth, suggesting it to be a novel TSG. The outliers based on their epigenome statuses contained unique TSGs, including DZIP1, compared with those identified by the expression microarray data. These results showed that the epigenome-based outlier approach is capable of identifying a different set of TSGs, compared to the expression-based outlier approach. (C) 2012 Elsevier Ireland Ltd. All rights reserved.