Genome-wide promoter analysis uncovers portions of the cancer methylome
Genome-wide promoter analysis uncovers portions of the cancer methylome
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DOI：
10.1158/0008-5472.can-07-5913
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发表时间：
2008-04-15
期刊：
影响因子：
11.2
通讯作者：
Sidransky, David
中科院分区：
文献类型：
--
作者：
Hoque, Mohammad Obaidul;Kim, Myoung Sook;Sidransky, David
DNA甲基化在癌症和其他疾病中介导CpG岛基因的表观遗传沉默中起作用。鉴定癌细胞中所有甲基化的基因启动子“癌症甲基化组”将极大地促进我们对肿瘤发生中基因调控网络的理解。我们以前描述了一种新的方法，确定甲基化的肿瘤抑制基因的基础上，药理学解蔽的启动子区域和微阵列分析的再表达检测。在这项研究中，我们修改和大大提高了候选人的选择新的启动子结构算法和微阵列数据产生的5种主要癌症类型的20种癌细胞系的基础上。我们确定了一组200个候选基因，这些基因在整个基因组中聚集，其中25个先前被报道为具有癌症特异性启动子甲基化。通过亚硫酸氢盐测序或甲基化特异性PCR（MSP）测试其余175个基因的启动子甲基化。175个基因中有82个（47%）在细胞系中被发现甲基化，这82个基因中有53个（65%）在原发性肿瘤组织中被甲基化。在这53个基因中，在28个基因中鉴定出癌症特异性甲基化（53个基因中的28个; 53%）。此外，我们在代表13种癌症类型的300个原发性肿瘤中用定量MSP测试了28个新鉴定的癌症特异性甲基化基因中的8个。我们发现至少一个基因的癌症特异性甲基化在所有癌症类型中都有很高的频率。大量具有癌症特异性甲基化的基因的鉴定为诊断和治疗干预提供了新的靶点，并为肿瘤生物学的基础研究开辟了肥沃的途径。
DNA methylation has a role in mediating epigenetic silencing of CpG island genes in cancer and other diseases. Identification of all gene promoters methylated in cancer cells "the cancer methylome" would greatly advance our understanding of gene regulatory networks in tumorigenesis. We previously described a new method of identifying methylated tumor suppressor genes based on pharmacologic unmasking of the promoter region and detection of re-expression on microarray analysis. In this study, we modified and greatly improved the selection of candidates based on new promoter structure algorithm and microarray data generated from 20 cancer cell lines of 5 major cancer types. We identified a set of 200 candidate genes that cluster throughout the genome of which 25 were previously reported as harboring cancer-specific promoter methylation. The remaining 175 genes were tested for promoter methylation by bisulfite sequencing or methylation-specific PCR (MSP). Eighty-two of 175 (47%) genes were found to be methylated in cell lines, and 53 of these 82 genes (65%) were methylated in primary tumor tissues. From these 53 genes, cancer-specific methylation was identified in 28 genes (28 of 53; 53%). Furthermore, we tested 8 of the 28 newly identified cancer-specific methylated genes with quantitative MSP in a panel of 300 primary tumors representing 13 types of cancer. We found cancer-specific methylation of at least one gene with high frequency in all cancer types. Identification of a large number of genes with cancer-specific methylation provides new targets for diagnostic and therapeutic intervention, and opens fertile avenues for basic research in tumor biology.