Medical and Molecular Genetics, School of Clinical and Experimental Medicine, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom.
Cancer Res. 2011 Apr 15;71(8):2988-99. doi: 10.1158/0008-5472.CAN-10-4026. Epub 2011 Mar 1.
Epigenetic profiling of tumor DNAs may reveal important new theranostic targets to improve prognosis and treatment of advanced cancer patients. In this study, we performed a genome-wide profile of DNA methylation patterns in sporadic breast tumors by using the HumanMethylation27 BeadChips to assess relationships between DNA methylation changes and patient tumor characteristics. The arrays identified 264 hypermethylated loci/genes present in genomic CpG islands. Hierarchical clustering based on methylation levels divided the specimens into three distinct groups, within which certain clinical features also clustered. Statistically significant differences were determined between overall methylation levels of these clusters and estrogen receptor and progesterone receptor (ER/PR) status (P = 0.001), tumor relapse (P = 0.035), and lymph node metastasis (P = 0.042). We identified several individual methylated genes associated with clinical features, including six genes (RECK, SFRP2, UAP1L1, ACADL, ITR, and UGT3A1) that showed statistical significance between methylation and relapse-free survival. Notably, the RECK gene in this group has been associated in other cancers with poorest prognosis. Among the leading relapse-associated genes and the genes associated with ER/PR status, we sequenced an independent set of paired normal/tumor breast DNA samples to confirm tumor specificity of methylation. Further, we carried out quantitative real-time reverse transcriptase PCR to confirm reduced expression in methylated tumors. Our findings suggest the utility for the DNA methylation patterns in these genes as clinically useful surrogate markers in breast cancer, as well as new molecular pathways for further investigation as therapeutic targets.
肿瘤 DNA 的表观遗传谱分析可能揭示重要的新治疗靶点，以改善晚期癌症患者的预后和治疗效果。在这项研究中，我们使用 HumanMethylation27 BeadChips 对散发性乳腺癌肿瘤的 DNA 甲基化模式进行了全基因组分析，以评估 DNA 甲基化变化与患者肿瘤特征之间的关系。该阵列确定了 264 个存在于基因组 CpG 岛中的高甲基化基因/位点。基于甲基化水平的层次聚类将标本分为三个不同的组，其中某些临床特征也存在聚类。这些聚类的总体甲基化水平与雌激素受体和孕激素受体（ER/PR）状态（P=0.001）、肿瘤复发（P=0.035）和淋巴结转移（P=0.042）之间存在统计学显著差异。我们鉴定了一些与临床特征相关的个体甲基化基因，包括与复发无进展生存相关的 6 个基因（RECK、SFRP2、UAP1L1、ACADL、ITR 和 UGT3A1）。特别是，该组中的 RECK 基因在其他癌症中与最差的预后相关。在主要与复发相关的基因和与 ER/PR 状态相关的基因中，我们对一组独立的配对正常/肿瘤乳腺 DNA 样本进行了测序，以确认甲基化的肿瘤特异性。此外，我们进行了定量实时逆转录 PCR 以确认甲基化肿瘤中的表达降低。我们的研究结果表明，这些基因中的 DNA 甲基化模式可用作乳腺癌的临床有用替代标志物，以及作为进一步研究的新分子途径和治疗靶点。
