Laboratory of Clinical Genomics, Section on Developmental Genomics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA.
Br J Cancer. 2010 Jan 19;102(2):419-27. doi: 10.1038/sj.bjc.6605505. Epub 2010 Jan 5.
Testicular germ cell tumour (TGCT) is the most common malignant tumour in young males. Although aberrant DNA methylation is implicated in the pathophysiology of many cancers, only a limited number of genes are known to be epigenetically changed in TGCT. This report documents the genome-wide analysis of differential methylation in an in vitro model culture system. Interesting genes were validated in TGCT patient samples.
In this study, we used methylated DNA immunoprecipitation (MeDIP) and whole-genome tiling arrays to identify differentially methylated regions (DMRs).
We identified 35 208 DMRs. However, only a small number of DMRs mapped to promoters. A genome-wide analysis of gene expression revealed a group of differentially expressed genes that were regulated by DNA methylation. We identified several candidate genes, including APOLD1, PCDH10 and RGAG1, which were dysregulated in TGCT patient samples. Surprisingly, APOLD1 had previously been mapped to the TGCT susceptibility locus at 12p13.1, suggesting that it may be important in TGCT pathogenesis. We also observed aberrant methylation in the loci of some non-coding RNAs (ncRNAs). One of the ncRNAs, hsa-mir-199a, was downregulated in TGCT patient samples, and also in our in vitro model culture system.
This report is the first application of MeDIP-chip for identifying epigenetically regulated genes and ncRNAs in TGCT. We also demonstrated the function of intergenic and intronic DMRs in the regulation of ncRNAs.
睾丸生殖细胞肿瘤（TGCT）是年轻男性中最常见的恶性肿瘤。虽然异常的 DNA 甲基化与许多癌症的病理生理学有关，但已知只有少数基因在 TGCT 中发生表观遗传改变。本报告记录了在体外模型培养系统中差异甲基化的全基因组分析。在 TGCT 患者样本中验证了有趣的基因。
在这项研究中，我们使用甲基化 DNA 免疫沉淀（MeDIP）和全基因组平铺阵列来识别差异甲基化区域（DMR）。
我们鉴定了 35208 个 DMR。然而，只有少数 DMR 映射到启动子。全基因组基因表达分析揭示了一组受 DNA 甲基化调控的差异表达基因。我们鉴定了几个候选基因，包括 APOLD1、PCDH10 和 RGAG1，它们在 TGCT 患者样本中失调。令人惊讶的是，APOLD1 先前已被映射到 12p13.1 的 TGCT 易感性位点，表明它可能在 TGCT 发病机制中很重要。我们还观察到一些非编码 RNA（ncRNA）位点的异常甲基化。其中一个 ncRNA，hsa-mir-199a，在 TGCT 患者样本中下调，在我们的体外模型培养系统中也是如此。
本报告是首次应用 MeDIP-chip 鉴定 TGCT 中表观遗传调控基因和 ncRNA。我们还证明了基因间和内含子 DMR 在 ncRNA 调控中的功能。
Zotero 插件
