Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
Deep sequencing reveals distinct patterns of DNA methylation in prostate cancer
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DOI：
10.1101/gr.119347.110
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发表时间：
2011-07-01
期刊：
影响因子：
7
通讯作者：
Chinnaiyan, Arul M.
中科院分区：
文献类型：
--
作者：
Kim, Jung H.;Dhanasekaran, Saravana M.;Chinnaiyan, Arul M.
从前驱病变开始，异常DNA甲基化标志着前列腺癌进展的整个谱。我们使用methylplex -下一代测序（M-NGS）在选定的前列腺组织和细胞系中绘制了全球DNA甲基化模式。基于隐马尔可夫模型的下一代序列分析鉴定出每个样本有68000个甲基化区域。虽然良性癌旁组织和癌旁组织的CpG岛（CGI）甲基化没有差异，但总体启动子CGI甲基化显著增加，从良性癌旁组织的12.6%增加到局部癌和转移癌组织的19.3%和21.8% （p值< 2 3 10(-16)）。我们在转录起始位点周围发现了明显的启动子甲基化模式，其中甲基化不仅发生在CGI上，也发生在CGI的侧翼区域和稀疏启动子上。在前列腺组织中6691个甲基化启动子中，2481个差异甲基化区域（DMRs）是癌症特异性的，包括许多新的DMRs。WFDC2启动子中的一种新的癌症特异性DMR在癌症（17/22组织，6/6细胞系）中显示频繁的甲基化，但在良性组织（0/10）和正常PrEC细胞中没有甲基化。LNCaP DNA甲基化和H3K4me3数据的整合表明了交替转录起始位点利用的表观遗传机制，当这些修饰出现在同一启动子上时，它们会分离到不同的区域。最后，我们观察到ERG基因融合阳性和阴性癌症之间重复元件甲基化的差异，特别是LINE-1，我们在组织面板上使用焦磷酸测序证实了这一观察结果。这一全面的甲基组图谱将进一步加深我们对前列腺癌进展中的表观遗传调控的理解。
Beginning with precursor lesions, aberrant DNA methylation marks the entire spectrum of prostate cancer progression. We mapped the global DNA methylation patterns in select prostate tissues and cell lines using MethylPlex-next-generation sequencing (M-NGS). Hidden Markov model-based next-generation sequence analysis identified similar to 68,000 methylated regions per sample. While global CpG island (CGI) methylation was not differential between benign adjacent and cancer samples, overall promoter CGI methylation significantly increased from similar to 12.6% in benign samples to 19.3% and 21.8% in localized and metastatic cancer tissues, respectively (P-value < 2 3 10(-16)). We found distinct patterns of promoter methylation around transcription start sites, where methylation occurred not only on the CGIs, but also on flanking regions and CGI sparse promoters. Among the 6691 methylated promoters in prostate tissues, 2481 differentially methylated regions (DMRs) are cancer-specific, including numerous novel DMRs. A novel cancer-specific DMR in the WFDC2 promoter showed frequent methylation in cancer (17/22 tissues, 6/6 cell lines), but not in the benign tissues (0/10) and normal PrEC cells. Integration of LNCaP DNA methylation and H3K4me3 data suggested an epigenetic mechanism for alternate transcription start site utilization, and these modifications segregated into distinct regions when present on the same promoter. Finally, we observed differences in repeat element methylation, particularly LINE-1, between ERG gene fusion-positive and -negative cancers, and we confirmed this observation using pyrosequencing on a tissue panel. This comprehensive methylome map will further our understanding of epigenetic regulation in prostate cancer progression.