Systems Biology Division, Zhejiang-California International Nanosystems Institute (ZCNI), Zhejiang University, Hangzhou, Zhejiang Providence, China.
PLoS One. 2011;6(12):e29450. doi: 10.1371/journal.pone.0029450. Epub 2011 Dec 22.
Cisplatin resistance is one of the major reasons leading to the high death rate of ovarian cancer. Methyl-Capture sequencing (MethylCap-seq), which combines precipitation of methylated DNA by recombinant methyl-CpG binding domain of MBD2 protein with NGS, global and unbiased analysis of global DNA methylation patterns. We applied MethylCap-seq to analyze genome-wide DNA methylation profile of cisplatin sensitive ovarian cancer cell line A2780 and its isogenic derivative resistant line A2780CP. We obtained 21,763,035 raw reads for the drug resistant cell line A2780CP and 18,821,061reads for the sensitive cell line A2780. We identified 1224 hyper-methylated and 1216 hypomethylated DMRs (differentially methylated region) in A2780CP compared to A2780. Our MethylCap-seq data on this ovarian cancer cisplatin resistant model provided a good resource for the research community. We also found that A2780CP, compared to A2780, has lower observed to expected methylated CpG ratios, suggesting a lower global CpG methylation in A2780CP cells. Methylation specific PCR and bisulfite sequencing confirmed hypermethylation of PTK6, PRKCE and BCL2L1 in A2780 compared with A2780CP. Furthermore, treatment with the demethylation reagent 5-aza-dC in A2780 cells demethylated the promoters and restored the expression of PTK6, PRKCE and BCL2L1.
顺铂耐药是导致卵巢癌死亡率居高不下的主要原因之一。甲基化捕获测序（MethylCap-seq）结合了重组 MBD2 蛋白的甲基化 DNA 沉淀与 NGS，实现了对全基因组 DNA 甲基化模式的全面、无偏分析。我们应用 MethylCap-seq 分析了顺铂敏感卵巢癌细胞系 A2780 及其同源耐药系 A2780CP 的全基因组 DNA 甲基化谱。我们获得了耐药细胞系 A2780CP 的 21763035 个原始读数和敏感细胞系 A2780 的 18821061 个读数。与 A2780 相比，我们在 A2780CP 中鉴定出了 1224 个高甲基化和 1216 个低甲基化 DMR（差异甲基化区域）。我们在这个卵巢癌顺铂耐药模型上的 MethylCap-seq 数据为研究界提供了一个很好的资源。我们还发现，与 A2780 相比，A2780CP 的观测到的与预期的甲基化 CpG 比值更低，这表明 A2780CP 细胞中的全局 CpG 甲基化水平更低。甲基化特异性 PCR 和亚硫酸氢盐测序证实，与 A2780CP 相比，A2780 中的 PTK6、PRKCE 和 BCL2L1 发生了高甲基化。此外，在 A2780 细胞中用去甲基化试剂 5-aza-dC 处理可使 PTK6、PRKCE 和 BCL2L1 的启动子去甲基化并恢复其表达。
