Global analysis of DNA methylation by Methyl-Capture sequencing reveals epigenetic control of cisplatin resistance in ovarian cancer cell

• Published in: PloS one 2011-12, Vol.6 (12), p.e29450-e29450
• Main Authors: Yu, Wei, Jin, Chengmeng, Lou, Xiaoyan, Han, Xu, Li, Lisha, He, Yinghua, Zhang, Hongyu, Ma, Kelong, Zhu, Jingde, Cheng, Lihua, Lin, Biaoyang
• Format: Article
• Language: English
• Subjects: Antineoplastic Agents - pharmacology; Azacytidine; Bioinformatics; Biology; Bisulfite; Cancer; Cancer genetics; Cell growth; Cell Line, Tumor; Cisplatin; Cisplatin - pharmacology; CpG islands; Cytotoxicity; Demethylation; Deoxyribonucleic acid; Development and progression; DNA; DNA damage; DNA Methylation; DNA sequencing; Drug resistance; Drug Resistance, Neoplasm; Encyclopedias; Epidermal growth factor; Epigenesis, Genetic; Epigenetic inheritance; Epigenetics; Female; Gene expression; Gene sequencing; Genomes; Genomics; Humans; Kinases; Mass Spectrometry; MBD2 protein; Medicine; Methylation; Mortality; Ovarian cancer; Ovarian carcinoma; Ovarian Neoplasms - genetics; Ovarian Neoplasms - pathology; Phosphorylation; Polymerase Chain Reaction; Protein binding; Proteins; Reagents; Signal transduction; Sulfites
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0029450

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.