Global Analysis of DNA Methylation by Methyl-Capture Sequencing Reveals Epigenetic Control of Cisplatin Resistance in Ovarian Cancer Cell

Wei Yu,Xu Han,Lihua Cheng,Yinghua He,Jingde Zhu,Biaoyang Lin,Chengmeng Jin,Lisha Li,Hongyu Zhang,Xiaoyan Lou,Kelong Ma,Matteo Pellegrini

doi:10.1371/journal.pone.0029450

Abstract

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.

Highlights

Drug resistance is the major reason leading to the high death rate of ovarian cancer
Our data is consistent with the previous reported cisplatin response profiles of A2780CP [17], indicating that the cell lines we had in the laboratory retains the difference in cisplatin resistance
The global MDB-seq data set generated for this pair of isogenic cells will be a useful resource for the research community interested in cisplatin resistance and epigenetics, and in ovarian cancer in general

Summary

Introduction

Drug resistance is the major reason leading to the high death rate of ovarian cancer. The chemotherapeutic agent cisplatin (cisdiamminedi-chloroplatinum(II)) is effective against ovarian carcinoma with an initial response rate of up to 70% [1]. DNA methylation of several genes in ovarian cancers including HSulf-1 [8], ABCG2 [9], EZH2 [10] have been found to be associated with drug resistance. Chang et al used global gene expression profiling to analyze cancer cells before and after treatment of DNA methyltransferase inhibitor5aza-29-deoxycytidine, which re-activates methylation silenced gene [12]. They identified several hundred genes that were downregulated in cisplatin resistant cancer cells and reactivated by the DNA methyltransferase inhibitor 5-aza-29-deoxycytidine [12]. Li et al compared the methylation pattern of A2780 and their derived resistant cell line after several cycles of drug selections using global CGI methylation arrays and mRNA expression microarrays [13]

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Conclusion