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

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.

Radiation-induced epigenetic DNA methylation modification of radiation-response pathways

“…In one study, methyl-capture sequencing was used to compare differences between 2 isogenic ovarian cancer cell lines, one of which has been rendered more resistant to cisplatin. 3 They found 2440 differentially methylated regions that mapped to several cell signaling pathways, among others.…”

“…Cisplatin resistance has been shown to have an epigenetic DNA methylation component in ovarian cancer. 3 Other evidence suggesting DNA methylation plays a role in radiation resistance have been studies showing treatment with 5-azacitidine to reduce global methylation has a radiosensitizing effect. 4,5 DNA methylation profiling technology with the Illumina HumanMethylation450 array allows us to query >450 000 loci within the genome and to cover 99% of RefSeq genes.…”

Upregulation of endogenous ICAM‐1 reduces ovarian cancer cell growth in the absence of immune cells

“…13,14 This might be caused by DNA demethylation, since the promoter of the ICAM-1 gene is one of the promoters that were found hypomethylated in a cisplatin resistant ovarian cancer cell line compared with its cisplatin-sensitive parental line. 42 Thus, either cisplatin induces ICAM-1 expression (through DNA demethylation or indirect) or cisplatin treatment selects for high ICAM-1 expressing cells by killing the ICAM-1 low expressing cells. By means of ATF-induced ICAM-1 expression, we show that it is likely that cisplatin treatment selects for ICAM-1 positive cells, since these are less sensitive to the treatment.…”

Long-term exposure to gefitinib induces acquired resistance through DNA methylation changes in the EGFR-mutant PC9 lung cancer cell line

“…Since most studies have focused on a limited number of candidate genes, many epigenetically silenced tumor suppressor genes involved in cancer-chemoresistance remain unidentified (12,14). Microarray-based screen pairing of the differential genetic profile of chemosensitive and chemoresistant cell lines have been reported (16)(17)(18)(19)(20) (21). However, only few reports focused on the relationship between egfr-tKi resistance and aberrant DNA methylation (22,23).…”