Identification Of Aberrant DNA Methylation Events Driving Breast Cancer Drug Resistance

Epigenetic plays an important role in the drug response of the tumor.DNA methylation is one of the most general epigenetic modifications,and its aberrant change was first discovered marker associated with chemo-resistance.Drug induced global DNA hyper-methylation is known to propel cancer drug resistance.Identification of the drug resistance driving DNA methylation events from massive random DNA methylation background is critical and challenging.In view of this challenge,we use strategy to screen DNA methylation events that stably existed or continuously increased in gradient chemo-resistance cell model.Using high throughput technology Methylated DNA Immunoprecipitation sequencing(MeDIP-seq),we analysed the methylome of MCF-7/PTX 90nM(90R)and MCF-7/PTX 150nM(150R),two cell lines with progressively increased drug resistance indexes.We identified stably exited DNA methylation events of 205 gene promoters 59 of them were further methylated in 150R.In combine with RNA sequencing(RNA-seq)data,8 promoter stably hypermethylated and expression down-regulated genes were filtered,include C8orf34,CNTNAP2,DOC2B,ELOVL4,PPP1R14C,RIMS2,SLC22A31 and VANGL2,5 of them:C8orf34,CNTNAP2,RIMS2,SLC22A31,VANGL2 showed more dramatic expression reduction,consistent with the increased DNA methylation degree.Using transmethylase inhibitor proved that these methylation events inhibited the expression of the corresponding genes.Further analysis confirmed that these specific abnormal DNA methylation events acted as important driving force in the formation of breast cancer chemoresistance phenotype,recovery of their expression could partly reverse the resistant phenotype of drug resistant cell lines.Clinical prognostic analysis using the Kaplan-Meier database further supported our laboratory results,indicated that the down-regulation of these gene expression levels was significantly associated with poor prognosis in breast cancer patients who received chemotherapy.Our study provide an effective system for the identification of the driving methylation events in tumor chemo-resistance,which will be helpful for the mechanism study and clinical application.