Candidate DNA methylation drivers of acquired cisplatin resistance in ovarian cancer identified by methylome and expression profiling

Oncogene. 2012 Oct 18;31(42):4567-76. doi: 10.1038/onc.2011.611. Epub 2012 Jan 16.

Abstract

Multiple DNA methylation changes in the cancer methylome are associated with the acquisition of drug resistance; however it remains uncertain how many represent critical DNA methylation drivers of chemoresistance. Using isogenic, cisplatin-sensitive/resistant ovarian cancer cell lines and inducing resensitizaton with demethylating agents, we aimed to identify consistent methylation and expression changes associated with chemoresistance. Using genome-wide DNA methylation profiling across 27 578 CpG sites, we identified loci at 4092 genes becoming hypermethylated in chemoresistant A2780/cp70 compared with the parental-sensitive A2780 cell line. Hypermethylation at gene promoter regions is often associated with transcriptional silencing; however, expression of only 245 of these hypermethylated genes becomes downregulated in A2780/cp70 as measured by microarray expression profiling. Treatment of A2780/cp70 with the demethylating agent 2-deoxy-5'-azacytidine induces resensitization to cisplatin and re-expression of 41 of the downregulated genes. A total of 13/41 genes were consistently hypermethylated in further independent cisplatin-resistant A2780 cell derivatives. CpG sites at 9 of the 13 genes (ARHGDIB, ARMCX2, COL1A, FLNA, FLNC, MEST, MLH1, NTS and PSMB9) acquired methylation in ovarian tumours at relapse following chemotherapy or chemoresistant cell lines derived at the time of patient relapse. Furthermore, 5/13 genes (ARMCX2, COL1A1, MDK, MEST and MLH1) acquired methylation in drug-resistant ovarian cancer-sustaining (side population) cells. MLH1 has a direct role in conferring cisplatin sensitivity when reintroduced into cells in vitro. This combined genomics approach has identified further potential key drivers of chemoresistance whose expression is silenced by DNA methylation that should be further evaluated as clinical biomarkers of drug resistance.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adaptor Proteins, Signal Transducing / genetics
  • Antineoplastic Agents / pharmacology
  • Azacitidine / analogs & derivatives
  • Azacitidine / pharmacology
  • Cell Line, Tumor
  • Cisplatin / pharmacology*
  • Collagen Type I / genetics
  • CpG Islands / genetics
  • DNA Methylation*
  • Decitabine
  • Drug Resistance, Neoplasm / genetics*
  • Epigenomics / methods*
  • Female
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation, Neoplastic / drug effects
  • Humans
  • Hydroxamic Acids / pharmacology
  • Midkine
  • MutL Protein Homolog 1
  • Nerve Growth Factors / genetics
  • Nuclear Proteins / genetics
  • Oligonucleotide Array Sequence Analysis
  • Ovarian Neoplasms / drug therapy
  • Ovarian Neoplasms / genetics*
  • Ovarian Neoplasms / pathology
  • Proteins / genetics
  • Reverse Transcriptase Polymerase Chain Reaction
  • Sulfonamides / pharmacology

Substances

  • Adaptor Proteins, Signal Transducing
  • Antineoplastic Agents
  • Collagen Type I
  • Hydroxamic Acids
  • MDK protein, human
  • MLH1 protein, human
  • Nerve Growth Factors
  • Nuclear Proteins
  • Proteins
  • Sulfonamides
  • collagen type I, alpha 1 chain
  • mesoderm specific transcript protein
  • Midkine
  • Decitabine
  • MutL Protein Homolog 1
  • belinostat
  • Azacitidine
  • Cisplatin

Associated data

  • GEO/GSE28648