Epigenetic inactivation of the putative DNA/RNA helicase SLFN11 in human cancer confers resistance to platinum drugs

Oncotarget. 2016 Jan 19;7(3):3084-97. doi: 10.18632/oncotarget.6413.


Platinum-derived drugs such as cisplatin and carboplatin are among the most commonly used cancer chemotherapy drugs, but very few specific molecular and cellular markers predicting differential sensitivity to these agents in a given tumor type have been clearly identified. Epigenetic gene silencing is increasingly being recognized as a factor conferring distinct tumoral drug sensitivity, so we have used a comprehensive DNA methylation microarray platform to interrogate the widely characterized NCI60 panel of human cancer cell lines with respect to CpG methylation status and cisplatin/carboplatin sensitivity. Using this approach, we have found promoter CpG island hypermethylation-associated silencing of the putative DNA/RNA helicase Schlafen-11 (SLFN11) to be associated with increased resistance to platinum compounds. We have also experimentally validated these findings in vitro. In this setting, we also identified the BRCA1 interacting DHX9 RNA helicase (also known as RHA) as a protein partner for SLFN11, suggesting a mechanistic pathway for the observed chemoresistance effect. Most importantly, we have been able to extend these findings clinically, following the observation that those patients with ovarian and non-small cell lung cancer carrying SLFN11 hypermethylation had a poor response to both cisplatin and carboplatin treatments. Overall, these results identify SLFN11 epigenetic inactivation as a predictor of resistance to platinum drugs in human cancer.

Keywords: CpG island methylation; DNA-damaging agents; SLFN11; chemoresistance; epigenetics.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antineoplastic Agents / pharmacology*
  • Carboplatin / pharmacology*
  • Carcinoma, Non-Small-Cell Lung / drug therapy*
  • Carcinoma, Non-Small-Cell Lung / genetics
  • Cell Line, Tumor
  • Cisplatin / pharmacology*
  • CpG Islands / drug effects
  • DEAD-box RNA Helicases / metabolism
  • DNA / metabolism
  • DNA Methylation / genetics
  • Drug Resistance, Neoplasm / genetics*
  • Epigenesis, Genetic
  • Female
  • Gene Expression Regulation, Neoplastic
  • HCT116 Cells
  • HEK293 Cells
  • Humans
  • Lung Neoplasms / drug therapy*
  • Lung Neoplasms / genetics
  • MCF-7 Cells
  • Male
  • Middle Aged
  • Neoplasm Proteins / metabolism
  • Nuclear Proteins / genetics*
  • Nuclear Proteins / metabolism
  • Ovarian Neoplasms / drug therapy*
  • Ovarian Neoplasms / genetics
  • RNA Interference
  • RNA, Small Interfering / genetics


  • Antineoplastic Agents
  • Neoplasm Proteins
  • Nuclear Proteins
  • RNA, Small Interfering
  • SLFN11 protein, human
  • DNA
  • Carboplatin
  • DHX9 protein, human
  • DEAD-box RNA Helicases
  • Cisplatin