Small molecule inhibitors uncover synthetic genetic interactions of human flap endonuclease 1 (FEN1) with DNA damage response genes

PLoS One. 2017 Jun 19;12(6):e0179278. doi: 10.1371/journal.pone.0179278. eCollection 2017.

Abstract

Flap endonuclease 1 (FEN1) is a structure selective endonuclease required for proficient DNA replication and the repair of DNA damage. Cellularly active inhibitors of this enzyme have previously been shown to induce a DNA damage response and, ultimately, cell death. High-throughput screens of human cancer cell-lines identify colorectal and gastric cell-lines with microsatellite instability (MSI) as enriched for cellular sensitivity to N-hydroxyurea series inhibitors of FEN1, but not the PARP inhibitor olaparib or other inhibitors of the DNA damage response. This sensitivity is due to a synthetic lethal interaction between FEN1 and MRE11A, which is often mutated in MSI cancers through instabilities at a poly(T) microsatellite repeat. Disruption of ATM is similarly synthetic lethal with FEN1 inhibition, suggesting that disruption of FEN1 function leads to the accumulation of DNA double-strand breaks. These are likely a result of the accumulation of aberrant replication forks, that accumulate as a consequence of a failure in Okazaki fragment maturation, as inhibition of FEN1 is toxic in cells disrupted for the Fanconi anemia pathway and post-replication repair. Furthermore, RAD51 foci accumulate as a consequence of FEN1 inhibition and the toxicity of FEN1 inhibitors increases in cells disrupted for the homologous recombination pathway, suggesting a role for homologous recombination in the resolution of damage induced by FEN1 inhibition. Finally, FEN1 appears to be required for the repair of damage induced by olaparib and cisplatin within the Fanconi anemia pathway, and may play a role in the repair of damage associated with its own disruption.

MeSH terms

  • Cell Line, Tumor
  • Cell Survival / drug effects
  • Cisplatin / toxicity
  • DNA / drug effects
  • DNA / metabolism
  • DNA Breaks, Double-Stranded / drug effects
  • DNA Damage / drug effects
  • DNA Repair / drug effects*
  • DNA Replication / drug effects
  • DNA-Binding Proteins / antagonists & inhibitors
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Down-Regulation / drug effects
  • Flap Endonucleases / antagonists & inhibitors
  • Flap Endonucleases / genetics
  • Flap Endonucleases / metabolism*
  • Humans
  • Hydroxyurea / chemistry
  • Hydroxyurea / toxicity*
  • MRE11 Homologue Protein
  • Microsatellite Instability / drug effects
  • Mutation
  • Phthalazines / toxicity
  • Piperazines / toxicity
  • Poly(ADP-ribose) Polymerase Inhibitors / toxicity
  • RNA Interference
  • RNA, Small Interfering / metabolism
  • Rad51 Recombinase / genetics

Substances

  • DNA-Binding Proteins
  • MRE11 protein, human
  • Okazaki fragments
  • Phthalazines
  • Piperazines
  • Poly(ADP-ribose) Polymerase Inhibitors
  • RNA, Small Interfering
  • DNA
  • Rad51 Recombinase
  • Flap Endonucleases
  • MRE11 Homologue Protein
  • FEN1 protein, human
  • Cisplatin
  • olaparib
  • Hydroxyurea

Grants and funding

Work performed in the laboratory of PJM was supported by Cancer Research UK Programme Grant CA9047/A10111 (http://science.cancerresearchuk.org/). Work performed by TAW at AstraZeneca Pharmaceuticals was funded by the AstraZeneca Postdoctoral Research Program. AstraZeneca provided financial support in the form of salaries and research materials for TAW and STD, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.