Replication gaps are a key determinant of PARP inhibitor synthetic lethality with BRCA deficiency

Mol Cell. 2021 Aug 5;81(15):3128-3144.e7. doi: 10.1016/j.molcel.2021.06.011. Epub 2021 Jul 2.

Abstract

Mutations in BRCA1 or BRCA2 (BRCA) is synthetic lethal with poly(ADP-ribose) polymerase inhibitors (PARPi). Lethality is thought to derive from DNA double-stranded breaks (DSBs) necessitating BRCA function in homologous recombination (HR) and/or fork protection (FP). Here, we report instead that toxicity derives from replication gaps. BRCA1- or FANCJ-deficient cells, with common repair defects but distinct PARPi responses, reveal gaps as a distinguishing factor. We further uncouple HR, FP, and fork speed from PARPi response. Instead, gaps characterize BRCA-deficient cells, are diminished upon resistance, restored upon resensitization, and, when exposed, augment PARPi toxicity. Unchallenged BRCA1-deficient cells have elevated poly(ADP-ribose) and chromatin-associated PARP1, but aberrantly low XRCC1 consistent with defects in backup Okazaki fragment processing (OFP). 53BP1 loss resuscitates OFP by restoring XRCC1-LIG3 that suppresses the sensitivity of BRCA1-deficient cells to drugs targeting OFP or generating gaps. We highlight gaps as a determinant of PARPi toxicity changing the paradigm for synthetic lethal interactions.

Keywords: BRCA1/BRCA2; Fanconi anemia (FA); Okazaki fragment processing; PARP inhibitor; fork protection; homologous recombination; parylation; replication gaps; ssDNA; synthetic lethal.

Publication types

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

MeSH terms

  • Animals
  • BRCA1 Protein / genetics*
  • Cell Line
  • Cisplatin / pharmacology
  • DNA / genetics
  • DNA / metabolism
  • DNA Replication / drug effects*
  • DNA, Single-Stranded / genetics
  • Drug Resistance, Neoplasm / drug effects
  • Drug Resistance, Neoplasm / genetics
  • Fanconi Anemia Complementation Group Proteins / genetics
  • Homologous Recombination / drug effects
  • Humans
  • Mice, Inbred NOD
  • Poly(ADP-ribose) Polymerase Inhibitors / pharmacology*
  • RNA Helicases / genetics
  • Rad51 Recombinase / genetics
  • Replication Protein A / genetics
  • Tumor Suppressor p53-Binding Protein 1 / genetics

Substances

  • BRCA1 Protein
  • BRCA1 protein, human
  • DNA, Single-Stranded
  • Fanconi Anemia Complementation Group Proteins
  • Okazaki fragments
  • Poly(ADP-ribose) Polymerase Inhibitors
  • RPA1 protein, human
  • Replication Protein A
  • TP53BP1 protein, human
  • Tumor Suppressor p53-Binding Protein 1
  • DNA
  • RAD51 protein, human
  • Rad51 Recombinase
  • BRIP1 protein, human
  • RNA Helicases
  • Cisplatin