Loss of nuclear DNA ligase III reverts PARP inhibitor resistance in BRCA1/53BP1 double-deficient cells by exposing ssDNA gaps

Mol Cell. 2021 Nov 18;81(22):4692-4708.e9. doi: 10.1016/j.molcel.2021.09.005. Epub 2021 Sep 22.

Abstract

Inhibitors of poly(ADP-ribose) (PAR) polymerase (PARPi) have entered the clinic for the treatment of homologous recombination (HR)-deficient cancers. Despite the success of this approach, preclinical and clinical research with PARPi has revealed multiple resistance mechanisms, highlighting the need for identification of novel functional biomarkers and combination treatment strategies. Functional genetic screens performed in cells and organoids that acquired resistance to PARPi by loss of 53BP1 identified loss of LIG3 as an enhancer of PARPi toxicity in BRCA1-deficient cells. Enhancement of PARPi toxicity by LIG3 depletion is dependent on BRCA1 deficiency but independent of the loss of 53BP1 pathway. Mechanistically, we show that LIG3 loss promotes formation of MRE11-mediated post-replicative ssDNA gaps in BRCA1-deficient and BRCA1/53BP1 double-deficient cells exposed to PARPi, leading to an accumulation of chromosomal abnormalities. LIG3 depletion also enhances efficacy of PARPi against BRCA1-deficient mammary tumors in mice, suggesting LIG3 as a potential therapeutic target.

Keywords: 53BP1; BRCA1; DNA damage response; DNA ligase III; PARP1, PARP inhibitor; drug resistance; replication fork; ssDNA gaps; vulnerabilities.

Publication types

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

MeSH terms

  • Animals
  • BRCA1 Protein / genetics*
  • Biopsy
  • CRISPR-Cas Systems
  • Cell Line
  • Cell Nucleus / metabolism
  • Cell Proliferation
  • Chromosome Aberrations
  • DNA Damage
  • DNA Ligase ATP / genetics*
  • DNA Ligase ATP / metabolism
  • DNA, Single-Stranded*
  • Female
  • Humans
  • Lentivirus / genetics
  • MRE11 Homologue Protein / genetics*
  • Mammary Neoplasms, Animal
  • Mice
  • Mutation
  • Ovarian Neoplasms / metabolism*
  • Poly(ADP-ribose) Polymerase Inhibitors / pharmacology*
  • Poly-ADP-Ribose Binding Proteins / genetics*
  • Poly-ADP-Ribose Binding Proteins / metabolism
  • RNA, Small Interfering / metabolism
  • Transgenes
  • Triple Negative Breast Neoplasms / metabolism*
  • Tumor Suppressor p53-Binding Protein 1 / genetics*

Substances

  • BRCA1 Protein
  • Brca1 protein, mouse
  • DNA, Single-Stranded
  • Mre11a protein, mouse
  • Poly(ADP-ribose) Polymerase Inhibitors
  • Poly-ADP-Ribose Binding Proteins
  • RNA, Small Interfering
  • Trp53bp1 protein, mouse
  • Tumor Suppressor p53-Binding Protein 1
  • MRE11 Homologue Protein
  • DNA Ligase ATP
  • Lig3 protein, mouse