DNA Repair Network Analysis Reveals Shieldin as a Key Regulator of NHEJ and PARP Inhibitor Sensitivity

Cell. 2018 May 3;173(4):972-988.e23. doi: 10.1016/j.cell.2018.03.050. Epub 2018 Apr 12.

Abstract

Repair of damaged DNA is essential for maintaining genome integrity and for preventing genome-instability-associated diseases, such as cancer. By combining proximity labeling with quantitative mass spectrometry, we generated high-resolution interaction neighborhood maps of the endogenously expressed DNA repair factors 53BP1, BRCA1, and MDC1. Our spatially resolved interaction maps reveal rich network intricacies, identify shared and bait-specific interaction modules, and implicate previously concealed regulators in this process. We identified a novel vertebrate-specific protein complex, shieldin, comprising REV7 plus three previously uncharacterized proteins, RINN1 (CTC-534A2.2), RINN2 (FAM35A), and RINN3 (C20ORF196). Recruitment of shieldin to DSBs, via the ATM-RNF8-RNF168-53BP1-RIF1 axis, promotes NHEJ-dependent repair of intrachromosomal breaks, immunoglobulin class-switch recombination (CSR), and fusion of unprotected telomeres. Shieldin functions as a downstream effector of 53BP1-RIF1 in restraining DNA end resection and in sensitizing BRCA1-deficient cells to PARP inhibitors. These findings have implications for understanding cancer-associated PARPi resistance and the evolution of antibody CSR in higher vertebrates.

Keywords: 53BP1; BRCA1; DNA damage repair; NHEJ; PARP inhibitors; antibody class-switch recombination; proteomics; proximity labeling; shieldin; telomere maintenance.

Publication types

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

MeSH terms

  • BRCA1 Protein / antagonists & inhibitors
  • BRCA1 Protein / genetics
  • BRCA1 Protein / metabolism
  • Cell Line, Tumor
  • DNA Breaks, Double-Stranded
  • DNA End-Joining Repair / drug effects*
  • DNA-Binding Proteins / antagonists & inhibitors
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism*
  • Humans
  • Immunoglobulin Class Switching / drug effects
  • Mad2 Proteins / antagonists & inhibitors
  • Mad2 Proteins / genetics
  • Mad2 Proteins / metabolism
  • Mutagenesis, Site-Directed
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism
  • Poly(ADP-ribose) Polymerase Inhibitors / pharmacology*
  • RNA Interference
  • RNA, Small Interfering / metabolism
  • Telomere-Binding Proteins / antagonists & inhibitors
  • Telomere-Binding Proteins / genetics
  • Telomere-Binding Proteins / metabolism
  • Trans-Activators / genetics
  • Trans-Activators / metabolism
  • Tumor Suppressor p53-Binding Protein 1 / antagonists & inhibitors
  • Tumor Suppressor p53-Binding Protein 1 / genetics
  • Tumor Suppressor p53-Binding Protein 1 / metabolism
  • Ubiquitin-Protein Ligases / antagonists & inhibitors
  • Ubiquitin-Protein Ligases / genetics
  • Ubiquitin-Protein Ligases / metabolism

Substances

  • BRCA1 Protein
  • BRCA1 protein, human
  • DNA-Binding Proteins
  • MAD2L2 protein, human
  • MDC1 protein, human
  • Mad2 Proteins
  • Nuclear Proteins
  • Poly(ADP-ribose) Polymerase Inhibitors
  • RNA, Small Interfering
  • RNF8 protein, human
  • Rif1 protein, human
  • TP53BP1 protein, human
  • Telomere-Binding Proteins
  • Trans-Activators
  • Tumor Suppressor p53-Binding Protein 1
  • Ubiquitin-Protein Ligases