CRISPR screens identify genomic ribonucleotides as a source of PARP-trapping lesions

Research output: Contribution to journalArticle

Authors

  • Michal Zimmermann
  • Olga Murina
  • Martin A M Reijns
  • Rachel Challis
  • Žygimantė Tarnauskaitė
  • Morwenna Muir
  • Adeline Fluteau
  • Michael Aregger
  • Andrea McEwan
  • Wei Yuan
  • Matthew Clarke
  • Maryou B Lambros
  • Shankara Paneesha
  • Megha Chandrashekhar
  • Stephane Angers
  • Jason Moffat
  • Valerie G Brunton
  • Traver Hart
  • Johann de Bono
  • Andrew P Jackson
  • Daniel Durocher

External organisations

  • The Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada.
  • MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom.
  • a Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, Medical and Dental School, University of Birmingham , Edgbaston , Birmingham , United Kingdom.
  • Edinburgh Cancer Research Centre, University of Edinburgh
  • The Institute of Cancer Research, London, United Kingdom.
  • Birmingham Heartlands Hospital, Birmingham, UK.
  • Banting and Best Department of Medical Research and Department of Molecular Genetics, University of Toronto, Ontario, Canada.
  • Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy & Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada.
  • Canadian Institute for Advanced Research, Toronto, Ontario, Canada.
  • Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
  • Department of Medicine, Royal Marsden NHS Foundation Trust, London
  • MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK. andrew.jackson@igmm.ed.ac.uk.
  • Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
  • Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

Abstract

The observation that BRCA1- and BRCA2-deficient cells are sensitive to inhibitors of poly(ADP-ribose) polymerase (PARP) has spurred the development of cancer therapies that use these inhibitors to target deficiencies in homologous recombination1. The cytotoxicity of PARP inhibitors depends on PARP trapping, the formation of non-covalent protein-DNA adducts composed of inhibited PARP1 bound to DNA lesions of unclear origins1,2,3,4. To address the nature of such lesions and the cellular consequences of PARP trapping, we undertook three CRISPR (clustered regularly interspersed palindromic repeats) screens to identify genes and pathways that mediate cellular resistance to olaparib, a clinically approved PARP inhibitor1. Here we present a high-confidence set of 73 genes, which when mutated cause increased sensitivity to PARP inhibitors. In addition to an expected enrichment for genes related to homologous recombination, we discovered that mutations in all three genes encoding ribonuclease H2 sensitized cells to PARP inhibition. We establish that the underlying cause of the PARP-inhibitor hypersensitivity of cells deficient in ribonuclease H2 is impaired ribonucleotide excision repair5. Embedded ribonucleotides, which are abundant in the genome of cells deficient in ribonucleotide excision repair, are substrates for cleavage by topoisomerase 1, resulting in PARP-trapping lesions that impede DNA replication and endanger genome integrity. We conclude that genomic ribonucleotides are a hitherto unappreciated source of PARP-trapping DNA lesions, and that the frequent deletion of RNASEH2B in metastatic prostate cancer and chronic lymphocytic leukaemia could provide an opportunity to exploit these findings therapeutically.

Details

Original languageEnglish
Pages (from-to)285-289
Number of pages5
JournalNature
Volume559
Issue number7713
Publication statusPublished - 4 Jul 2018