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

Michal Zimmermann, Olga Murina, Martin A. M. Reijns, Angelo Agathanggelou, Rachel Challis, Žygimantė Tarnauskaitė, Morwenna Muir, Adeline Fluteau, Michael Aregger, Andrea McEwan, Wei Yuan, Matthew Clarke, Maryou B. Lambros, Shankara Paneesha, Paul Moss, Megha Chandrashekhar, Stephane Angers, Jason Moffat, Valerie G. Brunton, Traver Hart, Johann Bono, Tatjana Stankovic, Andrew P. Jackson () and Daniel Durocher ()
Additional contact information
Michal Zimmermann: The Lunenfeld–Tanenbaum Research Institute, Mount Sinai Hospital
Olga Murina: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh
Martin A. M. Reijns: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh
Angelo Agathanggelou: Institute for Cancer and Genomic Sciences, University of Birmingham
Rachel Challis: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh
Žygimantė Tarnauskaitė: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh
Morwenna Muir: Cancer Research UK Edinburgh Centre, University of Edinburgh
Adeline Fluteau: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh
Michael Aregger: Donnelly Centre, University of Toronto
Andrea McEwan: The Lunenfeld–Tanenbaum Research Institute, Mount Sinai Hospital
Wei Yuan: The Institute of Cancer Research
Matthew Clarke: The Institute of Cancer Research
Maryou B. Lambros: The Institute of Cancer Research
Shankara Paneesha: Heartlands Hospital
Paul Moss: Institute of Immunology and Immunotherapy, University of Birmingham
Megha Chandrashekhar: Donnelly Centre, University of Toronto
Stephane Angers: Faculty of Medicine, University of Toronto
Jason Moffat: Donnelly Centre, University of Toronto
Valerie G. Brunton: Cancer Research UK Edinburgh Centre, University of Edinburgh
Traver Hart: The University of Texas MD Anderson Cancer Center
Johann Bono: The Institute of Cancer Research
Tatjana Stankovic: Institute for Cancer and Genomic Sciences, University of Birmingham
Andrew P. Jackson: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh
Daniel Durocher: The Lunenfeld–Tanenbaum Research Institute, Mount Sinai Hospital

Nature, 2018, vol. 559, issue 7713, 285-289

Abstract: 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 origins1–4. 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.

Date: 2018
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DOI: 10.1038/s41586-018-0291-z

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