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Genome-wide CRISPR screens reveal synthetic lethality of RNASEH2 deficiency and ATR inhibition

Oncogene (2018) | Download Citation

Abstract

Ataxia telangiectasia mutated and RAD3 related (ATR) protein kinase plays critical roles in ensuring DNA replication, DNA repair, and cell cycle control in response to replication stress, making ATR inhibition a promising therapeutic strategy for cancer treatment. To identify genes whose loss makes tumor cells hypersensitive to ATR inhibition, we performed CRISPR/Cas9-based whole-genome screens in 3 independent cell lines treated with a highly selective ATR inhibitor, AZD6738. These screens uncovered a comprehensive genome-wide profile of ATR inhibitor sensitivity. From the candidate genes, we demonstrated that RNASEH2 deficiency is synthetic lethal with ATR inhibition both in vitro and in vivo. RNASEH2-deficient cells exhibited elevated levels of DNA damage and, when treated with AZD6738, underwent apoptosis (short-time treated) or senescence (long-time treated). Notably, RNASEH2 deficiency is frequently found in prostate adenocarcinoma; we found decreased RNASEH2B protein levels in prostate adenocarcinoma patient-derived xenograft (PDX) samples. Our findings suggest that ATR inhibition may be beneficial for cancer patients with reduced levels of RNASEH2 and that RNASEH2 merits further exploration as a potential biomarker for ATR inhibitor-based therapy.

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Data availability

All relevant data not presented in the main figures or Supplementary Data are available from the authors.

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Acknowledgements

We thank the members of Dr. Junjie Chen’s lab for their kind help and Dr. Lei Li for his suggestions regarding the experimental design. We also thank Amy Ninetto from the Department of Scientific Publications at MD Anderson for editing the manuscript. This work was supported in part by CPRIT (RP160667) and NIH grants (CA157448, CA193124, CA210929, CA216911, and CA216437) to JC and MD Anderson’s NIH Cancer Center Support Grant (CA016672).

Author contributions

CW and JC conceived the project. CW, JZ, XF, MT, ZC, and MS performed the experiments. MEM provided technical support for the screen work. GW and GTH analyzed the deep-sequencing results. PS and NMN provided and analyzed the PDX samples. CW and JC wrote the manuscript with input from all authors.

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Affiliations

  1. Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA

    • Chao Wang
    • , Xu Feng
    • , Jie Zhang
    • , Mengfan Tang
    • , Zhen Chen
    • , Mrinal Srivastava
    •  & Junjie Chen
  2. Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA

    • Gang Wang
    • , Megan E. McLaughlin
    •  & Glen Traver Hart
  3. Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA

    • Peter Shepherd
    •  & Nora M. Navone

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The authors declare that they have no conflict of interest.

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Correspondence to Junjie Chen.

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DOI

https://doi.org/10.1038/s41388-018-0606-4