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CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer

Takuya Tsujino, Tomoaki Takai, Kunihiko Hinohara, Fu Gui, Takeshi Tsutsumi, Xiao Bai, Chenkui Miao, Chao Feng, Bin Gui, Zsofia Sztupinszki, Antoine Simoneau, Ning Xie, Ladan Fazli, Xuesen Dong, Haruhito Azuma, Atish D. Choudhury, Kent W. Mouw, Zoltan Szallasi, Lee Zou, Adam S. Kibel, Li Jia
doi: https://doi.org/10.1101/2022.04.13.488115
Takuya Tsujino
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
2Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
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Tomoaki Takai
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
2Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
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Kunihiko Hinohara
3Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
4Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Fu Gui
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
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Takeshi Tsutsumi
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
2Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
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Xiao Bai
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
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Chenkui Miao
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
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Chao Feng
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
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Bin Gui
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
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Zsofia Sztupinszki
5Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, USA
6Danish Cancer Society Research Center, Copenhagen, Denmark
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Antoine Simoneau
7Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
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Ning Xie
8Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
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Ladan Fazli
8Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
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Xuesen Dong
8Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
9Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
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Haruhito Azuma
2Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
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Atish D. Choudhury
3Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
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Kent W. Mouw
10Department of Radiation Oncology, Dana-Farber Cancer Institute & Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
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Zoltan Szallasi
5Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, USA
6Danish Cancer Society Research Center, Copenhagen, Denmark
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Lee Zou
7Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
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Adam S. Kibel
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
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Li Jia
1Division of Urology, Department of Surgery, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
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  • For correspondence: ljia@bwh.harvard.edu
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ABSTRACT

Prostate cancer (PCa) harboring BRCA1/2 mutations is often exquisitely sensitive to PARP inhibition. However, genomic alterations in other DNA damage response genes have not been consistently predictive of clinical response to PARP inhibitors (PARPis). Here, we perform genome-wide CRISPR-Cas9 knockout screens in BRCA1/2-proficient PCa cell lines and identify novel genes whose loss has a profound impact on PARPi sensitivity and resistance. Specifically, MMS22L deletion, frequently observed (up to 14%) in PCa, renders cells hypersensitive to PARPis by disrupting RAD51 loading required for homologous recombination repair, although this response is TP53-dependent. Unexpectedly, loss of CHEK2 confers resistance rather than sensitivity to PARPis in PCa cells through increased expression of BRCA2, a target of CHEK2-TP53-E2F7-mediated transcriptional repression. Combined PARP and ATR inhibition overcomes PARPi resistance caused by CHEK2 loss. Our findings may inform the use of PARPis beyond BRCA1/2-deficient tumors and support reevaluation of currently used biomarkers for PARPi treatment in PCa.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • We corrected the errors in Figure 5j and Supplementary Figure 8. The total case number has been changed from 111 to 146. Accordingly, the sample numbers have changed in the figures. No changes were made in the text.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted December 23, 2022.
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CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer
Takuya Tsujino, Tomoaki Takai, Kunihiko Hinohara, Fu Gui, Takeshi Tsutsumi, Xiao Bai, Chenkui Miao, Chao Feng, Bin Gui, Zsofia Sztupinszki, Antoine Simoneau, Ning Xie, Ladan Fazli, Xuesen Dong, Haruhito Azuma, Atish D. Choudhury, Kent W. Mouw, Zoltan Szallasi, Lee Zou, Adam S. Kibel, Li Jia
bioRxiv 2022.04.13.488115; doi: https://doi.org/10.1101/2022.04.13.488115
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CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer
Takuya Tsujino, Tomoaki Takai, Kunihiko Hinohara, Fu Gui, Takeshi Tsutsumi, Xiao Bai, Chenkui Miao, Chao Feng, Bin Gui, Zsofia Sztupinszki, Antoine Simoneau, Ning Xie, Ladan Fazli, Xuesen Dong, Haruhito Azuma, Atish D. Choudhury, Kent W. Mouw, Zoltan Szallasi, Lee Zou, Adam S. Kibel, Li Jia
bioRxiv 2022.04.13.488115; doi: https://doi.org/10.1101/2022.04.13.488115

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