Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability

Yi Qing Lü; Tiffany Cho; Saptaparna Mukherjee; Carmen Florencia Suarez; Nicolas S. Gonzalez-Foutel; Ahmad Malik; Sebastien Martinez; Dzana Dervovic; Robin Hyunseo Oh; Ellen Langille; Khalid N. Al-Zahrani; Lisa Hoeg; Zhen Yuan Lin; Ricky Tsai; Geraldine Mbamalu; Varda Rotter; Patricia Ashton-Prolla; Jason Moffat; Lucia Beatriz Chemes; Anne Claude Gingras; Moshe Oren; Daniel Durocher; Daniel Schramek

doi:10.1038/s44320-024-00032-x

Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability

Yi Qing Lü, Tiffany Cho, Saptaparna Mukherjee, Carmen Florencia Suarez, Nicolas S. Gonzalez-Foutel, Ahmad Malik, Sebastien Martinez, Dzana Dervovic, Robin Hyunseo Oh, Ellen Langille, Khalid N. Al-Zahrani, Lisa Hoeg, Zhen Yuan Lin, Ricky Tsai, Geraldine Mbamalu, Varda Rotter, Patricia Ashton-Prolla, Jason Moffat, Lucia Beatriz Chemes, Anne Claude GingrasMoshe Oren, Daniel Durocher, Daniel Schramek^*

^*Corresponding author for this work

Department of Molecular Cell Biology

Research output: Contribution to journal › Article › peer-review

Abstract

Tumor suppressor p53 (TP53) is frequently mutated in cancer, often resulting not only in loss of its tumor-suppressive function but also acquisition of dominant-negative and even oncogenic gain-of-function traits. While wild-type p53 levels are tightly regulated, mutants are typically stabilized in tumors, which is crucial for their oncogenic properties. Here, we systematically profiled the factors that regulate protein stability of wild-type and mutant p53 using marker-based genome-wide CRISPR screens. Most regulators of wild-type p53 also regulate p53 mutants, except for p53 R337H regulators, which are largely private to this mutant. Mechanistically, FBXO42 emerged as a positive regulator for a subset of p53 mutants, working with CCDC6 to control USP28-mediated mutant p53 stabilization. Additionally, C16orf72/HAPSTR1 negatively regulates both wild-type p53 and all tested mutants. C16orf72/HAPSTR1 is commonly amplified in breast cancer, and its overexpression reduces p53 levels in mouse mammary epithelium leading to accelerated breast cancer. This study offers a network perspective on p53 stability regulation, potentially guiding strategies to reinforce wild-type p53 or target mutant p53 in cancer.

Original language	English
Pages (from-to)	719-740
Number of pages	22
Journal	Molecular Systems Biology
Volume	20
Issue number	6
DOIs	https://doi.org/10.1038/s44320-024-00032-x
Publication status	Published Online - 5 Apr 2024

Bibliographical note

We would like to thank all members of our laboratories, as well as Mikko Taipale (University of Toronto), Brian Raught (University of Toronto/University Health Network), Yael Aylon (Weizmann Institute of Science), and The Centre for Phenogenomics (TCP), for helpful discussions. We want to thank Henrique Melo, Zheng Luo, Mingkun Wu and Matthew Guo for assistance with data analysis, Annie Bang, Michael Parsons and Dione White in the Lunenfeld-Tanenbaum Research Institute Flow Cytometry Facilities for assistance with FACS, Kin Chan at the Lunenfeld Network Biology Centre for assistance with next-generation sequencing, Andrew Elia at the University Health Network for assistance with histology, and Sampath Loganathan for general experiment helps. The FLAG-USP7 construct is a generous gift from Lori Frappier (University of Toronto). Research in this work is supported by funding from the Joint Canada-Israel Research Program (DS, MO, VR, ACG, PA-P, and LBC, CIHR IRDC 384428). DS was supported by the Canada Research Chairs Program. DD was supported by a grant from the Canadian Cancer Society (705644). YQL is the recipient of doctoral fellowships from the Canadian Institute of Health Research (CIHR 157921 and MSFSS 431649), the Government of Ontario (OGS) and the University of Toronto. DS is supported by the Canada Research Chair Program. PA-P was supported by a scholarship from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil, # 307826/2017-1).

Publisher Copyright:
© The Author(s) 2024.

All Science Journal Classification (ASJC) codes

Information Systems
General Biochemistry,Genetics and Molecular Biology
General Immunology and Microbiology
General Agricultural and Biological Sciences
Computational Theory and Mathematics
Applied Mathematics

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Cite this

Lü, Y. Q., Cho, T., Mukherjee, S., Suarez, C. F., Gonzalez-Foutel, N. S., Malik, A., Martinez, S., Dervovic, D., Oh, R. H., Langille, E., Al-Zahrani, K. N., Hoeg, L., Lin, Z. Y., Tsai, R., Mbamalu, G., Rotter, V., Ashton-Prolla, P., Moffat, J., Chemes, L. B., ... Schramek, D. (2024). Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability. Molecular Systems Biology, 20(6), 719-740. Advance online publication. https://doi.org/10.1038/s44320-024-00032-x

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title = "Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability",

abstract = "Tumor suppressor p53 (TP53) is frequently mutated in cancer, often resulting not only in loss of its tumor-suppressive function but also acquisition of dominant-negative and even oncogenic gain-of-function traits. While wild-type p53 levels are tightly regulated, mutants are typically stabilized in tumors, which is crucial for their oncogenic properties. Here, we systematically profiled the factors that regulate protein stability of wild-type and mutant p53 using marker-based genome-wide CRISPR screens. Most regulators of wild-type p53 also regulate p53 mutants, except for p53 R337H regulators, which are largely private to this mutant. Mechanistically, FBXO42 emerged as a positive regulator for a subset of p53 mutants, working with CCDC6 to control USP28-mediated mutant p53 stabilization. Additionally, C16orf72/HAPSTR1 negatively regulates both wild-type p53 and all tested mutants. C16orf72/HAPSTR1 is commonly amplified in breast cancer, and its overexpression reduces p53 levels in mouse mammary epithelium leading to accelerated breast cancer. This study offers a network perspective on p53 stability regulation, potentially guiding strategies to reinforce wild-type p53 or target mutant p53 in cancer.",

author = "L{\"u}, {Yi Qing} and Tiffany Cho and Saptaparna Mukherjee and Suarez, {Carmen Florencia} and Gonzalez-Foutel, {Nicolas S.} and Ahmad Malik and Sebastien Martinez and Dzana Dervovic and Oh, {Robin Hyunseo} and Ellen Langille and Al-Zahrani, {Khalid N.} and Lisa Hoeg and Lin, {Zhen Yuan} and Ricky Tsai and Geraldine Mbamalu and Varda Rotter and Patricia Ashton-Prolla and Jason Moffat and Chemes, {Lucia Beatriz} and Gingras, {Anne Claude} and Moshe Oren and Daniel Durocher and Daniel Schramek",

note = "We would like to thank all members of our laboratories, as well as Mikko Taipale (University of Toronto), Brian Raught (University of Toronto/University Health Network), Yael Aylon (Weizmann Institute of Science), and The Centre for Phenogenomics (TCP), for helpful discussions. We want to thank Henrique Melo, Zheng Luo, Mingkun Wu and Matthew Guo for assistance with data analysis, Annie Bang, Michael Parsons and Dione White in the Lunenfeld-Tanenbaum Research Institute Flow Cytometry Facilities for assistance with FACS, Kin Chan at the Lunenfeld Network Biology Centre for assistance with next-generation sequencing, Andrew Elia at the University Health Network for assistance with histology, and Sampath Loganathan for general experiment helps. The FLAG-USP7 construct is a generous gift from Lori Frappier (University of Toronto). Research in this work is supported by funding from the Joint Canada-Israel Research Program (DS, MO, VR, ACG, PA-P, and LBC, CIHR IRDC 384428). DS was supported by the Canada Research Chairs Program. DD was supported by a grant from the Canadian Cancer Society (705644). YQL is the recipient of doctoral fellowships from the Canadian Institute of Health Research (CIHR 157921 and MSFSS 431649), the Government of Ontario (OGS) and the University of Toronto. DS is supported by the Canada Research Chair Program. PA-P was supported by a scholarship from CNPq (Conselho Nacional de Desenvolvimento Cient{\'i}fico e Tecnol{\'o}gico, Brazil, # 307826/2017-1). Publisher Copyright: {\textcopyright} The Author(s) 2024.",

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doi = "10.1038/s44320-024-00032-x",

language = "English",

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Lü, YQ, Cho, T, Mukherjee, S, Suarez, CF, Gonzalez-Foutel, NS, Malik, A, Martinez, S, Dervovic, D, Oh, RH, Langille, E, Al-Zahrani, KN, Hoeg, L, Lin, ZY, Tsai, R, Mbamalu, G, Rotter, V, Ashton-Prolla, P, Moffat, J, Chemes, LB, Gingras, AC, Oren, M, Durocher, D & Schramek, D 2024, 'Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability', Molecular Systems Biology, vol. 20, no. 6, pp. 719-740. https://doi.org/10.1038/s44320-024-00032-x

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T1 - Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability

AU - Lü, Yi Qing

AU - Cho, Tiffany

AU - Mukherjee, Saptaparna

AU - Suarez, Carmen Florencia

AU - Gonzalez-Foutel, Nicolas S.

AU - Malik, Ahmad

AU - Martinez, Sebastien

AU - Dervovic, Dzana

AU - Oh, Robin Hyunseo

AU - Langille, Ellen

AU - Al-Zahrani, Khalid N.

AU - Hoeg, Lisa

AU - Lin, Zhen Yuan

AU - Tsai, Ricky

AU - Mbamalu, Geraldine

AU - Rotter, Varda

AU - Ashton-Prolla, Patricia

AU - Moffat, Jason

AU - Chemes, Lucia Beatriz

AU - Gingras, Anne Claude

AU - Oren, Moshe

AU - Durocher, Daniel

AU - Schramek, Daniel

N1 - We would like to thank all members of our laboratories, as well as Mikko Taipale (University of Toronto), Brian Raught (University of Toronto/University Health Network), Yael Aylon (Weizmann Institute of Science), and The Centre for Phenogenomics (TCP), for helpful discussions. We want to thank Henrique Melo, Zheng Luo, Mingkun Wu and Matthew Guo for assistance with data analysis, Annie Bang, Michael Parsons and Dione White in the Lunenfeld-Tanenbaum Research Institute Flow Cytometry Facilities for assistance with FACS, Kin Chan at the Lunenfeld Network Biology Centre for assistance with next-generation sequencing, Andrew Elia at the University Health Network for assistance with histology, and Sampath Loganathan for general experiment helps. The FLAG-USP7 construct is a generous gift from Lori Frappier (University of Toronto). Research in this work is supported by funding from the Joint Canada-Israel Research Program (DS, MO, VR, ACG, PA-P, and LBC, CIHR IRDC 384428). DS was supported by the Canada Research Chairs Program. DD was supported by a grant from the Canadian Cancer Society (705644). YQL is the recipient of doctoral fellowships from the Canadian Institute of Health Research (CIHR 157921 and MSFSS 431649), the Government of Ontario (OGS) and the University of Toronto. DS is supported by the Canada Research Chair Program. PA-P was supported by a scholarship from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brazil, # 307826/2017-1). Publisher Copyright: © The Author(s) 2024.

PY - 2024/4/5

Y1 - 2024/4/5

N2 - Tumor suppressor p53 (TP53) is frequently mutated in cancer, often resulting not only in loss of its tumor-suppressive function but also acquisition of dominant-negative and even oncogenic gain-of-function traits. While wild-type p53 levels are tightly regulated, mutants are typically stabilized in tumors, which is crucial for their oncogenic properties. Here, we systematically profiled the factors that regulate protein stability of wild-type and mutant p53 using marker-based genome-wide CRISPR screens. Most regulators of wild-type p53 also regulate p53 mutants, except for p53 R337H regulators, which are largely private to this mutant. Mechanistically, FBXO42 emerged as a positive regulator for a subset of p53 mutants, working with CCDC6 to control USP28-mediated mutant p53 stabilization. Additionally, C16orf72/HAPSTR1 negatively regulates both wild-type p53 and all tested mutants. C16orf72/HAPSTR1 is commonly amplified in breast cancer, and its overexpression reduces p53 levels in mouse mammary epithelium leading to accelerated breast cancer. This study offers a network perspective on p53 stability regulation, potentially guiding strategies to reinforce wild-type p53 or target mutant p53 in cancer.

AB - Tumor suppressor p53 (TP53) is frequently mutated in cancer, often resulting not only in loss of its tumor-suppressive function but also acquisition of dominant-negative and even oncogenic gain-of-function traits. While wild-type p53 levels are tightly regulated, mutants are typically stabilized in tumors, which is crucial for their oncogenic properties. Here, we systematically profiled the factors that regulate protein stability of wild-type and mutant p53 using marker-based genome-wide CRISPR screens. Most regulators of wild-type p53 also regulate p53 mutants, except for p53 R337H regulators, which are largely private to this mutant. Mechanistically, FBXO42 emerged as a positive regulator for a subset of p53 mutants, working with CCDC6 to control USP28-mediated mutant p53 stabilization. Additionally, C16orf72/HAPSTR1 negatively regulates both wild-type p53 and all tested mutants. C16orf72/HAPSTR1 is commonly amplified in breast cancer, and its overexpression reduces p53 levels in mouse mammary epithelium leading to accelerated breast cancer. This study offers a network perspective on p53 stability regulation, potentially guiding strategies to reinforce wild-type p53 or target mutant p53 in cancer.

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Genome-wide CRISPR screens identify novel regulators of wild-type and mutant p53 stability

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Bibliographical note

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