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Choi S, Bae HG, Jo DG, Kim WY. The Role of IRF9 Upregulation in Modulating Sensitivity to Olaparib and Platinum-Based Chemotherapies in Breast Cancer. Genes (Basel) 2024; 15:959. [PMID: 39062738 PMCID: PMC11276373 DOI: 10.3390/genes15070959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2024] [Revised: 07/19/2024] [Accepted: 07/20/2024] [Indexed: 07/28/2024] Open
Abstract
Poly(ADP-ribose) polymerase (PARP) inhibitors are targeted therapies that accumulate DNA damage by interfering with DNA repair mechanisms and are approved for treating several cancers with BRCA1/2 mutations. In this study, we utilized CRISPR-dCas9 interference screening to identify genes regulating sensitivity to PARP inhibitors in breast cancer cell lines. Our findings indicated that the interferon (IFN) signaling gene IRF9 was critically involved in modulating sensitivity to these inhibitors. We revealed that the loss of IRF9 leads to increased resistance to the PARP inhibitor in MDA-MB-468 cells, and a similar desensitization was observed in another breast cancer cell line, MDA-MB-231. Further analysis indicated that while the basal expression of IRF9 did not correlate with the response to the PARP inhibitor olaparib, its transcriptional induction was significantly associated with increased sensitivity to the DNA-damaging agent cisplatin in the NCI-60 cell line panel. This finding suggests a mechanistic link between IRF9 induction and cellular responses to DNA damage. Additionally, data from the METABRIC patient tissue study revealed a complex network of IFN-responsive gene expressions postchemotherapy, with seven upregulated genes, including IRF9, and three downregulated genes. These findings underscore the intricate role of IFN signaling in the cellular response to chemotherapy. Collectively, our CRISPR screening data and subsequent bioinformatic analyses suggest that IRF9 is a novel biomarker for sensitivity to DNA-damaging agents, such as olaparib and platinum-based chemotherapeutic agents. Our findings for IRF9 not only enhance our understanding of the genetic basis of drug sensitivity, but also elucidate the role of IRF9 as a critical effector within IFN signaling pathways, potentially influencing the association between the host immune system and chemotherapeutic efficacy.
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Affiliation(s)
- SeokGyeong Choi
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Republic of Korea;
| | - Han-Gyu Bae
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea; (H.-G.B.); (D.-G.J.)
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea; (H.-G.B.); (D.-G.J.)
| | - Woo-Young Kim
- College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Republic of Korea;
- Muscle Physiome Research Center, Sookmyung Women’s University, Seoul 04310, Republic of Korea
- Drug Information Research Institute, Sookmyung Women’s University, Seoul 04310, Republic of Korea
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2
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Mamar H, Fajka-Boja R, Mórocz M, Jurado E, Zentout S, Mihuţ A, Kopasz AG, Mérey M, Smith R, Sharma AB, Lakin N, Bowman A, Haracska L, Huet S, Timinszky G. The loss of DNA polymerase epsilon accessory subunits POLE3-POLE4 leads to BRCA1-independent PARP inhibitor sensitivity. Nucleic Acids Res 2024; 52:6994-7011. [PMID: 38828775 PMCID: PMC11229324 DOI: 10.1093/nar/gkae439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 05/02/2024] [Accepted: 05/09/2024] [Indexed: 06/05/2024] Open
Abstract
The clinical success of PARP1/2 inhibitors (PARPi) prompts the expansion of their applicability beyond homologous recombination deficiency. Here, we demonstrate that the loss of the accessory subunits of DNA polymerase epsilon, POLE3 and POLE4, sensitizes cells to PARPi. We show that the sensitivity of POLE4 knockouts is not due to compromised response to DNA damage or homologous recombination deficiency. Instead, POLE4 loss affects replication speed leading to the accumulation of single-stranded DNA gaps behind replication forks upon PARPi treatment, due to impaired post-replicative repair. POLE4 knockouts elicit elevated replication stress signaling involving ATR and DNA-PK. We find POLE4 to act parallel to BRCA1 in inducing sensitivity to PARPi and counteracts acquired resistance associated with restoration of homologous recombination. Altogether, our findings establish POLE4 as a promising target to improve PARPi driven therapies and hamper acquired PARPi resistance.
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Affiliation(s)
- Hasan Mamar
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Biology, University of Szeged, 6720 Szeged, Hungary
| | - Roberta Fajka-Boja
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Department of Immunology, Albert Szent-Györgyi Medical School, Faculty of Science and Informatics, University of Szeged, 6720 Szeged, Hungary
| | - Mónika Mórocz
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
| | - Eva Pinto Jurado
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSITUMS 3480 Rennes, France
| | - Siham Zentout
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSITUMS 3480 Rennes, France
| | - Alexandra Mihuţ
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Anna Georgina Kopasz
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Mihály Mérey
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
- Doctoral School of Multidisciplinary Medical Sciences, University of Szeged, Szeged, Hungary
| | - Rebecca Smith
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSITUMS 3480 Rennes, France
| | | | - Nicholas D Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Andrew James Bowman
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, UK
| | - Lajos Haracska
- HCEMM-BRC Mutagenesis and Carcinogenesis Research Group, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
| | - Sébastien Huet
- Univ Rennes, CNRS, IGDR (Institut de génétique et développement de Rennes) - UMR 6290, BIOSITUMS 3480 Rennes, France
| | - Gyula Timinszky
- Laboratory of DNA Damage and Nuclear Dynamics, Institute of Genetics, HUN-REN Biological Research Centre, 6276 Szeged, Hungary
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3
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Kim C, Wang XD, Liu Z, Hao J, Wang S, Li P, Zi Z, Ding Q, Jang S, Kim J, Luo Y, Huffman KE, Pal Choudhuri S, del Rio S, Cai L, Liang H, Drapkin BJ, Minna JD, Yu Y. Induced degradation of lineage-specific oncoproteins drives the therapeutic vulnerability of small cell lung cancer to PARP inhibitors. SCIENCE ADVANCES 2024; 10:eadh2579. [PMID: 38241363 PMCID: PMC10798557 DOI: 10.1126/sciadv.adh2579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024]
Abstract
Although BRCA1/2 mutations are not commonly found in small cell lung cancer (SCLC), a substantial fraction of SCLC shows clinically relevant response to PARP inhibitors (PARPis). However, the underlying mechanism(s) of PARPi sensitivity in SCLC is poorly understood. We performed quantitative proteomic analyses and identified proteomic changes that signify PARPi responses in SCLC cells. We found that the vulnerability of SCLC to PARPi could be explained by the degradation of lineage-specific oncoproteins (e.g., ASCL1). PARPi-induced activation of the E3 ligase HUWE1 mediated the ubiquitin-proteasome system (UPS)-dependent ASCL1 degradation. Although PARPi induced a general DNA damage response in SCLC cells, this signal generated a cell-specific response in ASCL1 degradation, leading to the identification of HUWE1 expression as a predictive biomarker for PARPi. Combining PARPi with agents targeting these pathways markedly improved therapeutic response in SCLC. The degradation of lineage-specific oncoproteins therefore represents a previously unidentified mechanism for PARPi efficacy in SCLC.
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Affiliation(s)
- Chiho Kim
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Xu-Dong Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Zhengshuai Liu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Jianwei Hao
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Shuai Wang
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Peng Li
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Zhenzhen Zi
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Qing Ding
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Seoyeon Jang
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jiwoong Kim
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yikai Luo
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Kenneth E. Huffman
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Shreoshi Pal Choudhuri
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sofia del Rio
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Ling Cai
- Quantitative Biomedical Research Center, Department of Population and Data Sciences, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Han Liang
- Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Benjamin J. Drapkin
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - John D. Minna
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Departments of Internal Medicine and Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
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4
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Beneyton A, Nonfoux L, Gagné JP, Rodrigue A, Kothari C, Atalay N, Hendzel M, Poirier G, Masson JY. The dynamic process of covalent and non-covalent PARylation in the maintenance of genome integrity: a focus on PARP inhibitors. NAR Cancer 2023; 5:zcad043. [PMID: 37609662 PMCID: PMC10440794 DOI: 10.1093/narcan/zcad043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/25/2023] [Accepted: 07/31/2023] [Indexed: 08/24/2023] Open
Abstract
Poly(ADP-ribosylation) (PARylation) by poly(ADP-ribose) polymerases (PARPs) is a highly regulated process that consists of the covalent addition of polymers of ADP-ribose (PAR) through post-translational modifications of substrate proteins or non-covalent interactions with PAR via PAR binding domains and motifs, thereby reprogramming their functions. This modification is particularly known for its central role in the maintenance of genomic stability. However, how genomic integrity is controlled by an intricate interplay of covalent PARylation and non-covalent PAR binding remains largely unknown. Of importance, PARylation has caught recent attention for providing a mechanistic basis of synthetic lethality involving PARP inhibitors (PARPi), most notably in homologous recombination (HR)-deficient breast and ovarian tumors. The molecular mechanisms responsible for the anti-cancer effect of PARPi are thought to implicate both catalytic inhibition and trapping of PARP enzymes on DNA. However, the relative contribution of each on tumor-specific cytotoxicity is still unclear. It is paramount to understand these PAR-dependent mechanisms, given that resistance to PARPi is a challenge in the clinic. Deciphering the complex interplay between covalent PARylation and non-covalent PAR binding and defining how PARP trapping and non-trapping events contribute to PARPi anti-tumour activity is essential for developing improved therapeutic strategies. With this perspective, we review the current understanding of PARylation biology in the context of the DNA damage response (DDR) and the mechanisms underlying PARPi activity and resistance.
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Affiliation(s)
- Adèle Beneyton
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Louis Nonfoux
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Philippe Gagné
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Amélie Rodrigue
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Charu Kothari
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Nurgul Atalay
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Michael J Hendzel
- Department of Oncology, Faculty of Medicine and Dentistry, University of Alberta, 11560 University Avenue, Edmonton, AlbertaT6G 1Z2, Canada
| | - Guy G Poirier
- CHU de Québec Research Center, CHUL Pavilion, Oncology Division, Laval University Cancer Research Center, 2705 Boulevard Laurier, Québec City, QC G1V 4G2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Laval University Cancer Research Center, 9 McMahon, Québec City, QC G1R 3S3, Canada
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5
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Pettitt SJ, Shao N, Zatreanu D, Frankum J, Bajrami I, Brough R, Krastev DB, Roumeliotis TI, Choudhary JS, Lorenz S, Rust A, de Bono JS, Yap TA, Tutt ANJ, Lord CJ. A HUWE1 defect causes PARP inhibitor resistance by modulating the BRCA1-∆11q splice variant. Oncogene 2023; 42:2701-2709. [PMID: 37491606 PMCID: PMC10473960 DOI: 10.1038/s41388-023-02782-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
Although PARP inhibitors (PARPi) now form part of the standard-of-care for the treatment of homologous recombination defective cancers, de novo and acquired resistance limits their overall effectiveness. Previously, overexpression of the BRCA1-∆11q splice variant has been shown to cause PARPi resistance. How cancer cells achieve increased BRCA1-∆11q expression has remained unclear. Using isogenic cells with different BRCA1 mutations, we show that reduction in HUWE1 leads to increased levels of BRCA1-∆11q and PARPi resistance. This effect is specific to cells able to express BRCA1-∆11q (e.g. BRCA1 exon 11 mutant cells) and is not seen in BRCA1 mutants that cannot express BRCA1-∆11q, nor in BRCA2 mutant cells. As well as increasing levels of BRCA1-∆11q protein in exon 11 mutant cells, HUWE1 silencing also restores RAD51 nuclear foci and platinum salt resistance. HUWE1 catalytic domain mutations were also seen in a case of PARPi resistant, BRCA1 exon 11 mutant, high grade serous ovarian cancer. These results suggest how elevated levels of BRCA1-∆11q and PARPi resistance can be achieved, identify HUWE1 as a candidate biomarker of PARPi resistance for assessment in future clinical trials and illustrate how some PARPi resistance mechanisms may only operate in patients with particular BRCA1 mutations.
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Affiliation(s)
- Stephen J Pettitt
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Nan Shao
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Diana Zatreanu
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Jessica Frankum
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Dragomir B Krastev
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK
| | | | | | - Sonja Lorenz
- Max Planck Institute for Multidisciplinary Sciences, 37077, Göttingen, Germany
| | - Alistair Rust
- The Institute of Cancer Research, London, SW3 6JB, UK
| | - Johann S de Bono
- The Institute of Cancer Research, The Royal Marsden Hospital, Downs Road, Sutton, Surrey, SM2 5PT, UK
| | - Timothy A Yap
- The Institute of Cancer Research, The Royal Marsden Hospital, Downs Road, Sutton, Surrey, SM2 5PT, UK
- University of Texas MD Anderson Cancer Center, 1400 Holcombe Blvd, Houston, TX, 77030, USA
| | - Andrew N J Tutt
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, SW3 6JB, UK.
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6
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Simpson D, Ling J, Jing Y, Adamson B. Mapping the Genetic Interaction Network of PARP inhibitor Response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.19.553986. [PMID: 37645833 PMCID: PMC10462155 DOI: 10.1101/2023.08.19.553986] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/31/2023]
Abstract
Genetic interactions have long informed our understanding of the coordinated proteins and pathways that respond to DNA damage in mammalian cells, but systematic interrogation of the genetic network underlying that system has yet to be achieved. Towards this goal, we measured 147,153 pairwise interactions among genes implicated in PARP inhibitor (PARPi) response. Evaluating genetic interactions at this scale, with and without exposure to PARPi, revealed hierarchical organization of the pathways and complexes that maintain genome stability during normal growth and defined changes that occur upon accumulation of DNA lesions due to cytotoxic doses of PARPi. We uncovered unexpected relationships among DNA repair genes, including context-specific buffering interactions between the minimally characterized AUNIP and BRCA1-A complex genes. Our work thus establishes a foundation for mapping differential genetic interactions in mammalian cells and provides a comprehensive resource for future studies of DNA repair and PARP inhibitors.
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Affiliation(s)
- Danny Simpson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Jia Ling
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
| | - Yangwode Jing
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Britt Adamson
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA
- Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
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7
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Awwad SW, Serrano-Benitez A, Thomas JC, Gupta V, Jackson SP. Revolutionizing DNA repair research and cancer therapy with CRISPR-Cas screens. Nat Rev Mol Cell Biol 2023; 24:477-494. [PMID: 36781955 DOI: 10.1038/s41580-022-00571-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/08/2022] [Indexed: 02/15/2023]
Abstract
All organisms possess molecular mechanisms that govern DNA repair and associated DNA damage response (DDR) processes. Owing to their relevance to human disease, most notably cancer, these mechanisms have been studied extensively, yet new DNA repair and/or DDR factors and functional interactions between them are still being uncovered. The emergence of CRISPR technologies and CRISPR-based genetic screens has enabled genome-scale analyses of gene-gene and gene-drug interactions, thereby providing new insights into cellular processes in distinct DDR-deficiency genetic backgrounds and conditions. In this Review, we discuss the mechanistic basis of CRISPR-Cas genetic screening approaches and describe how they have contributed to our understanding of DNA repair and DDR pathways. We discuss how DNA repair pathways are regulated, and identify and characterize crosstalk between them. We also highlight the impacts of CRISPR-based studies in identifying novel strategies for cancer therapy, and in understanding, overcoming and even exploiting cancer-drug resistance, for example in the contexts of PARP inhibition, homologous recombination deficiencies and/or replication stress. Lastly, we present the DDR CRISPR screen (DDRcs) portal , in which we have collected and reanalysed data from CRISPR screen studies and provide a tool for systematically exploring them.
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Affiliation(s)
- Samah W Awwad
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Almudena Serrano-Benitez
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - John C Thomas
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Vipul Gupta
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Stephen P Jackson
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK.
- The Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, UK.
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8
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Chen JZ, Wang LN, Luo XQ, Tang YL. The genomic landscape of sensitivity to arsenic trioxide uncovered by genome-wide CRISPR-Cas9 screening. Front Oncol 2023; 13:1178686. [PMID: 37251921 PMCID: PMC10214836 DOI: 10.3389/fonc.2023.1178686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Introduction Arsenic trioxide (ATO) is a promising anticancer drug for hematological malignancy. Given the dramatic efficacy of acute promyelocytic leukemia (APL), ATO has been utilized in other types of cancers, including solid tumors. Unfortunately, the results were not comparable with the effects on APL, and the resistance mechanism has not been clarified yet. This study intends to identify relevant genes and pathways affecting ATO drug sensitivity through genome-wide CRISPR-Cas9 knockdown screening to provide a panoramic view for further study of ATO targets and improved clinical outcomes. Methods A genome-wide CRISPR-Cas9 knockdown screening system was constructed for ATO screening. The screening results were processed with MAGeCK, and the results were subjected to pathway enrichment analysis using WebGestalt and KOBAS. We also performed protein-protein interaction (PPI) network analysis using String and Cytoscape, followed by expression profiling and survival curve analysis of critical genes. Virtual screening was used to recognize drugs that may interact with the hub gene. Results We applied enrichment analysis and identified vital ATO-related pathways such as metabolism, chemokines and cytokines production and signaling, and immune system responses. In addition, we identified KEAP1 as the top gene relating to ATO resistance. We found that KEAP1 expression was higher in the pan-cancer, including ALL, than in normal tissue. Patients with acute myeloid leukemia (AML) with higher KEAP1 expression had worse overall survival (OS). A virtual screen showed that etoposide and eltrombopag could bind to KEAP1 and potentially interact with ATO. Discussion ATO is a multi-target anticancer drug, and the key pathways regulating its sensitivity include oxidative stress, metabolism, chemokines and cytokines, and the immune system. KEAP1 is the most critical gene regulating ATO drug sensitivity, which is related to AML prognosis and may bind to some clinical drugs leading to an interaction with ATO. These integrated results provided new insights into the pharmacological mechanism of ATO and potentiate for further applications in cancer treatments.
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9
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Zelceski A, Francica P, Lingg L, Mutlu M, Stok C, Liptay M, Alexander J, Baxter JS, Brough R, Gulati A, Haider S, Raghunandan M, Song F, Sridhar S, Forment JV, O'Connor MJ, Davies BR, van Vugt MATM, Krastev DB, Pettitt SJ, Tutt ANJ, Rottenberg S, Lord CJ. MND1 and PSMC3IP control PARP inhibitor sensitivity in mitotic cells. Cell Rep 2023; 42:112484. [PMID: 37163373 DOI: 10.1016/j.celrep.2023.112484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 12/22/2022] [Accepted: 04/24/2023] [Indexed: 05/12/2023] Open
Abstract
The PSMC3IP-MND1 heterodimer promotes meiotic D loop formation before DNA strand exchange. In genome-scale CRISPR-Cas9 mutagenesis and interference screens in mitotic cells, depletion of PSMC3IP or MND1 causes sensitivity to poly (ADP-Ribose) polymerase inhibitors (PARPi) used in cancer treatment. PSMC3IP or MND1 depletion also causes ionizing radiation sensitivity. These effects are independent of PSMC3IP/MND1's role in mitotic alternative lengthening of telomeres. PSMC3IP- or MND1-depleted cells accumulate toxic RAD51 foci in response to DNA damage, show impaired homology-directed DNA repair, and become PARPi sensitive, even in cells lacking both BRCA1 and TP53BP1. Epistasis between PSMC3IP-MND1 and BRCA1/BRCA2 defects suggest that abrogated D loop formation is the cause of PARPi sensitivity. Wild-type PSMC3IP reverses PARPi sensitivity, whereas a PSMC3IP p.Glu201del mutant associated with D loop defects and ovarian dysgenesis does not. These observations suggest that meiotic proteins such as MND1 and PSMC3IP have a greater role in mitotic DNA repair.
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Affiliation(s)
- Anabel Zelceski
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Paola Francica
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; Departement of Biomedical Research (DBMR), Cancer Therapy Resistance Cluster, University of Bern, 3012 Bern, Switzerland
| | - Lea Lingg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; Departement of Biomedical Research (DBMR), Cancer Therapy Resistance Cluster, University of Bern, 3012 Bern, Switzerland
| | - Merve Mutlu
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - Colin Stok
- Department of Medical Oncology, University Medical Center Groningen, University of Groningen, Hanzeplein 1, 9713GZ Groningen, the Netherlands
| | - Martin Liptay
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | - John Alexander
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Joseph S Baxter
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Rachel Brough
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Aditi Gulati
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Syed Haider
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Maya Raghunandan
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Feifei Song
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Sandhya Sridhar
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | | | | | | | | | - Dragomir B Krastev
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK.
| | - Andrew N J Tutt
- Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK.
| | - Sven Rottenberg
- Institute of Animal Pathology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland; Departement of Biomedical Research (DBMR), Cancer Therapy Resistance Cluster, University of Bern, 3012 Bern, Switzerland; Division of Molecular Pathology, The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands; Bern Center for Precision Medicine, University of Bern, 3012 Bern, Switzerland.
| | - Christopher J Lord
- The CRUK Gene Function Laboratory, The Institute of Cancer Research, London SW3 6JB, UK; Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London SW3 6JB, UK.
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10
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Wang L, Wang P, Chen X, Yang H, Song S, Song Z, Jia L, Chen H, Bao X, Guo N, Huan X, Xi Y, Shen Y, Yang X, Su Y, Sun Y, Gao Y, Chen Y, Ding J, Lang J, Miao Z, Zhang A, He J. Thioparib inhibits homologous recombination repair, activates the type I IFN response, and overcomes olaparib resistance. EMBO Mol Med 2023; 15:e16235. [PMID: 36652375 PMCID: PMC9994488 DOI: 10.15252/emmm.202216235] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 12/19/2022] [Accepted: 12/21/2022] [Indexed: 01/19/2023] Open
Abstract
Poly-ADP-ribose polymerase (PARP) inhibitors (PARPi) have shown great promise for treating BRCA-deficient tumors. However, over 40% of BRCA-deficient patients fail to respond to PARPi. Here, we report that thioparib, a next-generation PARPi with high affinity against multiple PARPs, including PARP1, PARP2, and PARP7, displays high antitumor activities against PARPi-sensitive and -resistant cells with homologous recombination (HR) deficiency both in vitro and in vivo. Thioparib treatment elicited PARP1-dependent DNA damage and replication stress, causing S-phase arrest and apoptosis. Conversely, thioparib strongly inhibited HR-mediated DNA repair while increasing RAD51 foci formation. Notably, the on-target inhibition of PARP7 by thioparib-activated STING/TBK1-dependent phosphorylation of STAT1, triggered a strong induction of type I interferons (IFNs), and resulted in tumor growth retardation in an immunocompetent mouse model. However, the inhibitory effect of thioparib on tumor growth was more pronounced in PARP1 knockout mice, suggesting that a specific PARP7 inhibitor, rather than a pan inhibitor such as thioparib, would be more relevant for clinical applications. Finally, genome-scale CRISPR screening identified PARP1 and MCRS1 as genes capable of modulating thioparib sensitivity. Taken together, thioparib, a next-generation PARPi acting on both DNA damage response and antitumor immunity, serves as a therapeutic potential for treating hyperactive HR tumors, including those resistant to earlier-generation PARPi.
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Affiliation(s)
- Li‐Min Wang
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Pingyuan Wang
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- Pharm‐X Center, School of PharmacyShanghai Jiao Tong UniversityShanghaiChina
- Institute of Evolution and Marine BiodiversityOcean University of ChinaQingdaoChina
| | - Xiao‐Min Chen
- University of Chinese Academy of SciencesBeijingChina
- The CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and HealthUniversity of Chinese Academy of Sciences, Chinese Academy of SciencesShanghaiChina
| | - Hui Yang
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Shan‐Shan Song
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zilan Song
- Pharm‐X Center, School of PharmacyShanghai Jiao Tong UniversityShanghaiChina
| | - Li Jia
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hua‐Dong Chen
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xu‐Bin Bao
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ne Guo
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia‐Juan Huan
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yong Xi
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yan‐Yan Shen
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xin‐Ying Yang
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Su
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi‐Ming Sun
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ying‐Lei Gao
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yi Chen
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jian Ding
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Jing‐Yu Lang
- University of Chinese Academy of SciencesBeijingChina
- The CAS Key Laboratory of Tissue Microenvironment and Tumor, Shanghai Institute of Nutrition and HealthUniversity of Chinese Academy of Sciences, Chinese Academy of SciencesShanghaiChina
| | - Ze‐Hong Miao
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ao Zhang
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
- Pharm‐X Center, School of PharmacyShanghai Jiao Tong UniversityShanghaiChina
| | - Jin‐Xue He
- State Key Laboratory of Drug Research, Cancer Research Center, Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesBeijingChina
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11
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Guantay L, Garro C, Siri S, Pansa MF, Ghidelli-Disse S, Paviolo N, Racca A, Nicotra V, Radu C, Bocco JL, Felice R, Jansson KH, Remlinger K, Amador A, Stronach E, Coleman K, Muelbaier M, Drewes G, Gloger I, Madauss K, García M, Gottifredi V, Soria G. Deoxycytidine kinase (dCK) inhibition is synthetic lethal with BRCA2 deficiency. Drug Resist Updat 2023; 67:100932. [PMID: 36706533 DOI: 10.1016/j.drup.2023.100932] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/10/2023] [Accepted: 01/20/2023] [Indexed: 01/23/2023]
Abstract
BRCA2 is a well-established cancer driver in several human malignancies. While the remarkable success of PARP inhibitors proved the clinical potential of targeting BRCA deficiencies, the emergence of resistance mechanisms underscores the importance of seeking novel Synthetic Lethal (SL) targets for future drug development efforts. In this work, we performed a BRCA2-centric SL screen with a collection of plant-derived compounds from South America. We identified the steroidal alkaloid Solanocapsine as a selective SL inducer, and we were able to substantially increase its potency by deriving multiple analogs. The use of two complementary chemoproteomic approaches led to the identification of the nucleotide salvage pathway enzyme deoxycytidine kinase (dCK) as Solanocapsine's target responsible for its BRCA2-linked SL induction. Additional confirmatory evidence was obtained by using the highly specific dCK inhibitor (DI-87), which induces SL in multiple BRCA2-deficient and KO contexts. Interestingly, dCK-induced SL is mechanistically different from the one induced by PARP inhibitors. dCK inhibition generates substantially lower levels of DNA damage, and cytotoxic phenotypes are associated exclusively with mitosis, thus suggesting that the fine-tuning of nucleotide supply in mitosis is critical for the survival of BRCA2-deficient cells. Moreover, by using a xenograft model of contralateral tumors, we show that dCK impairment suffices to trigger SL in-vivo. Taken together, our findings unveil dCK as a promising new target for BRCA2-deficient cancers, thus setting the ground for future therapeutic alternatives to PARP inhibitors.
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Affiliation(s)
- Laura Guantay
- Centro de Investigaciones en Bioquímica Clínica e Inmunología, CIBICI-CONICET, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | | | - Sebastián Siri
- Fundación Instituto Leloir - CONICET, Buenos Aires, Argentina
| | - María Florencia Pansa
- Centro de Investigaciones en Bioquímica Clínica e Inmunología, CIBICI-CONICET, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; GlaxoSmithKline, Global Health R&D, Upper Providence, PA, United States
| | | | - Natalia Paviolo
- Fundación Instituto Leloir - CONICET, Buenos Aires, Argentina
| | - Ana Racca
- Centro de Investigaciones en Bioquímica Clínica e Inmunología, CIBICI-CONICET, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Viviana Nicotra
- Facultad de Ciencias Químicas, Instituto Multidisciplinario de Biología Vegetal (IMBIV-CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Caius Radu
- University of California, Los Angeles, CA, United States
| | - José Luis Bocco
- Centro de Investigaciones en Bioquímica Clínica e Inmunología, CIBICI-CONICET, Departamento de Bioquímica Clínica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Rosana Felice
- GlaxoSmithKline, Southern Cone LatAm, Buenos Aires, Argentina
| | - Keith H Jansson
- GlaxoSmithKline, Global Health R&D, Upper Providence, PA, United States
| | - Katja Remlinger
- GlaxoSmithKline, Global Health R&D, Upper Providence, PA, United States
| | - Alejandro Amador
- GlaxoSmithKline, Global Health R&D, Upper Providence, PA, United States
| | - Euan Stronach
- GlaxoSmithKline, Global Health R&D, Stevenage, United Kingdom
| | - Kevin Coleman
- GlaxoSmithKline, Synthetic Lethal RU, Waltham, MA, United States
| | | | - Gerard Drewes
- Cellzome GmbH - a GSK Company, 69117 Heidelberg, Germany
| | - Isro Gloger
- GlaxoSmithKline, Global Health R&D, Stevenage, United Kingdom
| | - Kevin Madauss
- GlaxoSmithKline, Global Health R&D, Upper Providence, PA, United States
| | - Manuela García
- Facultad de Ciencias Químicas, Instituto Multidisciplinario de Biología Vegetal (IMBIV-CONICET), Universidad Nacional de Córdoba, Córdoba, Argentina
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12
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Tsujino T, Takai T, Hinohara K, Gui F, Tsutsumi T, Bai X, Miao C, Feng C, Gui B, Sztupinszki Z, Simoneau A, Xie N, Fazli L, Dong X, Azuma H, Choudhury AD, Mouw KW, Szallasi Z, Zou L, Kibel AS, Jia L. CRISPR screens reveal genetic determinants of PARP inhibitor sensitivity and resistance in prostate cancer. Nat Commun 2023; 14:252. [PMID: 36650183 PMCID: PMC9845315 DOI: 10.1038/s41467-023-35880-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Prostate cancer harboring BRCA1/2 mutations are often exceptionally sensitive to PARP inhibitors. However, genomic alterations in other DNA damage response genes have not been consistently predictive of clinical response to PARP inhibition. Here, we perform genome-wide CRISPR-Cas9 knockout screens in BRCA1/2-proficient prostate cancer cells and identify previously unknown genes whose loss has a profound impact on PARP inhibitor response. Specifically, MMS22L deletion, frequently observed (up to 14%) in prostate cancer, renders cells hypersensitive to PARP inhibitors 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 PARP inhibition through increased expression of BRCA2, a target of CHEK2-TP53-E2F7-mediated transcriptional repression. Combined PARP and ATR inhibition overcomes PARP inhibitor resistance caused by CHEK2 loss. Our findings may inform the use of PARP inhibitors beyond BRCA1/2-deficient tumors and support reevaluation of current biomarkers for PARP inhibition in prostate cancer.
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Affiliation(s)
- Takuya Tsujino
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Tomoaki Takai
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Kunihiko Hinohara
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
- Department of Immunology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fu Gui
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Takeshi Tsutsumi
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Xiao Bai
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Chenkui Miao
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Chao Feng
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Bin Gui
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Zsofia Sztupinszki
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Antoine Simoneau
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Ning Xie
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ladan Fazli
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia, Canada
- Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Haruhito Azuma
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Atish D Choudhury
- Department of Medical Oncology, Dana-Farber Cancer Institute & Harvard Medical School, Boston, MA, USA
| | - Kent W Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute & Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children's Hospital, Boston, MA, USA
- Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Lee Zou
- Department of Pathology, Massachusetts General Hospital & Harvard Medical School, Boston, MA, USA
| | - Adam S Kibel
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA
| | - Li Jia
- Division of Urology, Department of Surgery, Brigham and Women's Hospital & Harvard Medical School, Boston, MA, USA.
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13
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Veneziani AC, Scott C, Wakefield MJ, Tinker AV, Lheureux S. Fighting resistance: post-PARP inhibitor treatment strategies in ovarian cancer. Ther Adv Med Oncol 2023; 15:17588359231157644. [PMID: 36872947 PMCID: PMC9983116 DOI: 10.1177/17588359231157644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 01/30/2023] [Indexed: 03/06/2023] Open
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPis) represent a therapeutic milestone in the management of epithelial ovarian cancer. The concept of 'synthetic lethality' is exploited by PARPi in tumors with defects in DNA repair pathways, particularly homologous recombination deficiency. The use of PARPis has been increasing since its approval as maintenance therapy, particularly in the first-line setting. Therefore, resistance to PARPi is an emerging issue in clinical practice. It brings an urgent need to elucidate and identify the mechanisms of PARPi resistance. Ongoing studies address this challenge and investigate potential therapeutic strategies to prevent, overcome, or re-sensitize tumor cells to PARPi. This review aims to summarize the mechanisms of resistance to PARPi, discuss emerging strategies to treat patients post-PARPi progression, and discuss potential biomarkers of resistance.
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Affiliation(s)
- Ana C Veneziani
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Clare Scott
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Medical Biology, University of Melbourne, Parkville, VIC, Australia.,Royal Women's Hospital, Parkville, VIC, Australia.,Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Matthew J Wakefield
- Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia
| | - Anna V Tinker
- BC Cancer Agency, Medical Oncology Vancouver, Canada
| | - Stephanie Lheureux
- Division of Medical Oncology and Haematology, Princess Margaret Cancer Centre, 610 University Ave, Toronto, ON M5B 2M9, Canada
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14
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Jackson LM, Moldovan GL. Mechanisms of PARP1 inhibitor resistance and their implications for cancer treatment. NAR Cancer 2022; 4:zcac042. [PMID: 36568963 PMCID: PMC9773381 DOI: 10.1093/narcan/zcac042] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The discovery of synthetic lethality as a result of the combined loss of PARP1 and BRCA has revolutionized the treatment of DNA repair-deficient cancers. With the development of PARP inhibitors, patients displaying germline or somatic mutations in BRCA1 or BRCA2 were presented with a novel therapeutic strategy. However, a large subset of patients do not respond to PARP inhibitors. Furthermore, many of those who do respond eventually acquire resistance. As such, combating de novo and acquired resistance to PARP inhibitors remains an obstacle in achieving durable responses in patients. In this review, we touch on some of the key mechanisms of PARP inhibitor resistance, including restoration of homologous recombination, replication fork stabilization and suppression of single-stranded DNA gap accumulation, as well as address novel approaches for overcoming PARP inhibitor resistance.
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Affiliation(s)
- Lindsey M Jackson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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15
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Schleicher EM, Moldovan GL. CRISPR screens guide the way for PARP and ATR inhibitor biomarker discovery. FEBS J 2022; 289:7854-7868. [PMID: 34601817 PMCID: PMC9003637 DOI: 10.1111/febs.16217] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/28/2021] [Accepted: 09/30/2021] [Indexed: 02/06/2023]
Abstract
DNA repair pathways are heavily studied for their role in cancer initiation and progression. Due to the large amount of inherent DNA damage in cancer cells, tumor cells profoundly rely on proper DNA repair for efficient cell cycle progression. Several current chemotherapeutics promote excessive DNA damage in cancer cells, thus leading to cell death during cell cycle progression. However, if the tumor has efficient DNA repair mechanisms, DNA-damaging therapeutics may not be as effective. Therefore, directly inhibiting DNA repair pathways alone and in combination with chemotherapeutics that cause DNA damage may result in improved clinical outcomes. Nevertheless, tumors can acquire resistance to DNA repair inhibitors. It is essential to understand the genetic mechanisms underlying this resistance. Genome-wide CRISPR screening has emerged as a powerful tool to identify biomarkers of resistance or sensitivity to DNA repair inhibitors. CRISPR knockout and CRISPR activation screens can be designed to investigate how the loss or overexpression of any human gene impacts resistance or sensitivity to specific inhibitors. This review will address the role of CRISPR screening in identifying biomarkers of resistance and sensitivity to DNA repair pathway inhibitors. We will focus on inhibitors targeting the PARP1 and ATR enzymes, and how the biomarkers identified from CRISPR screens can help inform the treatment plan for cancer patients.
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Affiliation(s)
- Emily M. Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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16
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McLean B, Istadi A, Clack T, Vankan M, Schramek D, Neely GG, Pajic M. A CRISPR Path to Finding Vulnerabilities and Solving Drug Resistance: Targeting the Diverse Cancer Landscape and Its Ecosystem. ADVANCED GENETICS (HOBOKEN, N.J.) 2022; 3:2200014. [PMID: 36911295 PMCID: PMC9993475 DOI: 10.1002/ggn2.202200014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 10/11/2022] [Indexed: 11/11/2022]
Abstract
Cancer is the second leading cause of death globally, with therapeutic resistance being a major cause of treatment failure in the clinic. The dynamic signaling that occurs between tumor cells and the diverse cells of the surrounding tumor microenvironment actively promotes disease progression and therapeutic resistance. Improving the understanding of how tumors evolve following therapy and the molecular mechanisms underpinning de novo or acquired resistance is thus critical for the identification of new targets and for the subsequent development of more effective combination regimens. Simultaneously targeting multiple hallmark capabilities of cancer to circumvent adaptive or evasive resistance may lead to significantly improved treatment response in the clinic. Here, the latest applications of functional genomics tools, such as clustered regularly interspaced short palindromic repeats (CRISPR) editing, to characterize the dynamic cancer resistance mechanisms, from improving the understanding of resistance to classical chemotherapeutics, to deciphering unique mechanisms that regulate tumor responses to new targeted agents and immunotherapies, are discussed. Potential avenues of future research in combating therapeutic resistance, the contribution of tumor-stroma signaling in this setting, and how advanced functional genomics tools can help streamline the identification of key molecular determinants of drug response are explored.
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Affiliation(s)
- Benjamin McLean
- The Kinghorn Cancer Centre The Garvan Institute of Medical Research 384 Victoria St, Darlinghurst Sydney New South Wales 2010 Australia
| | - Aji Istadi
- The Kinghorn Cancer Centre The Garvan Institute of Medical Research 384 Victoria St, Darlinghurst Sydney New South Wales 2010 Australia
| | - Teleri Clack
- Dr. John and Anne Chong Lab for Functional Genomics Charles Perkins Centre Centenary Institute University of Sydney Camperdown New South Wales 2006 Australia
| | - Mezzalina Vankan
- Dr. John and Anne Chong Lab for Functional Genomics Charles Perkins Centre Centenary Institute University of Sydney Camperdown New South Wales 2006 Australia
| | - Daniel Schramek
- Centre for Molecular and Systems Biology Lunenfeld-Tanenbaum Research Institute Mount Sinai Hospital Toronto Ontario M5G 1X5 Canada.,Department of Molecular Genetics Faculty of Medicine University of Toronto Toronto Ontario M5S 1A8 Canada
| | - G Gregory Neely
- Dr. John and Anne Chong Lab for Functional Genomics Charles Perkins Centre Centenary Institute University of Sydney Camperdown New South Wales 2006 Australia
| | - Marina Pajic
- The Kinghorn Cancer Centre The Garvan Institute of Medical Research 384 Victoria St, Darlinghurst Sydney New South Wales 2010 Australia.,St Vincent's Clinical School Faculty of Medicine University of NSW Sydney Sydney New South Wales 2052 Australia
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17
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Zhang H, Gao H, Gu Y, John A, Wei L, Huang M, Yu J, Adeosun AA, Weinshilboum RM, Wang L. 3D CRISPR screen in prostate cancer cells reveals PARP inhibitor sensitization through TBL1XR1-SMC3 interaction. Front Oncol 2022; 12:999302. [PMID: 36523978 PMCID: PMC9746894 DOI: 10.3389/fonc.2022.999302] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 11/14/2022] [Indexed: 08/24/2023] Open
Abstract
Poly(ADP-ribose) (PAR) polymerase inhibitors (PARPi) either have been approved or being tested in the clinic for the treatment of a variety of cancers with homologous recombination deficiency (HRD). However, cancer cells can develop resistance to PARPi drugs through various mechanisms, and new biomarkers and combination therapeutic strategies need to be developed to support personalized treatment. In this study, a genome-wide CRISPR screen was performed in a prostate cancer cell line with 3D culture condition which identified novel signals involved in DNA repair pathways. One of these genes, TBL1XR1, regulates sensitivity to PARPi in prostate cancer cells. Mechanistically, we show that TBL1XR1 interacts with and stabilizes SMC3 on chromatin and promotes γH2AX spreading along the chromatin of the cells under DNA replication stress. TBL1XR1-SMC3 double knockdown (knockout) cells have comparable sensitivity to PARPi compared to SMC3 knockdown or TBL1XR1 knockout cells, and more sensitivity than WT cells. Our findings provide new insights into mechanisms underlying response to PARPi or platin compounds in the treatment of malignancies.
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Affiliation(s)
- Huan Zhang
- School of Medicine, Nantong University, Nantong, China
| | - Huanyao Gao
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Yayun Gu
- School of Medicine, Nantong University, Nantong, China
| | - August John
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Lixuan Wei
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Minhong Huang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Jia Yu
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Adeyemi A. Adeosun
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Richard M. Weinshilboum
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
| | - Liewei Wang
- Division of Clinical Pharmacology, Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, United States
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18
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Wilson J, Loizou JI. Exploring the genetic space of the DNA damage response for cancer therapy through CRISPR-based screens. Mol Oncol 2022; 16:3778-3791. [PMID: 35708734 PMCID: PMC9627789 DOI: 10.1002/1878-0261.13272] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/11/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
The concepts of synthetic lethality and viability have emerged as powerful approaches to identify vulnerabilities and resistances within the DNA damage response for the treatment of cancer. Historically, interactions between two genes have had a longstanding presence in genetics and have been identified through forward genetic screens that rely on the molecular basis of the characterized phenotypes, typically caused by mutations in single genes. While such complex genetic interactions between genes have been studied extensively in model organisms, they have only recently been prioritized as therapeutic strategies due to technological advancements in genetic screens. Here, we discuss synthetic lethal and viable interactions within the DNA damage response and present how CRISPR-based genetic screens and chemical compounds have allowed for the systematic identification and targeting of such interactions for the treatment of cancer.
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Affiliation(s)
- Jordan Wilson
- Center for Cancer Research, Comprehensive Cancer CentreMedical University of ViennaAustria,CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
| | - Joanna I. Loizou
- Center for Cancer Research, Comprehensive Cancer CentreMedical University of ViennaAustria,CeMM Research Center for Molecular Medicine of the Austrian Academy of SciencesViennaAustria
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19
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Huang TT, Burkett SS, Tandon M, Yamamoto TM, Gupta N, Bitler BG, Lee JM, Nair JR. Distinct roles of treatment schemes and BRCA2 on the restoration of homologous recombination DNA repair and PARP inhibitor resistance in ovarian cancer. Oncogene 2022; 41:5020-5031. [PMID: 36224341 PMCID: PMC9669252 DOI: 10.1038/s41388-022-02491-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 09/26/2022] [Accepted: 09/28/2022] [Indexed: 11/09/2022]
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPis) represent a major advance in ovarian cancer, now as a treatment and as a maintenance therapy in the upfront and recurrent settings. However, patients often develop resistance to PARPis, underlining the importance of dissecting resistance mechanisms. Here, we report different dosing/timing schemes of PARPi treatment in BRCA2-mutant PEO1 cells, resulting in the simultaneous development of distinct resistance mechanisms. PARPi-resistant variants PEO1/OlaJR, established by higher initial doses and short-term PARPi treatment, develops PARPi resistance by rapidly restoring functional BRCA2 and promoting drug efflux activity. In contrast, PEO1/OlaR, developed by lower initial doses with long-term PARPi exposure, shows no regained BRCA2 function but a mesenchymal-like phenotype with greater invasion ability, and exhibits activated ATR/CHK1 and suppressed EZH2/MUS81 signaling cascades to regain HR repair and fork stabilization, respectively. Our study suggests that PARPi resistance mechanisms can be governed by treatment strategies and have a molecular basis on BRCA2 functionality. Further, we define different mechanisms that may serve as useful biomarkers to assess subsequent treatment strategies in PARPi-resistant ovarian cancer.
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Affiliation(s)
- Tzu-Ting Huang
- Women's Malignancies Branch (WMB), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | | | - Mayank Tandon
- Center for Cancer Research Collaborative Bioinformatics Resource, CCR, NCI, NIH, Bethesda, MD, USA
| | - Tomomi M Yamamoto
- Department of OB/GYN, Division of Reproductive Sciences, The University of Colorado, Aurora, CO, USA
| | - Nitasha Gupta
- Women's Malignancies Branch (WMB), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Benjamin G Bitler
- Department of OB/GYN, Division of Reproductive Sciences, The University of Colorado, Aurora, CO, USA
| | - Jung-Min Lee
- Women's Malignancies Branch (WMB), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Jayakumar R Nair
- Women's Malignancies Branch (WMB), Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
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20
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Dhoonmoon A, Nicolae CM, Moldovan GL. The KU-PARP14 axis differentially regulates DNA resection at stalled replication forks by MRE11 and EXO1. Nat Commun 2022; 13:5063. [PMID: 36030235 PMCID: PMC9420157 DOI: 10.1038/s41467-022-32756-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Suppression of nascent DNA degradation has emerged as an essential role of the BRCA pathway in genome protection. In BRCA-deficient cells, the MRE11 nuclease is responsible for both resection of reversed replication forks, and accumulation of single stranded DNA gaps behind forks. Here, we show that the mono-ADP-ribosyltransferase PARP14 is a critical co-factor of MRE11. PARP14 is recruited to nascent DNA upon replication stress in BRCA-deficient cells, and through its catalytic activity, mediates the engagement of MRE11. Loss or inhibition of PARP14 suppresses MRE11-mediated fork degradation and gap accumulation, and promotes genome stability and chemoresistance of BRCA-deficient cells. Moreover, we show that the KU complex binds reversed forks and protects them against EXO1-catalyzed degradation. KU recruits the PARP14-MRE11 complex, which initiates partial resection to release KU and allow long-range resection by EXO1. Our work identifies a multistep process of nascent DNA processing at stalled replication forks in BRCA-deficient cells. Protection of replication forks against nucleolytic degradation is crucial for genome stability. Here, Dhoonmoon et al identify PARP14 and the KU complex as essential regulators of fork degradation by MRE11 and EXO1 nucleases in BRCA-deficient cells.
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Affiliation(s)
- Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.
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21
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Wang N, Yang Y, Jin D, Zhang Z, Shen K, Yang J, Chen H, Zhao X, Yang L, Lu H. PARP inhibitor resistance in breast and gynecological cancer: Resistance mechanisms and combination therapy strategies. Front Pharmacol 2022; 13:967633. [PMID: 36091750 PMCID: PMC9455597 DOI: 10.3389/fphar.2022.967633] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/04/2022] [Indexed: 12/02/2022] Open
Abstract
Breast cancer and gynecological tumors seriously endanger women’s physical and mental health, fertility, and quality of life. Due to standardized surgical treatment, chemotherapy, and radiotherapy, the prognosis and overall survival of cancer patients have improved compared to earlier, but the management of advanced disease still faces great challenges. Recently, poly (ADP-ribose) polymerase (PARP) inhibitors (PARPis) have been clinically approved for breast and gynecological cancer patients, significantly improving their quality of life, especially of patients with BRCA1/2 mutations. However, drug resistance faced by PARPi therapy has hindered its clinical promotion. Therefore, developing new drug strategies to resensitize cancers affecting women to PARPi therapy is the direction of our future research. Currently, the effects of PARPi in combination with other drugs to overcome drug resistance are being studied. In this article, we review the mechanisms of PARPi resistance and summarize the current combination of clinical trials that can improve its resistance, with a view to identify the best clinical treatment to save the lives of patients.
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Affiliation(s)
- Nannan Wang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yan Yang
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Dongdong Jin
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Endometrial Disease Prevention and Treatment, Zhengzhou, China
| | - Zhenan Zhang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ke Shen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jing Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Huanhuan Chen
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinyue Zhao
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Li Yang
- Department of Obstetrics and Gynecology, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Zhengzhou Key Laboratory of Endometrial Disease Prevention and Treatment, Zhengzhou, China
- *Correspondence: Li Yang, ; Huaiwu Lu,
| | - Huaiwu Lu
- Department of Gynaecological Oncology, Sun Yat Sen Memorial Hospital, Guangzhou, China
- *Correspondence: Li Yang, ; Huaiwu Lu,
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22
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The TIP60-ATM axis regulates replication fork stability in BRCA-deficient cells. Oncogenesis 2022; 11:33. [PMID: 35717336 PMCID: PMC9206655 DOI: 10.1038/s41389-022-00410-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022] Open
Abstract
Maintenance of replication fork stability is essential for genome preservation. Stalled replication forks can be reversed by translocases such as SMARCAL1, and unless protected through the activity of the BRCA pathway, are subsequently subjected to nucleolytic degradation. The ATM and ATR kinases are master regulators of the DNA damage response. ATM activation upon DNA damage is mediated by the acetyltransferase TIP60. Here, we show that the TIP60-ATM pathway promotes replication fork reversal by recruiting SMARCAL1 to stalled forks. This enables fork degradation in BRCA-deficient cells. We also show that this ATM activity is not shared by ATR. Moreover, we performed a series of genome-wide CRISPR knockout genetic screens to identify genetic determinants of the cellular sensitivity to ATM inhibition in wildtype and BRCA2-knockout cells, and validated the top hits from multiple screens. We provide a valuable list of common genes which regulate the response to multiple ATM inhibitors. Importantly, we identify a differential response of wildtype and BRCA2-deficient cells to these inhibitors. In BRCA2-knockout cells, DNA repair genes (including RAD17, MDC1, and USP28) were essential for survival upon ATM inhibitor treatment, which was not the case in wild-type cells. These findings may eventually help guide the way for rational deployment of ATM inhibitors in the clinic.
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23
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Lei T, Du S, Peng Z, Chen L. Multifaceted regulation and functions of 53BP1 in NHEJ‑mediated DSB repair (Review). Int J Mol Med 2022; 50:90. [PMID: 35583003 PMCID: PMC9162042 DOI: 10.3892/ijmm.2022.5145] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 04/29/2022] [Indexed: 12/02/2022] Open
Abstract
The repair of DNA double-strand breaks (DSBs) is crucial for the preservation of genomic integrity and the maintenance of cellular homeostasis. Non-homologous DNA end joining (NHEJ) is the predominant repair mechanism for any type of DNA DSB during the majority of the cell cycle. NHEJ defects regulate tumor sensitivity to ionizing radiation and anti-neoplastic agents, resulting in immunodeficiencies and developmental abnormalities in malignant cells. p53-binding protein 1 (53BP1) is a key mediator involved in DSB repair, which functions to maintain a balance in the repair pathway choices and in preserving genomic stability. 53BP1 promotes DSB repair via NHEJ and antagonizes DNA end overhang resection. At present, novel lines of evidence have revealed the molecular mechanisms underlying the recruitment of 53BP1 and DNA break-responsive effectors to DSB sites, and the promotion of NHEJ-mediated DSB repair via 53BP1, while preventing homologous recombination. In the present review article, recent advances made in the elucidation of the structural and functional characteristics of 53BP1, the mechanisms of 53BP1 recruitment and interaction with the reshaping of the chromatin architecture around DSB sites, the post-transcriptional modifications of 53BP1, and the up- and downstream pathways of 53BP1 are discussed. The present review article also focuses on the application perspectives, current challenges and future directions of 53BP1 research.
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Affiliation(s)
- Tiantian Lei
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Suya Du
- Department of Clinical Pharmacy, Sichuan Cancer Hospital and Institute, Sichuan Cancer Center, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan 610041, P.R. China
| | - Zhe Peng
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
| | - Lin Chen
- Department of Pharmacy, Women and Children's Hospital of Chongqing Medical University, Chongqing 401147, P.R. China
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24
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Miao C, Tsujino T, Takai T, Gui F, Tsutsumi T, Sztupinszki Z, Wang Z, Azuma H, Szallasi Z, Mouw KW, Zou L, Kibel AS, Jia L. RB1 loss overrides PARP inhibitor sensitivity driven by RNASEH2B loss in prostate cancer. SCIENCE ADVANCES 2022; 8:eabl9794. [PMID: 35179959 PMCID: PMC8856618 DOI: 10.1126/sciadv.abl9794] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Current targeted cancer therapies are largely guided by mutations of a single gene, which overlooks concurrent genomic alterations. Here, we show that RNASEH2B, RB1, and BRCA2, three closely located genes on chromosome 13q, are frequently deleted in prostate cancer individually or jointly. Loss of RNASEH2B confers cancer cells sensitivity to poly(ADP-ribose) polymerase (PARP) inhibition due to impaired ribonucleotide excision repair and PARP trapping. When co-deleted with RB1, however, cells lose their sensitivity, in part, through E2F1-induced BRCA2 expression, thereby enhancing homologous recombination repair capacity. Nevertheless, loss of BRCA2 resensitizes RNASEH2B/RB1 co-deleted cells to PARP inhibition. Our results may explain some of the disparate clinical results from PARP inhibition due to interaction between multiple genomic alterations and support a comprehensive genomic test to determine who may benefit from PARP inhibition. Last, we show that ATR inhibition can disrupt E2F1-induced BRCA2 expression and overcome PARP inhibitor resistance caused by RB1 loss.
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Affiliation(s)
- Chenkui Miao
- Division of Urology, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Takuya Tsujino
- Division of Urology, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Tomoaki Takai
- Division of Urology, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Fu Gui
- Division of Urology, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Takeshi Tsutsumi
- Division of Urology, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Zsofia Sztupinszki
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, USA
| | - Zengjun Wang
- Department of Urology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Haruhito Azuma
- Department of Urology, Osaka Medical and Pharmaceutical University, Osaka, Japan
| | - Zoltan Szallasi
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA, USA
| | - Kent W. Mouw
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Lee Zou
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Adam S. Kibel
- Division of Urology, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
| | - Li Jia
- Division of Urology, Department of Surgery, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA, USA
- Corresponding author.
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25
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Xie J, DiMaio D. Traptamer screening: a new functional genomics approach to study virus entry and other cellular processes. FEBS J 2022; 289:355-362. [PMID: 33604985 PMCID: PMC8371075 DOI: 10.1111/febs.15775] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/26/2021] [Accepted: 02/17/2021] [Indexed: 01/03/2023]
Abstract
Historically, the genetic analysis of mammalian cells entailed the isolation of randomly arising mutant cell lines with altered properties, followed by laborious genetic mapping experiments to identify the mutant gene responsible for the phenotype. In recent years, somatic cell genetics has been revolutionized by functional genomics screens, in which expression of every protein-coding gene is systematically perturbed, and the phenotype of the perturbed cells is determined. We outline here a novel functional genomics screening strategy that differs fundamentally from commonly used approaches. In this strategy, we express libraries of artificial transmembrane proteins named traptamers and select rare cells with the desired phenotype because, by chance, a traptamer specifically perturbs the expression or activity of a target protein. Active traptamers are then recovered from the selected cells and can be used as tools to dissect the biological process under study. We also briefly describe how we have used this new strategy to provide insights into the complex process by which human papillomaviruses enter cells.
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Affiliation(s)
- Jian Xie
- Department of Genetics, Yale School of Medicine, New Haven, CT USA
| | - Daniel DiMaio
- Department of Genetics, Yale School of Medicine, New Haven, CT USA
- Department of Therapeutic Radiology, Yale School of Medicine, New Haven, CT USA
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT USA
- Yale Cancer Center, New Haven, CT USA
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26
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Jackson LM, Dhoonmoon A, Hale A, Dennis KA, Schleicher EM, Nicolae CM, Moldovan GL. Loss of MED12 activates the TGFβ pathway to promote chemoresistance and replication fork stability in BRCA-deficient cells. Nucleic Acids Res 2021; 49:12855-12869. [PMID: 34871431 PMCID: PMC8682781 DOI: 10.1093/nar/gkab1184] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 11/23/2022] Open
Abstract
Understanding chemoresistance mechanisms in BRCA-deficient cells will allow for identification of biomarkers for predicting tumor response to therapy, as well as the design of novel therapeutic approaches targeting this chemoresistance. Here, we show that the protein MED12, a component of the Mediator transcription regulation complex, plays an unexpected role in regulating chemosensitivity in BRCA-deficient cells. We found that loss of MED12 confers resistance to cisplatin and PARP inhibitors in both BRCA1- and BRCA2-deficient cells, which is associated with restoration of both homologous recombination and replication fork stability. Surprisingly, MED12-controlled chemosensitivity does not involve a function of the Mediator complex, but instead reflects a distinct role of MED12 in suppression of the TGFβ pathway. Importantly, we show that ectopic activation of the TGFβ pathway is enough to overcome the fork protection and DNA repair defects of BRCA-mutant cells, resulting in chemoresistance. Our work identifies the MED12-TGFβ module as an important regulator of genomic stability and chemosensitivity in BRCA-deficient cells.
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Affiliation(s)
- Lindsey M Jackson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Anastasia Hale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Kady A Dennis
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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27
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Hayward SB, Ciccia A. Towards a CRISPeR understanding of homologous recombination with high-throughput functional genomics. Curr Opin Genet Dev 2021; 71:171-181. [PMID: 34583241 PMCID: PMC8671205 DOI: 10.1016/j.gde.2021.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]
Abstract
CRISPR-dependent genome editing enables the study of genes and mutations on a large scale. Here we review CRISPR-based functional genomics technologies that generate gene knockouts and single nucleotide variants (SNVs) and discuss how their use has provided new important insights into the function of homologous recombination (HR) genes. In particular, we highlight discoveries from CRISPR screens that have contributed to define the response to PARP inhibition in cells deficient for the HR genes BRCA1 and BRCA2, uncover genes whose loss causes synthetic lethality in combination with BRCA1/2 deficiency, and characterize the function of BRCA1/2 SNVs of uncertain clinical significance. Further use of these approaches, combined with next-generation CRISPR-based technologies, will aid to dissect the genetic network of the HR pathway, define the impact of HR mutations on cancer etiology and treatment, and develop novel targeted therapies for HR-deficient tumors.
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Affiliation(s)
- Samuel B Hayward
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, United States
| | - Alberto Ciccia
- Department of Genetics and Development, Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, United States.
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28
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Biegała Ł, Gajek A, Marczak A, Rogalska A. PARP inhibitor resistance in ovarian cancer: Underlying mechanisms and therapeutic approaches targeting the ATR/CHK1 pathway. Biochim Biophys Acta Rev Cancer 2021; 1876:188633. [PMID: 34619333 DOI: 10.1016/j.bbcan.2021.188633] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/14/2021] [Accepted: 10/01/2021] [Indexed: 01/01/2023]
Abstract
Ovarian cancer (OC) constitutes the most common cause of gynecologic cancer-related death in women worldwide. Despite consistent developments in treatment strategies for OC, the management of advanced-stage disease remains a significant challenge. Recent improvements in targeted treatments based on poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) have provided invaluable benefits to patients with OC. Unfortunately, numerous patients do not respond to PARPi due to intrinsic resistance or acquisition of resistance. Here, we discuss mechanisms of resistance to PARPi that have specifically emerged in OC including increased drug efflux, restoration of HR repair, re-establishment of replication fork stability, reduced PARP1 trapping, abnormalities in PARP signaling, and less common pathways associated with alternative DNA sensing and repair pathways. Elucidation of the precise mechanisms is essential for the development of novel strategies to re-sensitize OC cells to PARPi agents. Additionally, novel potential concepts for preventing and combating resistance to PARPi under development and relevant clinical reports on treatment strategies have been reviewed, with emphasis on the exploitation of the ATR/CHK1 kinase pathway in sensitization to PARPi to overcome resistance-induced vulnerability in ovarian cancer.
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Affiliation(s)
- Łukasz Biegała
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
| | - Arkadiusz Gajek
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
| | - Agnieszka Marczak
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
| | - Aneta Rogalska
- Department of Medical Biophysics, Institute of Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland.
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29
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Wattenberg MM, Reiss KA. Determinants of Homologous Recombination Deficiency in Pancreatic Cancer. Cancers (Basel) 2021; 13:4716. [PMID: 34572943 PMCID: PMC8466888 DOI: 10.3390/cancers13184716] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/10/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
Pancreatic cancer is a treatment-resistant malignancy associated with high mortality. However, defective homologous recombination (HR), a DNA repair mechanism required for high-fidelity repair of double-strand DNA breaks, is a therapeutic vulnerability. Consistent with this, a subset of patients with pancreatic cancer show unique tumor responsiveness to HR-dependent DNA damage triggered by certain treatments (platinum chemotherapy and PARP inhibitors). While pathogenic mutations in HR genes are a major driver of this sensitivity, another layer of diverse tumor intrinsic and extrinsic factors regulate the HR deficiency (HRD) phenotype. Defining the mechanisms that drive HRD may guide the development of novel strategies and therapeutics to induce treatment sensitivity in non-HRD tumors. Here, we discuss the complexity underlying HRD in pancreatic cancer and highlight implications for identifying and treating this distinct subset of patients.
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Affiliation(s)
- Max M. Wattenberg
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kim A. Reiss
- Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA;
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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30
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Thakar T, Moldovan GL. The emerging determinants of replication fork stability. Nucleic Acids Res 2021; 49:7224-7238. [PMID: 33978751 PMCID: PMC8287955 DOI: 10.1093/nar/gkab344] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/21/2022] Open
Abstract
A universal response to replication stress is replication fork reversal, where the nascent complementary DNA strands are annealed to form a protective four-way junction allowing forks to avert DNA damage while replication stress is resolved. However, reversed forks are in turn susceptible to nucleolytic digestion of the regressed nascent DNA arms and rely on dedicated mechanisms to protect their integrity. The most well studied fork protection mechanism involves the BRCA pathway and its ability to catalyze RAD51 nucleofilament formation on the reversed arms of stalled replication forks. Importantly, the inability to prevent the degradation of reversed forks has emerged as a hallmark of BRCA deficiency and underlies genome instability and chemosensitivity in BRCA-deficient cells. In the past decade, multiple factors underlying fork stability have been discovered. These factors either cooperate with the BRCA pathway, operate independently from it to augment fork stability in its absence, or act as enablers of fork degradation. In this review, we examine these novel determinants of fork stability, explore the emergent conceptual underpinnings underlying fork protection, as well as the impact of fork protection on cellular viability and cancer therapy.
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Affiliation(s)
- Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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31
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Cheng X, Côté V, Côté J. NuA4 and SAGA acetyltransferase complexes cooperate for repair of DNA breaks by homologous recombination. PLoS Genet 2021; 17:e1009459. [PMID: 34228704 PMCID: PMC8284799 DOI: 10.1371/journal.pgen.1009459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 07/16/2021] [Accepted: 06/21/2021] [Indexed: 12/30/2022] Open
Abstract
Chromatin modifying complexes play important yet not fully defined roles in DNA repair processes. The essential NuA4 histone acetyltransferase (HAT) complex is recruited to double-strand break (DSB) sites and spreads along with DNA end resection. As predicted, NuA4 acetylates surrounding nucleosomes upon DSB induction and defects in its activity correlate with altered DNA end resection and Rad51 recombinase recruitment. Importantly, we show that NuA4 is also recruited to the donor sequence during recombination along with increased H4 acetylation, indicating a direct role during strand invasion/D-loop formation after resection. We found that NuA4 cooperates locally with another HAT, the SAGA complex, during DSB repair as their combined action is essential for DNA end resection to occur. This cooperation of NuA4 and SAGA is required for recruitment of ATP-dependent chromatin remodelers, targeted acetylation of repair factors and homologous recombination. Our work reveals a multifaceted and conserved cooperation mechanism between acetyltransferase complexes to allow repair of DNA breaks by homologous recombination. DNA double-strand breaks (DSBs) are among the most dangerous types of DNA lesions as they can produce genomic instability that leads to cancer and genetic diseases. It is therefore crucial to understand the precise molecular mechanisms used by cells to detect and repair this type of damages. Homologous recombination using sister chromatid as template is the most accurate pathway to repair these breaks but has to occur within the context of the DNA compacted structure in chromosomes. Here, we show that two enzymes, NuA4 and SAGA, that acetylate the structural components of chromosomes in the vicinity of the DNA breaks are together essential for recombination-mediated repair to occur. We found that they are recruited at an early step after damage detection and their action allows subsequent remodeling of local structural organisation by other enzymes, providing DNA access to the recombination machinery. These results highlight the cooperation of enzymes for a same goal, providing robustness in the repair process as only the loss of both leads to major defects.
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Affiliation(s)
- Xue Cheng
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Valérie Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
| | - Jacques Côté
- St-Patrick Research Group in Basic Oncology, Laval University Cancer Research Center, Oncology Division of CHU de Québec-Université Laval Research Center, Quebec City, Canada
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32
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Wenmaekers S, Viergever BJ, Kumar G, Kranenburg O, Black PC, Daugaard M, Meijer RP. A Potential Role for HUWE1 in Modulating Cisplatin Sensitivity. Cells 2021; 10:cells10051262. [PMID: 34065298 PMCID: PMC8160634 DOI: 10.3390/cells10051262] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/17/2021] [Accepted: 05/18/2021] [Indexed: 12/25/2022] Open
Abstract
Cisplatin is a widely used antineoplastic agent, whose efficacy is limited by primary and acquired therapeutic resistance. Recently, a bladder cancer genome-wide CRISPR/Cas9 knock-out screen correlated cisplatin sensitivity to multiple genetic biomarkers. Among the screen’s top hits was the HECT domain-containing ubiquitin E3 ligase (HUWE1). In this review, HUWE1 is postulated as a therapeutic response modulator, affecting the collision between platinum-DNA adducts and the replication fork, the primary cytotoxic action of platins. HUWE1 can alter the cytotoxic response to platins by targeting essential components of the DNA damage response including BRCA1, p53, and Mcl-1. Deficiency of HUWE1 could lead to enhanced DNA damage repair and a dysfunctional apoptotic apparatus, thereby inducing resistance to platins. Future research on the relationship between HUWE1 and platins could generate new mechanistic insights into therapy resistance. Ultimately, HUWE1 might serve as a clinical biomarker to tailor cancer treatment strategies, thereby improving cancer care and patient outcomes.
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Affiliation(s)
- Stijn Wenmaekers
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Bastiaan J. Viergever
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Gunjan Kumar
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Onno Kranenburg
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
| | - Peter C. Black
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
| | - Mads Daugaard
- Department of Urologic Sciences, University of British Columbia, Vancouver, BC V5Z 1M9, Canada; (G.K.); (P.C.B.)
- Vancouver Prostate Centre, Vancouver, BC V6H 3Z6, Canada
- Correspondence: (M.D.); (R.P.M.)
| | - Richard P. Meijer
- Laboratory Translational Oncology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands; (S.W.); (B.J.V.); (O.K.)
- Department of Oncological Urology, University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
- Correspondence: (M.D.); (R.P.M.)
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The dystonia gene THAP1 controls DNA double-strand break repair choice. Mol Cell 2021; 81:2611-2624.e10. [PMID: 33857404 DOI: 10.1016/j.molcel.2021.03.034] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 02/01/2021] [Accepted: 03/19/2021] [Indexed: 12/26/2022]
Abstract
The Shieldin complex shields double-strand DNA breaks (DSBs) from nucleolytic resection. Curiously, the penultimate Shieldin component, SHLD1, is one of the least abundant mammalian proteins. Here, we report that the transcription factors THAP1, YY1, and HCF1 bind directly to the SHLD1 promoter, where they cooperatively maintain the low basal expression of SHLD1, thereby ensuring a proper balance between end protection and resection during DSB repair. The loss of THAP1-dependent SHLD1 expression confers cross-resistance to poly (ADP-ribose) polymerase (PARP) inhibitor and cisplatin in BRCA1-deficient cells and shorter progression-free survival in ovarian cancer patients. Moreover, the embryonic lethality and PARPi sensitivity of BRCA1-deficient mice is rescued by ablation of SHLD1. Our study uncovers a transcriptional network that directly controls DSB repair choice and suggests a potential link between DNA damage and pathogenic THAP1 mutations, found in patients with the neurodevelopmental movement disorder adult-onset torsion dystonia type 6.
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