1
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Olvera-León R, Zhang F, Offord V, Zhao Y, Tan HK, Gupta P, Pal T, Robles-Espinoza CD, Arriaga-González FG, Matsuyama LSAS, Delage E, Dicks E, Ezquina S, Rowlands CF, Turnbull C, Pharoah P, Perry JRB, Jasin M, Waters AJ, Adams DJ. High-resolution functional mapping of RAD51C by saturation genome editing. Cell 2024; 187:5719-5734.e19. [PMID: 39299233 DOI: 10.1016/j.cell.2024.08.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 02/29/2024] [Accepted: 08/20/2024] [Indexed: 09/22/2024]
Abstract
Pathogenic variants in RAD51C confer an elevated risk of breast and ovarian cancer, while individuals homozygous for specific RAD51C alleles may develop Fanconi anemia. Using saturation genome editing (SGE), we functionally assess 9,188 unique variants, including >99.5% of all possible coding sequence single-nucleotide alterations. By computing changes in variant abundance and Gaussian mixture modeling (GMM), we functionally classify 3,094 variants to be disruptive and use clinical truth sets to reveal an accuracy/concordance of variant classification >99.9%. Cell fitness was the primary assay readout allowing us to observe a phenomenon where specific missense variants exhibit distinct depletion kinetics potentially suggesting that they represent hypomorphic alleles. We further explored our exhaustive functional map, revealing critical residues on the RAD51C structure and resolving variants found in cancer-segregating kindred. Furthermore, through interrogation of UK Biobank and a large multi-center ovarian cancer cohort, we find significant associations between SGE-depleted variants and cancer diagnoses.
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Affiliation(s)
- Rebeca Olvera-León
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, Querétaro, Mexico
| | - Fang Zhang
- Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, USA; Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Victoria Offord
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Yajie Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, UK
| | - Hong Kee Tan
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Prashant Gupta
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Tuya Pal
- Department of Medicine, Division of Genetic Medicine, Vanderbilt University Medical Center (VUMC)/Vanderbilt-Ingram Cancer Center (VICC), Nashville, TN, USA
| | - Carla Daniela Robles-Espinoza
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, Querétaro, Mexico
| | - Fernanda G Arriaga-González
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK; Laboratorio Internacional de Investigación sobre el Genoma Humano, Universidad Nacional Autónoma de México, Campus Juriquilla, Querétaro, Querétaro, Mexico
| | | | - Erwan Delage
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
| | - Ed Dicks
- Department of Public Health and Primary Care, University of Cambridge, Robinson Way, Cambridge, UK
| | - Suzana Ezquina
- Department of Public Health and Primary Care, University of Cambridge, Robinson Way, Cambridge, UK
| | - Charlie F Rowlands
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK; National Cancer Registration and Analysis Service, National Health Service (NHS) England, London, UK; Cancer Genetics Unit, The Royal Marsden NHS Foundation Trust, London, UK
| | - Paul Pharoah
- Department of Computational Biomedicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge, UK
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Andrew J Waters
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
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2
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Hengel SR, Oppenheimer KG, Smith CM, Schaich MA, Rein HL, Martino J, Darrah KE, Witham M, Ezekwenna OC, Burton KR, Van Houten B, Spies M, Bernstein KA. The human Shu complex promotes RAD51 activity by modulating RPA dynamics on ssDNA. Nat Commun 2024; 15:7197. [PMID: 39169038 PMCID: PMC11339404 DOI: 10.1038/s41467-024-51595-0] [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: 06/13/2023] [Accepted: 08/09/2024] [Indexed: 08/23/2024] Open
Abstract
Templated DNA repair that occurs during homologous recombination and replication stress relies on RAD51. RAD51 activity is positively regulated by BRCA2 and the RAD51 paralogs. The Shu complex is a RAD51 paralog-containing complex consisting of SWSAP1, SWS1, and SPIDR. We demonstrate that SWSAP1-SWS1 binds RAD51, maintains RAD51 filament stability, and enables strand exchange. Using single-molecule confocal fluorescence microscopy combined with optical tweezers, we show that SWSAP1-SWS1 decorates RAD51 filaments proficient for homologous recombination. We also find SWSAP1-SWS1 enhances RPA diffusion on ssDNA. Importantly, we show human sgSWSAP1 and sgSWS1 knockout cells are sensitive to pharmacological inhibition of PARP and APE1. Lastly, we identify cancer variants in SWSAP1 that alter Shu complex formation. Together, we show that SWSAP1-SWS1 stimulates RAD51-dependent high-fidelity repair and may be an important new cancer therapeutic target.
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Affiliation(s)
- Sarah R Hengel
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA.
- Tufts University, Department of Biology, Medford, MA, USA.
| | - Katherine G Oppenheimer
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
| | - Chelsea M Smith
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
- University of North Carolina at Chapel Hill, Department of Pathology and Laboratory Medicine, Chapel Hill, NC, USA
| | - Matthew A Schaich
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
| | - Hayley L Rein
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
| | - Julieta Martino
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
- GeneDx, Gaithersburg, MD, USA
| | - Kristie E Darrah
- University of Pennsylvania School of Medicine, Penn Center for Genome Integrity, Department of Biochemistry and Biophysics, 421 Curie Boulevard, Philadelphia, PA, USA
| | - Maggie Witham
- Tufts University, Department of Biology, Medford, MA, USA
| | | | - Kyle R Burton
- Tufts University, Department of Biology, Medford, MA, USA
| | - Bennett Van Houten
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA
| | - Maria Spies
- University of Iowa, Department of Biochemistry and Molecular Biology, Iowa City, IA, USA
| | - Kara A Bernstein
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, UPMC-Hillman Cancer Center, Pittsburgh, PA, USA.
- University of Pennsylvania School of Medicine, Penn Center for Genome Integrity, Department of Biochemistry and Biophysics, 421 Curie Boulevard, Philadelphia, PA, USA.
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3
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Manneh R, Verson CA, Martin A, Delgado A, Isaacsson Velho PH, Manduley A, Tejado L, Rodríguez Y, Vargas C, Barata PC. Prospective Study of Homologous Recombination Repair Gene Mutation Prevalence in Patients With Advanced Prostate Cancer From Latin America: Challenges and Future Approaches. JCO Precis Oncol 2024; 8:e2300628. [PMID: 38748947 PMCID: PMC11371117 DOI: 10.1200/po.23.00628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 01/05/2024] [Accepted: 03/15/2024] [Indexed: 07/15/2024] Open
Abstract
PURPOSE The prevalence of homologous recombination repair gene mutations (HRRm) in patients with metastatic castration-resistant prostate cancer (mCRPC) in Latin America and the Caribbean (LAC) is unknown. Prevalence of homologous Recombination repair (HRR) gene mutatiOns in patientS with metastatic castration resistant ProstatE Cancer in LaTin America (PROSPECT) aimed to determine this prevalence and to describe the demographic and clinical characteristics of the participants. MATERIALS AND METHODS This was a prospective, cross-sectional, multicenter study across 11 cancer centers in seven LAC countries. After informed consent, all eligible participants underwent genomic testing by provided blood samples for germline HRR testing; they also provided PC tissue blocks if available for somatic HRR testing. RESULTS Between April 2021 and April 2022, 387 patients (median age, 70 years [49-89], 94.3% Eastern Cooperative Oncology Group 0-1) with mCRPC were enrolled in the study. Almost 40% of them had a family history of cancer, and the overall time from their initial PC and mCRPC diagnosis was 3 years and 1 year, respectively. The overall prevalence of germline HRRm was 4.2%. The mutations detected included the genes CHEK2 (n = 4, 1%), ATM (n = 3, 0.8%), BRCA2 (n = 3, 0.8%), BRIP1 (n = 2, 0.5%), RAD51B (n = 2, 0.5%), BRCA1 (n = 1, 0.3%), and MRE11 (n = 1, 0.3%). The prevalence of somatic HRRm could not be assessed because of high HRR testing failure rates (79%, 199/251) associated with insufficient DNA, absence of tumor cells, and poor-quality DNA. CONCLUSION Despite the study's limitations, to our knowledge, PROSPECT was the first attempt to describe the prevalence of HRRm in patients with PC from LAC. Notably, the germline HRRm prevalence in this study was inferior to that observed in North American and European populations. The somatic HRR testing barriers identified are being addressed by several projects to improve access to HRR testing and biomarker-based therapies in LAC.
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Affiliation(s)
- Ray Manneh
- Sociedad de Oncología y Hematología del Cesar, Valledupar, Colombia
| | - Carmen Alaez Verson
- Laboratorio de Diagnóstico Genómico, Instituto Nacional de Medicina Genómica, Ciudad de Mexico, Mexico
| | - Angel Martin
- Instituto Alexander Fleming, Buenos Aires, Argentina
| | - Arturo Delgado
- Centro Médico Nacional Siglo XXI, Ciudad de Mexico, Mexico
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4
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Hengel SR, Oppenheimer K, Smith C, Schaich MA, Rein HL, Martino J, Darrah K, Ezekwenna O, Burton K, Van Houten B, Spies M, Bernstein KA. The human Shu complex promotes RAD51 activity by modulating RPA dynamics on ssDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.14.580393. [PMID: 38405734 PMCID: PMC10888808 DOI: 10.1101/2024.02.14.580393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Templated DNA repair that occurs during homologous recombination and replication stress relies on RAD51. RAD51 activity is positively regulated by BRCA2 and the RAD51 paralogs. The Shu complex is a RAD51 paralog-containing complex consisting of SWSAP1 and SWS1. We demonstrate that SWSAP1-SWS1 binds RAD51, maintains RAD51 filament stability, and enables strand exchange. Using single molecule confocal fluorescence microscopy combined with optical tweezers, we show that SWSAP1-SWS1 decorates RAD51 filaments proficient for homologous recombination. We also find SWSAP1-SWS1 enhances RPA diffusion on ssDNA. Importantly, we show human sgSWSAP1 and sgSWS1 knockout cells are sensitive to pharmacological inhibition of PARP and APE1. Lastly, we identify cancer variants in SWSAP1 that alter SWS1 complex formation. Together, we show that SWSAP1-SWS1 stimulates RAD51-dependent high-fidelity repair and may be an important new cancer therapeutic target.
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5
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Ito M, Fujita Y, Shinohara A. Positive and negative regulators of RAD51/DMC1 in homologous recombination and DNA replication. DNA Repair (Amst) 2024; 134:103613. [PMID: 38142595 DOI: 10.1016/j.dnarep.2023.103613] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 12/10/2023] [Accepted: 12/10/2023] [Indexed: 12/26/2023]
Abstract
RAD51 recombinase plays a central role in homologous recombination (HR) by forming a nucleoprotein filament on single-stranded DNA (ssDNA) to catalyze homology search and strand exchange between the ssDNA and a homologous double-stranded DNA (dsDNA). The catalytic activity of RAD51 assembled on ssDNA is critical for the DNA-homology-mediated repair of DNA double-strand breaks in somatic and meiotic cells and restarting stalled replication forks during DNA replication. The RAD51-ssDNA complex also plays a structural role in protecting the regressed/reversed replication fork. Two types of regulators control RAD51 filament formation, stability, and dynamics, namely positive regulators, including mediators, and negative regulators, so-called remodelers. The appropriate balance of action by the two regulators assures genome stability. This review describes the roles of positive and negative RAD51 regulators in HR and DNA replication and its meiosis-specific homolog DMC1 in meiotic recombination. We also provide future study directions for a comprehensive understanding of RAD51/DMC1-mediated regulation in maintaining and inheriting genome integrity.
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Affiliation(s)
- Masaru Ito
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Yurika Fujita
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
| | - Akira Shinohara
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
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6
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Peng TW, Ma QF, Li J, Wang X, Zhang CH, Ma J, Li JY, Wang W, Zhu CL, Liu XH. HBV promotes its replication by up-regulating RAD51C gene expression. Sci Rep 2024; 14:2607. [PMID: 38297111 PMCID: PMC10831117 DOI: 10.1038/s41598-024-53047-7] [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: 07/30/2023] [Accepted: 01/27/2024] [Indexed: 02/02/2024] Open
Abstract
Chronic hepatitis B virus (HBV) infection is a major cause of hepatocellular carcinoma (HCC), pegylated-interferon-α(PEG-IFNα) and long-term nucleos(t)ide analogs (NUCs) are mainly drugs used to treat HBV infection, but the effectiveness is unsatisfactory in different populations, the exploration of novel therapeutic approaches is necessary. RAD51C is associated with DNA damage repair and plays an important role in the development and progression of tumors. Early cDNA microarray results showed that RAD51C expression was significantly increased in HBV-infected HCC cells, however, the relationship between HBV infection and abnormal expression of RAD51C has not been reported. Therefore, we conducted RT-PCR, western blot, Co-immunoprecipitation(Co-IP), and immunofluorescence(IF) to detect HBV-RAD51C interaction in RAD51C overexpression or interfering HCC cells. Our results showed that RAD51C and HBV X protein(HBX) produced a direct interaction in the nucleus, the HBV infection of HCC cells promoted RAD51C expression, and the increased expression of RAD51C promoted HBV replication. This indicated that RAD51C is closely related to the occurrence and development of HCC caused by HBV infection, and may bring a breakthrough in the the prevention and treatment study of HCC.
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Affiliation(s)
- Ting-Wei Peng
- Department of Clinical Laboratory, Shanghai Gongli Hospital, the Second Military Medical University, Shanghai, 200135, China
| | - Qing-Feng Ma
- Department of Clinical Laboratory, Liyuan Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430077, China
| | - Jie Li
- China Medical Tribune, Beijing, 100009, China
| | - Xue Wang
- Department of Clinical Laboratory, Shanghai Gongli Hospital, the Second Military Medical University, Shanghai, 200135, China
| | - Cong-Hui Zhang
- Department of Clinical Laboratory, Shanghai Gongli Hospital, the Second Military Medical University, Shanghai, 200135, China
| | - Junwen Ma
- Department of Clinical Laboratory, Liyuan Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430077, China
| | - Jun-Yi Li
- Department of Clinical Laboratory, Liyuan Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430077, China
| | - Wei Wang
- Department of Clinical Laboratory, Wuhan Fourth Hospital, Wuhan, 430034, China.
| | - Cheng-Liang Zhu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, China.
| | - Xing-Hui Liu
- Department of Clinical Laboratory, Shanghai Gongli Hospital, the Second Military Medical University, Shanghai, 200135, China.
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7
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Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y. High-throughput PRIME-editing screens identify functional DNA variants in the human genome. Mol Cell 2023; 83:4633-4645.e9. [PMID: 38134886 PMCID: PMC10766087 DOI: 10.1016/j.molcel.2023.11.021] [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: 05/12/2023] [Revised: 10/07/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023]
Abstract
Despite tremendous progress in detecting DNA variants associated with human disease, interpreting their functional impact in a high-throughput and single-base resolution manner remains challenging. Here, we develop a pooled prime-editing screen method, PRIME, that can be applied to characterize thousands of coding and non-coding variants in a single experiment with high reproducibility. To showcase its applications, we first identified essential nucleotides for a 716 bp MYC enhancer via PRIME-mediated single-base resolution analysis. Next, we applied PRIME to functionally characterize 1,304 genome-wide association study (GWAS)-identified non-coding variants associated with breast cancer and 3,699 variants from ClinVar. We discovered that 103 non-coding variants and 156 variants of uncertain significance are functional via affecting cell fitness. Collectively, we demonstrate that PRIME is capable of characterizing genetic variants at single-base resolution and scale, advancing accurate genome annotation for disease risk prediction, diagnosis, and therapeutic target identification.
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Affiliation(s)
- Xingjie Ren
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Han Yang
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jovia L Nierenberg
- Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Yifan Sun
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Cooper Beaman
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Thu Pham
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Mai Nobuhara
- Pharmaceutical Sciences and Pharmacogenomics Graduate Program, University of California, San Francisco, San Francisco, CA, USA
| | - Maya Asami Takagi
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Vivek Narayan
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA
| | - Yun Li
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA; Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Elad Ziv
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Division of General Internal Medicine, Department of Medicine, and Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Yin Shen
- Institute for Human Genetics, University of California, San Francisco, San Francisco, CA, USA; Department of Neurology, University of California, San Francisco, San Francisco, CA, USA; Weill Institute for Neurosciences, University of California, San Francisco, San Francisco, CA, USA.
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8
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Guh CL, Lei KH, Chen YA, Jiang YZ, Chang HY, Liaw H, Li HW, Yen HY, Chi P. RAD51 paralogs synergize with RAD51 to protect reversed forks from cellular nucleases. Nucleic Acids Res 2023; 51:11717-11731. [PMID: 37843130 PMCID: PMC10681713 DOI: 10.1093/nar/gkad856] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/12/2023] [Accepted: 09/23/2023] [Indexed: 10/17/2023] Open
Abstract
Fork reversal is a conserved mechanism to prevent stalled replication forks from collapsing. Formation and protection of reversed forks are two crucial steps in ensuring fork integrity and stability. Five RAD51 paralogs, namely, RAD51B, RAD51C, RAD51D, XRCC2 and XRCC3, which share sequence and structural similarity to the recombinase RAD51, play poorly defined mechanistic roles in these processes. Here, using purified BCDX2 (RAD51BCD-XRCC2) and CX3 (RAD51C-XRCC3) complexes and in vitro reconstituted biochemical systems, we mechanistically dissect their functions in forming and protecting reversed forks. We show that both RAD51 paralog complexes lack fork reversal activities. Whereas CX3 exhibits modest fork protection activity, BCDX2 significantly synergizes with RAD51 to protect DNA against attack by the nucleases MRE11 and EXO1. DNA protection is contingent upon the ability of RAD51 to form a functional nucleoprotein filament on DNA. Collectively, our results provide evidence for a hitherto unknown function of RAD51 paralogs in synergizing with RAD51 nucleoprotein filament to prevent degradation of stressed replication forks.
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Affiliation(s)
- Chia-Lun Guh
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Kai-Hang Lei
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Yi-An Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yi-Zhen Jiang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Hao-Yen Chang
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Hung-Wen Li
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | - Hsin-Yung Yen
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
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9
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Szakal B, Branzei D. Hot on RAD51C: structure and functions of RAD51C-XRCC3. Mol Oncol 2023; 17:1950-1952. [PMID: 37681281 PMCID: PMC10552886 DOI: 10.1002/1878-0261.13518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023] Open
Abstract
A new study by Longo, Roy et al. has solved the structure of the RAD51C-XRCC3 (CX3) heterodimer with a bound ATP analog, identifying two main structural interfaces and defining separable replication fork stability roles. One function relates to the ability of RAD51C to bind and assemble CX3 on nascent DNA, with an impact on the ability of forks to restart upon replication stress. The other relates to effective CX3 heterodimer formation, required for 5' RAD51 filament capping, with effects on RAD51 filament disassembly, fork protection and influencing the persistence of reversed forks.
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Affiliation(s)
- Barnabas Szakal
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
| | - Dana Branzei
- IFOM ETS, The AIRC Institute of Molecular OncologyMilanItaly
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM‐CNR)PaviaItaly
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10
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Rein HL, Bernstein KA. Finding significance: New perspectives in variant classification of the RAD51 regulators, BRCA2 and beyond. DNA Repair (Amst) 2023; 130:103563. [PMID: 37651978 PMCID: PMC10529980 DOI: 10.1016/j.dnarep.2023.103563] [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: 04/25/2023] [Revised: 08/11/2023] [Accepted: 08/15/2023] [Indexed: 09/02/2023]
Abstract
For many individuals harboring a variant of uncertain functional significance (VUS) in a homologous recombination (HR) gene, their risk of developing breast and ovarian cancer is unknown. Integral to the process of HR are BRCA1 and regulators of the central HR protein, RAD51, including BRCA2, PALB2, RAD51C and RAD51D. Due to advancements in sequencing technology and the continued expansion of cancer screening panels, the number of VUS identified in these genes has risen significantly. Standard practices for variant classification utilize different types of predictive, population, phenotypic, allelic and functional evidence. While variant analysis is improving, there remains a struggle to keep up with demand. Understanding the effects of an HR variant can aid in preventative care and is critical for developing an effective cancer treatment plan. In this review, we discuss current perspectives in the classification of variants in the breast and ovarian cancer genes BRCA1, BRCA2, PALB2, RAD51C and RAD51D.
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Affiliation(s)
- Hayley L Rein
- University of Pittsburgh, School of Medicine, Department of Pharmacology and Chemical Biology, Pittsburgh, PA, USA
| | - Kara A Bernstein
- University of Pennsylvania School of Medicine, Department of Biochemistry and Biophysics, 421 Curie Boulevard, Philadelphia, PA, USA.
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11
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Hu C, Nagaraj AB, Shimelis H, Montalban G, Lee KY, Huang H, Lumby CA, Na J, Susswein LR, Roberts ME, Marshall ML, Hiraki S, LaDuca H, Chao E, Yussuf A, Pesaran T, Neuhausen SL, Haiman CA, Kraft P, Lindstrom S, Palmer JR, Teras LR, Vachon CM, Yao S, Ong I, Nathanson KL, Weitzel JN, Boddicker N, Gnanaolivu R, Polley EC, Mer G, Cui G, Karam R, Richardson ME, Domchek SM, Yadav S, Hruska KS, Dolinsky J, Weroha SJ, Hart SN, Simard J, Masson JY, Pang YP, Couch FJ. Functional and Clinical Characterization of Variants of Uncertain Significance Identifies a Hotspot for Inactivating Missense Variants in RAD51C. Cancer Res 2023; 83:2557-2571. [PMID: 37253112 PMCID: PMC10390864 DOI: 10.1158/0008-5472.can-22-2319] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 10/07/2022] [Accepted: 05/25/2023] [Indexed: 06/01/2023]
Abstract
Pathogenic protein-truncating variants of RAD51C, which plays an integral role in promoting DNA damage repair, increase the risk of breast and ovarian cancer. A large number of RAD51C missense variants of uncertain significance (VUS) have been identified, but the effects of the majority of these variants on RAD51C function and cancer predisposition have not been established. Here, analysis of 173 missense variants by a homology-directed repair (HDR) assay in reconstituted RAD51C-/- cells identified 30 nonfunctional (deleterious) variants, including 18 in a hotspot within the ATP-binding region. The deleterious variants conferred sensitivity to cisplatin and olaparib and disrupted formation of RAD51C/XRCC3 and RAD51B/RAD51C/RAD51D/XRCC2 complexes. Computational analysis indicated the deleterious variant effects were consistent with structural effects on ATP-binding to RAD51C. A subset of the variants displayed similar effects on RAD51C activity in reconstituted human RAD51C-depleted cancer cells. Case-control association studies of deleterious variants in women with breast and ovarian cancer and noncancer controls showed associations with moderate breast cancer risk [OR, 3.92; 95% confidence interval (95% CI), 2.18-7.59] and high ovarian cancer risk (OR, 14.8; 95% CI, 7.71-30.36), similar to protein-truncating variants. This functional data supports the clinical classification of inactivating RAD51C missense variants as pathogenic or likely pathogenic, which may improve the clinical management of variant carriers. SIGNIFICANCE Functional analysis of the impact of a large number of missense variants on RAD51C function provides insight into RAD51C activity and information for classification of the cancer relevance of RAD51C variants.
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Affiliation(s)
| | | | | | - Gemma Montalban
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | | | | | | | - Jie Na
- Mayo Clinic, Rochester, Minnesota
| | | | | | | | | | | | | | | | | | | | | | - Peter Kraft
- T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts
| | - Sara Lindstrom
- Department of Epidemiology, University of Washington, Seattle, Washington
| | - Julie R. Palmer
- Slone Epidemiology Center at Boston University, Boston, Massachusetts
| | - Lauren R. Teras
- Behavioral and Epidemiology Research Group, American Cancer Society, Atlanta, Georgia
| | | | - Song Yao
- Roswell Park Comprehensive Cancer Center, Buffalo, New York
| | - Irene Ong
- University of Wisconsin-Madison, Madison, Wisconsin
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Jacques Simard
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
| | - Jean Yves Masson
- CHU de Quebec-Université Laval Research Center, Université Laval, Quebec City, Quebec, Canada
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12
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Longo MA, Roy S, Chen Y, Tomaszowski KH, Arvai AS, Pepper JT, Boisvert RA, Kunnimalaiyaan S, Keshvani C, Schild D, Bacolla A, Williams GJ, Tainer JA, Schlacher K. RAD51C-XRCC3 structure and cancer patient mutations define DNA replication roles. Nat Commun 2023; 14:4445. [PMID: 37488098 PMCID: PMC10366140 DOI: 10.1038/s41467-023-40096-1] [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: 04/12/2023] [Accepted: 07/07/2023] [Indexed: 07/26/2023] Open
Abstract
RAD51C is an enigmatic predisposition gene for breast, ovarian, and prostate cancer. Currently, missing structural and related functional understanding limits patient mutation interpretation to homology-directed repair (HDR) function analysis. Here we report the RAD51C-XRCC3 (CX3) X-ray co-crystal structure with bound ATP analog and define separable RAD51C replication stability roles informed by its three-dimensional structure, assembly, and unappreciated polymerization motif. Mapping of cancer patient mutations as a functional guide confirms ATP-binding matching RAD51 recombinase, yet highlights distinct CX3 interfaces. Analyses of CRISPR/Cas9-edited human cells with RAD51C mutations combined with single-molecule, single-cell and biophysics measurements uncover discrete CX3 regions for DNA replication fork protection, restart and reversal, accomplished by separable functions in DNA binding and implied 5' RAD51 filament capping. Collective findings establish CX3 as a cancer-relevant replication stress response complex, show how HDR-proficient variants could contribute to tumor development, and identify regions to aid functional testing and classification of cancer mutations.
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Affiliation(s)
- Michael A Longo
- Department of Molecular & Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Sunetra Roy
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Yue Chen
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | - Andrew S Arvai
- The Department of Integrative Structural & Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Jordan T Pepper
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Rebecca A Boisvert
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | | | - Caezanne Keshvani
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - David Schild
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Albino Bacolla
- Department of Molecular & Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Gareth J Williams
- Department of Biochemistry and Molecular Biology, Robson DNA Science Centre, Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada.
| | - John A Tainer
- Department of Molecular & Cellular Oncology, UT MD Anderson Cancer Center, Houston, TX, USA.
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA.
| | - Katharina Schlacher
- Department of Cancer Biology, UT MD Anderson Cancer Center, Houston, TX, USA.
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13
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Rawal Y, Jia L, Meir A, Zhou S, Kaur H, Ruben EA, Kwon Y, Bernstein KA, Jasin M, Taylor AB, Burma S, Hromas R, Mazin AV, Zhao W, Zhou D, Wasmuth EV, Greene EC, Sung P, Olsen SK. Structural insights into BCDX2 complex function in homologous recombination. Nature 2023; 619:640-649. [PMID: 37344589 PMCID: PMC10712684 DOI: 10.1038/s41586-023-06219-w] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 05/15/2023] [Indexed: 06/23/2023]
Abstract
Homologous recombination (HR) fulfils a pivotal role in the repair of DNA double-strand breaks and collapsed replication forks1. HR depends on the products of several paralogues of RAD51, including the tetrameric complex of RAD51B, RAD51C, RAD51D and XRCC2 (BCDX2)2. BCDX2 functions as a mediator of nucleoprotein filament assembly by RAD51 and single-stranded DNA (ssDNA) during HR, but its mechanism remains undefined. Here we report cryogenic electron microscopy reconstructions of human BCDX2 in apo and ssDNA-bound states. The structures reveal how the amino-terminal domains of RAD51B, RAD51C and RAD51D participate in inter-subunit interactions that underpin complex formation and ssDNA-binding specificity. Single-molecule DNA curtain analysis yields insights into how BCDX2 enhances RAD51-ssDNA nucleoprotein filament assembly. Moreover, our cryogenic electron microscopy and functional analyses explain how RAD51C alterations found in patients with cancer3-6 inactivate DNA binding and the HR mediator activity of BCDX2. Our findings shed light on the role of BCDX2 in HR and provide a foundation for understanding how pathogenic alterations in BCDX2 impact genome repair.
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Affiliation(s)
- Yashpal Rawal
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Lijia Jia
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Aviv Meir
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA
| | - Shuo Zhou
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Hardeep Kaur
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Eliza A Ruben
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Youngho Kwon
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Kara A Bernstein
- Department of Biochemistry & Biophysics, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexander B Taylor
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Sandeep Burma
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
- Department of Neurosurgery, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Robert Hromas
- Department of Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Alexander V Mazin
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Weixing Zhao
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Daohong Zhou
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Elizabeth V Wasmuth
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Eric C Greene
- Department of Biochemistry and Molecular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.
| | - Patrick Sung
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Shaun K Olsen
- Department of Biochemistry & Structural Biology and Greehey Children's Cancer Research Institute, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, San Antonio, TX, USA.
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14
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Greenhough LA, Liang CC, Belan O, Kunzelmann S, Maslen S, Rodrigo-Brenni MC, Anand R, Skehel M, Boulton SJ, West SC. Structure and function of the RAD51B-RAD51C-RAD51D-XRCC2 tumour suppressor. Nature 2023; 619:650-657. [PMID: 37344587 PMCID: PMC7614784 DOI: 10.1038/s41586-023-06179-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 05/08/2023] [Indexed: 06/23/2023]
Abstract
Homologous recombination is a fundamental process of life. It is required for the protection and restart of broken replication forks, the repair of chromosome breaks and the exchange of genetic material during meiosis. Individuals with mutations in key recombination genes, such as BRCA2 (also known as FANCD1), or the RAD51 paralogues RAD51B, RAD51C (also known as FANCO), RAD51D, XRCC2 (also known as FANCU) and XRCC3, are predisposed to breast, ovarian and prostate cancers1-10 and the cancer-prone syndrome Fanconi anaemia11-13. The BRCA2 tumour suppressor protein-the product of BRCA2-is well characterized, but the cellular functions of the RAD51 paralogues remain unclear. Genetic knockouts display growth defects, reduced RAD51 focus formation, spontaneous chromosome abnormalities, sensitivity to PARP inhibitors and replication fork defects14,15, but the precise molecular roles of RAD51 paralogues in fork stability, DNA repair and cancer avoidance remain unknown. Here we used cryo-electron microscopy, AlphaFold2 modelling and structural proteomics to determine the structure of the RAD51B-RAD51C-RAD51D-XRCC2 complex (BCDX2), revealing that RAD51C-RAD51D-XRCC2 mimics three RAD51 protomers aligned within a nucleoprotein filament, whereas RAD51B is highly dynamic. Biochemical and single-molecule analyses showed that BCDX2 stimulates the nucleation and extension of RAD51 filaments-which are essential for recombinational DNA repair-in reactions that depend on the coupled ATPase activities of RAD51B and RAD51C. Our studies demonstrate that BCDX2 orchestrates RAD51 assembly on single stranded DNA for replication fork protection and double strand break repair, in reactions that are critical for tumour avoidance.
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Affiliation(s)
| | | | - Ondrej Belan
- The Francis Crick Institute, London, UK
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Boston, MA, USA
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15
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RAD51 paralogs: Expanding roles in replication stress responses and repair. Curr Opin Pharmacol 2022; 67:102313. [PMID: 36343481 DOI: 10.1016/j.coph.2022.102313] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/26/2022] [Accepted: 09/29/2022] [Indexed: 11/06/2022]
Abstract
Mammalian RAD51 paralogs are essential for cell survival and are critical for RAD51-mediated repair of DNA double-strand breaks (DSBs) by homologous recombination (HR). However, the molecular mechanism by which RAD51 paralogs participate in HR is largely unclear. Germline mutations in RAD51 paralogs are associated with breast and ovarian cancers and Fanconi anemia-like disorder, underscoring the crucial roles of RAD51 paralogs in genome maintenance and tumor suppression. Despite their discovery over three decades ago, the essential functions of RAD51 paralogs in cell survival and genome stability remain obscure. Recent studies unravel DSB repair independent functions of RAD51 paralogs in replication stress responses. Here, we highlight the recent findings that uncovered the novel functions of RAD51 paralogs in replication fork progression, its stability, and restart and discuss RAD51 paralogs as a potential therapeutic target for cancer treatment.
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