1
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Honda M, Razzaghi M, Gaur P, Malacaria E, Marozzi G, Biagi LD, Aiello FA, Paintsil EA, Stanfield AJ, Deppe BJ, Gakhar L, Schnicker NJ, Ashley Spies M, Pichierri P, Spies M. A double-ring of human RAD52 remodels replication forks restricting fork reversal. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.14.566657. [PMID: 38014173 PMCID: PMC10680749 DOI: 10.1101/2023.11.14.566657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Human RAD52 1,2 is a multifunctional DNA repair protein involved in several cellular events that support genome stability including protection of stalled DNA replication forks from excessive degradation 3-7 . In its gatekeeper role, RAD52 binds to and stabilizes stalled replication forks during replication stress protecting them from reversal by SMARCAL1 5 . The structural and molecular mechanism of the RAD52-mediated fork protection remains elusive. Here, using P1 nuclease sensitivity, biochemical and single-molecule analyses we show that RAD52 dynamically remodels replication forks through its strand exchange activity. The presence of the ssDNA binding protein RPA at the fork modulates the kinetics of the strand exchange without impeding the reaction outcome. Mass photometry and single-particle cryo-electron microscopy show that the replication fork promotes a unique nucleoprotein structure containing head-to-head arrangement of two undecameric RAD52 rings with an extended positively charged surface that accommodates all three arms of the replication fork. We propose that the formation and continuity of this surface is important for the strand exchange reaction and for competition with SMARCAL1. One Sentence Summary Using cryo-EM, biochemical and single-molecule approaches we show that the structure of stalled DNA replication fork promotes a unique two-ring organization of human RAD52 protein which remodels the fork via DNA strand exchange.
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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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Di Biagi L, Marozzi G, Malacaria E, Honda M, Aiello FA, Valenzisi P, Spies M, Franchitto A, Pichierri P. RAD52 prevents accumulation of Polα -dependent replication gaps at perturbed replication forks in human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.12.536536. [PMID: 37090680 PMCID: PMC10120653 DOI: 10.1101/2023.04.12.536536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Replication gaps can arise as a consequence of perturbed DNA replication and their accumulation might undermine the stability of the genome. Loss of RAD52, a protein involved in the regulation of fork reversal, promotes accumulation of parental ssDNA gaps during replication perturbation. Here, we demonstrate that this is due to the engagement of Polα downstream of the extensive degradation of perturbed replication forks after their reversal, and is not dependent on PrimPol. Polα is hyper-recruited at parental ssDNA in the absence of RAD52, and this recruitment is dependent on fork reversal enzymes and RAD51. Of note, we report that the interaction between Polα and RAD51 is stimulated by RAD52 inhibition, and Polα -dependent gap accumulation requires nucleation of RAD51 suggesting that it occurs downstream strand invasion. Altogether, our data indicate that RAD51- Polα -dependent repriming is essential to promote fork restart and limit DNA damage accumulation when RAD52 function is disabled.
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Affiliation(s)
- Ludovica Di Biagi
- Mechanisms, Biomarkers and Models Section, Genome Stability Group, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Giorgia Marozzi
- Mechanisms, Biomarkers and Models Section, Genome Stability Group, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Section, Genome Stability Group, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Masayoshi Honda
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242 (USA)
| | - Francesca Antonella Aiello
- Mechanisms, Biomarkers and Models Section, Genome Stability Group, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Pasquale Valenzisi
- Mechanisms, Biomarkers and Models Section, Genome Stability Group, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242 (USA)
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Section, Genome Stability Group, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Section, Genome Stability Group, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome (Italy)
- Istituto Nazionale Biostrutture e Biosistemi - Roma Area Research - Via delle Medaglie d’Oro 305, 00136 Rome (Italy)
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4
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Previtali V, Bagnolini G, Ciamarone A, Ferrandi G, Rinaldi F, Myers SH, Roberti M, Cavalli A. New Horizons of Synthetic Lethality in Cancer: Current Development and Future Perspectives. J Med Chem 2024; 67:11488-11521. [PMID: 38955347 DOI: 10.1021/acs.jmedchem.4c00113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
In recent years, synthetic lethality has been recognized as a solid paradigm for anticancer therapies. The discovery of a growing number of synthetic lethal targets has led to a significant expansion in the use of synthetic lethality, far beyond poly(ADP-ribose) polymerase inhibitors used to treat BRCA1/2-defective tumors. In particular, molecular targets within DNA damage response have provided a source of inhibitors that have rapidly reached clinical trials. This Perspective focuses on the most recent progress in synthetic lethal targets and their inhibitors, within and beyond the DNA damage response, describing their design and associated therapeutic strategies. We will conclude by discussing the current challenges and new opportunities for this promising field of research, to stimulate discussion in the medicinal chemistry community, allowing the investigation of synthetic lethality to reach its full potential.
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Affiliation(s)
- Viola Previtali
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Greta Bagnolini
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Ciamarone
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Giovanni Ferrandi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Francesco Rinaldi
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Samuel Harry Myers
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
| | - Marinella Roberti
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
| | - Andrea Cavalli
- Computational & Chemical Biology, Istituto Italiano di Tecnologia, 16163 Genova, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, 40126 Bologna, Italy
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5
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Cavalcante BRR, Freitas RD, Siquara da Rocha LO, Santos RSB, Souza BSDF, Ramos PIP, Rocha GV, Gurgel Rocha CA. In silico approaches for drug repurposing in oncology: a scoping review. Front Pharmacol 2024; 15:1400029. [PMID: 38919258 PMCID: PMC11196849 DOI: 10.3389/fphar.2024.1400029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 05/14/2024] [Indexed: 06/27/2024] Open
Abstract
Introduction: Cancer refers to a group of diseases characterized by the uncontrolled growth and spread of abnormal cells in the body. Due to its complexity, it has been hard to find an ideal medicine to treat all cancer types, although there is an urgent need for it. However, the cost of developing a new drug is high and time-consuming. In this sense, drug repurposing (DR) can hasten drug discovery by giving existing drugs new disease indications. Many computational methods have been applied to achieve DR, but just a few have succeeded. Therefore, this review aims to show in silico DR approaches and the gap between these strategies and their ultimate application in oncology. Methods: The scoping review was conducted according to the Arksey and O'Malley framework and the Joanna Briggs Institute recommendations. Relevant studies were identified through electronic searching of PubMed/MEDLINE, Embase, Scopus, and Web of Science databases, as well as the grey literature. We included peer-reviewed research articles involving in silico strategies applied to drug repurposing in oncology, published between 1 January 2003, and 31 December 2021. Results: We identified 238 studies for inclusion in the review. Most studies revealed that the United States, India, China, South Korea, and Italy are top publishers. Regarding cancer types, breast cancer, lymphomas and leukemias, lung, colorectal, and prostate cancer are the top investigated. Additionally, most studies solely used computational methods, and just a few assessed more complex scientific models. Lastly, molecular modeling, which includes molecular docking and molecular dynamics simulations, was the most frequently used method, followed by signature-, Machine Learning-, and network-based strategies. Discussion: DR is a trending opportunity but still demands extensive testing to ensure its safety and efficacy for the new indications. Finally, implementing DR can be challenging due to various factors, including lack of quality data, patient populations, cost, intellectual property issues, market considerations, and regulatory requirements. Despite all the hurdles, DR remains an exciting strategy for identifying new treatments for numerous diseases, including cancer types, and giving patients faster access to new medications.
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Affiliation(s)
- Bruno Raphael Ribeiro Cavalcante
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Department of Pathology and Forensic Medicine of the School of Medicine, Federal University of Bahia, Salvador, Brazil
| | - Raíza Dias Freitas
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Department of Social and Pediatric Dentistry of the School of Dentistry, Federal University of Bahia, Salvador, Brazil
| | - Leonardo de Oliveira Siquara da Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Department of Pathology and Forensic Medicine of the School of Medicine, Federal University of Bahia, Salvador, Brazil
| | | | - Bruno Solano de Freitas Souza
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- D’Or Institute for Research and Education (IDOR), Salvador, Brazil
| | - Pablo Ivan Pereira Ramos
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Center of Data and Knowledge Integration for Health (CIDACS), Salvador, Brazil
| | - Gisele Vieira Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- D’Or Institute for Research and Education (IDOR), Salvador, Brazil
| | - Clarissa Araújo Gurgel Rocha
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (IGM-FIOCRUZ/BA), Salvador, Brazil
- Department of Pathology and Forensic Medicine of the School of Medicine, Federal University of Bahia, Salvador, Brazil
- D’Or Institute for Research and Education (IDOR), Salvador, Brazil
- Department of Propaedeutics, School of Dentistry of the Federal University of Bahia, Salvador, Brazil
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6
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Liang CC, Greenhough LA, Masino L, Maslen S, Bajrami I, Tuppi M, Skehel M, Taylor IA, West SC. Mechanism of single-stranded DNA annealing by RAD52-RPA complex. Nature 2024; 629:697-703. [PMID: 38658755 PMCID: PMC11096129 DOI: 10.1038/s41586-024-07347-7] [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: 06/06/2023] [Accepted: 03/22/2024] [Indexed: 04/26/2024]
Abstract
RAD52 is important for the repair of DNA double-stranded breaks1,2, mitotic DNA synthesis3-5 and alternative telomere length maintenance6,7. Central to these functions, RAD52 promotes the annealing of complementary single-stranded DNA (ssDNA)8,9 and provides an alternative to BRCA2/RAD51-dependent homologous recombination repair10. Inactivation of RAD52 in homologous-recombination-deficient BRCA1- or BRCA2-defective cells is synthetically lethal11,12, and aberrant expression of RAD52 is associated with poor cancer prognosis13,14. As a consequence, RAD52 is an attractive therapeutic target against homologous-recombination-deficient breast, ovarian and prostate cancers15-17. Here we describe the structure of RAD52 and define the mechanism of annealing. As reported previously18-20, RAD52 forms undecameric (11-subunit) ring structures, but these rings do not represent the active form of the enzyme. Instead, cryo-electron microscopy and biochemical analyses revealed that ssDNA annealing is driven by RAD52 open rings in association with replication protein-A (RPA). Atomic models of the RAD52-ssDNA complex show that ssDNA sits in a positively charged channel around the ring. Annealing is driven by the RAD52 N-terminal domains, whereas the C-terminal regions modulate the open-ring conformation and RPA interaction. RPA associates with RAD52 at the site of ring opening with critical interactions occurring between the RPA-interacting domain of RAD52 and the winged helix domain of RPA2. Our studies provide structural snapshots throughout the annealing process and define the molecular mechanism of ssDNA annealing by the RAD52-RPA complex.
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Affiliation(s)
| | | | | | | | | | - Marcel Tuppi
- The Francis Crick Institute, London, UK
- Abcam, Cambridge Biomedical Campus, Cambridge, UK
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7
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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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8
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Ronson GE, Starowicz K, Anthony EJ, Piberger AL, Clarke LC, Garvin AJ, Beggs AD, Whalley CM, Edmonds MJ, Beesley JFJ, Morris JR. Mechanisms of synthetic lethality between BRCA1/2 and 53BP1 deficiencies and DNA polymerase theta targeting. Nat Commun 2023; 14:7834. [PMID: 38030626 PMCID: PMC10687250 DOI: 10.1038/s41467-023-43677-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 11/16/2023] [Indexed: 12/01/2023] Open
Abstract
A synthetic lethal relationship exists between disruption of polymerase theta (Polθ), and loss of either 53BP1 or homologous recombination (HR) proteins, including BRCA1; however, the mechanistic basis of these observations are unclear. Here we reveal two distinct mechanisms of Polθ synthetic lethality, identifying dual influences of 1) whether Polθ is lost or inhibited, and 2) the underlying susceptible genotype. Firstly, we find that the sensitivity of BRCA1/2- and 53BP1-deficient cells to Polθ loss, and 53BP1-deficient cells to Polθ inhibition (ART558) requires RAD52, and appropriate reduction of RAD52 can ameliorate these phenotypes. We show that in the absence of Polθ, RAD52 accumulations suppress ssDNA gap-filling in G2/M and encourage MRE11 nuclease accumulation. In contrast, the survival of BRCA1-deficient cells treated with Polθ inhibitor are not restored by RAD52 suppression, and ssDNA gap-filling is prevented by the chemically inhibited polymerase itself. These data define an additional role for Polθ, reveal the mechanism underlying synthetic lethality between 53BP1, BRCA1/2 and Polθ loss, and indicate genotype-dependent Polθ inhibitor mechanisms.
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Affiliation(s)
- George E Ronson
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Katarzyna Starowicz
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Adthera Bio, Lyndon House, 62 Hagley Road, Birmingham, B16 8PE, UK
| | - Elizabeth J Anthony
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ann Liza Piberger
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Lucy C Clarke
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- West Midlands Regional Genetics Laboratory, Birmingham Women's Hospital, Mindelsohn Way, Birmingham, B15 2TG, UK
| | - Alexander J Garvin
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- University of Leeds, Leeds, UK
| | - Andrew D Beggs
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Genomics Birmingham, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Celina M Whalley
- Genomics Birmingham, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Matthew J Edmonds
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
- Certara Insight, Danebrook Court, Oxford Office Village, Kidlington, Oxfordshire, OX5 1LQ, UK
| | - James F J Beesley
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- Birmingham Centre for Genome Biology and Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
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9
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Palovcak A, Yuan F, Verdun R, Luo L, Zhang Y. Fanconi anemia associated protein 20 (FAAP20) plays an essential role in homology-directed repair of DNA double-strand breaks. Commun Biol 2023; 6:873. [PMID: 37620397 PMCID: PMC10449828 DOI: 10.1038/s42003-023-05252-9] [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: 12/19/2022] [Accepted: 08/17/2023] [Indexed: 08/26/2023] Open
Abstract
FAAP20 is a Fanconi anemia (FA) protein that associates with the FA core complex to promote FANCD2/FANCI monoubiquitination and activate the damage response to interstrand crosslink damage. Here, we report that FAAP20 has a marked role in homologous recombination at a DNA double-strand break not associated with an ICL and separable from its binding partner FANCA. While FAAP20's role in homologous recombination is not dependent on FANCA, we found that FAAP20 stimulates FANCA's biochemical activity in vitro and participates in the single-strand annealing pathway of double-strand break repair in a FANCA-dependent manner. This indicates that FAAP20 has roles in several homology-directed repair pathways. Like other homology-directed repair factors, FAAP20 loss causes a reduction in nuclear RAD51 Irradiation-induced foci; and sensitizes cancer cells to ionizing radiation and PARP inhibition. In summary, FAAP20 participates in DNA double strand break repair by supporting homologous recombination in a non-redundant manner to FANCA, and single-strand annealing repair via FANCA-mediated strand annealing activity.
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Affiliation(s)
- Anna Palovcak
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Fenghua Yuan
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Ramiro Verdun
- Department of Medicine, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Liang Luo
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Yanbin Zhang
- Department of Biochemistry & Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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10
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Richards F, Llorca-Cardenosa MJ, Langton J, Buch-Larsen SC, Shamkhi NF, Sharma AB, Nielsen ML, Lakin ND. Regulation of Rad52-dependent replication fork recovery through serine ADP-ribosylation of PolD3. Nat Commun 2023; 14:4310. [PMID: 37463936 DOI: 10.1038/s41467-023-40071-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/06/2023] [Indexed: 07/20/2023] Open
Abstract
Although Poly(ADP-ribose)-polymerases (PARPs) are key regulators of genome stability, how site-specific ADP-ribosylation regulates DNA repair is unclear. Here, we describe a novel role for PARP1 and PARP2 in regulating Rad52-dependent replication fork repair to maintain cell viability when homologous recombination is dysfunctional, suppress replication-associated DNA damage, and maintain genome stability. Mechanistically, Mre11 and ATM are required for induction of PARP activity in response to replication stress that in turn promotes break-induced replication (BIR) through assembly of Rad52 at stalled/damaged replication forks. Further, by mapping ADP-ribosylation sites induced upon replication stress, we identify that PolD3 is a target for PARP1/PARP2 and that its site-specific ADP-ribosylation is required for BIR activity, replication fork recovery and genome stability. Overall, these data identify a critical role for Mre11-dependent PARP activation and site-specific ADP-ribosylation in regulating BIR to maintain genome integrity during DNA synthesis.
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Affiliation(s)
- Frederick Richards
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | | | - Jamie Langton
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Sara C Buch-Larsen
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Noor F Shamkhi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | | | - Michael L Nielsen
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200, Copenhagen, Denmark
| | - Nicholas D Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK.
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11
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Bhat D, Malacaria E, Biagi L, Razzaghi M, Honda M, Hobbs K, Hengel S, Pichierri P, Spies M, Spies M. Therapeutic disruption of RAD52-ssDNA complexation via novel drug-like inhibitors. NAR Cancer 2023; 5:zcad018. [PMID: 37139244 PMCID: PMC10150327 DOI: 10.1093/narcan/zcad018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/09/2023] [Accepted: 04/14/2023] [Indexed: 05/05/2023] Open
Abstract
RAD52 protein is a coveted target for anticancer drug discovery. Similar to poly-ADP-ribose polymerase (PARP) inhibitors, pharmacological inhibition of RAD52 is synthetically lethal with defects in genome caretakers BRCA1 and BRCA2 (∼25% of breast and ovarian cancers). Emerging structure activity relationships for RAD52 are complex, making it challenging to transform previously identified disruptors of the RAD52-ssDNA interaction into drug-like leads using traditional medicinal chemistry approaches. Using pharmacophoric informatics on the RAD52 complexation by epigallocatechin (EGC), and the Enamine in silico REAL database, we identified six distinct chemical scaffolds that occupy the same physical space on RAD52 as EGC. All six were RAD52 inhibitors (IC50 ∼23-1200 μM) with two of the compounds (Z56 and Z99) selectively killing BRCA-mutant cells and inhibiting cellular activities of RAD52 at micromolar inhibitor concentrations. While Z56 had no effect on the ssDNA-binding protein RPA and was toxic to BRCA-mutant cells only, Z99 inhibited both proteins and displayed toxicity towards BRCA-complemented cells. Optimization of the Z99 scaffold resulted in a set of more powerful and selective inhibitors (IC50 ∼1.3-8 μM), which were only toxic to BRCA-mutant cells. RAD52 complexation by Z56, Z99 and its more specific derivatives provide a roadmap for next generation of cancer therapeutics.
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Affiliation(s)
- Divya S Bhat
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Ludovica Di Biagi
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Mortezaali Razzaghi
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Masayoshi Honda
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Kathryn F Hobbs
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, IA 52242, USA
| | - Sarah R Hengel
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Section, Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - M Ashley Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, IA 52242, USA
- Naturis Informatika LLC, 401 Mullin Ave., Iowa City, IA 52246, USA
| | - Maria Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
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12
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Balboni B, Rinaldi F, Previtali V, Ciamarone A, Girotto S, Cavalli A. Novel Insights into RAD52’s Structure, Function, and Druggability for Synthetic Lethality and Innovative Anticancer Therapies. Cancers (Basel) 2023; 15:cancers15061817. [PMID: 36980703 PMCID: PMC10046612 DOI: 10.3390/cancers15061817] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 03/08/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
In recent years, the RAD52 protein has been highlighted as a mediator of many DNA repair mechanisms. While RAD52 was initially considered to be a non-essential auxiliary factor, its inhibition has more recently been demonstrated to be synthetically lethal in cancer cells bearing mutations and inactivation of specific intracellular pathways, such as homologous recombination. RAD52 is now recognized as a novel and critical pharmacological target. In this review, we comprehensively describe the available structural and functional information on RAD52. The review highlights the pathways in which RAD52 is involved and the approaches to RAD52 inhibition. We discuss the multifaceted role of this protein, which has a complex, dynamic, and functional 3D superstructural arrangement. This complexity reinforces the need to further investigate and characterize RAD52 to solve a challenging mechanistic puzzle and pave the way for a robust drug discovery campaign.
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Affiliation(s)
- Beatrice Balboni
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Francesco Rinaldi
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Viola Previtali
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy
| | - Andrea Ciamarone
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
| | - Stefania Girotto
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy
- Structural Biophysics and Translational Pharmacology Facility, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy
- Correspondence: (S.G.); (A.C.); Tel.: +39-010-2896-983 (S.G.); +39-010-2897-403 (A.C.)
| | - Andrea Cavalli
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, 16163 Genoa, Italy
- Department of Pharmacy and Biotechnology, University of Bologna, via Belmeloro 6, 40126 Bologna, Italy
- Correspondence: (S.G.); (A.C.); Tel.: +39-010-2896-983 (S.G.); +39-010-2897-403 (A.C.)
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13
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van de Kooij B, Schreuder A, Pavani RS, Garzero V, Van Hoeck A, San Martin Alonso M, Koerse D, Wendel TJ, Callen E, Boom J, Mei H, Cuppen E, Nussenzweig A, van Attikum H, Noordermeer SM. EXO1-mediated DNA repair by single-strand annealing is essential for BRCA1-deficient cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.24.529205. [PMID: 37720033 PMCID: PMC10503826 DOI: 10.1101/2023.02.24.529205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/19/2023]
Abstract
Deficiency for the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR) leads to chromosomal instability and diseases such as cancer. Yet, defective HR also results in vulnerabilities that can be exploited for targeted therapy. Here, we identify such a vulnerability and show that BRCA1-deficient cells are dependent on the long-range end-resection factor EXO1 for survival. EXO1 loss results in DNA replication-induced lesions decorated by poly(ADP-ribose)-chains. In cells that lack both BRCA1 and EXO1, this is accompanied by unresolved DSBs due to impaired single-strand annealing (SSA), a DSB repair process that requires the activity of both proteins. In contrast, BRCA2-deficient cells have increased SSA, also in the absence of EXO1, and hence are not dependent on EXO1 for survival. In agreement with our mechanistic data, BRCA1-mutated tumours have elevated EXO1 expression and contain more genomic signatures of SSA compared to BRCA1-proficient tumours. Collectively, our data indicate that EXO1 is a promising novel target for treatment of BRCA1-deficient tumours.
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14
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Bhat DS, Spies MA, Spies M. A moving target for drug discovery: Structure activity relationship and many genome (de)stabilizing functions of the RAD52 protein. DNA Repair (Amst) 2022; 120:103421. [PMID: 36327799 PMCID: PMC9888176 DOI: 10.1016/j.dnarep.2022.103421] [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: 07/29/2022] [Revised: 10/18/2022] [Accepted: 10/24/2022] [Indexed: 02/02/2023]
Abstract
BRCA-ness phenotype, a signature of many breast and ovarian cancers, manifests as deficiency in homologous recombination, and as defects in protection and repair of damaged DNA replication forks. A dependence of such cancers on DNA repair factors less important for survival of BRCA-proficient cells, offers opportunities for development of novel chemotherapeutic interventions. The first drugs targeting BRCA-deficient cancers, poly-ADP-ribose polymerase (PARP) inhibitors have been approved for the treatment of advanced, chemotherapy resistant cancers in patients with BRCA1/2 germline mutations. Nine additional proteins that can be targeted to selectively kill BRCA-deficient cancer cells have been identified. Among them, a DNA repair protein RAD52 is an especially attractive target due to general tolerance of the RAD52 loss of function, and protective role of an inactivating mutation. Yet, the effective pharmacological inhibitors of RAD52 have not been forthcoming. In this review, we discuss advances in the state of our knowledge of the RAD52 structure, activities and cellular functions, with a specific focus on the features that make RAD52 an attractive, but difficult drug target.
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Affiliation(s)
- Divya S Bhat
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - M Ashley Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA; Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, Iowa 52242, USA
| | - Maria Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA.
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15
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Skoko JJ, Cao J, Gaboriau D, Attar M, Asan A, Hong L, Paulsen CE, Ma H, Liu Y, Wu H, Harkness T, Furdui CM, Manevich Y, Morrison CG, Brown ET, Normolle D, Spies M, Spies MA, Carroll K, Neumann CA. Redox regulation of RAD51 Cys319 and homologous recombination by peroxiredoxin 1. Redox Biol 2022; 56:102443. [PMID: 36058112 PMCID: PMC9450138 DOI: 10.1016/j.redox.2022.102443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 08/01/2022] [Accepted: 08/11/2022] [Indexed: 11/28/2022] Open
Abstract
RAD51 is a critical recombinase that functions in concert with auxiliary mediator proteins to direct the homologous recombination (HR) DNA repair pathway. We show that Cys319 RAD51 possesses nucleophilic characteristics and is important for irradiation-induced RAD51 foci formation and resistance to inhibitors of poly (ADP-ribose) polymerase (PARP). We have previously identified that cysteine (Cys) oxidation of proteins can be important for activity and modulated via binding to peroxiredoxin 1 (PRDX1). PRDX1 reduces peroxides and coordinates the signaling actions of protein binding partners. Loss of PRDX1 inhibits irradiation-induced RAD51 foci formation and represses HR DNA repair. PRDX1-deficient human breast cancer cells and mouse embryonic fibroblasts display disrupted RAD51 foci formation and decreased HR, resulting in increased DNA damage and sensitization of cells to irradiation. Following irradiation cells deficient in PRDX1 had increased incorporation of the sulfenylation probe DAz-2 in RAD51 Cys319, a functionally-significant, thiol that PRDX1 is critical for maintaining in a reduced state. Molecular dynamics (MD) simulations of dT-DNA bound to a non-oxidized RAD51 protein showed tight binding throughout the simulation, while dT-DNA dissociated from an oxidized Cys319 RAD51 filament. These novel data establish RAD51 Cys319 as a functionally-significant site for the redox regulation of HR and cellular responses to IR. A functionally-significant Cys319 was identified in RAD51 that possesses nucleophilic characteristics. RAD51 Cys319 plays a central role in RAD51-mediated repair of DNA double strand breaks (DSB). Loss of peroxiredoxin 1 (PRDX1) impairs DNA DSB repair by homologous recombination and results in DNA damage. PRDX1 is critical for maintaining RAD51 Cys319 in a reduced state. Molecular dynamic (MD) simulations suggest ssDNA to dissociate from sulfenylated and not reduced RAD51 Cys319.
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Affiliation(s)
- John J Skoko
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Juxiang Cao
- Department of Cell and Molecular Pharmacology, The Medical University of South Carolina, Charleston, SC, 29425, USA
| | - David Gaboriau
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland; Facility for Imaging By Light Microscopy, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Myriam Attar
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Alparslan Asan
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Lisa Hong
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA
| | - Candice E Paulsen
- Department of Chemistry, Scripps Research Institute Florida, Jupiter, FL, 33458, USA
| | - Hongqiang Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Hanzhi Wu
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Trey Harkness
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA
| | - Cristina M Furdui
- Department of Internal Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA; Center for Redox Biology and Medicine, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Yefim Manevich
- Department of Cell and Molecular Pharmacology, The Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Ciaran G Morrison
- Centre for Chromosome Biology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Erika T Brown
- Dartmouth Geisel School of Medicine, Hanover, NH, 03755, USA
| | - Daniel Normolle
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa, IA, 52242, USA
| | - Michael Ashley Spies
- Department of Biochemistry and Molecular Biology, Department of Pharmaceutical Sciences and Experimental Therapeutics, University of Iowa, IA, 52242, USA
| | - Kate Carroll
- Department of Chemistry, Scripps Research Institute Florida, Jupiter, FL, 33458, USA
| | - Carola A Neumann
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, 15261, USA; Women's Cancer Research Center, University of Pittsburgh Cancer Institute, Pittsburgh, PA, 15213, USA; Magee-Women's Research Institute, Magee-Women's Research Hospital of University of Pittsburgh Medical Center, Pittsburgh, PA, 15213, USA.
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16
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Li E, Xia M, Du Y, Long K, Ji F, Pan F, He L, Hu Z, Guo Z. METTL3 promotes homologous recombination repair and modulates chemotherapeutic response in breast cancer by regulating the EGF/Rad51 axis. eLife 2022; 11:75231. [PMID: 35502895 PMCID: PMC9094751 DOI: 10.7554/elife.75231] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
METTL3 and N6-methyladenosine (m6A) are involved in many types of biological and pathological processes, including DNA repair. However, the function and mechanism of METTL3 in DNA repair and chemotherapeutic response remain largely unknown. In present study, we identified that METTL3 participates in the regulation of homologous recombination repair (HR), which further influences chemotherapeutic response in both MCF-7 and MDA-MB-231 breast cancer (BC) cells. Knockdown of METTL3 sensitized these BC cells to Adriamycin (ADR; also named as doxorubicin) treatment and increased accumulation of DNA damage. Mechanically, we demonstrated that inhibition of METTL3 impaired HR efficiency and increased ADR-induced DNA damage by regulating m6A modification of EGF/RAD51 axis. METTL3 promoted EGF expression through m6A modification, which further upregulated RAD51 expression, resulting in enhanced HR activity. We further demonstrated that the m6A 'reader', YTHDC1, bound to the m6A modified EGF transcript and promoted EGF synthesis, which enhanced HR and cell survival during ADR treatment in breast cancer cells. Our findings reveal a pivotal mechanism of METTL3-mediated HR and chemotherapeutic drug response, which may contribute to cancer therapy.
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Affiliation(s)
- Enjie Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Mingyue Xia
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Yu Du
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Kaili Long
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Feng Ji
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Feiyan Pan
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Lingfeng He
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Zhigang Hu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, Nanjing, China
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17
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Kelm JM, Samarbakhsh A, Pillai A, VanderVere-Carozza PS, Aruri H, Pandey DS, Pawelczak KS, Turchi JJ, Gavande NS. Recent Advances in the Development of Non-PIKKs Targeting Small Molecule Inhibitors of DNA Double-Strand Break Repair. Front Oncol 2022; 12:850883. [PMID: 35463312 PMCID: PMC9020266 DOI: 10.3389/fonc.2022.850883] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 02/22/2022] [Indexed: 01/09/2023] Open
Abstract
The vast majority of cancer patients receive DNA-damaging drugs or ionizing radiation (IR) during their course of treatment, yet the efficacy of these therapies is tempered by DNA repair and DNA damage response (DDR) pathways. Aberrations in DNA repair and the DDR are observed in many cancer subtypes and can promote de novo carcinogenesis, genomic instability, and ensuing resistance to current cancer therapy. Additionally, stalled or collapsed DNA replication forks present a unique challenge to the double-strand DNA break (DSB) repair system. Of the various inducible DNA lesions, DSBs are the most lethal and thus desirable in the setting of cancer treatment. In mammalian cells, DSBs are typically repaired by the error prone non-homologous end joining pathway (NHEJ) or the high-fidelity homology directed repair (HDR) pathway. Targeting DSB repair pathways using small molecular inhibitors offers a promising mechanism to synergize DNA-damaging drugs and IR while selective inhibition of the NHEJ pathway can induce synthetic lethality in HDR-deficient cancer subtypes. Selective inhibitors of the NHEJ pathway and alternative DSB-repair pathways may also see future use in precision genome editing to direct repair of resulting DSBs created by the HDR pathway. In this review, we highlight the recent advances in the development of inhibitors of the non-phosphatidylinositol 3-kinase-related kinases (non-PIKKs) members of the NHEJ, HDR and minor backup SSA and alt-NHEJ DSB-repair pathways. The inhibitors described within this review target the non-PIKKs mediators of DSB repair including Ku70/80, Artemis, DNA Ligase IV, XRCC4, MRN complex, RPA, RAD51, RAD52, ERCC1-XPF, helicases, and DNA polymerase θ. While the DDR PIKKs remain intensely pursued as therapeutic targets, small molecule inhibition of non-PIKKs represents an emerging opportunity in drug discovery that offers considerable potential to impact cancer treatment.
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Affiliation(s)
- Jeremy M. Kelm
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Amirreza Samarbakhsh
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Athira Pillai
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | | | - Hariprasad Aruri
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | - Deepti S. Pandey
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States
| | | | - John J. Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States,NERx Biosciences, Indianapolis, IN, United States,Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Navnath S. Gavande
- Department of Pharmaceutical Sciences, Eugene Applebaum College of Pharmacy and Health Sciences, Wayne State University, Detroit, MI, United States,Molecular Therapeutics Program, Barbara Ann Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, United States,*Correspondence: Navnath S. Gavande, ; orcid.org/0000-0002-2413-0235
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18
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Chheda PR, Cooling GT, Dean SF, Propp J, Hobbs KF, Spies MA. Decrypting a Cryptic Allosteric Pocket in H. pylori Glutamate Racemase. Commun Chem 2021; 4:172. [PMID: 35673630 PMCID: PMC9169614 DOI: 10.1038/s42004-021-00605-z] [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: 08/13/2021] [Accepted: 11/08/2021] [Indexed: 01/27/2023] Open
Abstract
One of our greatest challenges in drug design is targeting cryptic allosteric pockets in enzyme targets. Drug leads that do bind to these cryptic pockets are often discovered during HTS campaigns, and the mechanisms of action are rarely understood. Nevertheless, it is often the case that the allosteric pocket provides the best option for drug development against a given target. In the current studies we present a successful way forward in rationally exploiting the cryptic allosteric pocket of H. pylori glutamate racemase, an essential enzyme in this pathogen's life cycle. A wide range of computational and experimental methods are employed in a workflow leading to the discovery of a series of natural product allosteric inhibitors which occupy the allosteric pocket of this essential racemase. The confluence of these studies reveals a fascinating source of the allosteric inhibition, which centers on the abolition of essential monomer-monomer coupled motion networks.
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Affiliation(s)
- Pratik Rajesh Chheda
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, IA 52242 USA
| | - Grant T. Cooling
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, IA 52242 USA
| | - Sondra F. Dean
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, IA 52242 USA
| | - Jonah Propp
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, IA 52242 USA
| | - Kathryn F. Hobbs
- Department of Biochemistry, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242 USA
| | - M. Ashley Spies
- Division of Medicinal and Natural Products Chemistry, Department of Pharmaceutical Sciences and Experimental Therapeutics, The University of Iowa, Iowa City, IA 52242 USA
- Department of Biochemistry, Carver College of Medicine, The University of Iowa, Iowa City, IA 52242 USA
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19
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Huang F, Nguyen TT, Echeverria I, Rakesh R, Cary DC, Paculova H, Sali A, Weiss A, Peterlin BM, Fujinaga K. Reversible phosphorylation of cyclin T1 promotes assembly and stability of P-TEFb. eLife 2021; 10:68473. [PMID: 34821217 PMCID: PMC8648303 DOI: 10.7554/elife.68473] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 11/19/2021] [Indexed: 01/06/2023] Open
Abstract
The positive transcription elongation factor b (P-TEFb) is a critical coactivator for transcription of most cellular and viral genes, including those of HIV. While P-TEFb is regulated by 7SK snRNA in proliferating cells, P-TEFb is absent due to diminished levels of CycT1 in quiescent and terminally differentiated cells, which has remained unexplored. In these cells, we found that CycT1 not bound to CDK9 is rapidly degraded. Moreover, productive CycT1:CDK9 interactions are increased by PKC-mediated phosphorylation of CycT1 in human cells. Conversely, dephosphorylation of CycT1 by PP1 reverses this process. Thus, PKC inhibitors or removal of PKC by chronic activation results in P-TEFb disassembly and CycT1 degradation. This finding not only recapitulates P-TEFb depletion in resting CD4+ T cells but also in anergic T cells. Importantly, our studies reveal mechanisms of P-TEFb inactivation underlying T cell quiescence, anergy, and exhaustion as well as proviral latency and terminally differentiated cells.
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Affiliation(s)
- Fang Huang
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
| | - Trang Tt Nguyen
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States.,The Howard Hughes Medical Institute, San Francisco, United States
| | - Ignacia Echeverria
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Departmentof Cellular Molecular Pharmacology, California Institute for Quantitative Biosciences (QBI), and Department of Bioengineering and Therapeutic Sciences, San Francisco, United States
| | - Ramachandran Rakesh
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Departmentof Cellular Molecular Pharmacology, California Institute for Quantitative Biosciences (QBI), and Department of Bioengineering and Therapeutic Sciences, San Francisco, United States
| | - Daniele C Cary
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
| | - Hana Paculova
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, United States.,Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences (QBI), San Francisco, United States
| | - Arthur Weiss
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States.,The Howard Hughes Medical Institute, San Francisco, United States
| | - Boris Matija Peterlin
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
| | - Koh Fujinaga
- Departments of Medicine, Microbiology and Immunology, University of California, San Francisco, San Francisco, United States.,Department of Medicine, San Francisco, United States
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20
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Rossi MJ, DiDomenico SF, Patel M, Mazin AV. RAD52: Paradigm of Synthetic Lethality and New Developments. Front Genet 2021; 12:780293. [PMID: 34887904 PMCID: PMC8650160 DOI: 10.3389/fgene.2021.780293] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/05/2021] [Indexed: 12/31/2022] Open
Abstract
DNA double-strand breaks and inter-strand cross-links are the most harmful types of DNA damage that cause genomic instability that lead to cancer development. The highest fidelity pathway for repairing damaged double-stranded DNA is termed Homologous recombination (HR). Rad52 is one of the key HR proteins in eukaryotes. Although it is critical for most DNA repair and recombination events in yeast, knockouts of mammalian RAD52 lack any discernable phenotypes. As a consequence, mammalian RAD52 has been long overlooked. That is changing now, as recent work has shown RAD52 to be critical for backup DNA repair pathways in HR-deficient cancer cells. Novel findings have shed light on RAD52's biochemical activities. RAD52 promotes DNA pairing (D-loop formation), single-strand DNA and DNA:RNA annealing, and inverse strand exchange. These activities contribute to its multiple roles in DNA damage repair including HR, single-strand annealing, break-induced replication, and RNA-mediated repair of DNA. The contributions of RAD52 that are essential to the viability of HR-deficient cancer cells are currently under investigation. These new findings make RAD52 an attractive target for the development of anti-cancer therapies against BRCA-deficient cancers.
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Affiliation(s)
- Matthew J. Rossi
- Department of Biochemistry and Structural Biology, University of Texas Health Science Center, San Antonio, TX, United States
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21
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Llorens-Agost M, Ensminger M, Le HP, Gawai A, Liu J, Cruz-García A, Bhetawal S, Wood RD, Heyer WD, Löbrich M. POLθ-mediated end joining is restricted by RAD52 and BRCA2 until the onset of mitosis. Nat Cell Biol 2021; 23:1095-1104. [PMID: 34616022 PMCID: PMC8675436 DOI: 10.1038/s41556-021-00764-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/30/2021] [Indexed: 01/25/2023]
Abstract
BRCA2-mutant cells are defective in homologous recombination, making them vulnerable to the inactivation of other pathways for the repair of DNA double-strand breaks (DSBs). This concept can be clinically exploited but is currently limited due to insufficient knowledge about how DSBs are repaired in the absence of BRCA2. We show that DNA polymerase θ (POLθ)-mediated end joining (TMEJ) repairs DSBs arising during the S phase in BRCA2-deficient cells only after the onset of the ensuing mitosis. This process is regulated by RAD52, whose loss causes the premature usage of TMEJ and the formation of chromosomal fusions. Purified RAD52 and BRCA2 proteins both block the DNA polymerase function of POLθ, suggesting a mechanism explaining their synthetic lethal relationships. We propose that the delay of TMEJ until mitosis ensures the conversion of originally one-ended DSBs into two-ended DSBs. Mitotic chromatin condensation might further serve to juxtapose correct break ends and limit chromosomal fusions.
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Affiliation(s)
- Marta Llorens-Agost
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Michael Ensminger
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Hang Phuong Le
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Anugrah Gawai
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Jie Liu
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Andrés Cruz-García
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany
| | - Sarita Bhetawal
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Richard D Wood
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, TX, USA
| | - Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, Davis, CA, USA
| | - Markus Löbrich
- Radiation Biology and DNA Repair, Technical University of Darmstadt, Darmstadt, Germany.
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22
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Nickoloff JA, Sharma N, Allen CP, Taylor L, Allen SJ, Jaiswal AS, Hromas R. Roles of homologous recombination in response to ionizing radiation-induced DNA damage. Int J Radiat Biol 2021; 99:903-914. [PMID: 34283012 PMCID: PMC9629169 DOI: 10.1080/09553002.2021.1956001] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/04/2021] [Accepted: 07/05/2021] [Indexed: 02/06/2023]
Abstract
PURPOSE Ionizing radiation induces a vast array of DNA lesions including base damage, and single- and double-strand breaks (SSB, DSB). DSBs are among the most cytotoxic lesions, and mis-repair causes small- and large-scale genome alterations that can contribute to carcinogenesis. Indeed, ionizing radiation is a 'complete' carcinogen. DSBs arise immediately after irradiation, termed 'frank DSBs,' as well as several hours later in a replication-dependent manner, termed 'secondary' or 'replication-dependent DSBs. DSBs resulting from replication fork collapse are single-ended and thus pose a distinct problem from two-ended, frank DSBs. DSBs are repaired by error-prone nonhomologous end-joining (NHEJ), or generally error-free homologous recombination (HR), each with sub-pathways. Clarifying how these pathways operate in normal and tumor cells is critical to increasing tumor control and minimizing side effects during radiotherapy. CONCLUSIONS The choice between NHEJ and HR is regulated during the cell cycle and by other factors. DSB repair pathways are major contributors to cell survival after ionizing radiation, including tumor-resistance to radiotherapy. Several nucleases are important for HR-mediated repair of replication-dependent DSBs and thus replication fork restart. These include three structure-specific nucleases, the 3' MUS81 nuclease, and two 5' nucleases, EEPD1 and Metnase, as well as three end-resection nucleases, MRE11, EXO1, and DNA2. The three structure-specific nucleases evolved at very different times, suggesting incremental acceleration of replication fork restart to limit toxic HR intermediates and genome instability as genomes increased in size during evolution, including the gain of large numbers of HR-prone repetitive elements. Ionizing radiation also induces delayed effects, observed days to weeks after exposure, including delayed cell death and delayed HR. In this review we highlight the roles of HR in cellular responses to ionizing radiation, and discuss the importance of HR as an exploitable target for cancer radiotherapy.
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Affiliation(s)
- Jac A. Nickoloff
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Neelam Sharma
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Christopher P. Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
- Department of Microbiology, Immunology and Pathology, Flow Cytometry and Cell Sorting Facility, Colorado State University, Fort Collins, CO, USA
| | - Lynn Taylor
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sage J. Allen
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Aruna S. Jaiswal
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
| | - Robert Hromas
- Division of Hematology and Medical Oncology, Department of Medicine and the Mays Cancer Center, University of Texas Health Science Center, San Antonio, TX, USA
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23
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Raimundo L, Calheiros J, Saraiva L. Exploiting DNA Damage Repair in Precision Cancer Therapy: BRCA1 as a Prime Therapeutic Target. Cancers (Basel) 2021; 13:cancers13143438. [PMID: 34298653 PMCID: PMC8303227 DOI: 10.3390/cancers13143438] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 06/21/2021] [Accepted: 07/07/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Chemical inhibition of central DNA damage repair (DDR) proteins has become a promising approach in precision cancer therapy. In particular, BRCA1 and its DDR-associated proteins constitute important targets for developing DNA repair inhibiting drugs. This review provides relevant insights on DDR biology and pharmacology, aiming to boost the development of more effective DDR targeted therapies. Abstract Precision medicine aims to identify specific molecular alterations, such as driver mutations, allowing tailored and effective anticancer therapies. Poly(ADP)-ribose polymerase inhibitors (PARPi) are the prototypical example of targeted therapy, exploiting the inability of cancer cells to repair DNA damage. Following the concept of synthetic lethality, PARPi have gained great relevance, particularly in BRCA1 dysfunctional cancer cells. In fact, BRCA1 mutations culminate in DNA repair defects that can render cancer cells more vulnerable to therapy. However, the efficacy of these drugs has been greatly affected by the occurrence of resistance due to multi-connected DNA repair pathways that may compensate for each other. Hence, the search for additional effective agents targeting DNA damage repair (DDR) is of crucial importance. In this context, BRCA1 has assumed a central role in developing drugs aimed at inhibiting DNA repair activity. Collectively, this review provides an in-depth understanding of the biology and regulatory mechanisms of DDR pathways, highlighting the potential of DDR-associated molecules, particularly BRCA1 and its interconnected partners, in precision cancer medicine. It also affords an overview about what we have achieved and a reflection on how much remains to be done in this field, further addressing encouraging clues for the advance of DDR targeted therapy.
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24
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Sharp MF, Bythell-Douglas R, Deans AJ, Crismani W. The Fanconi anemia ubiquitin E3 ligase complex as an anti-cancer target. Mol Cell 2021; 81:2278-2289. [PMID: 33984284 DOI: 10.1016/j.molcel.2021.04.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 03/27/2021] [Accepted: 04/21/2021] [Indexed: 10/21/2022]
Abstract
Agents that induce DNA damage can cure some cancers. However, the side effects of chemotherapy are severe because of the indiscriminate action of DNA-damaging agents on both healthy and cancerous cells. DNA repair pathway inhibition provides a less toxic and targeted alternative to chemotherapy. A compelling DNA repair target is the Fanconi anemia (FA) E3 ligase core complex due to its critical-and likely singular-role in the efficient removal of specific DNA lesions. FA pathway inactivation has been demonstrated to specifically kill some types of cancer cells without the addition of exogenous DNA damage, including cells that lack BRCA1, BRCA2, ATM, or functionally related genes. In this perspective, we discuss the genetic and biochemical evidence in support of the FA core complex as a compelling drug target for cancer therapy. In particular, we discuss the genetic, biochemical, and structural data that could rapidly advance our capacity to identify and implement the use of FA core complex inhibitors in the clinic.
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Affiliation(s)
- Michael F Sharp
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Rohan Bythell-Douglas
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia
| | - Andrew J Deans
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia; Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC, Australia
| | - Wayne Crismani
- Genome Stability Unit, St. Vincent's Institute of Medical Research, Fitzroy, VIC, Australia; Department of Medicine (St. Vincent's), University of Melbourne, Fitzroy, VIC, Australia.
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25
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Yang Q, Li Y, Sun R, Li J. Identification of a RAD52 Inhibitor Inducing Synthetic Lethality in BRCA2-Deficient Cancer Cells. Front Pharmacol 2021; 12:637825. [PMID: 33995041 PMCID: PMC8118686 DOI: 10.3389/fphar.2021.637825] [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: 12/04/2020] [Accepted: 04/12/2021] [Indexed: 11/16/2022] Open
Abstract
The breast cancer susceptibility gene 1/2 (BRCA1/2) is frequently mutated in many malignant tumors, such as breast cancer and ovarian cancer. Studies have demonstrated that inhibition of RAD52 gene function in BRCA2-deficient cancer causes synthetic lethality, suggesting a potential application of RAD52 in cancer-targeted therapy. In this study, we have performed a virtual screening by targeting the self-association domain (residues 85-159) of RAD52 with a library of 66,608 compounds and found one compound, C791-0064, that specifically inhibited the proliferation of BRCA2-deficient cancer cells. Our biochemical and cell-based experimental data suggested that C791-0064 specifically bound to RAD52 and disrupted the single-strand annealing activity of RAD52. Taken together, C791-0064 is a promising leading compound worthy of further exploitation in the context of BRCA-deficient targeted cancer therapy.
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Affiliation(s)
- Qianye Yang
- Institute of Cancer Biology and Drug Discovery, Chengdu University, Chengdu, China
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
| | - Yu Li
- West China School of Pharmacy, Sichuan University, Chengdu, China
| | - Rong Sun
- Basic medical research center, School of medicine, Nantong University, Nantong, China
| | - Jian Li
- Institute of Cancer Biology and Drug Discovery, Chengdu University, Chengdu, China
- Sichuan Industrial Institute of Antibiotics, Chengdu University, Chengdu, China
- School of Medicine, Chengdu University, Chengdu, China
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26
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Al-Mugotir M, Lovelace JJ, George J, Bessho M, Pal D, Struble L, Kolar C, Rana S, Natarajan A, Bessho T, Borgstahl GEO. Selective killing of homologous recombination-deficient cancer cell lines by inhibitors of the RPA:RAD52 protein-protein interaction. PLoS One 2021; 16:e0248941. [PMID: 33784323 DOI: 10.1371/journal.pone.0248941] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 03/09/2021] [Indexed: 12/29/2022] Open
Abstract
Synthetic lethality is a successful strategy employed to develop selective chemotherapeutics against cancer cells. Inactivation of RAD52 is synthetically lethal to homologous recombination (HR) deficient cancer cell lines. Replication protein A (RPA) recruits RAD52 to repair sites, and the formation of this protein-protein complex is critical for RAD52 activity. To discover small molecules that inhibit the RPA:RAD52 protein-protein interaction (PPI), we screened chemical libraries with our newly developed Fluorescence-based protein-protein Interaction Assay (FluorIA). Eleven compounds were identified, including FDA-approved drugs (quinacrine, mitoxantrone, and doxorubicin). The FluorIA was used to rank the compounds by their ability to inhibit the RPA:RAD52 PPI and showed mitoxantrone and doxorubicin to be the most effective. Initial studies using the three FDA-approved drugs showed selective killing of BRCA1-mutated breast cancer cells (HCC1937), BRCA2-mutated ovarian cancer cells (PE01), and BRCA1-mutated ovarian cancer cells (UWB1.289). It was noteworthy that selective killing was seen in cells known to be resistant to PARP inhibitors (HCC1937 and UWB1 SYr13). A cell-based double-strand break (DSB) repair assay indicated that mitoxantrone significantly suppressed RAD52-dependent single-strand annealing (SSA) and mitoxantrone treatment disrupted the RPA:RAD52 PPI in cells. Furthermore, mitoxantrone reduced radiation-induced foci-formation of RAD52 with no significant activity against RAD51 foci formation. The results indicate that the RPA:RAD52 PPI could be a therapeutic target for HR-deficient cancers. These data also suggest that RAD52 is one of the targets of mitoxantrone and related compounds.
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Affiliation(s)
- Mona Al-Mugotir
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Jeffrey J Lovelace
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Joseph George
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Mika Bessho
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Dhananjaya Pal
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Lucas Struble
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Carol Kolar
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Sandeep Rana
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Amarnath Natarajan
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Tadayoshi Bessho
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
| | - Gloria E O Borgstahl
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska, United States of America
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27
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Doi G, Okada S, Yasukawa T, Sugiyama Y, Bala S, Miyazaki S, Kang D, Ito T. Catalytically inactive Cas9 impairs DNA replication fork progression to induce focal genomic instability. Nucleic Acids Res 2021; 49:954-968. [PMID: 33398345 PMCID: PMC7826275 DOI: 10.1093/nar/gkaa1241] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/05/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Catalytically inactive Cas9 (dCas9) has become an increasingly popular tool for targeted gene activation/inactivation, live-cell imaging, and base editing. While dCas9 was reported to induce base substitutions and indels, it has not been associated with structural variations. Here, we show that dCas9 impedes replication fork progression to destabilize tandem repeats in budding yeast. When targeted to the CUP1 array comprising ∼16 repeat units, dCas9 induced its contraction in most cells, especially in the presence of nicotinamide. Replication intermediate analysis demonstrated replication fork stalling in the vicinity of dCas9-bound sites. Genetic analysis indicated that while destabilization is counteracted by the replisome progression complex components Ctf4 and Mrc1 and the accessory helicase Rrm3, it involves single-strand annealing by the recombination proteins Rad52 and Rad59. Although dCas9-mediated replication fork stalling is a potential risk in conventional applications, it may serve as a novel tool for both mechanistic studies and manipulation of genomic instability.
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Affiliation(s)
- Goro Doi
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Satoshi Okada
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takehiro Yasukawa
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Yuki Sugiyama
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Siqin Bala
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Shintaro Miyazaki
- Kyushu University School of Medicine, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Dongchon Kang
- Department of Clinical Chemistry and Laboratory Medicine, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Ito
- Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
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28
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Wang J, Oh YT, Li Z, Dou J, Tang S, Wang X, Wang H, Takeda S, Wang Y. RAD52 Adjusts Repair of Single-Strand Breaks via Reducing DNA-Damage-Promoted XRCC1/LIG3α Co-localization. Cell Rep 2021; 34:108625. [PMID: 33440161 PMCID: PMC7872142 DOI: 10.1016/j.celrep.2020.108625] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/20/2020] [Accepted: 12/17/2020] [Indexed: 11/07/2022] Open
Abstract
Radiation sensitive 52 (RAD52) is an important factor for double-strand break repair (DSBR). However, deficiency in vertebrate/mammalian Rad52 has no apparent phenotype. The underlying mechanism remains elusive. Here, we report that RAD52 deficiency increased cell survival after camptothecin (CPT) treatment. CPT generates single-strand breaks (SSBs) that further convert to double-strand breaks (DSBs) if they are not repaired. RAD52 inhibits SSB repair (SSBR) through strong single-strand DNA (ssDNA) and/or poly(ADP-ribose) (PAR) binding affinity to reduce DNA-damage-promoted X-Ray Repair Cross Complementing 1 (XRCC1)/ligase IIIα (LIG3α) co-localization. The inhibitory effects of RAD52 on SSBR neutralize the role of RAD52 in DSBR, suggesting that RAD52 may maintain a balance between cell survival and genomic integrity. Furthermore, we demonstrate that blocking RAD52 oligomerization that disrupts RAD52’s DSBR, while retaining its ssDNA binding capacity that is required for RAD52’s inhibitory effects on SSBR, sensitizes cells to different DNA-damaging agents. This discovery provides guidance for developing efficient RAD52 inhibitors in cancer therapy. Wang et al. show that vertebrate/mammalian RAD52 promotes CPT-induced cell death via inhibition of PARP-mediated SSBR, which involves RAD52’s strong ssDNA/PAR binding affinity that reduces DNA-damage-promoted XRCC1-LIG3a interaction. Blocking of RAD52 oligomerization, while retaining the ssDNA binding capacity of RAD52, efficiently sensitizes cells to different DNA-damaging agents.
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Affiliation(s)
- Jian Wang
- Department of Radiation Oncology, Emory University School of Medicine and the Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - You-Take Oh
- Department of Radiation Oncology, Emory University School of Medicine and the Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Zhentian Li
- Department of Radiation Oncology, Emory University School of Medicine and the Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Juan Dou
- Department of Radiation Oncology, Emory University School of Medicine and the Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Siyuan Tang
- Department of Radiation Oncology, Emory University School of Medicine and the Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Xiang Wang
- Department of Radiation Oncology, Emory University School of Medicine and the Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Hongyan Wang
- Department of Radiation Oncology, Emory University School of Medicine and the Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA
| | - Shunichi Takeda
- CREST Research Project, Radiation Genetics, Faculty of Medicine, Kyoto University, Yoshida-konoe, Sakyo-ku, Kyoto 606-8501, Japan.
| | - Ya Wang
- Department of Radiation Oncology, Emory University School of Medicine and the Winship Cancer Institute of Emory University, Atlanta, GA 30322, USA.
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29
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Myers S, Ortega JA, Cavalli A. Synthetic Lethality through the Lens of Medicinal Chemistry. J Med Chem 2020; 63:14151-14183. [PMID: 33135887 PMCID: PMC8015234 DOI: 10.1021/acs.jmedchem.0c00766] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 02/07/2023]
Abstract
Personalized medicine and therapies represent the goal of modern medicine, as drug discovery strives to move away from one-cure-for-all and makes use of the various targets and biomarkers within differing disease areas. This approach, especially in oncology, is often undermined when the cells make use of alternative survival pathways. As such, acquired resistance is unfortunately common. In order to combat this phenomenon, synthetic lethality is being investigated, making use of existing genetic fragilities within the cancer cell. This Perspective highlights exciting targets within synthetic lethality, (PARP, ATR, ATM, DNA-PKcs, WEE1, CDK12, RAD51, RAD52, and PD-1) and discusses the medicinal chemistry programs being used to interrogate them, the challenges these programs face, and what the future holds for this promising field.
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Affiliation(s)
- Samuel
H. Myers
- Computational
& Chemical Biology, Istituto Italiano
di Tecnologia, 16163 Genova, Italy
| | - Jose Antonio Ortega
- Computational
& Chemical Biology, Istituto Italiano
di Tecnologia, 16163 Genova, Italy
| | - Andrea Cavalli
- Computational
& Chemical Biology, Istituto Italiano
di Tecnologia, 16163 Genova, Italy
- Department
of Pharmacy and Biotechnology, University
of Bologna, 40126 Bologna, Italy
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30
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Kondratick CM, Washington MT, Spies M. Making Choices: DNA Replication Fork Recovery Mechanisms. Semin Cell Dev Biol 2020; 113:27-37. [PMID: 33967572 DOI: 10.1016/j.semcdb.2020.10.001] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
DNA replication is laden with obstacles that slow, stall, collapse, and break DNA replication forks. At each obstacle, there is a decision to be made whether to bypass the lesion, repair or restart the damaged fork, or to protect stalled forks from further demise. Each "decision" draws upon multitude of proteins participating in various mechanisms that allow repair and restart of replication forks. Specific functions for many of these proteins have been described and an understanding of how they come together in supporting replication forks is starting to emerge. Many questions, however, remain regarding selection of the mechanisms that enable faithful genome duplication and how "normal" intermediates in these mechanisms are sometimes funneled into "rogue" processes that destabilize the genome and lead to cancer, cell death, and emergence of chemotherapeutic resistance. In this review we will discuss molecular mechanisms of DNA damage bypass and replication fork protection and repair. We will specifically focus on the key players that define which mechanism is employed including: PCNA and its control by posttranslational modifications, translesion synthesis DNA polymerases, molecular motors that catalyze reversal of stalled replication forks, proteins that antagonize fork reversal and protect reversed forks from nucleolytic degradation, and the machinery of homologous recombination that helps to reestablish broken forks. We will also discuss risks to genome integrity inherent in each of these mechanisms.
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Affiliation(s)
- Christine M Kondratick
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - M Todd Washington
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242.,Department of Radiation Oncology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242.,Department of Radiation Oncology, Carver College of Medicine, University of Iowa, Iowa City, Iowa 52242
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31
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Harnessing DNA Replication Stress for Novel Cancer Therapy. Genes (Basel) 2020; 11:genes11090990. [PMID: 32854236 PMCID: PMC7564951 DOI: 10.3390/genes11090990] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/03/2020] [Accepted: 08/20/2020] [Indexed: 12/16/2022] Open
Abstract
DNA replication is the fundamental process for accurate duplication and transfer of genetic information. Its fidelity is under constant stress from endogenous and exogenous factors which can cause perturbations that lead to DNA damage and defective replication. This can compromise genomic stability and integrity. Genomic instability is considered as one of the hallmarks of cancer. In normal cells, various checkpoints could either activate DNA repair or induce cell death/senescence. Cancer cells on the other hand potentiate DNA replicative stress, due to defective DNA damage repair mechanism and unchecked growth signaling. Though replicative stress can lead to mutagenesis and tumorigenesis, it can be harnessed paradoxically for cancer treatment. Herein, we review the mechanism and rationale to exploit replication stress for cancer therapy. We discuss both established and new approaches targeting DNA replication stress including chemotherapy, radiation, and small molecule inhibitors targeting pathways including ATR, Chk1, PARP, WEE1, MELK, NAE, TLK etc. Finally, we review combination treatments, biomarkers, and we suggest potential novel methods to target DNA replication stress to treat cancer.
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32
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Harumoto T, Sato A, Takayama Y, Miyagi H, Saito JI, Shinohara F. Structure-guided screening strategy combining surface plasmon resonance with nuclear magnetic resonance for identification of small-molecule Argonaute 2 inhibitors. PLoS One 2020; 15:e0236710. [PMID: 32735606 PMCID: PMC7394379 DOI: 10.1371/journal.pone.0236710] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 07/13/2020] [Indexed: 01/07/2023] Open
Abstract
Argonaute (AGO) proteins are the key component of the RNA interference machinery that suppresses gene expression by forming an RNA-induced silencing complex (RISC) with microRNAs (miRNAs). Each miRNA is involved in various cellular processes, such as development, differentiation, tumorigenesis, and viral infection. Thus, molecules that regulate miRNA function are expected to have therapeutic potential. In addition, the biogenesis of miRNA is a multistep process involving various proteins, although the complete pathway remains to be elucidated. Therefore, identification of molecules that can specifically modulate each step will help understand the mechanism of gene suppression. To date, several AGO2 inhibitors have been identified. However, these molecules were identified through a single screening method, and no studies have specifically evaluated a combinatorial strategy. Here, we demonstrated a combinatorial screening (SCR) approach comprising an in silico molecular docking study, surface plasmon resonance (SPR) analysis, and nuclear magnetic resonance (NMR) analysis, focusing on the strong binding between the 5'-terminal phosphate of RNA and the AGO2 middle (MID) domain. By combining SPR and NMR, we identified binding modes of amino acid residues binding to AGO2. First, using a large chemical library (over 6,000,000 compounds), 171 compounds with acidic functional groups were screened using in silico SCR. Next, we constructed an SPR inhibition system that could analyze only the 5'-terminal binding site of RNA, and nine molecules that strongly bound to the AGO2 MID domain were selected. Finally, using NMR, three molecules that bound to the desired site were identified. The RISC inhibitory ability of the “hit” compounds was analyzed in human cell lysate, and all three hit compounds strongly inhibited the binding between double-stranded RNA and AGO2.
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Affiliation(s)
- Toshimasa Harumoto
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Machida-shi, Tokyo, Japan
- * E-mail:
| | - Atsuko Sato
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Nagaizumi-cho, Suntou-gun, Shizuoka, Japan
| | - Yuki Takayama
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Nagaizumi-cho, Suntou-gun, Shizuoka, Japan
| | - Hikaru Miyagi
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Machida-shi, Tokyo, Japan
| | - Jun-ichi Saito
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Nagaizumi-cho, Suntou-gun, Shizuoka, Japan
| | - Fumikazu Shinohara
- Research Functions Unit, R&D Division, Kyowa Kirin Co., Ltd., Otemachi, Chiyoda-ku, Tokyo, Japan
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33
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Clear AD, Manthey GM, Lewis O, Lopez IY, Rico R, Owens S, Negritto MC, Wolf EW, Xu J, Kenjić N, Perry JJP, Adamson AW, Neuhausen SL, Bailis AM. Variants of the human RAD52 gene confer defects in ionizing radiation resistance and homologous recombination repair in budding yeast. ACTA ACUST UNITED AC 2020; 7:270-285. [PMID: 33015141 PMCID: PMC7517009 DOI: 10.15698/mic2020.10.732] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
RAD52 is a structurally and functionally conserved component of the DNA double-strand break (DSB) repair apparatus from budding yeast to humans. We recently showed that expressing the human gene, HsRAD52 in rad52 mutant budding yeast cells can suppress both their ionizing radiation (IR) sensitivity and homologous recombination repair (HRR) defects. Intriguingly, we observed that HsRAD52 supports DSB repair by a mechanism of HRR that conserves genome structure and is independent of the canonical HR machinery. In this study we report that naturally occurring variants of HsRAD52, one of which suppresses the pathogenicity of BRCA2 mutations, were unable to suppress the IR sensitivity and HRR defects of rad52 mutant yeast cells, but fully suppressed a defect in DSB repair by single-strand annealing (SSA). This failure to suppress both IR sensitivity and the HRR defect correlated with an inability of HsRAD52 protein to associate with and drive an interaction between genomic sequences during DSB repair by HRR. These results suggest that HsRAD52 supports multiple, distinct DSB repair apparatuses in budding yeast cells and help further define its mechanism of action in HRR. They also imply that disruption of HsRAD52-dependent HRR in BRCA2-defective human cells may contribute to protection against tumorigenesis and provide a target for killing BRCA2-defective cancers.
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Affiliation(s)
- Alissa D Clear
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.,bioStrategies Group, Chicago, IL, USA
| | - Glenn M Manthey
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Olivia Lewis
- City of Hope - Duarte High School NIH Science Education Partnership Award Program, Duarte, CA, USA.,Barbara Bush Houston Literacy Foundation, Houston, TX, USA
| | - Isabelle Y Lopez
- City of Hope - Duarte High School NIH Science Education Partnership Award Program, Duarte, CA, USA.,California State Polytechnic University at Pomona, Pomona, CA, USA
| | - Rossana Rico
- City of Hope - Duarte High School NIH Science Education Partnership Award Program, Duarte, CA, USA.,Henry Samueli School of Engineering and Applied Sciences, University of California at Los Angeles, Los Angeles, CA, USA
| | - Shannon Owens
- Eugene and Ruth Roberts Summer Student Academy, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Department of Microbiology and Molecular Genetics, College of Biological Sciences, University of California at Davis, Davis, CA, USA
| | | | - Elise W Wolf
- Molecular Biology Program, Pomona College, Claremont, CA, USA.,Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, CA, USA
| | - Jason Xu
- Molecular Biology Program, Pomona College, Claremont, CA, USA.,Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikola Kenjić
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - J Jefferson P Perry
- Department of Biochemistry, University of California at Riverside, Riverside, CA, USA
| | - Aaron W Adamson
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Susan L Neuhausen
- Department of Population Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA
| | - Adam M Bailis
- Department of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, Duarte, CA, USA.,Irell & Manella Graduate School of Biological Sciences, Beckman Research Institute of City of Hope, Duarte, CA, USA.,College of Health Professions, Thomas Jefferson University, Philadelphia, PA, USA
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34
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Current Understanding of RAD52 Functions: Fundamental and Therapeutic Insights. Cancers (Basel) 2020; 12:cancers12030705. [PMID: 32192055 PMCID: PMC7140074 DOI: 10.3390/cancers12030705] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 02/07/2023] Open
Abstract
In this Special Issue, we would like to focus on the various functions of the RAD52 helicase-like protein and the current implications of such findings for cancer treatment. Over the last few years, various laboratories have discovered particular activities of mammalian RAD52—both in S and M phase—that are distinct from the auxiliary role of yeast RAD52 in homologous recombination. At DNA double-strand breaks, RAD52 was demonstrated to spur alternative pathways to compensate for the loss of homologous recombination functions. At collapsed replication forks, RAD52 activates break-induced replication. In the M phase, RAD52 promotes the finalization of DNA replication. Its compensatory role in the resolution of DNA double-strand breaks has put RAD52 in the focus of synthetic lethal strategies, which is particularly relevant for cancer treatment.
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35
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From R-Loops to G-Quadruplexes: Emerging New Threats for the Replication Fork. Int J Mol Sci 2020; 21:ijms21041506. [PMID: 32098397 PMCID: PMC7073102 DOI: 10.3390/ijms21041506] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 12/12/2022] Open
Abstract
Replicating the entire genome is one of the most complex tasks for all organisms. Research carried out in the last few years has provided us with a clearer picture on how cells preserve genomic information from the numerous insults that may endanger its stability. Different DNA repair pathways, coping with exogenous or endogenous threat, have been dissected at the molecular level. More recently, there has been an increasing interest towards intrinsic obstacles to genome replication, paving the way to a novel view on genomic stability. Indeed, in some cases, the movement of the replication fork can be hindered by the presence of stable DNA: RNA hybrids (R-loops), the folding of G-rich sequences into G-quadruplex structures (G4s) or repetitive elements present at Common Fragile Sites (CFS). Although differing in their nature and in the way they affect the replication fork, all of these obstacles are a source of replication stress. Replication stress is one of the main hallmarks of cancer and its prevention is becoming increasingly important as a target for future chemotherapeutics. Here we will try to summarize how these three obstacles are generated and how the cells handle replication stress upon their encounter. Finally, we will consider their role in cancer and their exploitation in current chemotherapeutic approaches.
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36
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Physiological and Pathological Roles of RAD52 at DNA Replication Forks. Cancers (Basel) 2020; 12:cancers12020402. [PMID: 32050645 PMCID: PMC7072239 DOI: 10.3390/cancers12020402] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 02/07/2023] Open
Abstract
Understanding basic molecular mechanisms underlying the biology of cancer cells is of outmost importance for identification of novel therapeutic targets and biomarkers for patient stratification and better therapy selection. One of these mechanisms, the response to replication stress, fuels cancer genomic instability. It is also an Achille’s heel of cancer. Thus, identification of pathways used by the cancer cells to respond to replication-stress may assist in the identification of new biomarkers and discovery of new therapeutic targets. Alternative mechanisms that act at perturbed DNA replication forks and involve fork degradation by nucleases emerged as crucial for sensitivity of cancer cells to chemotherapeutics agents inducing replication stress. Despite its important role in homologous recombination and recombinational repair of DNA double strand breaks in lower eukaryotes, RAD52 protein has been considered dispensable in human cells and the full range of its cellular functions remained unclear. Very recently, however, human RAD52 emerged as an important player in multiple aspects of replication fork metabolism under physiological and pathological conditions. In this review, we describe recent advances on RAD52’s key functions at stalled or collapsed DNA replication forks, in particular, the unexpected role of RAD52 as a gatekeeper, which prevents unscheduled processing of DNA. Last, we will discuss how these functions can be exploited using specific inhibitors in targeted therapy or for an informed therapy selection.
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37
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Stefanovie B, Hengel SR, Mlcouskova J, Prochazkova J, Spirek M, Nikulenkov F, Nemecek D, Koch BG, Bain FE, Yu L, Spies M, Krejci L. DSS1 interacts with and stimulates RAD52 to promote the repair of DSBs. Nucleic Acids Res 2020; 48:694-708. [PMID: 31799622 PMCID: PMC6954417 DOI: 10.1093/nar/gkz1052] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 10/21/2019] [Accepted: 10/23/2019] [Indexed: 12/12/2022] Open
Abstract
The proper repair of deleterious DNA lesions such as double strand breaks prevents genomic instability and carcinogenesis. In yeast, the Rad52 protein mediates DSB repair via homologous recombination. In mammalian cells, despite the presence of the RAD52 protein, the tumour suppressor protein BRCA2 acts as the predominant mediator during homologous recombination. For decades, it has been believed that the RAD52 protein played only a back-up role in the repair of DSBs performing an error-prone single strand annealing (SSA). Recent studies have identified several new functions of the RAD52 protein and have drawn attention to its important role in genome maintenance. Here, we show that RAD52 activities are enhanced by interacting with a small and highly acidic protein called DSS1. Binding of DSS1 to RAD52 changes the RAD52 oligomeric conformation, modulates its DNA binding properties, stimulates SSA activity and promotes strand invasion. Our work introduces for the first time RAD52 as another interacting partner of DSS1 and shows that both proteins are important players in the SSA and BIR pathways of DSB repair.
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Affiliation(s)
- Barbora Stefanovie
- Department of Biology, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500 Brno, Czech Republic
| | - Sarah R Hengel
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Jarmila Mlcouskova
- Department of Biology, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500 Brno, Czech Republic
| | - Jana Prochazkova
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500 Brno, Czech Republic
| | - Mario Spirek
- Department of Biology, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500 Brno, Czech Republic
| | - Fedor Nikulenkov
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500 Brno, Czech Republic
| | | | - Brandon G Koch
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Fletcher E Bain
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Liping Yu
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
- NMR Core Facility, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Maria Spies
- Department of Biochemistry, University of Iowa Carver College of Medicine, 51 Newton Road, Iowa City, IA 52242, USA
| | - Lumir Krejci
- Department of Biology, Masaryk University, 62500 Brno, Czech Republic
- International Clinical Research Center, St. Anne's University Hospital in Brno, 62500 Brno, Czech Republic
- National Centre for Biomolecular Research, Masaryk University, 62500 Brno, Czech Republic
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38
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Trenner A, Sartori AA. Harnessing DNA Double-Strand Break Repair for Cancer Treatment. Front Oncol 2019; 9:1388. [PMID: 31921645 PMCID: PMC6921965 DOI: 10.3389/fonc.2019.01388] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 11/25/2019] [Indexed: 12/20/2022] Open
Abstract
DNA double-strand breaks (DSBs) are highly deleterious, with a single unrepaired DSB being sufficient to trigger cell death. Compared to healthy cells, cancer cells have a higher DSB burden due to oncogene-induced replication stress and acquired defects in DNA damage response (DDR) mechanisms. Consequently, hyperproliferating cancer cells rely on efficient DSB repair for their survival. Moreover, augmented DSB repair capacity is a major cause of radio- and chemoresistance and, ultimately, cancer recurrence. Although inherited DDR defects can predispose individuals to develop certain cancers, the very same vulnerability may be therapeutically exploited to preferentially kill tumor cells. A paradigm for DNA repair targeted therapy has emerged in cancers that exhibit mutations in BRCA1 or BRCA2 tumor suppressor genes, conferring a strong defect in homologous recombination, a major and error-free DSB repair pathway. Clinical validation of such approaches, commonly described as synthetic lethality (SL), has been provided by the regulatory approval of poly(ADP-ribose) polymerase 1 inhibitors (PARPi) as monotherapy for BRCA1/2-mutated breast and ovarian tumors. In this review, we will describe the different DSB repair mechanisms and discuss how their specific features could be exploited for cancer therapy. A major emphasis is put on advances in combinatorial treatment modalities and SL approaches arising from DSB repair pathway interdependencies.
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Affiliation(s)
- Anika Trenner
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Alessandro A Sartori
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
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39
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Toma M, Sullivan-Reed K, Śliwiński T, Skorski T. RAD52 as a Potential Target for Synthetic Lethality-Based Anticancer Therapies. Cancers (Basel) 2019; 11:E1561. [PMID: 31615159 PMCID: PMC6827130 DOI: 10.3390/cancers11101561] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/11/2019] [Accepted: 10/11/2019] [Indexed: 12/15/2022] Open
Abstract
Alterations in DNA repair systems play a key role in the induction and progression of cancer. Tumor-specific defects in DNA repair mechanisms and activation of alternative repair routes create the opportunity to employ a phenomenon called "synthetic lethality" to eliminate cancer cells. Targeting the backup pathways may amplify endogenous and drug-induced DNA damage and lead to specific eradication of cancer cells. So far, the synthetic lethal interaction between BRCA1/2 and PARP1 has been successfully applied as an anticancer treatment. Although PARP1 constitutes a promising target in the treatment of tumors harboring deficiencies in BRCA1/2-mediated homologous recombination (HR), some tumor cells survive, resulting in disease relapse. It has been suggested that alternative RAD52-mediated HR can protect BRCA1/2-deficient cells from the accumulation of DNA damage and the synthetic lethal effect of PARPi. Thus, simultaneous inhibition of RAD52 and PARP1 might result in a robust dual synthetic lethality, effectively eradicating BRCA1/2-deficient tumor cells. In this review, we will discuss the role of RAD52 and its potential application in synthetic lethality-based anticancer therapies.
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Affiliation(s)
- Monika Toma
- Sol Sherry Thrombosis Research Center and Fels Institute for Cancer Research and Molecular Biology Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
- Laboratory of Medical Genetics Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland.
| | - Katherine Sullivan-Reed
- Sol Sherry Thrombosis Research Center and Fels Institute for Cancer Research and Molecular Biology Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
| | - Tomasz Śliwiński
- Laboratory of Medical Genetics Faculty of Biology and Environmental Protection, University of Lodz, 90-236 Lodz, Poland.
| | - Tomasz Skorski
- Sol Sherry Thrombosis Research Center and Fels Institute for Cancer Research and Molecular Biology Lewis Katz School of Medicine, Temple University, Philadelphia, PA 19140, USA.
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40
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Kohzaki M, Ootsuyama A, Sun L, Moritake T, Okazaki R. Human RECQL4 represses the RAD52-mediated single-strand annealing pathway after ionizing radiation or cisplatin treatment. Int J Cancer 2019; 146:3098-3113. [PMID: 31495919 DOI: 10.1002/ijc.32670] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 08/06/2019] [Accepted: 09/04/2019] [Indexed: 11/12/2022]
Abstract
Ionizing radiation (IR) and cisplatin are frequently used cancer treatments, although the mechanisms of error-prone DNA repair-mediated genomic instability after anticancer treatment are not fully clarified yet. RECQL4 mutations mainly in the C-terminal region of the RECQL4 gene lead to the cancer-predisposing Rothmund-Thomson syndrome, but the function of RECQL4ΔC (C-terminus deleted) in error-prone DNA repair remains unclear. We established several RECQL4ΔC cell lines and found that RECQL4ΔC cancer cells, but not RECQL4ΔC nontumorigenic cells, exhibited IR/cisplatin hypersensitivity. Notably, RECQL4ΔC cancer cells presented increased RPA2/RAD52 foci after cancer treatments. RECQL4ΔC HCT116 cells exhibited increased error-prone single-strand annealing (SSA) activity and decreased alternative end-joining activities, suggesting that RECQL4 regulates the DNA repair pathway choice at double-strand breaks. RAD52 depletion by siRNA or RAD52 inhibitors (5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside [AICAR], (-)-epigallocatechin [EGC]) or a RAD52-phenylalanine 79 aptamer significantly restrained the growth of RAD52-upregulated RECQL4ΔC HCT116 cells in vitro and in mouse xenografts. Remarkably, compared to single-agent cisplatin or EGC treatment, cisplatin followed by low-concentration EGC had a significant suppressive effect on RECQL4ΔC HCT116 cell growth in vivo. Together, the regimens targeting the RAD52-mediated SSA pathway after anticancer treatment may be applicable for cancer patients with RECQL4 gene mutations.
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Affiliation(s)
- Masaoki Kohzaki
- Department of Radiological Health Science, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Akira Ootsuyama
- Department of Radiation Biology and Health, School of Medicine, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Lue Sun
- Department of Radiological Health Science, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan.,Health Research Institute, Department of Life Science and Biotechnology, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
| | - Takashi Moritake
- Department of Radiological Health Science, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
| | - Ryuji Okazaki
- Department of Radiological Health Science, Institute of Industrial Ecological Sciences, University of Occupational and Environmental Health, Japan, Kitakyushu, Japan
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41
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Replication Stress Response Links RAD52 to Protecting Common Fragile Sites. Cancers (Basel) 2019; 11:cancers11101467. [PMID: 31569559 PMCID: PMC6826974 DOI: 10.3390/cancers11101467] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 09/20/2019] [Accepted: 09/23/2019] [Indexed: 12/20/2022] Open
Abstract
Rad52 in yeast is a key player in homologous recombination (HR), but mammalian RAD52 is dispensable for HR as shown by the lack of a strong HR phenotype in RAD52-deficient cells and in RAD52 knockout mice. RAD52 function in mammalian cells first emerged with the discovery of its important backup role to BRCA (breast cancer genes) in HR. Recent new evidence further demonstrates that RAD52 possesses multiple activities to cope with replication stress. For example, replication stress-induced DNA repair synthesis in mitosis (MiDAS) and oncogene overexpression-induced DNA replication are dependent on RAD52. RAD52 becomes essential in HR to repair DSBs containing secondary structures, which often arise at collapsed replication forks. RAD52 is also implicated in break-induced replication (BIR) and is found to inhibit excessive fork reversal at stalled replication forks. These various functions of RAD52 to deal with replication stress have been linked to the protection of genome stability at common fragile sites, which are often associated with the DNA breakpoints in cancer. Therefore, RAD52 has important recombination roles under special stress conditions in mammalian cells, and presents as a promising anti-cancer therapy target.
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42
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Palma A, Pugliese GM, Murfuni I, Marabitti V, Malacaria E, Rinalducci S, Minoprio A, Sanchez M, Mazzei F, Zolla L, Franchitto A, Pichierri P. Phosphorylation by CK2 regulates MUS81/EME1 in mitosis and after replication stress. Nucleic Acids Res 2019; 46:5109-5124. [PMID: 29850896 PMCID: PMC6007509 DOI: 10.1093/nar/gky280] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 04/04/2018] [Indexed: 12/21/2022] Open
Abstract
The MUS81 complex is crucial for preserving genome stability through the resolution of branched DNA intermediates in mitosis. However, untimely activation of the MUS81 complex in S-phase is dangerous. Little is known about the regulation of the human MUS81 complex and how deregulated activation affects chromosome integrity. Here, we show that the CK2 kinase phosphorylates MUS81 at Serine 87 in late-G2/mitosis, and upon mild replication stress. Phosphorylated MUS81 interacts with SLX4, and this association promotes the function of the MUS81 complex. In line with a role in mitosis, phosphorylation at Serine 87 is suppressed in S-phase and is mainly detected in the MUS81 molecules associated with EME1. Loss of CK2-dependent MUS81 phosphorylation contributes modestly to chromosome integrity, however, expression of the phosphomimic form induces DSBs accumulation in S-phase, because of unscheduled targeting of HJ-like DNA intermediates, and generates a wide chromosome instability phenotype. Collectively, our findings describe a novel regulatory mechanism controlling the MUS81 complex function in human cells. Furthermore, they indicate that, genome stability depends mainly on the ability of cells to counteract targeting of branched intermediates by the MUS81/EME1 complex in S-phase, rather than on a correct MUS81 function in mitosis.
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Affiliation(s)
- Anita Palma
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Giusj Monia Pugliese
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Ivana Murfuni
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Veronica Marabitti
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Eva Malacaria
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Sara Rinalducci
- Proteomics, Metabolomics and Interactomics Lab, Department of Ecology and Biology, Università della Tuscia, Viale dell'Università snc, 01100 Viterbo, Italy
| | - Anna Minoprio
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Massimo Sanchez
- Core Facilities Center - Section of Cytometry, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Filomena Mazzei
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Lello Zolla
- Proteomics, Metabolomics and Interactomics Lab, Department of Ecology and Biology, Università della Tuscia, Viale dell'Università snc, 01100 Viterbo, Italy
| | - Annapaola Franchitto
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
| | - Pietro Pichierri
- Mechanisms, Biomarkers and Models Unit, Department of Environment and Health, Istituto Superiore di Sanità - Viale Regina Elena 299, 00161 Rome, Italy
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43
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Jalan M, Olsen KS, Powell SN. Emerging Roles of RAD52 in Genome Maintenance. Cancers (Basel) 2019; 11:E1038. [PMID: 31340507 PMCID: PMC6679097 DOI: 10.3390/cancers11071038] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/17/2019] [Accepted: 07/18/2019] [Indexed: 12/22/2022] Open
Abstract
The maintenance of genome integrity is critical for cell survival. Homologous recombination (HR) is considered the major error-free repair pathway in combatting endogenously generated double-stranded lesions in DNA. Nevertheless, a number of alternative repair pathways have been described as protectors of genome stability, especially in HR-deficient cells. One of the factors that appears to have a role in many of these pathways is human RAD52, a DNA repair protein that was previously considered to be dispensable due to a lack of an observable phenotype in knock-out mice. In later studies, RAD52 deficiency has been shown to be synthetically lethal with defects in BRCA genes, making RAD52 an attractive therapeutic target, particularly in the context of BRCA-deficient tumors.
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Affiliation(s)
- Manisha Jalan
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kyrie S Olsen
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Simon N Powell
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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44
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Liang F, Miller AS, Longerich S, Tang C, Maranon D, Williamson EA, Hromas R, Wiese C, Kupfer GM, Sung P. DNA requirement in FANCD2 deubiquitination by USP1-UAF1-RAD51AP1 in the Fanconi anemia DNA damage response. Nat Commun 2019; 10:2849. [PMID: 31253762 PMCID: PMC6599204 DOI: 10.1038/s41467-019-10408-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2019] [Accepted: 05/08/2019] [Indexed: 02/02/2023] Open
Abstract
Fanconi anemia (FA) is a multigenic disease of bone marrow failure and cancer susceptibility stemming from a failure to remove DNA crosslinks and other chromosomal lesions. Within the FA DNA damage response pathway, DNA-dependent monoubiquitinaton of FANCD2 licenses downstream events, while timely FANCD2 deubiquitination serves to extinguish the response. Here, we show with reconstituted biochemical systems, which we developed, that efficient FANCD2 deubiquitination by the USP1-UAF1 complex is dependent on DNA and DNA binding by UAF1. Surprisingly, we find that the DNA binding activity of the UAF1-associated protein RAD51AP1 can substitute for that of UAF1 in FANCD2 deubiquitination in our biochemical system. We also reveal the importance of DNA binding by UAF1 and RAD51AP1 in FANCD2 deubiquitination in the cellular setting. Our results provide insights into a key step in the FA pathway and help define the multifaceted role of the USP1-UAF1-RAD51AP1 complex in DNA damage tolerance and genome repair. In the Fanconi anemia pathway, deubiquitination of FANCD2 is a fundamental regulatory step. Here, the authors have developed a set of biochemical tools to reconstitute FANCD2 deubiquitination by recombinant USP1-UAF1-RAD51AP1 and reveal critical mechanistic details of the process.
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Affiliation(s)
- Fengshan Liang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA.,Department of Pediatrics, Section of Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA
| | - Adam S Miller
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Simonne Longerich
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
| | - Caroline Tang
- Department of Pediatrics, Section of Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA.,Department of Pathology, Yale University School of Medicine, New Haven, CT, USA
| | - David Maranon
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Elizabeth A Williamson
- Department of Medicine, 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
| | - Claudia Wiese
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO, USA
| | - Gary M Kupfer
- Department of Pediatrics, Section of Hematology-Oncology, Yale University School of Medicine, New Haven, CT, USA. .,Department of Pathology, Yale University School of Medicine, New Haven, CT, USA.
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA. .,Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
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45
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Toma M, Skorski T, Sliwinski T. DNA Double Strand Break Repair - Related Synthetic Lethality. Curr Med Chem 2019; 26:1446-1482. [PMID: 29421999 DOI: 10.2174/0929867325666180201114306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 12/25/2022]
Abstract
Cancer is a heterogeneous disease with a high degree of diversity between and within tumors. Our limited knowledge of their biology results in ineffective treatment. However, personalized approach may represent a milestone in the field of anticancer therapy. It can increase specificity of treatment against tumor initiating cancer stem cells (CSCs) and cancer progenitor cells (CPCs) with minimal effect on normal cells and tissues. Cancerous cells carry multiple genetic and epigenetic aberrations which may disrupt pathways essential for cell survival. Discovery of synthetic lethality has led a new hope of creating effective and personalized antitumor treatment. Synthetic lethality occurs when simultaneous inactivation of two genes or their products causes cell death whereas individual inactivation of either gene is not lethal. The effectiveness of numerous anti-tumor therapies depends on induction of DNA damage therefore tumor cells expressing abnormalities in genes whose products are crucial for DNA repair pathways are promising targets for synthetic lethality. Here, we discuss mechanistic aspects of synthetic lethality in the context of deficiencies in DNA double strand break repair pathways. In addition, we review clinical trials utilizing synthetic lethality interactions and discuss the mechanisms of resistance.
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Affiliation(s)
- Monika Toma
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Tomasz Skorski
- Department of Microbiology and Immunology, 3400 North Broad Street, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, United States
| | - Tomasz Sliwinski
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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46
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Rad52 prevents excessive replication fork reversal and protects from nascent strand degradation. Nat Commun 2019; 10:1412. [PMID: 30926821 PMCID: PMC6441034 DOI: 10.1038/s41467-019-09196-9] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 02/26/2019] [Indexed: 01/02/2023] Open
Abstract
Stabilisation of stalled replication forks prevents excessive fork reversal and their pathological degradation, which can undermine genome integrity. Here we investigate a physiological role of RAD52 at stalled replication forks by using human cell models depleted of RAD52, a specific small-molecule inhibitor of the RAD52-ssDNA interaction, in vitro and single-molecule analyses. We demonstrate that RAD52 prevents excessive degradation of reversed replication forks by MRE11. Mechanistically, RAD52 binds to the stalled replication fork, promotes its occlusion and counteracts loading of SMARCAL1 in vitro and in vivo. Loss of the RAD52 function results in a slightly-defective replication restart, persistence of under-replicated regions and chromosome instability. Moreover, the RAD52-inhibited cells rely on RAD51 for completion of replication and viability upon replication arrest. Collectively, our data suggest an unexpected gatekeeper mechanism by which RAD52 limits excessive remodelling of stalled replication forks, thus indirectly assisting RAD51 and BRCA2 in protecting forks from unscheduled degradation and preventing genome instability. Stabilisation of stalled replication forks prevents excessive fork reversal and genome instability. Here authors reveal a RAD52-dependent replication fork protection mechanism.
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47
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Pokhrel N, Caldwell CC, Corless EI, Tillison EA, Tibbs J, Jocic N, Tabei SMA, Wold MS, Spies M, Antony E. Dynamics and selective remodeling of the DNA-binding domains of RPA. Nat Struct Mol Biol 2019; 26:129-136. [PMID: 30723327 PMCID: PMC6368398 DOI: 10.1038/s41594-018-0181-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 12/19/2018] [Indexed: 12/16/2022]
Abstract
Replication protein A (RPA) coordinates important DNA metabolic events by stabilizing single-stranded DNA (ssDNA) intermediates, activating the DNA-damage response and handing off ssDNA to the appropriate downstream players. Six DNA-binding domains (DBDs) in RPA promote high-affinity binding to ssDNA yet also allow RPA displacement by lower affinity proteins. We generated fluorescent versions of Saccharomyces cerevisiae RPA and visualized the conformational dynamics of individual DBDs in the context of the full-length protein. We show that both DBD-A and DBD-D rapidly bind to and dissociate from ssDNA while RPA remains bound to ssDNA. The recombination mediator protein Rad52 selectively modulates the dynamics of DBD-D. These findings reveal how RPA-interacting proteins with lower ssDNA binding affinities can access the occluded ssDNA and remodel individual DBDs to replace RPA.
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Affiliation(s)
- Nilisha Pokhrel
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Colleen C Caldwell
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Elliot I Corless
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Emma A Tillison
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA
| | - Joseph Tibbs
- Department of Physics, University of Northern Iowa, Cedar Falls, IA, USA
| | - Nina Jocic
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Physics, University of Northern Iowa, Cedar Falls, IA, USA
| | - S M Ali Tabei
- Department of Physics, University of Northern Iowa, Cedar Falls, IA, USA
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.
| | - Edwin Antony
- Department of Biological Sciences, Marquette University, Milwaukee, WI, USA.
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48
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Ducy M, Sesma-Sanz L, Guitton-Sert L, Lashgari A, Gao Y, Brahiti N, Rodrigue A, Margaillan G, Caron MC, Côté J, Simard J, Masson JY. The Tumor Suppressor PALB2: Inside Out. Trends Biochem Sci 2019; 44:226-240. [PMID: 30638972 DOI: 10.1016/j.tibs.2018.10.008] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/14/2018] [Accepted: 10/20/2018] [Indexed: 12/26/2022]
Abstract
Partner and Localizer of BRCA2 (PALB2) has emerged as an important and versatile player in genome integrity maintenance. Biallelic mutations in PALB2 cause Fanconi anemia (FA) subtype FA-N, whereas monoallelic mutations predispose to breast, and pancreatic familial cancers. Herein, we review recent developments in our understanding of the mechanisms of regulation of the tumor suppressor PALB2 and its functional domains. Regulation of PALB2 functions in DNA damage response and repair occurs on multiple levels, including homodimerization, phosphorylation, and ubiquitylation. With a molecular emphasis, we present PALB2-associated cancer mutations and their detailed analysis by functional assays.
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Affiliation(s)
- Mandy Ducy
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; CHU de Québec Research Center, Endocrinology and Nephrology Division, 2705 Bld Laurier, Québec City, QC, G1V 4G2, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Laura Sesma-Sanz
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Laure Guitton-Sert
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Anahita Lashgari
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Yuandi Gao
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Nadine Brahiti
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Amélie Rodrigue
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Guillaume Margaillan
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; CHU de Québec Research Center, Endocrinology and Nephrology Division, 2705 Bld Laurier, Québec City, QC, G1V 4G2, Canada
| | - Marie-Christine Caron
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Jacques Côté
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada
| | - Jacques Simard
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; CHU de Québec Research Center, Endocrinology and Nephrology Division, 2705 Bld Laurier, Québec City, QC, G1V 4G2, Canada
| | - Jean-Yves Masson
- CHU de Québec Research Center, Oncology Division, 9 McMahon, Québec City, QC, G1R 3S3, Canada; Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Québec City, QC, G1V 0A6, Canada.
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49
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Datta A, Brosh RM. New Insights Into DNA Helicases as Druggable Targets for Cancer Therapy. Front Mol Biosci 2018; 5:59. [PMID: 29998112 PMCID: PMC6028597 DOI: 10.3389/fmolb.2018.00059] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 06/06/2018] [Indexed: 12/28/2022] Open
Abstract
Small molecules that deter the functions of DNA damage response machinery are postulated to be useful for enhancing the DNA damaging effects of chemotherapy or ionizing radiation treatments to combat cancer by impairing the proliferative capacity of rapidly dividing cells that accumulate replicative lesions. Chemically induced or genetic synthetic lethality is a promising area in personalized medicine, but it remains to be optimized. A new target in cancer therapy is DNA unwinding enzymes known as helicases. Helicases play critical roles in all aspects of nucleic acid metabolism. We and others have investigated small molecule targeted inhibition of helicase function by compound screens using biochemical and cell-based approaches. Small molecule-induced trapping of DNA helicases may represent a generalized mechanism exemplified by certain topoisomerase and PARP inhibitors that exert poisonous consequences, especially in rapidly dividing cancer cells. Taking the lead from the broader field of DNA repair inhibitors and new information gleaned from structural and biochemical studies of DNA helicases, we predict that an emerging strategy to identify useful helicase-interacting compounds will be structure-based molecular docking interfaced with a computational approach. Potency, specificity, drug resistance, and bioavailability of helicase inhibitor drugs and targeting such compounds to subcellular compartments where the respective helicases operate must be addressed. Beyond cancer therapy, continued and new developments in this area may lead to the discovery of helicase-interacting compounds that chemically rescue clinically relevant helicase missense mutant proteins or activate the catalytic function of wild-type DNA helicases, which may have novel therapeutic application.
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Affiliation(s)
- Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD, United States
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, NIH Biomedical Research Center, Baltimore, MD, United States
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50
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Prakash A, Garcia-Moreno JF, Brown JAL, Bourke E. Clinically Applicable Inhibitors Impacting Genome Stability. Molecules 2018; 23:E1166. [PMID: 29757235 PMCID: PMC6100577 DOI: 10.3390/molecules23051166] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/27/2018] [Accepted: 05/01/2018] [Indexed: 12/14/2022] Open
Abstract
Advances in technology have facilitated the molecular profiling (genomic and transcriptomic) of tumours, and has led to improved stratification of patients and the individualisation of treatment regimes. To fully realize the potential of truly personalised treatment options, we need targeted therapies that precisely disrupt the compensatory pathways identified by profiling which allow tumours to survive or gain resistance to treatments. Here, we discuss recent advances in novel therapies that impact the genome (chromosomes and chromatin), pathways targeted and the stage of the pathways targeted. The current state of research will be discussed, with a focus on compounds that have advanced into trials (clinical and pre-clinical). We will discuss inhibitors of specific DNA damage responses and other genome stability pathways, including those in development, which are likely to synergistically combine with current therapeutic options. Tumour profiling data, combined with the knowledge of new treatments that affect the regulation of essential tumour signalling pathways, is revealing fundamental insights into cancer progression and resistance mechanisms. This is the forefront of the next evolution of advanced oncology medicine that will ultimately lead to improved survival and may, one day, result in many cancers becoming chronic conditions, rather than fatal diseases.
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Affiliation(s)
- Anu Prakash
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| | - Juan F Garcia-Moreno
- Discipline of Surgery, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| | - James A L Brown
- Discipline of Surgery, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
| | - Emer Bourke
- Discipline of Pathology, Lambe Institute for Translational Research, School of Medicine, National University of Ireland Galway, H91 YR71 Galway, Ireland.
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