1
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Sharma R, Mishra A, Bhardwaj M, Singh G, Indira Harahap LV, Vanjani S, Pan CH, Nepali K. Medicinal chemistry breakthroughs on ATM, ATR, and DNA-PK inhibitors as prospective cancer therapeutics. J Enzyme Inhib Med Chem 2025; 40:2489720. [PMID: 40256842 PMCID: PMC12013171 DOI: 10.1080/14756366.2025.2489720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2025] [Revised: 03/28/2025] [Accepted: 04/01/2025] [Indexed: 04/22/2025] Open
Abstract
This review discusses the critical roles of Ataxia Telangiectasia Mutated Kinase (ATM), ATM and Rad3-related Kinase (ATR), and DNA-dependent protein kinase (DNA-PK) in the DNA damage response (DDR) and their implications in cancer. Emphasis is placed on the intricate interplay between these kinases, highlighting their collaborative and distinct roles in maintaining genomic integrity and promoting tumour development under dysregulated conditions. Furthermore, the review covers ongoing clinical trials, patent literature, and medicinal chemistry campaigns on ATM/ATR/DNA-PK inhibitors as antitumor agents. Notably, the medicinal chemistry campaigns employed robust drug design strategies and aimed at assembling new structural templates with amplified DDR kinase inhibitory ability, as well as outwitting the pharmacokinetic liabilities of the existing DDR kinase inhibitors. Given the success attained through such endeavours, the clinical pipeline of DNA repair kinase inhibitors is anticipated to be supplemented by a reasonable number of tractable entries (DDR kinase inhibitors) soon.
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Affiliation(s)
- Ram Sharma
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Anshul Mishra
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Monika Bhardwaj
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Gurpreet Singh
- Department of Pharmaceutical Chemistry, ISF College of Pharmacy, Moga, India
| | | | - Sakshi Vanjani
- Molecular Medicine, University of South Florida, Tampa, FL, USA
| | - Chun Hsu Pan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
| | - Kunal Nepali
- School of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
- Ph.D. Program in Drug Discovery and Development Industry, College of Pharmacy, Taipei Medical University, Taipei, Taiwan
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2
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Wang Y, Hess JD, Wang C, Ma L, Luo M, Jossart J, Perry JJ, Kwon D, Wang Z, Pei X, Shen C, Wang Y, Zhou M, Yin H, Horne D, Nussenzweig A, Zheng L, Shen B. Discovery and Characterization of Small Molecule Inhibitors Targeting Exonuclease 1 for Homologous Recombination-Deficient Cancer Therapy. ACS Chem Biol 2025. [PMID: 40378357 DOI: 10.1021/acschembio.5c00117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2025]
Abstract
Human exonuclease 1 (EXO1), a member of the structure-specific nuclease family, plays a critical role in maintaining genome stability by processing DNA double-strand breaks (DSBs), nicks, and replication intermediates during DNA replication and repair. As its exonuclease activity is essential for homologous recombination (HR) and replication fork processing, EXO1 has emerged as a compelling therapeutic target, especially in cancers marked by heightened DNA damage and replication stress. Through high-throughput screening of 45,000 compounds, we identified seven distinct chemical scaffolds that demonstrated effective and selective inhibition of EXO1. Representative compounds from two of the most potent scaffolds, C200 and F684, underwent a comprehensive docking analysis and subsequent site-directed mutagenesis studies to evaluate their binding mechanisms. Biochemical assays further validated their potent and selective inhibition of the EXO1 nuclease activity. Tumor cell profiling experiments revealed that these inhibitors exploit synthetic lethality in BRCA1-deficient cells, emphasizing their specificity and therapeutic potential for targeting genetically HR-deficient (HRD) cancers driven by deleterious mutations in HR genes like BRCA1/2. Mechanistically, EXO1 inhibition suppressed DNA end resection, stimulated the accumulation of DNA double-strand breaks, and triggered S-phase PARylation, effectively disrupting DNA repair pathways that are essential for cancer cell survival. These findings establish EXO1 inhibitors as promising candidates for the treatment of HRD cancers and lay the groundwork for the further optimization and development of these compounds as targeted therapeutics.
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Affiliation(s)
- Yixing Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Jessica D Hess
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Chen Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Lingzi Ma
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Megan Luo
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Jennifer Jossart
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - John J Perry
- Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - David Kwon
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Zhe Wang
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Xinyu Pei
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Changxian Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Yingying Wang
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Holly Yin
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - David Horne
- Department of Molecular Medicine, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - André Nussenzweig
- Laboratory of Genome Integrity, National Cancer Institute NIH, Bethesda, Maryland 20892, United States
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, Duarte, California 91010, United States
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3
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Tang Z, Wang H, Wang X, Ludlow RA, Liu Z, Zhang M, Cao Q, Liu W, Zhao Q. Melatonin Mitigates Cd-Induced Growth Repression and RNA m 6A Hypermethylation by Triggering MMR-Mediated DNA Damage Response. PLANTS (BASEL, SWITZERLAND) 2025; 14:1398. [PMID: 40364427 PMCID: PMC12073604 DOI: 10.3390/plants14091398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2025] [Revised: 05/03/2025] [Accepted: 05/05/2025] [Indexed: 05/15/2025]
Abstract
Melatonin (MT) has been found to mitigate cadmium (Cd) toxicity with negligible environmental risks. It remains poorly understood as to how MT mitigates Cd-induced growth repression and regulates RNA m6A methylation. We aimed to elucidate the effect of MT on growth repression and RNA m6A methylation in Arabidopsis (Arabidopsis thaliana) exposed to Cd stress. MT mitigated, on average, 13.96% and 8.42% of growth repression resulting from Cd and mismatch repair (MMR) deficiency. The ameliorative effect on Cd stress was reduced by 70.56% and 34.23% in msh2 and msh6 mutants, respectively. With distinct dose-effect relationships, m6A hypermethylation responded to Cd stress rather than Cu stress, which was further elevated in MMR-deficient seedlings. MT reduced m6A levels by 22.98% even without stress induction, whereas the depressed m6A levels in MMR-deficient seedlings, greatly exceeding those in the WT. The "writer" and "eraser" gene expression responsible for m6A methylation was reduced with the concentration of stresses due to MT, but VIR and ALKBH9B no longer responded to Cd stress in msh2 and msh6. Despite the remarkable repression, MMR gene expression was regularly promoted by MT under Cd and Cu stress. Our study provides novel insights into the molecular mechanisms underlying the restorative effects of MT on growth repression and m6A methylation regulation, which shed light on Cd phytoremediation.
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Affiliation(s)
- Zihan Tang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China; (Z.T.); (X.W.); (Z.L.); (M.Z.); (Q.C.)
| | - Hetong Wang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China; (Z.T.); (X.W.); (Z.L.); (M.Z.); (Q.C.)
| | - Xianpeng Wang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China; (Z.T.); (X.W.); (Z.L.); (M.Z.); (Q.C.)
| | - Richard A. Ludlow
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK;
| | - Zhouli Liu
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China; (Z.T.); (X.W.); (Z.L.); (M.Z.); (Q.C.)
- Northeast Geological S&T Innovation Center, China Geological Survey, Shenyang 110034, China
| | - Min Zhang
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China; (Z.T.); (X.W.); (Z.L.); (M.Z.); (Q.C.)
| | - Qijiang Cao
- Liaoning Key Laboratory of Urban Integrated Pest Management and Ecological Security, College of Life Science and Bioengineering, Shenyang University, Shenyang 110044, China; (Z.T.); (X.W.); (Z.L.); (M.Z.); (Q.C.)
| | - Wan Liu
- College of Agriculture and Biological Sciences, Dehong Normal University, Mangshi 678400, China;
| | - Qiang Zhao
- College of Agriculture, Heilongjiang Bayi Agricultural University, Daqing 163000, China
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4
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Wang G, Wang P, Zheng Z, Zhang Q, Xu C, Xu X, Jian L, Zhao Z, Cai G, Wang X. Molecular architecture and inhibition mechanism of human ATR-ATRIP. Sci Bull (Beijing) 2025:S2095-9273(25)00489-X. [PMID: 40379520 DOI: 10.1016/j.scib.2025.05.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2025] [Revised: 03/31/2025] [Accepted: 04/29/2025] [Indexed: 05/19/2025]
Abstract
The ataxia telangiectasia-mutated and Rad3-related (ATR) kinase is a master regulator of DNA damage response and replication stress in humans. Targeting ATR is the focus of oncology drug pipelines with a number of potent, selective ATR inhibitors currently in clinical development. Here, we determined the cryo-EM structures of the human ATR-ATRIP complex in the presence of VE-822 and RP-3500, two ATR inhibitors currently in Phase II clinical trials, achieving an overall resolution of approximately 3 Å. These structures yield a near-complete atomic model of the ATR-ATRIP complex, revealing subunit stoichiometry, intramolecular and intermolecular interactions, and critical regulatory sites including an insertion in the PIKK regulatory domain (PRD). Structural comparison provides insights into the modes of action and selectivity of ATR inhibitors. The divergent binding modes near the solvent side and in the rear pocket area of VE-822 and RP-3500, particularly their disparate binding orientations, lead to varying conformational changes in the active site. Surprisingly, one ATR-ATRIP complex binds four VE-822 molecules, with two in the ATR active site and two at the ATR-ATR dimer interface. The binding and selectivity of RP-3500 depend on two bound water molecules, which may be further enhanced by the substitution of these bound waters. Our study provides a structural framework for understanding ATR regulation and holds promise for assisting future efforts in rational drug design targeting ATR.
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Affiliation(s)
- Guangxian Wang
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Po Wang
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Zexuan Zheng
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Qingjun Zhang
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Chenchen Xu
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Xinyi Xu
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Lingfei Jian
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Zhanpeng Zhao
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China
| | - Gang Cai
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China; Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China.
| | - Xuejuan Wang
- Department of Radiation Oncology, the First Affiliated Hospital of USTC, MOE Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China; Key Laboratory of Anhui Province for Emerging and Reemerging Infectious Diseases, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230000, China.
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5
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Duthoo E, Beyls E, Backers L, Gudjónsson T, Huang P, Jonckheere L, Riemann S, Parton B, Du L, Debacker V, De Bruyne M, Hoste L, Baeyens A, Vral A, Van Braeckel E, Staal J, Mortier G, Kerre T, Pan-Hammarström Q, Sørensen CS, Haerynck F, Claes KB, Tavernier SJ. Replication stress, microcephalic primordial dwarfism, and compromised immunity in ATRIP deficient patients. J Exp Med 2025; 222:e20241432. [PMID: 40029331 PMCID: PMC11874998 DOI: 10.1084/jem.20241432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2024] [Revised: 11/13/2024] [Accepted: 12/23/2024] [Indexed: 03/05/2025] Open
Abstract
Ataxia telangiectasia and Rad3-related (ATR) kinase and its interacting protein ATRIP orchestrate the replication stress response. Homozygous splice variants in the ATRIP gene, resulting in ATRIP deficiency, were identified in two patients of independent ancestry with microcephaly, primordial dwarfism, and recurrent infections. The c.829+5G>T patient exhibited lymphopenia, poor vaccine responses, autoimmune features with hemolytic anemia, and neutropenia. Immunophenotyping revealed reduced CD16+/CD56dim NK cells and absent naïve T cells, MAIT cells, and iNKT cells. Lymphocytic defects were characterized by TCR oligoclonality, abnormal class switch recombination, and impaired T cell proliferation. ATRIP deficiency resulted in low-grade ATR activation but impaired CHK1 phosphorylation under genotoxic stress. ATRIP-deficient cells inadequately regulated DNA replication, leading to chromosomal instability, compromised cell cycle control, and impaired cell viability. CRISPR-SelectTIME confirmed reduced cell fitness for both variants. This study establishes ATRIP deficiency as a monogenic cause of microcephalic primordial dwarfism, highlights ATRIP's critical role in protecting immune cells from replication stress, and offers new insights into its canonical functions.
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Affiliation(s)
- Evi Duthoo
- Primary Immunodeficiency Research Lab (PIRL), Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, ERN-RITA Reference Center, Ghent University Hospital, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Elien Beyls
- Primary Immunodeficiency Research Lab (PIRL), Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, ERN-RITA Reference Center, Ghent University Hospital, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Lynn Backers
- Primary Immunodeficiency Research Lab (PIRL), Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Thorkell Gudjónsson
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Peiquan Huang
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leander Jonckheere
- Respiratory Infection and Defense Lab (RIDL), Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Sebastian Riemann
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
- Laboratory for Translational Research in Obstructive Pulmonary Diseases, Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
| | - Bram Parton
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Likun Du
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Veronique Debacker
- Primary Immunodeficiency Research Lab (PIRL), Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, ERN-RITA Reference Center, Ghent University Hospital, Ghent, Belgium
| | - Marieke De Bruyne
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Levi Hoste
- Primary Immunodeficiency Research Lab (PIRL), Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Department of Pediatrics, Ghent University Hospital, Ghent, Belgium
| | - Ans Baeyens
- Radiobiology Lab, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Anne Vral
- Radiobiology Lab, Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Eva Van Braeckel
- Respiratory Infection and Defense Lab (RIDL), Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Jens Staal
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
| | - Geert Mortier
- Center for Human Genetics, University Hospitals Leuven, Leuven, Belgium
| | - Tessa Kerre
- Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, ERN-RITA Reference Center, Ghent University Hospital, Ghent, Belgium
- Department of Hematology, Ghent University Hospital, Ghent, Belgium
| | - Qiang Pan-Hammarström
- Division of Immunology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Claus S. Sørensen
- Biotech Research and Innovation Centre (BRIC), Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Filomeen Haerynck
- Primary Immunodeficiency Research Lab (PIRL), Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, ERN-RITA Reference Center, Ghent University Hospital, Ghent, Belgium
- Department of Pediatric Respiratory and Infectious Medicine, Ghent University Hospital, Ghent, Belgium
| | - Kathleen B.M. Claes
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Simon J. Tavernier
- Primary Immunodeficiency Research Lab (PIRL), Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium
- Center for Primary Immunodeficiency, Jeffrey Modell Diagnosis and Research Center, ERN-RITA Reference Center, Ghent University Hospital, Ghent, Belgium
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
- Unit of Molecular Signal Transduction in Inflammation, VIB-UGent Center for Inflammation Research, Ghent, Belgium
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Zhang J, Chen B, Xu F, Wang R, Zhao X, Yao Z, Zhang J, Zhou S, Xu A, Wu L, Zhao G. Phospho-TRIM21 orchestrates RPA2 ubiquitination switch to promote homologous recombination and tumor radio/chemo-resistance. Oncogene 2025; 44:1106-1117. [PMID: 39900724 DOI: 10.1038/s41388-025-03288-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2024] [Revised: 01/05/2025] [Accepted: 01/23/2025] [Indexed: 02/05/2025]
Abstract
RPA2, a key component of the RPA complex, is essential for single-stranded DNA (ssDNA) binding and DNA repair. However, the regulation of RPA2-ssDNA interaction and the recruitment of repair proteins following DNA damage remain incompletely understood. Our study uncovers a novel mechanism by which phosphorylated TRIM21 (Phospho-TRIM21) regulates RPA2 ubiquitination, thereby modulating homologous recombination and tumor radio/chemo-resistance. In the absence of DNA damage, TRIM21 mediates K63-linked ubiquitination of RPA2, countering K6-linked ubiquitination. Upon DNA damage, ubiquitination-modified RPA2 binds ssDNA, stabilizing the DNA structure and facilitating ATRIP/ATR recruitment. ATR subsequently phosphorylates TRIM21 at Ser41, leading to the dissociation of the TRIM21-RPA2 complex and a shift in RPA2 ubiquitination from K63 to K6 linkage. This shift maintains RPA2 ubiquitination homeostasis and stabilizes the RPA2-ATRIP complex, which is crucial for efficient homologous recombination (HR) repair and enhanced tumor radio/chemo-resistance. We also demonstrate that TRIM21 is frequently upregulated in cancers, and its depletion sensitizes cancer cells to radio/chemotherapy, suggesting its potential as a therapeutic target. This study provides novel insights into TRIM21's role in the DNA damage response and its implications for cancer treatment.
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Affiliation(s)
- Jie Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Bin Chen
- Department of Oncology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Feng Xu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Ruru Wang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Xipeng Zhao
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Zhicheng Yao
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Jie Zhang
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - Shenglan Zhou
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
- University of Science and Technology of China, Hefei, Anhui, 230026, China
| | - An Xu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
| | - Lijun Wu
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui, 230601, China
| | - Guoping Zhao
- High Magnetic Field Laboratory, Key Laboratory of High Magnetic Field and Ion Beam Physical Biology, Chinese Academy of Sciences, Anhui Province Key Laboratory of Environmental Toxicology and Pollution Control Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, Anhui, 230031, China.
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7
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Jordan MR, Mendoza-Munoz PL, Pawelczak KS, Turchi JJ. Targeting DNA damage sensors for cancer therapy. DNA Repair (Amst) 2025; 149:103841. [PMID: 40339280 DOI: 10.1016/j.dnarep.2025.103841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Revised: 04/18/2025] [Accepted: 04/26/2025] [Indexed: 05/10/2025]
Abstract
DNA damage occurs from both endogenous and exogenous sources and DNA damaging agents are a mainstay in cancer therapeutics. DNA damage sensors (DDS) are proteins that recognize and bind to unique DNA structures that arise from direct DNA damage or replication stress and are the first step in the DNA damage response (DDR). DNA damage sensors are responsible for recruiting transducer proteins that signal downstream DNA repair pathways. As the initiating proteins, DDS are excellent candidates for anti-cancer drug targeting to limit DDR activation. Here, we review four major DDS: PARP1, RPA, Ku, and the MRN complex. We briefly describe the cellular DDS functions before analyzing the structural mechanisms of DNA damage sensing. Lastly, we examine the current state of the field towards inhibiting each DDS for anti-cancer therapeutics and broadly discuss the therapeutic potential for DDS targeting.
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Affiliation(s)
- Matthew R Jordan
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Pamela L Mendoza-Munoz
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | | | - John J Turchi
- Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States; NERx BioSciences, Indianapolis, IN, United States.
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8
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Chen Y, Wang L, Zhou Q, Wei W, Wei H, Ma Y, Han T, Ma S, Huang X, Zhang M, Gao F, Liu C, Li W. Dynamic R-loops at centromeres ensure chromosome alignment during oocyte meiotic divisions in mice. Sci Bull (Beijing) 2025; 70:1311-1327. [PMID: 39984387 DOI: 10.1016/j.scib.2025.02.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2024] [Revised: 01/12/2025] [Accepted: 01/24/2025] [Indexed: 02/23/2025]
Abstract
R-loops play various roles in many physiological processes, however, their role in meiotic division remains largely unknown. Here we show that R-loops and their regulator RNase H1 are present at centromeres during oocyte meiotic divisions. Proper centromeric R-loops are essential to ensure chromosome alignment in oocytes during metaphase I (MI). Remarkably, both Rnaseh1 knockout and overexpression in oocytes lead to severe spindle assembly defects and chromosome misalignment due to dysregulation of R-loops at centromeres. Furthermore, we find that replication protein A (RPA) is recruited to centromeric R-loops, facilitating the deposition of ataxia telangiectasia-mutated and Rad3-related (ATR) kinase at centromeres by interacting with the ATR-interaction protein (ATRIP). The ATR kinase deposition triggers the activity of CHK1, stimulating the phosphorylation of Aurora B to finally promote proper spindle assembly and chromosome alignment at the equatorial plate. Most importantly, the application of ATR, CHK1, and Aurora B inhibitors could efficiently rescue the defects in spindle assembly and chromosome alignment due to RNase H1 deficiency in oocytes. Overall, our findings uncover a critical role of R-loops during mouse oocyte meiotic divisions, suggesting that dysregulation of R-loops may be associated with female infertility. Additionally, ATR, CHK1, and Aurora B inhibitors may potentially be used to treat some infertile patients.
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Affiliation(s)
- Yinghong Chen
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Liying Wang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 511436, China
| | - Qiuxing Zhou
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Wei Wei
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Huafang Wei
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; Sino-French Hoffmann Institute, School of Basic Medical Science, Guangzhou Medical University, Guangzhou 511436, China
| | - Yanjie Ma
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tingting Han
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Shuang Ma
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; Beijing Hospital, National Center of Gerontology, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Xiaoming Huang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China
| | - Meijia Zhang
- The Innovation Centre of Ministry of Education for Development and Diseases, the Second Affiliated Hospital, School of Medicine, South China University of Technology, Guangzhou 510006, China.
| | - Fei Gao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Chao Liu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Wei Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou 510623, China; State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Tsukada K, Imamura R, Miyake T, Saikawa K, Saito M, Kase N, Fu L, Ishiai M, Matsumoto Y, Shimada M. CDK-mediated phosphorylation of PNKP is required for end-processing of single-strand DNA gaps on Okazaki fragments and genome stability. eLife 2025; 14:e99217. [PMID: 40146629 PMCID: PMC11949490 DOI: 10.7554/elife.99217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 03/11/2025] [Indexed: 03/29/2025] Open
Abstract
Polynucleotide kinase phosphatase (PNKP) has enzymatic activities as 3'-phosphatase and 5'-kinase of DNA ends to promote DNA ligation and repair. Here, we show that cyclin-dependent kinases (CDKs) regulate the phosphorylation of threonine 118 (T118) in PNKP. This phosphorylation allows recruitment to the gapped DNA structure found in single-strand DNA (ssDNA) nicks and/or gaps between Okazaki fragments (OFs) during DNA replication. T118A (alanine)-substituted PNKP-expressing cells exhibited an accumulation of ssDNA gaps in S phase and accelerated replication fork progression. Furthermore, PNKP is involved in poly (ADP-ribose) polymerase 1 (PARP1)-dependent replication gap filling as part of a backup pathway in the absence of OFs ligation. Altogether, our data suggest that CDK-mediated PNKP phosphorylation at T118 is important for its recruitment to ssDNA gaps to proceed with OFs ligation and its backup repairs via the gap-filling pathway to maintain genome stability.
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Affiliation(s)
- Kaima Tsukada
- Laboratory for Zero-Carbon Energy, Institute of Integrated Research, Institute of Science TokyoTokyoJapan
- Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of CopenhagenCopenhagenDenmark
| | - Rikiya Imamura
- Laboratory for Zero-Carbon Energy, Institute of Integrated Research, Institute of Science TokyoTokyoJapan
| | - Tomoko Miyake
- Laboratory for Zero-Carbon Energy, Institute of Integrated Research, Institute of Science TokyoTokyoJapan
| | - Kotaro Saikawa
- Laboratory for Zero-Carbon Energy, Institute of Integrated Research, Institute of Science TokyoTokyoJapan
| | - Mizuki Saito
- Laboratory for Zero-Carbon Energy, Institute of Integrated Research, Institute of Science TokyoTokyoJapan
| | - Naoya Kase
- Laboratory for Zero-Carbon Energy, Institute of Integrated Research, Institute of Science TokyoTokyoJapan
| | - Lingyan Fu
- Laboratory for Zero-Carbon Energy, Institute of Integrated Research, Institute of Science TokyoTokyoJapan
| | | | - Yoshihisa Matsumoto
- Laboratory for Zero-Carbon Energy, Institute of Integrated Research, Institute of Science TokyoTokyoJapan
| | - Mikio Shimada
- Laboratory for Zero-Carbon Energy, Institute of Integrated Research, Institute of Science TokyoTokyoJapan
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10
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Xu Z, Liu Y, Li F, Yang Y, Zhang H, Meng F, Liu X, Xie X, Chen X, Shi Y, Zhang L. Phase separation of hnRNPA1 and TERRA regulates telomeric stability. J Mol Cell Biol 2025; 16:mjae037. [PMID: 39313323 PMCID: PMC12019227 DOI: 10.1093/jmcb/mjae037] [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: 01/30/2024] [Revised: 09/15/2024] [Accepted: 09/20/2024] [Indexed: 09/25/2024] Open
Abstract
Telomeres are the complexes composed of repetitive DNA sequences and associated proteins located at the end of chromatin. As a result of the DNA replication ending issue, telomeric DNA shortens during each cell cycle. The shelterin protein complex caps telomeric ends and forms a high-order protein-DNA structure to protect telomeric DNA. The stability of telomeres is critical for cellular function and related to the progression of many human diseases. Telomeric repeat-containing RNA (TERRA) is a noncoding RNA transcribed from telomeric DNA regions. TERRA plays an essential role in regulating and maintaining the stability of telomeres. Heterogeneous nuclear ribonucleoproteins (hnRNPs) are RNA-binding proteins associated with complex and diverse biological processes. hnRNPA1 can recognize both TERRA and telomeric DNA. Previous research reported that hnRNPA1, TERRA, and POT1, a component of the shelterin complex, work coordinately and displace replication protein A from telomeric single-stranded DNA after DNA replication, promoting telomere capping to preserve genomic integrity. However, the detailed molecular mechanism has remained unclear for >20 years. Here, our study revealed the molecular structure through which the hnRNPA1 UP1 domain interacts with TERRA and identified critical residues on the interacting surface between UP1 and TERRA. Furthermore, we proved that nucleic acids significantly increase the phase-separating ability of hnRNPA1, while disrupting the UP1-TERRA interaction extraordinarily affects hnRNPA1 droplet formation both in vitro and in vivo. Taken together, these data reveal the molecular mechanism of the phase separation of hnRNPA1 and TERRA and the potential contribution of the droplets to maintaining genomic stability.
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Affiliation(s)
- Ziyan Xu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Hefei National Research Center for Cross-disciplinary Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yongrui Liu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Hefei National Research Center for Cross-disciplinary Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Fudong Li
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Hefei National Research Center for Cross-disciplinary Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Yi Yang
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Hong Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Feilong Meng
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Xing Liu
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Hefei National Research Center for Cross-disciplinary Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Xin Xie
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xianjun Chen
- Optogenetics and Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yunyu Shi
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Hefei National Research Center for Cross-disciplinary Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
| | - Liang Zhang
- Center for Advanced Interdisciplinary Science and Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Ministry of Education Key Laboratory for Membraneless Organelles and Cellular Dynamics, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
- Hefei National Research Center for Cross-disciplinary Science, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230027, China
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11
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Gong P, Guo Z, Wang S, Gao S, Cao Q. Histone Phosphorylation in DNA Damage Response. Int J Mol Sci 2025; 26:2405. [PMID: 40141048 PMCID: PMC11941871 DOI: 10.3390/ijms26062405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2025] [Revised: 03/01/2025] [Accepted: 03/05/2025] [Indexed: 03/28/2025] Open
Abstract
The DNA damage response (DDR) is crucial for maintaining genomic stability and preventing the accumulation of mutations that can lead to various diseases, including cancer. The DDR is a complex cellular regulatory network that involves DNA damage sensing, signal transduction, repair, and cell cycle arrest. Modifications in histone phosphorylation play important roles in these processes, facilitating DNA repair factor recruitment, damage signal transduction, chromatin remodeling, and cell cycle regulation. The precise regulation of histone phosphorylation is critical for the effective repair of DNA damage, genomic integrity maintenance, and the prevention of diseases such as cancer, where DNA repair mechanisms are often compromised. Thus, understanding histone phosphorylation in the DDR provides insights into DDR mechanisms and offers potential therapeutic targets for diseases associated with genomic instability, including cancers.
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Affiliation(s)
- Ping Gong
- Hunan Institute of Microbiology, Changsha 410009, China; (Z.G.); (S.W.); (S.G.)
| | - Zhaohui Guo
- Hunan Institute of Microbiology, Changsha 410009, China; (Z.G.); (S.W.); (S.G.)
| | - Shengping Wang
- Hunan Institute of Microbiology, Changsha 410009, China; (Z.G.); (S.W.); (S.G.)
| | - Shufeng Gao
- Hunan Institute of Microbiology, Changsha 410009, China; (Z.G.); (S.W.); (S.G.)
| | - Qinhong Cao
- College of Biological Sciences, China Agricultural University, No.2 Yuan-Ming-Yuan West Road, Beijing 100193, China
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12
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Zhao F, Cai C, Gao H, Moon J, Christyani G, Qin S, Hao Y, Liu T, Lou Z, Kim W. Mono-ubiquitination of TopBP1 by PHRF1 enhances ATR activation and genomic stability. Nucleic Acids Res 2025; 53:gkaf073. [PMID: 40052822 PMCID: PMC11886831 DOI: 10.1093/nar/gkaf073] [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: 03/12/2024] [Revised: 12/28/2024] [Accepted: 01/28/2025] [Indexed: 03/10/2025] Open
Abstract
The TopBP1-ATR axis is critical for maintaining genomic stability during DNA replication stress, yet the precise regulation of TopBP1 in replication stress responses remains poorly understood. In this study, we identified PHD and Ring Finger Domains 1 (PHRF1) as an important ATR activator through its interaction with TopBP1. Our analysis revealed a correlation between PHRF1 and genomic stability in cancer patients. Mechanistically, PHRF1 is recruited to DNA lesions in a manner dependent on its PHD domain and histone methylation. Subsequently, PHRF1 mono-ubiquitinates TopBP1 at lysine 73, which enhances the TopBP1-ATR interaction and activates ATR. Depletion of PHRF1 disrupts ATR activation and sensitizes cells to replication stress-inducing agents. Furthermore, conditional knockout of Phrf1 in mice leads to early lethality and impaired ATR-Chk1 axis signaling. Collectively, our findings establish PHRF1 as a novel E3 ligase for TopBP1, coordinating the replication stress response by enhancing TopBP1-ATR signaling.
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Affiliation(s)
- Fei Zhao
- College of Biology, Hunan University, Changsha 410082, China
| | - Chenghui Cai
- College of Biology, Hunan University, Changsha 410082, China
| | - Huanyao Gao
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, United States
| | - Jaeyoung Moon
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan 31151 Chungcheongnam-do, Republic of Korea
| | - Grania Christyani
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan 31151 Chungcheongnam-do, Republic of Korea
| | - Sisi Qin
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan 31151 Chungcheongnam-do, Republic of Korea
| | - Yalan Hao
- Analytical Instrumentation Center, Hunan University, Changsha 410082, China
| | - Tongzheng Liu
- College of Pharmacy/International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Ministry of Education (MOE) of China, Jinan University, Guangzhou 510632, China
| | - Zhenkun Lou
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, United States
| | - Wootae Kim
- Department of Integrated Biomedical Science, Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan 31151 Chungcheongnam-do, Republic of Korea
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13
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Cordes J, Zhao S, Engel CM, Stingele J. Cellular responses to RNA damage. Cell 2025; 188:885-900. [PMID: 39983673 DOI: 10.1016/j.cell.2025.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2024] [Revised: 11/26/2024] [Accepted: 01/02/2025] [Indexed: 02/23/2025]
Abstract
RNA plays a central role in protein biosynthesis and performs diverse regulatory and catalytic functions, making it essential for all processes of life. Like DNA, RNA is constantly subjected to damage from endogenous and environmental sources. However, while the DNA damage response has been extensively studied, it was long assumed that RNA lesions are relatively inconsequential due to the transient nature of most RNA molecules. Here, we review recent studies that challenge this view by revealing complex RNA damage responses that determine survival when cells are exposed to nucleic acid-damaging agents and promote the resolution of RNA lesions.
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Affiliation(s)
- Jacqueline Cordes
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Shubo Zhao
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany; College of Basic Medical Sciences, Medical Basic Research Innovation Center of Airway Disease in North China, Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, China
| | - Carla M Engel
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julian Stingele
- Gene Center and Department of Biochemistry, Ludwig-Maximilians-Universität München, 81377 Munich, Germany.
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14
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Bhandare P, Narain A, Hofstetter J, Rummel T, Wenzel J, Schülein-Völk C, Lamer S, Eilers U, Schlosser A, Eilers M, Erhard F, Wolf E. Phenotypic screens identify SCAF1 as critical activator of RNAPII elongation and global transcription. Nucleic Acids Res 2025; 53:gkae1219. [PMID: 39698826 PMCID: PMC11879057 DOI: 10.1093/nar/gkae1219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 10/30/2024] [Accepted: 12/03/2024] [Indexed: 12/20/2024] Open
Abstract
Transcripts produced by RNA polymerase II (RNAPII) are fundamental for cellular responses to environmental changes. It is therefore no surprise that there exist multiple avenues for the regulation of this process. To explore the regulation mediated by RNAPII-interacting proteins, we used a small interfering RNA (siRNA)-based screen to systematically evaluate their influence on RNA synthesis. We identified several proteins that strongly affected RNAPII activity. We evaluated one of the top hits, SCAF1 (SR-related C-terminal domain-associated factor 1), using an auxin-inducible degradation system and sequencing approaches. In agreement with our screen results, acute depletion of SCAF1 decreased RNA synthesis, and showed an increase of Serine-2 phosphorylated-RNAPII (pS2-RNAPII). We found that the accumulation of pS2-RNAPII within the gene body occurred at GC-rich regions and was indicative of stalled RNAPII complexes. The accumulation of stalled RNAPII complexes was accompanied by reduced recruitment of initiating RNAPII, explaining the observed global decrease in transcriptional output. Furthermore, upon SCAF1 depletion, RNAPII complexes showed increased association with components of the proteasomal-degradation machinery. We concluded that in cells lacking SCAF1, RNAPII undergoes a rather interrupted passage, resulting in intervention by the proteasomal-degradation machinery to clear stalled RNAPII. While cells survive the compromised transcription caused by absence of SCAF1, further inhibition of proteasomal-degradation machinery is synthetically lethal.
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Affiliation(s)
- Pranjali Bhandare
- Institute of Biochemistry, University of Kiel, Rudolf-Höber-Straße 1, Kiel 24118, Germany
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Ashwin Narain
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Julia Hofstetter
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, Würzburg 97074, Germany
- Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Teresa Rummel
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstraße 4, Regensburg 93040, Germany
| | - Julia Wenzel
- Institute of Biochemistry, University of Kiel, Rudolf-Höber-Straße 1, Kiel 24118, Germany
| | - Christina Schülein-Völk
- Core Unit High-Content Microscopy, Biocenter, Theodor Boveri Institute, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Stephanie Lamer
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Straße 2, Würzburg 97080, Germany
| | - Ursula Eilers
- Core Unit High-Content Microscopy, Biocenter, Theodor Boveri Institute, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Andreas Schlosser
- Rudolf-Virchow-Zentrum - Center for Integrative and Translational Bioimaging, University of Würzburg, Josef-Schneider-Straße 2, Würzburg 97080, Germany
| | - Martin Eilers
- Chair of Biochemistry and Molecular Biology, Theodor Boveri Institute, University of Würzburg, Am Hubland, Würzburg 97074, Germany
| | - Florian Erhard
- Faculty for Informatics and Data Science, University of Regensburg, Bajuwarenstraße 4, Regensburg 93040, Germany
| | - Elmar Wolf
- Institute of Biochemistry, University of Kiel, Rudolf-Höber-Straße 1, Kiel 24118, Germany
- Cancer Systems Biology Group, Theodor Boveri Institute, University of Würzburg, Am Hubland, Würzburg 97074, Germany
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15
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Karami Fath M, Najafiyan B, Morovatshoar R, Khorsandi M, Dashtizadeh A, Kiani A, Farzam F, Kazemi KS, Nabi Afjadi M. Potential promising of synthetic lethality in cancer research and treatment. NAUNYN-SCHMIEDEBERG'S ARCHIVES OF PHARMACOLOGY 2025; 398:1403-1431. [PMID: 39305329 DOI: 10.1007/s00210-024-03444-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2024] [Accepted: 09/08/2024] [Indexed: 02/14/2025]
Abstract
Cancer is a complex disease driven by multiple genetic changes, including mutations in oncogenes, tumor suppressor genes, DNA repair genes, and genes involved in cancer metabolism. Synthetic lethality (SL) is a promising approach in cancer research and treatment, where the simultaneous dysfunction of specific genes or pathways causes cell death. By targeting vulnerabilities created by these dysfunctions, SL therapies selectively kill cancer cells while sparing normal cells. SL therapies, such as PARP inhibitors, WEE1 inhibitors, ATR and ATM inhibitors, and DNA-PK inhibitors, offer a distinct approach to cancer treatment compared to conventional targeted therapies. Instead of directly inhibiting specific molecules or pathways, SL therapies exploit genetic or molecular vulnerabilities in cancer cells to induce selective cell death, offering benefits such as targeted therapy, enhanced treatment efficacy, and minimized harm to healthy tissues. SL therapies can be personalized based on each patient's unique genetic profile and combined with other treatment modalities to potentially achieve synergistic effects. They also broaden the effectiveness of treatment across different cancer types, potentially overcoming drug resistance and improving patient outcomes. This review offers an overview of the current understanding of SL mechanisms, advancements, and challenges, as well as the preclinical and clinical development of SL. It also discusses new directions and opportunities for utilizing SL in targeted therapy for anticancer treatment.
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Affiliation(s)
- Mohsen Karami Fath
- Department of Cellular and Molecular Biology, Faculty of Biological Sciences, Kharazmi University, Tehran, Iran
| | - Behnam Najafiyan
- Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Reza Morovatshoar
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Mahdieh Khorsandi
- Department of Biotechnology, Faculty of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Arash Kiani
- Student Research Committee, Yasuj University of Medical Sciences, Yasuj, Iran
| | - Farnoosh Farzam
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran
| | - Kimia Sadat Kazemi
- Faculty of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Mohsen Nabi Afjadi
- Department of Biochemistry, Faculty of Biological Science, Tarbiat Modares University, Tehran, Iran.
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16
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Coquel F, Ho SZ, Tsai KC, Yang CY, Aze A, Devin J, Chang TH, Kong-Hap M, Bioteau A, Moreaux J, Maiorano D, Pourquier P, Yang WC, Lin YL, Pasero P. Synergistic effect of inhibiting CHK2 and DNA replication on cancer cell growth. eLife 2025; 13:RP104718. [PMID: 39887032 PMCID: PMC11785374 DOI: 10.7554/elife.104718] [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] [Indexed: 02/01/2025] Open
Abstract
Cancer cells display high levels of oncogene-induced replication stress (RS) and rely on DNA damage checkpoint for viability. This feature is exploited by cancer therapies to either increase RS to unbearable levels or inhibit checkpoint kinases involved in the DNA damage response. Thus far, treatments that combine these two strategies have shown promise but also have severe adverse effects. To identify novel, better-tolerated anticancer combinations, we screened a collection of plant extracts and found two natural compounds from the plant, Psoralea corylifolia, that synergistically inhibit cancer cell proliferation. Bakuchiol inhibited DNA replication and activated the checkpoint kinase CHK1 by targeting DNA polymerases. Isobavachalcone interfered with DNA double-strand break repair by inhibiting the checkpoint kinase CHK2 and DNA end resection. The combination of bakuchiol and isobavachalcone synergistically inhibited cancer cell proliferation in vitro. Importantly, it also prevented tumor development in xenografted NOD/SCID mice. The synergistic effect of inhibiting DNA replication and CHK2 signaling identifies a vulnerability of cancer cells that might be exploited by using clinically approved inhibitors in novel combination therapies.
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Affiliation(s)
- Flavie Coquel
- Institut de Génétique Humaine, Univ. de Montpellier, CNRSMontpellierFrance
- ‘Maintenance of Genome Integrity during DNA replication’ laboratory, équipe labélisée Ligue contre le CancerMontpellierFrance
| | - Sing-Zong Ho
- Agricultural Biotechnology Research Center, Academia SinicaTaipeiTaiwan
| | - Keng-Chang Tsai
- Ph.D. Program in Medical Biotechnology, College of Medical Science and Technology, Taipei Medical UniversityTaipeiTaiwan
- National Research Institute of Chinese Medicine, Ministry of Health and WelfareTaipeiTaiwan
| | - Chun-Yen Yang
- Institut de Génétique Humaine, Univ. de Montpellier, CNRSMontpellierFrance
| | - Antoine Aze
- Institut de Génétique Humaine, Univ. de Montpellier, CNRSMontpellierFrance
- ‘Genome Surveillance and Stability’ Laboratory, IGH, Univ. de Montpellier, CNRSMontpellierFrance
| | - Julie Devin
- Institut de Génétique Humaine, Univ. de Montpellier, CNRSMontpellierFrance
- ‘Normal and Malignant B cells’ laboratory', IGH, Univ. de Montpellier, CNRSMontpellierFrance
| | - Ting-Hsiang Chang
- Agricultural Biotechnology Research Center, Academia SinicaTaipeiTaiwan
| | - Marie Kong-Hap
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de MontpellierMontpellierFrance
| | - Audrey Bioteau
- Institut de Génétique Humaine, Univ. de Montpellier, CNRSMontpellierFrance
- ‘Maintenance of Genome Integrity during DNA replication’ laboratory, équipe labélisée Ligue contre le CancerMontpellierFrance
| | - Jerome Moreaux
- Institut de Génétique Humaine, Univ. de Montpellier, CNRSMontpellierFrance
- ‘Normal and Malignant B cells’ laboratory', IGH, Univ. de Montpellier, CNRSMontpellierFrance
- Institut Universitaire de FranceParisFrance
- Department of Biological Hematology, CHU MontpellierMontpellierFrance
| | - Domenico Maiorano
- Institut de Génétique Humaine, Univ. de Montpellier, CNRSMontpellierFrance
- ‘Genome Surveillance and Stability’ Laboratory, IGH, Univ. de Montpellier, CNRSMontpellierFrance
| | - Philippe Pourquier
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Institut régional du Cancer de MontpellierMontpellierFrance
| | - Wen-Chin Yang
- Agricultural Biotechnology Research Center, Academia SinicaTaipeiTaiwan
- Graduate Institute of Integrated Medicine, China Medical UniversityTaichungTaiwan
- Department of Life Sciences, National Chung-Hsing UniversityTaichungTaiwan
| | - Yea-Lih Lin
- ‘Maintenance of Genome Integrity during DNA replication’ laboratory, équipe labélisée Ligue contre le CancerMontpellierFrance
| | - Philippe Pasero
- Institut de Génétique Humaine, Univ. de Montpellier, CNRSMontpellierFrance
- ‘Maintenance of Genome Integrity during DNA replication’ laboratory, équipe labélisée Ligue contre le CancerMontpellierFrance
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17
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Biller M, Kabir S, Nipper S, Allen S, Kayali Y, Kuncik S, Sasanuma H, Zhou P, Vaziri C, Tomida J. REV7 associates with ATRIP and inhibits ATR kinase activity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.17.633588. [PMID: 39868202 PMCID: PMC11761088 DOI: 10.1101/2025.01.17.633588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Integration of DNA replication with DNA repair, cell cycle progression, and other biological processes is crucial for preserving genome stability and fundamentally important for all life. Ataxia-telangiectasia mutated and RAD3-related (ATR) and its partner ATR-interacting protein (ATRIP) function as a critical proximal sensor and transducer of the DNA Damage Response (DDR). Several ATR substrates, including p53 and CHK1, are crucial for coordination of cell cycle phase transitions, transcription, and DNA repair when cells sustain DNA damage. While much is known about ATR activation mechanisms, it is less clear how ATR signaling is negatively regulated in cells. Here, we identify the DNA repair protein REV7 as a novel direct binding partner of ATRIP. We define a REV7-interaction motif in ATRIP, which when mutated abrogates the REV7-ATRIP interaction in vitro and in intact cells. Using in vitro kinase assays, we show that REV7 inhibits ATR-mediated phosphorylation of its substrates, including p53. Disruption of the REV7-ATRIP interaction also enhances phosphorylation of CHK1 at Ser317 (a known ATR target site) in intact cells. Taken together our results establish REV7 as a critical negative regulator of ATR signaling. REV7 has pleiotropic roles in multiple DDR pathways including Trans-Lesion Synthesis, DNA Double-Strand Break resection, and p53 stability and may play a central role in the integration of multiple genome maintenance pathways.
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18
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Li Z, Zhang Z. A tale of two strands: Decoding chromatin replication through strand-specific sequencing. Mol Cell 2025; 85:238-261. [PMID: 39824166 PMCID: PMC11750172 DOI: 10.1016/j.molcel.2024.10.035] [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: 08/15/2024] [Revised: 10/03/2024] [Accepted: 10/25/2024] [Indexed: 01/20/2025]
Abstract
DNA replication, a fundamental process in all living organisms, proceeds with continuous synthesis of the leading strand by DNA polymerase ε (Pol ε) and discontinuous synthesis of the lagging strand by polymerase δ (Pol δ). This inherent asymmetry at each replication fork necessitates the development of methods to distinguish between these two nascent strands in vivo. Over the past decade, strand-specific sequencing strategies, such as enrichment and sequencing of protein-associated nascent DNA (eSPAN) and Okazaki fragment sequencing (OK-seq), have become essential tools for studying chromatin replication in eukaryotic cells. In this review, we outline the foundational principles underlying these methodologies and summarize key mechanistic insights into DNA replication, parental histone transfer, epigenetic inheritance, and beyond, gained through their applications. Finally, we discuss the limitations and challenges of current techniques, highlighting the need for further technological innovations to better understand the dynamics and regulation of chromatin replication in eukaryotic cells.
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Affiliation(s)
- Zhiming Li
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; West China School of Public Health and West China Fourth Hospital, State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China
| | - Zhiguo Zhang
- Institute for Cancer Genetics and Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, NY 10032, USA; Department of Pediatrics and Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY 10032, USA.
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19
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Roshan P, Kaushik V, Mistry A, Vayyeti A, Antony A, Luebbers R, Deveryshetty J, Antony E, Origanti S. Mechanism of RPA phosphocode priming and tuning by Cdk1/Wee1 signaling circuit. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.16.633180. [PMID: 39868089 PMCID: PMC11761648 DOI: 10.1101/2025.01.16.633180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Replication protein A (RPA) is a heterotrimeric single-strand DNA binding protein that is integral to DNA metabolism. Segregation of RPA functions in response to DNA damage is fine-tuned by hyperphosphorylation of the RPA32 subunit that is dependent on Cyclin-dependent kinase (Cdk)-mediated priming phosphorylation at the Ser-23 and Ser-29 sites. However, the mechanism of priming-driven hyperphosphorylation of RPA remains unresolved. Furthermore, the modulation of cell cycle progression by the RPA-Cdk axis is not clearly understood. Here, we uncover that the RPA70 subunit is also phosphorylated by Cdk1 at Thr-191. This modification is crucial for the G2 to M phase transition. This function is enacted through reciprocal regulation of Cdk1 activity through a feedback circuit espoused by stabilization of Wee1 kinase. The Thr-191 phosphosite on RPA70 is also crucial for priming hyperphosphorylation of RPA32 in response to DNA damage. Structurally, phosphorylation by Cdk1 primes RPA by reconfiguring the domains to release the N-terminus of RPA32 and the two protein-interaction domains that markedly enhances the efficiency of multisite phosphorylation by other kinases. Our findings establish a unique phosphocode-dependent feedback mechanism between RPA and RPA-regulating kinases that is fine-tuned to enact bipartite functions in cell cycle progression and DNA damage response.
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20
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Dyankova-Danovska T, Uzunova S, Danovski G, Stamatov R, Kanev PB, Atemin A, Ivanova A, Aleksandrov R, Stoynov S. In and out of Replication Stress: PCNA/RPA1-Based Dynamics of Fork Stalling and Restart in the Same Cell. Int J Mol Sci 2025; 26:667. [PMID: 39859385 PMCID: PMC11765805 DOI: 10.3390/ijms26020667] [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: 12/04/2024] [Revised: 01/08/2025] [Accepted: 01/12/2025] [Indexed: 01/27/2025] Open
Abstract
Replication forks encounter various impediments, which induce fork stalling and threaten genome stability, yet the precise dynamics of fork stalling and restart at the single-cell level remain elusive. Herein, we devise a live-cell microscopy-based approach to follow hydroxyurea-induced fork stalling and subsequent restart at 30 s resolution. We measure two distinct processes during fork stalling. One is rapid PCNA removal, which reflects the drop in DNA synthesis. The other is gradual RPA1 accumulation up to 2400 nt of ssDNA per fork despite an active intra-S checkpoint. Restoring the nucleotide pool enables a prompt restart without post-replicative ssDNA and a smooth cell cycle progression. ATR, but not ATM inhibition, accelerates hydroxyurea-induced RPA1 accumulation nine-fold, leading to RPA1 exhaustion within 20 min. Fork restart under ATR inhibition led to the persistence of ~600 nt ssDNA per fork after S-phase, which reached 2500 nt under ATR/ATM co-inhibition, with both scenarios leading to mitotic catastrophe. MRE11 inhibition had no effect on PCNA/RPA1 dynamics regardless of ATR activity. E3 ligase RAD18 was recruited at stalled replication forks in parallel to PCNA removal. Our results shed light on fork dynamics during nucleotide depletion and provide a valuable tool for interrogating the effects of replication stress-inducing anti-cancer agents.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Stoyno Stoynov
- Institute of Molecular Biology, Bulgarian Academy of Sciences, Acad. G. Bonchev Str. Bl. 21, 1113 Sofia, Bulgaria; (T.D.-D.); (S.U.); (G.D.); (R.S.); (P.-B.K.); (A.A.); (A.I.); (R.A.)
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21
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Wan B, Guan D, Li S, Chwat-Edelstein T, Zhao X. Mms22-Rtt107 axis attenuates the DNA damage checkpoint and the stability of the Rad9 checkpoint mediator. Nat Commun 2025; 16:311. [PMID: 39746913 PMCID: PMC11697250 DOI: 10.1038/s41467-024-54624-0] [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: 05/14/2024] [Accepted: 11/15/2024] [Indexed: 01/04/2025] Open
Abstract
The DNA damage checkpoint is a highly conserved signaling pathway induced by genotoxin exposure or endogenous genome stress. It alters many cellular processes such as arresting the cell cycle progression and increasing DNA repair capacities. However, cells can downregulate the checkpoint after prolonged stress exposure to allow continued growth and alternative repair. Strategies that can dampen the DNA damage checkpoint are not well understood. Here, we report that budding yeast employs a pathway composed of the scaffold protein Rtt107, its binding partner Mms22, and an Mms22-associated ubiquitin ligase complex to downregulate the DNA damage checkpoint. Mechanistically, this pathway promotes the proteasomal degradation of a key checkpoint factor, Rad9. Furthermore, Rtt107 binding to Mms22 helps to enrich the ubiquitin ligase complex on chromatin for targeting the chromatin-bound form of Rad9. Finally, we provide evidence that the Rtt107-Mms22 axis operates in parallel with the Rtt107-Slx4 axis, which displaces Rad9 from chromatin. We thus propose that Rtt107 enables a bifurcated "anti-Rad9" strategy to optimally downregulate the DNA damage checkpoint.
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Affiliation(s)
- Bingbing Wan
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai, 200240, China.
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Danying Guan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Shibai Li
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Tzippora Chwat-Edelstein
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Programs in Biochemistry, Cell, and Molecular Biology, Weill Cornell Graduate School of Medical Sciences, New York, NY, 10065, USA
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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22
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Zhu X, Gao C, Peng B, Xue J, Xia D, Yang L, Zhang J, Gao X, Hu Y, Lin S, Gong P, Xu X. FOXP1 phosphorylation antagonizes its O-GlcNAcylation in regulating ATR activation in response to replication stress. EMBO J 2025; 44:457-483. [PMID: 39623140 PMCID: PMC11729909 DOI: 10.1038/s44318-024-00323-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 11/13/2024] [Accepted: 11/18/2024] [Indexed: 01/15/2025] Open
Abstract
ATR signaling is essential in sensing and responding to the replication stress; as such, any defects can impair cellular function and survival. ATR itself is activated via tightly regulated mechanisms. Here, we identify FOXP1, a forkhead-box-containing transcription factor, as a regulator coordinating ATR activation. We show that, unlike its role as a transcription factor, FOXP1 functions as a scaffold and directly binds to RPA-ssDNA and ATR-ATRIP complexes, facilitating the recruitment and activation of ATR. This process is regulated by FOXP1 O-GlcNAcylation, which represses its interaction with ATR, while CHK1-mediated phosphorylation of FOXP1 inhibits its O-GlcNAcylation upon replication stress. Supporting the physiological relevance of this loop, we find pathogenic FOXP1 mutants identified in various tumor tissues with compromised ATR activation and stalled replication fork stability. We thus conclude that FOXP1 may serve as a potential chemotherapeutic target in related tumors.
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Affiliation(s)
- Xuefei Zhu
- Carson International Cancer Center & Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Shenzhen University General Hospital, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China.
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China.
| | - Congwen Gao
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China
- College of Life Sciences, Institute of Life Sciences and Green Development, Hebei University, 071002, Baoding, China
| | - Bin Peng
- Carson International Cancer Center & Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Shenzhen University General Hospital, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China
| | - Jingwei Xue
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China
| | - Donghui Xia
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China
- Shenzhen University General Hospital-Dehua Hospital Joint Research Center on Precision Medicine (sgh-dhhCPM), Dehua Hospital, Dehua, 362500, Quanzhou, China
- State Key Laboratory of Agro-biotechnology and MOA Key Laboratory of Soil Microbiology, College of Biological Sciences, China Agricultural University, 100193, Beijing, China
| | - Liu Yang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China
| | - Jiexiang Zhang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China
- Shenzhen University-Friedrich Schiller Universität Jena Joint PhD Program in Biomedical Sciences, Shenzhen University School of Medicine, 518060, Shenzhen, Guangdong, China
| | - Xinrui Gao
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China
| | - Yilin Hu
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Shixian Lin
- Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Peng Gong
- Carson International Cancer Center & Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Shenzhen University General Hospital, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China.
| | - Xingzhi Xu
- Carson International Cancer Center & Department of General Surgery & Institute of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Shenzhen University General Hospital, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China.
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Marshall Laboratory of Biomedical Engineering, Shenzhen University Medical School, 518060, Shenzhen, Guangdong, China.
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23
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Ming H, Tan J, Cao SY, Yu CP, Qi YT, Wang C, Zhang L, Liu Y, Yuan J, Yin M, Lei QY. NUFIP1 integrates amino acid sensing and DNA damage response to maintain the intestinal homeostasis. Nat Metab 2025; 7:120-136. [PMID: 39753713 DOI: 10.1038/s42255-024-01179-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 11/15/2024] [Indexed: 01/30/2025]
Abstract
Nutrient availability strongly affects intestinal homeostasis. Here, we report that low-protein (LP) diets decrease amino acids levels, impair the DNA damage response (DDR), cause DNA damage and exacerbate inflammation in intestinal tissues of male mice with inflammatory bowel disease (IBD). Intriguingly, loss of nuclear fragile X mental retardation-interacting protein 1 (NUFIP1) contributes to the amino acid deficiency-induced impairment of the DDR in vivo and in vitro and induces necroptosis-related spontaneous enteritis. Mechanistically, phosphorylated NUFIP1 binds to replication protein A2 (RPA32) to recruit the ataxia telangiectasia and Rad3-related (ATR)-ATR-interacting protein (ATRIP) complex, triggering the DDR. Consistently, both reintroducing NUFIP1 but not its non-phospho-mutant and inhibition of necroptosis prevent bowel inflammation in male Nufip1 conditional knockout mice. Intestinal inflammation and DNA damage in male mice with IBD can be mitigated by NUFIP1 overexpression. Moreover, NUFIP1 protein levels in the intestine of patients with IBD were found to be significantly decreased. Conclusively, our study uncovers that LP diets contribute to intestinal inflammation by hijacking NUFIP1-DDR signalling and thereby activating necroptosis.
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Affiliation(s)
- Hui Ming
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; School of Basic Medical Sciences, Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jing Tan
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; School of Basic Medical Sciences, Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Si-Yi Cao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; School of Basic Medical Sciences, Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng-Ping Yu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; School of Basic Medical Sciences, Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yu-Ting Qi
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; School of Basic Medical Sciences, Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chao Wang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; School of Basic Medical Sciences, Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Zhang
- Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ying Liu
- Department of Pathology, School of Basic Medical Sciences, Fudan University, Shanghai, China
| | - Jian Yuan
- State Key Laboratory of Cardiology and Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Department of Biochemistry and Molecular Biology, Tongji University School of Medicine, Shanghai, China
| | - Miao Yin
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; School of Basic Medical Sciences, Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Qun-Ying Lei
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences; School of Basic Medical Sciences, Cancer Institutes; Key Laboratory of Breast Cancer in Shanghai; Shanghai Key Laboratory of Radiation Oncology; the Shanghai Key Laboratory of Medical Epigenetics, State Key Laboratory of Medical Neurobiology, Shanghai Medical College, Fudan University, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- New Cornerstone Science Laboratory, School of Basic Medical Sciences, Fudan University, Shanghai, China.
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24
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Huang PC, Hong S, Alnaser HF, Mimitou EP, Kim KP, Murakami H, Keeney S. Meiotic DNA break resection and recombination rely on chromatin remodeler Fun30. EMBO J 2025; 44:200-224. [PMID: 39613969 PMCID: PMC11695836 DOI: 10.1038/s44318-024-00318-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 10/03/2024] [Accepted: 11/12/2024] [Indexed: 12/01/2024] Open
Abstract
DNA double-strand breaks (DSBs) are nucleolytically processed to generate single-stranded DNA for homologous recombination. In Saccharomyces cerevisiae meiosis, this resection involves nicking by the Mre11-Rad50-Xrs2 complex (MRX), then exonucleolytic digestion by Exo1. Chromatin remodeling at meiotic DSBs is thought necessary for resection, but the remodeling enzyme was unknown. Here we show that the SWI/SNF-like ATPase Fun30 plays a major, nonredundant role in meiotic resection. A fun30 mutation shortened resection tracts almost as severely as an exo1-nd (nuclease-dead) mutation, and resection was further shortened in a fun30 exo1-nd double mutant. Fun30 associates with chromatin in response to DSBs, and the constitutive positioning of nucleosomes governs resection endpoint locations in the absence of Fun30. We infer that Fun30 promotes both the MRX- and Exo1-dependent steps in resection, possibly by removing nucleosomes from broken chromatids. Moreover, the extremely short resection in fun30 exo1-nd double mutants is accompanied by compromised interhomolog recombination bias, leading to defects in recombination and chromosome segregation. Thus, this study also provides insight about the minimal resection lengths needed for robust recombination.
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Affiliation(s)
- Pei-Ching Huang
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10021, USA
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Metagenomi, Emeryville, CA, 94608, USA
| | - Soogil Hong
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
| | - Hasan F Alnaser
- Chromosome and Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK
| | - Eleni P Mimitou
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
- Immunai, 430 E 29th St, New York, NY, 10016, USA
| | - Keun P Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, South Korea
- Research Center for Biomolecules and Biosystems, Chung-Ang University, Seoul, 06974, South Korea
| | - Hajime Murakami
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Chromosome and Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, AB25 2ZD, UK.
| | - Scott Keeney
- Weill Cornell Graduate School of Medical Sciences, Cornell University, New York, NY, 10021, USA.
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
- Howard Hughes Medical Institute, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA.
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25
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Yang H, Lan L. Transcription-coupled DNA repair protects genome stability upon oxidative stress-derived DNA strand breaks. FEBS Lett 2025; 599:168-176. [PMID: 38813713 PMCID: PMC11607181 DOI: 10.1002/1873-3468.14938] [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: 02/01/2024] [Revised: 03/27/2024] [Accepted: 04/29/2024] [Indexed: 05/31/2024]
Abstract
Elevated oxidative stress, which threatens genome stability, has been detected in almost all types of cancers. Cells employ various DNA repair pathways to cope with DNA damage induced by oxidative stress. Recently, a lot of studies have provided insights into DNA damage response upon oxidative stress, specifically in the context of transcriptionally active genomes. Here, we summarize recent studies to help understand how the transcription is regulated upon DNA double strand breaks (DSB) and how DNA repair pathways are selectively activated at the damage sites coupling with transcription. The role of RNA molecules, especially R-loops and RNA modifications during the DNA repair process, is critical for protecting genome stability. This review provides an update on how cells protect transcribed genome loci via transcription-coupled repair pathways.
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Affiliation(s)
- Haibo Yang
- Department of Urology, Brigham and Women’s Hospital & Harvard Medical School, Boston, MA, USA
| | - Li Lan
- Departments of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC, USA
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26
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Gong GQ, Anandapadamanaban M, Islam MS, Hay IM, Bourguet M, Špokaitė S, Dessus AN, Ohashi Y, Perisic O, Williams RL. Making PI3K superfamily enzymes run faster. Adv Biol Regul 2025; 95:101060. [PMID: 39592347 DOI: 10.1016/j.jbior.2024.101060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2024] [Accepted: 11/16/2024] [Indexed: 11/28/2024]
Abstract
The phosphoinositide 3-kinase (PI3K) superfamily includes lipid kinases (PI3Ks and type III PI4Ks) and a group of PI3K-like Ser/Thr protein kinases (PIKKs: mTOR, ATM, ATR, DNA-PKcs, SMG1 and TRRAP) that have a conserved C-terminal kinase domain. A common feature of the superfamily is that they have very low basal activity that can be greatly increased by a range of regulatory factors. Activators reconfigure the active site, causing a subtle realignment of the N-lobe of the kinase domain relative to the C-lobe. This realignment brings the ATP-binding loop in the N-lobe closer to the catalytic residues in the C-lobe. In addition, a conserved C-lobe feature known as the PIKK regulatory domain (PRD) also can change conformation, and PI3K activators can alter an analogous PRD-like region. Recent structures have shown that diverse activating influences can trigger these conformational changes, and a helical region clamping onto the kinase domain transmits regulatory interactions to bring about the active site realignment for more efficient catalysis. A recent report of a small-molecule activator of PI3Kα for application in nerve regeneration suggests that flexibility of these regulatory elements might be exploited to develop specific activators of all PI3K superfamily members. These activators could have roles in wound healing, anti-stroke therapy and treating neurodegeneration. We review common structural features of the PI3K superfamily that may make them amenable to activation.
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Affiliation(s)
- Grace Q Gong
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK; University College London Cancer Institute, University College London, London, UK
| | | | - Md Saiful Islam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Iain M Hay
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Maxime Bourguet
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Saulė Špokaitė
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Antoine N Dessus
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Yohei Ohashi
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Olga Perisic
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Roger L Williams
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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27
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Martínez-Carranza M, Vialle L, Madru C, Cordier F, Tekpinar AD, Haouz A, Legrand P, Le Meur RA, England P, Dulermo R, Guijarro JI, Henneke G, Sauguet L. Communication between DNA polymerases and Replication Protein A within the archaeal replisome. Nat Commun 2024; 15:10926. [PMID: 39738083 PMCID: PMC11686378 DOI: 10.1038/s41467-024-55365-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2024] [Accepted: 12/09/2024] [Indexed: 01/01/2025] Open
Abstract
Replication Protein A (RPA) plays a pivotal role in DNA replication by coating and protecting exposed single-stranded DNA, and acting as a molecular hub that recruits additional replication factors. We demonstrate that archaeal RPA hosts a winged-helix domain (WH) that interacts with two key actors of the replisome: the DNA primase (PriSL) and the replicative DNA polymerase (PolD). Using an integrative structural biology approach, combining nuclear magnetic resonance, X-ray crystallography and cryo-electron microscopy, we unveil how RPA interacts with PriSL and PolD through two distinct surfaces of the WH domain: an evolutionarily conserved interface and a novel binding site. Finally, RPA is shown to stimulate the activity of PriSL in a WH-dependent manner. This study provides a molecular understanding of the WH-mediated regulatory activity in central replication factors such as RPA, which regulate genome maintenance in Archaea and Eukaryotes.
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Affiliation(s)
- Markel Martínez-Carranza
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France
| | - Léa Vialle
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), Plouzané, France
| | - Clément Madru
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France
| | - Florence Cordier
- Biological NMR & HDX-MS Technological Platform, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France
- Structural Bioinformatics, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France
| | - Ayten Dizkirici Tekpinar
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France
- Department of Molecular Biology and Genetics, Van Yüzüncü Yil University, Van, Turkey
| | - Ahmed Haouz
- Crystallography Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France
| | - Pierre Legrand
- Synchrotron SOLEIL, HelioBio group, L'Orme des Merisiers, Saint-Aubin, France
| | - Rémy A Le Meur
- Biological NMR & HDX-MS Technological Platform, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France
| | - Patrick England
- Molecular Biophysics Platform, C2RT, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France
| | - Rémi Dulermo
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), Plouzané, France
| | - J Iñaki Guijarro
- Biological NMR & HDX-MS Technological Platform, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France
| | - Ghislaine Henneke
- Univ Brest, Ifremer, CNRS, Biologie et Ecologie des Ecoystèmes marins profonds (BEEP), Plouzané, France.
| | - Ludovic Sauguet
- Architecture and Dynamics of Biological Macromolecules, Institut Pasteur, Université Paris Cité, CNRS UMR 3528, Paris, France.
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28
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Latoszek M, Baginska-Drabiuk K, Sledziewska-Gojska E, Kaniak-Golik A. PCNA and Rnh1 independently participate in the protection of mitochondrial genome against UV-induced mutagenesis in yeast cells. Sci Rep 2024; 14:31017. [PMID: 39730600 DOI: 10.1038/s41598-024-82104-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 12/02/2024] [Indexed: 12/29/2024] Open
Abstract
In Saccharomyces cerevisiae cells, the bulk of mitochondrial DNA (mtDNA) replication is mediated by the replicative high-fidelity DNA polymerase γ. However, upon UV irradiation low-fidelity translesion polymerases: Polη, Polζ and Rev1, participate in an error-free replicative bypass of UV-induced lesions in mtDNA. We analysed how translesion polymerases could function in mitochondria. We show that, contrary to expectations, yeast PCNA is mitochondrially localized and, upon genotoxic stress, ubiquitinated PCNA can be detected in purified mitochondria. Moreover, the substitution K164R in PCNA leads to an increase of UV-induced point mutations in mtDNA. This UV-dependent effect is highly enhanced in cells in which the Mec1/Rad53/Dun1 checkpoint-dependent deoxynucleotide triphosphate (dNTP) increase in response to DNA damage is blocked and RNase H1 is lacking, suggesting that PCNA plays a role in a replication damage bypass pathway dealing with lesions in multiple ribonucleotides embedded in mtDNA. In addition, our analysis indicates that K164R in PCNA restricts mostly the anti-mutagenic Polη activity on UV-damaged mtDNA, whereas the inhibitory effect on Polζ's activity is only partial. We also show for the first time that in conditions of dNTP depletion yeast Rnh1 neutralizes deleterious effects of ribonucleotides for mtDNA replication, thereby preventing the enhanced instability of rho+ mitochondrial genomes.
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Affiliation(s)
- Martyna Latoszek
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Baginska-Drabiuk
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | | | - Aneta Kaniak-Golik
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland.
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29
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Zhu L, Dluzewska J, Fernández-Jiménez N, Ranjan R, Pelé A, Dziegielewski W, Szymanska-Lejman M, Hus K, Górna J, Pradillo M, Ziolkowski PA. The kinase ATR controls meiotic crossover distribution at the genome scale in Arabidopsis. THE PLANT CELL 2024; 37:koae292. [PMID: 39471331 DOI: 10.1093/plcell/koae292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2024] [Revised: 10/07/2024] [Accepted: 10/21/2024] [Indexed: 11/01/2024]
Abstract
Meiotic crossover, i.e. the reciprocal exchange of chromosome fragments during meiosis, is a key driver of genetic diversity. Crossover is initiated by the formation of programmed DNA double-strand breaks (DSBs). While the role of ATAXIA-TELANGIECTASIA AND RAD3-RELATED (ATR) kinase in DNA damage signaling is well-known, its impact on crossover formation remains understudied. Here, using measurements of recombination at chromosomal intervals and genome-wide crossover mapping, we showed that ATR inactivation in Arabidopsis (Arabidopsis thaliana) leads to dramatic crossover redistribution, with an increase in crossover frequency in chromosome arms and a decrease in pericentromeres. These global changes in crossover placement were not caused by alterations in DSB numbers, which we demonstrated by analyzing phosphorylated H2A.X foci in zygonema. Using the seed-typing technique, we found that hotspot usage remains mainly unchanged in atr mutants compared with wild-type individuals. Moreover, atr showed no change in the number of crossovers caused by two independent pathways, which implies no effect on crossover pathway choice. Analyses of genetic interaction indicate that while the effects of atr are independent of MMS AND UV SENSITIVE81 (MUS81), ZIPPER1 (ZYP1), FANCONI ANEMIA COMPLEMENTATION GROUP M (FANCM), and D2 (FANCD2), the underlying mechanism may be similar between ATR and FANCD2. This study extends our understanding of ATR's role in meiosis, uncovering functions in regulating crossover distribution.
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Affiliation(s)
- Longfei Zhu
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Julia Dluzewska
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Nadia Fernández-Jiménez
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Rajeev Ranjan
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Alexandre Pelé
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Wojciech Dziegielewski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Maja Szymanska-Lejman
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Karolina Hus
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Julia Górna
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
| | - Mónica Pradillo
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Piotr A Ziolkowski
- Laboratory of Genome Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University in Poznan, 61-614 Poznan, Poland
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30
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Nair JR, Huang TT, Sunkara A, Pruitt MR, Ibanez KR, Chiang CY, Cheng KCC, Wilson K, Cardillo TM, Hofsess S, Lee JM. Distinct effects of sacituzumab govitecan and berzosertib on DNA damage response in ovarian cancer. iScience 2024; 27:111283. [PMID: 39628575 PMCID: PMC11613210 DOI: 10.1016/j.isci.2024.111283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 09/10/2024] [Accepted: 10/25/2024] [Indexed: 12/06/2024] Open
Abstract
Antibody-drug conjugates (ADCs) have become an important class of anticancer drugs in solid tumors including drug-resistant gynecologic malignancies. TROP2 is a cell surface antigen that is highly expressed in ovarian carcinoma (OC) but minimally expressed in normal ovarian tissues. In this study, we aimed to identify how TROP2-specific ADC, sacituzumab govitecan (SG), modulates DNA damage response pathways in drug-resistant OC. We found that SG induces G2/M arrest, increases RPA1 foci, and decreases replication fork speed, resulting in replication stress in TROP2-positive cells while these were less evident in TROP2-negative cells. In OC in vitro and in vivo models, SN-38 sensitivity and TROP2 expression play key roles in response to either ATR inhibitor or SG alone, or in combination. Additionally, inhibition of translesion DNA synthesis enhances SG and PARP inhibitor (PARPi) sensitivity in PARPi-resistant OC cells. These findings provide mechanistic insights for clinical development of SG in drug-resistant OC.
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Affiliation(s)
- Jayakumar R. Nair
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Tzu-Ting Huang
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Anu Sunkara
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Margaret R. Pruitt
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Kristen R. Ibanez
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Chih-Yuan Chiang
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, NIH, Rockville, MD, USA
| | - Ken Chih-Chien Cheng
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, NIH, Rockville, MD, USA
| | - Kelli Wilson
- Functional Genomics Laboratory, National Center for Advancing Translational Sciences, NIH, Rockville, MD, USA
| | | | - Scott Hofsess
- Gilead Sciences, Inc., 333 Lakeside Dr., Foster City, CA 94404, USA
| | - Jung-Min Lee
- Women’s Malignancies Branch, Center for Cancer Research (CCR), National Cancer Institute (NCI), National Institutes of Health (NIH), Bethesda, MD, USA
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31
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Zhou FY, Waterman DP, Ashton M, Caban-Penix S, Memisoglu G, Eapen VV, Haber JE. Prolonged cell cycle arrest in response to DNA damage in yeast requires the maintenance of DNA damage signaling and the spindle assembly checkpoint. eLife 2024; 13:RP94334. [PMID: 39656839 PMCID: PMC11630823 DOI: 10.7554/elife.94334] [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] [Indexed: 12/12/2024] Open
Abstract
Cells evoke the DNA damage checkpoint (DDC) to inhibit mitosis in the presence of DNA double-strand breaks (DSBs) to allow more time for DNA repair. In budding yeast, a single irreparable DSB is sufficient to activate the DDC and induce cell cycle arrest prior to anaphase for about 12-15 hr, after which cells 'adapt' to the damage by extinguishing the DDC and resuming the cell cycle. While activation of the DNA damage-dependent cell cycle arrest is well understood, how it is maintained remains unclear. To address this, we conditionally depleted key DDC proteins after the DDC was fully activated and monitored changes in the maintenance of cell cycle arrest. Degradation of Ddc2ATRIP, Rad9, Rad24, or Rad53CHK2 results in premature resumption of the cell cycle, indicating that these DDC factors are required both to establish and maintain the arrest. Dun1 is required for the establishment, but not the maintenance, of arrest, whereas Chk1 is required for prolonged maintenance but not for initial establishment of the mitotic arrest. When the cells are challenged with two persistent DSBs, they remain permanently arrested. This permanent arrest is initially dependent on the continuous presence of Ddc2, Rad9, and Rad53; however, after 15 hr these proteins become dispensable. Instead, the continued mitotic arrest is sustained by spindle assembly checkpoint (SAC) proteins Mad1, Mad2, and Bub2 but not by Bub2's binding partner Bfa1. These data suggest that prolonged cell cycle arrest in response to 2 DSBs is achieved by a handoff from the DDC to specific components of the SAC. Furthermore, the establishment and maintenance of DNA damage-induced cell cycle arrest require overlapping but different sets of factors.
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Affiliation(s)
- Felix Y Zhou
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWalthamUnited States
| | - David P Waterman
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWalthamUnited States
| | - Marissa Ashton
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWalthamUnited States
| | - Suhaily Caban-Penix
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWalthamUnited States
| | - Gonen Memisoglu
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWalthamUnited States
- Department of Molecular Genetics & Cell Biology, University of ChicagoChicagoUnited States
| | - Vinay V Eapen
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWalthamUnited States
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWalthamUnited States
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32
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Keszthelyi A, Mansoubi S, Whale A, Houseley J, Baxter J. The fork protection complex generates DNA topological stress-induced DNA damage while ensuring full and faithful genome duplication. Proc Natl Acad Sci U S A 2024; 121:e2413631121. [PMID: 39589889 PMCID: PMC11626154 DOI: 10.1073/pnas.2413631121] [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: 07/08/2024] [Accepted: 10/14/2024] [Indexed: 11/28/2024] Open
Abstract
The fork protection complex (FPC), composed of Mrc1, Tof1, and Csm3, supports rapid and stable DNA replication. Here, we show that FPC activity also introduces DNA damage by increasing DNA topological stress during replication. Mrc1 action increases DNA topological stress during plasmid replication, while Mrc1 or Tof1 activity causes replication stress and DNA damage within topologically constrained regions. We show that the recruitment of Top1 to the fork by Tof1 suppresses the DNA damage generated in these loci. While FPC activity introduces some DNA damage due to increased topological stress, the FPC is also necessary to prevent DNA damage in long replicons across the genome, indicating that the FPC is required for complete and faithful genome duplication. We conclude that FPC regulation must balance ensuring full genome duplication through rapid replication with minimizing the consequential DNA topological stress-induced DNA damage caused by rapid replication through constrained regions.
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Affiliation(s)
- Andrea Keszthelyi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, East SussexBN1 9RQ, United Kingdom
| | - Sahar Mansoubi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, East SussexBN1 9RQ, United Kingdom
- Biology Department, North Tehran Branch, Islamic Azad University, Tehran1477893855, Iran
| | - Alex Whale
- Epigenetics Programme The Babraham Institute, Babraham Research Campus, CambridgeCB22 3AT, United Kingdom
| | - Jonathan Houseley
- Epigenetics Programme The Babraham Institute, Babraham Research Campus, CambridgeCB22 3AT, United Kingdom
| | - Jonathan Baxter
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, East SussexBN1 9RQ, United Kingdom
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33
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Zhao H, Richardson C, Marriott I, Yang IH, Yan S. APE1 is a master regulator of the ATR-/ATM-mediated DNA damage response. DNA Repair (Amst) 2024; 144:103776. [PMID: 39461278 PMCID: PMC11611674 DOI: 10.1016/j.dnarep.2024.103776] [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: 09/18/2024] [Revised: 10/14/2024] [Accepted: 10/15/2024] [Indexed: 10/29/2024]
Abstract
To maintain genomic integrity, cells have evolved several conserved DNA damage response (DDR) pathways in response to DNA damage and stress conditions. Apurinic/apyrimidinic endonuclease 1 (APE1) exhibits AP endonuclease, 3'-5' exonuclease, 3'-phosphodiesterase, and 3'-exoribonuclease activities and plays critical roles in the DNA repair and redox regulation of transcription. However, it remains unclear whether and how APE1 is involved in DDR pathways. In this perspective, we first updated our knowledge of APE1's functional domains and its nuclease activities and their specific associated substrates. We then summarized the newly discovered roles and mechanisms of action of APE1 in the global and nucleolar ATR-mediated DDR pathway. While the ATM-mediated DDR is well known to be activated by DNA double-strand breaks and oxidative stress, here we provided new perspectives as to how ATM DDR signaling is activated by indirect single-strand breaks (SSBs) resulting from genotoxic stress and defined SSB structures, and discuss how ATM kinase is directly activated and regulated by its activator, APE1. Together, accumulating body of new evidence supports the notion that APE1 is a master regulator protein of the ATR- and ATM-mediated DDR pathways. These new findings of APE1 in DDR signaling provide previously uncharacterized but critical functions and regulations of APE1 in genome integrity.
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Affiliation(s)
- Haichao Zhao
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Christine Richardson
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; School of Data Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Ian Marriott
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - In Hong Yang
- Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; Department of Mechanical Engineering and Engineering Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; Center for Biomedical Engineering and Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA; School of Data Science, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.
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34
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Ahmed SMQ, Sasikumar J, Laha S, Das SP. Multifaceted role of the DNA replication protein MCM10 in maintaining genome stability and its implication in human diseases. Cancer Metastasis Rev 2024; 43:1353-1371. [PMID: 39240414 DOI: 10.1007/s10555-024-10209-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 08/29/2024] [Indexed: 09/07/2024]
Abstract
MCM10 plays a vital role in genome duplication and is crucial for DNA replication initiation, elongation, and termination. It coordinates several proteins to assemble at the fork, form a functional replisome, trigger origin unwinding, and stabilize the replication bubble. MCM10 overexpression is associated with increased aggressiveness in breast, cervical, and several other cancers. Disruption of MCM10 leads to altered replication timing associated with initiation site gains and losses accompanied by genome instability. Knockdown of MCM10 affects the proliferation and migration of cancer cells, manifested by DNA damage and replication fork arrest, and has recently been shown to be associated with clinical conditions like CNKD and RCM. Loss of MCM10 function is associated with impaired telomerase activity, leading to the accumulation of abnormal replication forks and compromised telomere length. MCM10 interacts with histones, aids in nucleosome assembly, binds BRCA2 to maintain genome integrity during DNA damage, prevents lesion skipping, and inhibits PRIMPOL-mediated repriming. It also interacts with the fork reversal enzyme SMARCAL1 and inhibits fork regression. Additionally, MCM10 undergoes several post-translational modifications and contributes to transcriptional silencing by interacting with the SIR proteins. This review explores the mechanism associated with MCM10's multifaceted role in DNA replication initiation, chromatin organization, transcriptional silencing, replication stress, fork stability, telomere length maintenance, and DNA damage response. Finally, we discuss the role of MCM10 in the early detection of cancer, its prognostic significance, and its potential use in therapeutics for cancer treatment.
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Affiliation(s)
- Sumayyah M Q Ahmed
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Jayaprakash Sasikumar
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Suparna Laha
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India
| | - Shankar Prasad Das
- Cell Biology and Molecular Genetics (CBMG), Yenepoya Research Centre (YRC), Yenepoya (Deemed to be University), Mangalore, 575018, India.
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35
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Crawford MR, Harper JA, Cooper TJ, Marsolier-Kergoat MC, Llorente B, Neale MJ. Separable roles of the DNA damage response kinase Mec1ATR and its activator Rad24RAD17 during meiotic recombination. PLoS Genet 2024; 20:e1011485. [PMID: 39652586 DOI: 10.1371/journal.pgen.1011485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 12/19/2024] [Accepted: 11/04/2024] [Indexed: 12/21/2024] Open
Abstract
During meiosis, programmed DNA double-strand breaks (DSBs) are formed by the topoisomerase-like enzyme, Spo11, activating the DNA damage response (DDR) kinase Mec1ATR via the checkpoint clamp loader, Rad24RAD17. At single loci, loss of Mec1 and Rad24 activity alters DSB formation and recombination outcome, but their genome-wide roles have not been examined in detail. Here, we utilise two strategies-deletion of the mismatch repair protein, Msh2, and control of meiotic prophase length via regulation of the Ndt80 transcription factor-to help characterise the roles Mec1 and Rad24 play in meiotic recombination by enabling genome-wide mapping of meiotic progeny. In line with previous studies, we observe severely impacted spore viability and a reduction in the frequency of recombination upon deletion of RAD24-driven by a shortened prophase. By contrast, loss of Mec1 function increases recombination frequency, consistent with its role in DSB trans-interference, and has less effect on spore viability. Despite these differences, complex multi-chromatid events initiated by closely spaced DSBs-rare in wild-type cells-occur more frequently in the absence of either Rad24 or Mec1, suggesting a loss of spatial regulation at the level of DSB formation in both. Mec1 and Rad24 also have important roles in the spatial regulation of crossovers (COs). Upon loss of either Mec1 or Rad24, CO distributions become more random-suggesting reductions in the global manifestation of interference. Such effects are similar to, but less extreme than, the phenotype of 'ZMM' mutants such as zip3Δ, and may be driven by reductions in the proportion of interfering COs. Collectively, in addition to shared roles in CO regulation, our results highlight separable roles for Rad24 as a pro-CO factor, and for Mec1 as a regulator of recombination frequency, the loss of which helps to suppress any broader defects in CO regulation caused by abrogation of the DDR.
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Affiliation(s)
- Margaret R Crawford
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, United Kingdom
- Francis Crick Institute, London, United Kingdom
| | - Jon A Harper
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, United Kingdom
| | - Tim J Cooper
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, United Kingdom
| | - Marie-Claude Marsolier-Kergoat
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
- UMR7206 Eco-Anthropology and Ethno-Biology, CNRS-MNHN-University Paris Diderot, Musée de l'Homme, Paris, France
| | - Bertrand Llorente
- Cancer Research Centre of Marseille, CNRS, INSERM U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Matthew J Neale
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, United Kingdom
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36
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Fan J, Dhingra N, Yang T, Yang V, Zhao X. Srs2 binding to PCNA and its sumoylation contribute to RPA antagonism during the DNA damage response. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.28.587206. [PMID: 38586001 PMCID: PMC10996639 DOI: 10.1101/2024.03.28.587206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Activation of the DNA damage checkpoint upon genotoxin treatment induces a multitude of cellular changes, such as cell cycle arrest or delay, to cope with genome stress. After prolonged genotoxin treatment, the checkpoint can be downregulated to allow cell cycle and growth resumption. In yeast, downregulation of the DNA damage checkpoint requires the Srs2 DNA helicase, which removes the ssDNA binding complex RPA and the associated Mec1 checkpoint kinase from DNA, thus dampening Mec1-mediated checkpoint. However, it is unclear whether the 'anti-checkpoint' role of Srs2 is temporally and spatially regulated to both allow timely checkpoint termination and to prevent superfluous RPA removal. Here we address this question by examining regulatory elements of Srs2, such as its phosphorylation, sumoylation, and protein-interaction sites. Our genetic analyses and checkpoint level assessment suggest that the RPA countering role of Srs2 is promoted by Srs2 binding to PCNA, which recruits Srs2 to a subset of ssDNA regions. RPA antagonism is further fostered by Srs2 sumoylation, which we found depends on the Srs2-PCNA interaction. Srs2 sumoylation is additionally reliant on Mec1 and peaks after Mec1 activity reaches maximal levels. Based on these data, we propose a two-step model of checkpoint downregulation wherein Srs2 recruitment to PCNA proximal ssDNA-RPA filaments and subsequent sumoylation stimulated upon Mec1 hyperactivation facilitate checkpoint recovery. This model suggests that Srs2 removal of RPA is minimized at ssDNA regions with no proximal PCNA to permit RPA-mediated DNA protection at these sites.
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Affiliation(s)
- Jiayi Fan
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Nalini Dhingra
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Tammy Yang
- City University of New York Hunter College, New York, NY 10065
| | - Vicki Yang
- City University of New York Hunter College, New York, NY 10065
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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Elazab IM, El-Feky OA, Khedr EG, El-Ashmawy NE. Prostate cancer and the cell cycle: Focusing on the role of microRNAs. Gene 2024; 928:148785. [PMID: 39053658 DOI: 10.1016/j.gene.2024.148785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
Prostate cancer is the most frequent solid tumor in terms of incidence and ranks second only to lung cancer in terms of cancer mortality among men. It has a considerably high mortality rate; around 375,000 deaths occurred worldwide in 2020. In 2024, the American Cancer Society estimated that the number of new prostate cancer cases will be around 299,010 cases, and the estimated deaths will be around 32,250 deaths only in the USA. Cell cycle dysregulation is inevitable in cancer etiology and is targeted by various therapies in cancer treatment. MicroRNAs (miRNAs) are small, endogenous, non-coding regulatory molecules involved in both normal and abnormal cellular events. One of the cellular processes regulated by miRNAs is the cell cycle. Although there are some exceptions, tumor suppressor miRNAs could potentially arrest the cell cycle by downregulating several molecular machineries involved in catalyzing the cell cycle progression. In contrast, oncogenic miRNAs (oncomirs) help the cell cycle to progress by targeting various regulatory proteins such as retinoblastoma (Rb) or cell cycle inhibitors such as p21 or p27, and hence may contribute to prostate cancer progression; however, this is not always the case. In this review, we emphasize how a dysregulated miRNA expression profile is linked to an abnormal cell cycle progression in prostate cancer, which subsequently paves the way to a new therapeutic option for prostate cancer.
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Affiliation(s)
- Ibrahim M Elazab
- Department of Biochemistry, Faculty of Pharmacy, Tanta University, Al-Geish Street, Tanta, El-Gharbia, 31527, Egypt.
| | - Ola A El-Feky
- Department of Biochemistry, Faculty of Pharmacy, Tanta University, Al-Geish Street, Tanta, El-Gharbia, 31527, Egypt.
| | - Eman G Khedr
- Department of Biochemistry, Faculty of Pharmacy, Tanta University, Al-Geish Street, Tanta, El-Gharbia, 31527, Egypt.
| | - Nahla E El-Ashmawy
- Department of Biochemistry, Faculty of Pharmacy, Tanta University, Al-Geish Street, Tanta, El-Gharbia, 31527, Egypt; Department of Pharmacology and Biochemistry, Faculty of Pharmacy, The British University in Egypt, BUE, Cairo, 11837, Egypt.
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38
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Yang Y, Jayaprakash D, Jhujh S, Reynolds J, Chen S, Gao Y, Anand J, Mutter-Rottmayer E, Ariel P, An J, Cheng X, Pearce K, Blanchet SA, Nandakumar N, Zhou P, Fradet-Turcotte A, Stewart G, Vaziri C. PCNA-binding activity separates RNF168 functions in DNA replication and DNA double-stranded break signaling. Nucleic Acids Res 2024; 52:13019-13035. [PMID: 39445802 PMCID: PMC11602139 DOI: 10.1093/nar/gkae918] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Revised: 09/15/2024] [Accepted: 10/07/2024] [Indexed: 10/25/2024] Open
Abstract
RNF168 orchestrates a ubiquitin-dependent DNA damage response to regulate the recruitment of repair factors, such as 53BP1 to DNA double-strand breaks (DSBs). In addition to its canonical functions in DSB signaling, RNF168 may facilitate DNA replication fork progression. However, the precise role of RNF168 in DNA replication remains unclear. Here, we demonstrate that RNF168 is recruited to DNA replication factories in a manner that is independent of the canonical DSB response pathway regulated by Ataxia-Telangiectasia Mutated (ATM) and RNF8. We identify a degenerate Proliferating Cell Nuclear Antigen (PCNA)-interacting peptide (DPIP) motif in the C-terminus of RNF168, which together with its Motif Interacting with Ubiquitin (MIU) domain mediates binding to mono-ubiquitylated PCNA at replication factories. An RNF168 mutant harboring inactivating substitutions in its DPIP box and MIU1 domain (termed RNF168 ΔDPIP/ΔMIU1) is not recruited to sites of DNA synthesis and fails to support ongoing DNA replication. Notably, the PCNA interaction-deficient RNF168 ΔDPIP/ΔMIU1 mutant fully rescues the ability of RNF168-/- cells to form 53BP1 foci in response to DNA DSBs. Therefore, RNF168 functions in DNA replication and DSB signaling are fully separable. Our results define a new mechanism by which RNF168 promotes DNA replication independently of its canonical functions in DSB signaling.
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Affiliation(s)
- Yang Yang
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, 160 Medical Drive, Chapel Hill, NC 27599, USA
| | - Deepika Jayaprakash
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, 160 Medical Drive, Chapel Hill, NC 27599, USA
- Oral and Craniofacial Biomedicine Program, Adam’s School of Dentistry, University of North Carolina at Chapel Hill, 385 S Columbia Street, Chapel Hill, NC 27599, USA
| | - Satpal S Jhujh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK
| | - John J Reynolds
- Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK
| | - Steve Chen
- Cytiva Life Sciences, Global Life Sciences Solutions USA LLC, 100 Results Way, Marlborough, MA 01752, USA
| | - Yanzhe Gao
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, 160 Medical Drive, Chapel Hill, NC 27599, USA
| | - Jay Ramanlal Anand
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, 160 Medical Drive, Chapel Hill, NC 27599, USA
| | - Elizabeth Mutter-Rottmayer
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, 160 Medical Drive, Chapel Hill, NC 27599, USA
| | - Pablo Ariel
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, 160 Medical Drive, Chapel Hill, NC 27599, USA
| | - Jing An
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, 160 Medical Drive, Chapel Hill, NC 27599, USA
- Institute of Cancer Prevention and Treatment, Harbin Medical University, 6 Bao Jian Street, Nan Gang District, Harbin 150081, China
| | - Xing Cheng
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, 160 Medical Drive, Chapel Hill, NC 27599, USA
- Department of Neuro-Oncology, Chongqing University Cancer Hospital and Chongqing Cancer Institute and Chongqing Cancer Hospital,181 Hanyu Road, Shapingba District, Chongqing 400044, China
| | - Kenneth H Pearce
- Center For Integrated Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Marsico Hall, 125 Mason Farm Road, CB# 7363, Chapel Hill, NC 27599, USA
| | - Sophie-Anne Blanchet
- CHU de Québec-Université Laval Research Center (Oncology division), Université Laval Cancer Research Center and Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medecine, Université Laval, 9 McMahon, Québec, Canada
| | - Nandana Nandakumar
- CHU de Québec-Université Laval Research Center (Oncology division), Université Laval Cancer Research Center and Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medecine, Université Laval, 9 McMahon, Québec, Canada
| | - Pei Zhou
- Department of Biochemistry, Duke University School of Medicine, 307 Research Drive, Durham, NC 27710, USA
| | - Amélie Fradet-Turcotte
- CHU de Québec-Université Laval Research Center (Oncology division), Université Laval Cancer Research Center and Department of Molecular Biology, Medical Biochemistry and Pathology, Faculty of Medecine, Université Laval, 9 McMahon, Québec, Canada
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Vincent Drive, Edgbaston, Birmingham B15 2TT, UK
| | - Cyrus Vaziri
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, 614 Brinkhous-Bullitt Building, 160 Medical Drive, Chapel Hill, NC 27599, USA
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39
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Gong X, Peng C, Zeng Z. NU7441, a selective inhibitor of DNA-PKcs, alleviates intracerebral hemorrhage injury with suppression of ferroptosis in brain. PeerJ 2024; 12:e18489. [PMID: 39583099 PMCID: PMC11583913 DOI: 10.7717/peerj.18489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2024] [Accepted: 10/17/2024] [Indexed: 11/26/2024] Open
Abstract
Neuronal apoptosis, oxidative stress, and ferroptosis play a crucial role in the progression of secondary brain injury following intracerebral hemorrhage (ICH). Although studies have highlighted the important functions of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) in various experimental models, its precise role and mechanism in ICH remain unclear. In this study, we investigated the effects of DNA-PKcs on N2A cells under a hemin-induced hemorrhagic state in vitro and a rat model of collagenase-induced ICH in vivo. The results revealed a notable increase in DNA-PKcs levels during the acute phase of ICH. As anticipated, DNA-PKcs and γ-H2AX had consistent upregulations after ICH. Administration of NU7441, a selective inhibitor of DNA-PKcs, alleviated neurological impairment, histological damage, and ipsilateral brain edema in vivo. Mechanistically, NU7441 attenuated neuronal apoptosis both in vivo and in vitro, alleviated oxidative stress by decreasing ROS levels, and suppressed ferroptosis by enhancing GPX4 activity. These results suggest that inhibition of DNA-PKcs is a promising therapeutic target for ICH.
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Affiliation(s)
- Xiyu Gong
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
- Department of Neurology, Second Hospital of Jilin University, Changchun, Jilin Province, China
| | - Cuiying Peng
- Department of Neurology, Hunan Provincial Rehabilitation Hospital, Hunan University of Medicine, Changsha, Hunan, China
| | - Zhou Zeng
- Department of Neurology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
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40
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Wang Z, Wang C, Zhai Y, Bai Y, Wang H, Rong X. Loss of Brcc3 in Zebrafish Embryos Increases Their Susceptibility to DNA Damage Stress. Int J Mol Sci 2024; 25:12108. [PMID: 39596176 PMCID: PMC11594080 DOI: 10.3390/ijms252212108] [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: 10/13/2024] [Revised: 11/02/2024] [Accepted: 11/06/2024] [Indexed: 11/28/2024] Open
Abstract
DNA double-strand breaks (DSBs) represent one of the most severe forms of genetic damage in organisms, yet vertebrate models capable of monitoring DSBs in real-time remain scarce. BRCA1/BRCA2-containing complex subunit 3 (BRCC3), also known as BRCC36, functions within various multiprotein complexes to mediate diverse biological processes. However, the physiological role of BRCC3 in vertebrates, as well as the underlying mechanisms that govern its activity, are not well understood. To explore these questions, we generated brcc3-knockout zebrafish using CRISPR/Cas9 gene-editing technology. While brcc3 mutant zebrafish appear phenotypically normal and remain fertile, they exhibit significantly increased rates of mortality and deformity following exposure to DNA damage. Furthermore, embryos lacking Brcc3 display heightened p53 signaling, elevated γ-H2AX levels, and increased apoptosis in response to DNA-damaging agents such as ultraviolet (UV) light and Etoposide (ETO). Notably, genetic inactivation of p53 or pharmacological inhibition of Ataxia-telangiectasia mutated (ATM) activity rescues the hypersensitivity to UV and ETO observed in Brcc3-deficient embryos. These findings suggest that Brcc3 plays a critical role in DNA damage response (DDR), promoting cell survival during embryogenesis. Additionally, brcc3-null mutant zebrafish offer a promising vertebrate model for real-time monitoring of DSBs.
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Affiliation(s)
- Zhengyang Wang
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Caixia Wang
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Yanpeng Zhai
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Yan Bai
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
| | - Hongying Wang
- Hubei Provincial Key Laboratory for Protection and Application of Special Plants in Wuling Area of China, Key Laboratory of State Ethnic Affairs Commission for Biological Technology, College of Life Sciences, South-Central Minzu University, Wuhan 430074, China
| | - Xiaozhi Rong
- Key Laboratory of Marine Drugs (Ocean University of China), Chinese Ministry of Education, and School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Laboratory for Marine Drugs and Bioproducts, Qingdao Marine Science and Technology Center, Qingdao 266237, China
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41
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Elfar G, Aning O, Ngai T, Yeo P, Chan J, Sim S, Goh L, Yuan J, Phua C, Yeo J, Mak S, Goh B, Chow PH, Tam W, Ho Y, Cheok C. p53-dependent crosstalk between DNA replication integrity and redox metabolism mediated through a NRF2-PARP1 axis. Nucleic Acids Res 2024; 52:12351-12377. [PMID: 39315696 PMCID: PMC11551750 DOI: 10.1093/nar/gkae811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 08/24/2024] [Accepted: 09/10/2024] [Indexed: 09/25/2024] Open
Abstract
Mechanisms underlying p53-mediated protection of the replicating genome remain elusive, despite the quintessential role of p53 in maintaining genomic stability. Here, we uncover an unexpected function of p53 in curbing replication stress by limiting PARP1 activity and preventing the unscheduled degradation of deprotected stalled forks. We searched for p53-dependent factors and elucidated RRM2B as a prime factor. Deficiency in p53/RRM2B results in the activation of an NRF2 antioxidant transcriptional program, with a concomitant elevation in basal PARylation in cells. Dissecting the consequences of p53/RRM2B loss revealed a crosstalk between redox metabolism and genome integrity that is negotiated through a hitherto undescribed NRF2-PARP1 axis, and pinpoint G6PD as a primary oxidative stress-induced NRF2 target and activator of basal PARylation. This study elucidates how loss of p53 could be destabilizing for the replicating genome and, importantly, describes an unanticipated crosstalk between redox metabolism, PARP1 and p53 tumor suppressor pathway that is broadly relevant in cancers and can be leveraged therapeutically.
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Affiliation(s)
- Gamal Ahmed Elfar
- NUS Department of Pathology, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Obed Aning
- NUS Department of Pathology, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Tsz Wai Ngai
- NUS Department of Pathology, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Pearlyn Yeo
- NUS Department of Pathology, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Joel Wai Kit Chan
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Shang Hong Sim
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Leonard Goh
- NUS Department of Pathology, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | - Ju Yuan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Cheryl Zi Jin Phua
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Joanna Zhen Zhen Yeo
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Shi Ya Mak
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Brian Kim Poh Goh
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital, Singapore and National Cancer Centre Singapore, Singapore
| | - Pierce Kah-Hoe Chow
- Department of Hepatopancreatobiliary and Transplant Surgery, Singapore General Hospital, Singapore and National Cancer Centre Singapore, Singapore
- Surgery Academic ClinicalProgramme, Duke-NUS Medical School, National University of Singapore, Singapore
| | - Wai Leong Tam
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, Singapore
| | - Ying Swan Ho
- Bioprocessing Technology Institute (BTI), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Chit Fang Cheok
- NUS Department of Pathology, National University of Singapore, Yong Loo Lin School of Medicine, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
- NUS Center for Cancer Research, Yong Loo Lin School of Medicine, National University Singapore, Singapore
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42
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Granger S, Sharma R, Kaushik V, Razzaghi M, Honda M, Gaur P, Bhat D, Labenz S, Heinen J, Williams B, Tabei SMA, Wlodarski M, Antony E, Spies M. Human hnRNPA1 reorganizes telomere-bound replication protein A. Nucleic Acids Res 2024; 52:12422-12437. [PMID: 39329264 PMCID: PMC11551749 DOI: 10.1093/nar/gkae834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 09/04/2024] [Accepted: 09/11/2024] [Indexed: 09/28/2024] Open
Abstract
Human replication protein A (RPA) is a heterotrimeric ssDNA binding protein responsible for many aspects of cellular DNA metabolism. Dynamic interactions of the four RPA DNA binding domains (DBDs) with DNA control replacement of RPA by downstream proteins in various cellular metabolic pathways. RPA plays several important functions at telomeres where it binds to and melts telomeric G-quadruplexes, non-canonical DNA structures formed at the G-rich telomeric ssDNA overhangs. Here, we combine single-molecule total internal reflection fluorescence microscopy (smTIRFM) and mass photometry (MP) with biophysical and biochemical analyses to demonstrate that heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) specifically remodels RPA bound to telomeric ssDNA by dampening the RPA configurational dynamics and forming a ternary complex. Uniquely, among hnRNPA1 target RNAs, telomeric repeat-containing RNA (TERRA) is selectively capable of releasing hnRNPA1 from the RPA-telomeric DNA complex. We speculate that this telomere specific RPA-DNA-hnRNPA1 complex is an important structure in telomere protection.
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Affiliation(s)
- Sophie L Granger
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, IA City, IA 52242, USA
| | - Richa Sharma
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, 1250 Carr Lane, St. Louis, MO 63104, USA
| | - Mortezaali Razzaghi
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, IA City, IA 52242, USA
| | - Masayoshi Honda
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, IA City, IA 52242, USA
| | - Paras Gaur
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, IA City, IA 52242, USA
| | - Divya S Bhat
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, IA City, IA 52242, USA
| | - Sabryn M Labenz
- Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA
| | - Jenna E Heinen
- Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA
| | - Blaine A Williams
- Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA
| | - S M Ali Tabei
- Department of Physics, University of Northern Iowa, Cedar Falls, IA 50614, USA
| | - Marcin W Wlodarski
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, St. Louis University School of Medicine, 1250 Carr Lane, St. Louis, MO 63104, USA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, University of Iowa Carver College of Medicine, 51 Newton Road, IA City, IA 52242, USA
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43
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Shih CT, Huang TT, Nair JR, Ibanez KR, Lee JM. Poly (ADP-Ribose) Polymerase Inhibitor Olaparib-Resistant BRCA1-Mutant Ovarian Cancer Cells Demonstrate Differential Sensitivity to PARP Inhibitor Rechallenge. Cells 2024; 13:1847. [PMID: 39594596 PMCID: PMC11592949 DOI: 10.3390/cells13221847] [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: 09/11/2024] [Revised: 10/31/2024] [Accepted: 11/04/2024] [Indexed: 11/28/2024] Open
Abstract
Poly (ADP-ribose) polymerase inhibitors (PARPis) show cytotoxicity in homologous recombination deficiency (HRD) seen in BRCA-mutant ovarian cancer (OvCa). Despite initial responses, resistance often develops. The reintroduction of different PARPis, such as niraparib or rucaparib, has shown some clinical activity in BRCA mutation-associated OvCa patients with prior olaparib treatment, yet the underlying mechanisms remain unclear. To investigate the differential sensitivity to different PARPis, we established an olaparib-resistant BRCA1-mutant OvCa cell line (UWB-OlaJR) by exposing UWB1.289 cells to gradually increasing concentrations of olaparib. UWB-OlaJR exhibited restored HR capability without BRCA1 reversion mutation or increased drug efflux. We examined cell viability, DNA damage, and DNA replication fork dynamics in UWB-OlaJR treated with various PARPis. UWB-OlaJR exhibits varying sensitivity to PARPis, showing cross-resistance to veliparib and talazoparib, and sensitivity with increased cytotoxicity to niraparib and rucaparib. Indeed, DNA fiber assay reveals that niraparib and rucaparib cause higher replication stress than the others. Moreover, S1 nuclease fiber assay shows that niraparib and rucaparib induce greater DNA single-strand gaps than other PARPis, leading to increased DNA damage and cell death. Our study provides novel insights into differential PARPi sensitivity in olaparib-resistant BRCA-mutant OvCa, which requires further investigation of inter-agent differences in large prospective studies.
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Affiliation(s)
- Chi-Ting Shih
- Women’s Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA; (T.-T.H.); (J.R.N.); (K.R.I.); (J.-M.L.)
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Meng J, Zhou W, Mao X, Lei P, An X, Xue H, Qi Y, Yu F, Liu X. PRL1 interacts with and stabilizes RPA2A to regulate carbon deprivation-induced senescence in Arabidopsis. THE NEW PHYTOLOGIST 2024; 244:855-869. [PMID: 39229867 DOI: 10.1111/nph.20082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Accepted: 08/11/2024] [Indexed: 09/05/2024]
Abstract
Leaf senescence is a developmental program regulated by both endogenous and environmental cues. Abiotic stresses such as nutrient deprivation can induce premature leaf senescence, which profoundly impacts plant growth and crop yield. However, the molecular mechanisms underlying stress-induced senescence are not fully understood. In this work, employing a carbon deprivation (C-deprivation)-induced senescence assay in Arabidopsis seedlings, we identified PLEIOTROPIC REGULATORY LOCUS 1 (PRL1), a component of the NineTeen Complex, as a negative regulator of C-deprivation-induced senescence. Furthermore, we demonstrated that PRL1 directly interacts with the RPA2A subunit of the single-stranded DNA-binding Replication Protein A (RPA) complex. Consistently, the loss of RPA2A leads to premature senescence, while increased expression of RPA2A inhibits senescence. Moreover, overexpression of RPA2A reverses the accelerated senescence in prl1 mutants, and the interaction with PRL1 stabilizes RPA2A under C-deprivation. In summary, our findings reveal the involvement of the PRL1-RPA2A functional module in C-deprivation-induced plant senescence.
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Affiliation(s)
- Jingjing Meng
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Wenhui Zhou
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xinhao Mao
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Pei Lei
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xue An
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Hui Xue
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Yafei Qi
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Fei Yu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
- Institute of Future Agriculture, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - Xiayan Liu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production and College of Life Sciences, Northwest A&F University, Yangling, Shaanxi, 712100, China
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45
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Federica G, Michela C, Giovanna D. Targeting the DNA damage response in cancer. MedComm (Beijing) 2024; 5:e788. [PMID: 39492835 PMCID: PMC11527828 DOI: 10.1002/mco2.788] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 09/26/2024] [Accepted: 09/26/2024] [Indexed: 11/05/2024] Open
Abstract
DNA damage response (DDR) pathway is the coordinated cellular network dealing with the identification, signaling, and repair of DNA damage. It tightly regulates cell cycle progression and promotes DNA repair to minimize DNA damage to daughter cells. Key proteins involved in DDR are frequently mutated/inactivated in human cancers and promote genomic instability, a recognized hallmark of cancer. Besides being an intrinsic property of tumors, DDR also represents a unique therapeutic opportunity. Indeed, inhibition of DDR is expected to delay repair, causing persistent unrepaired breaks, to interfere with cell cycle progression, and to sensitize cancer cells to several DNA-damaging agents, such as radiotherapy and chemotherapy. In addition, DDR defects in cancer cells have been shown to render these cells more dependent on the remaining pathways, which could be targeted very specifically (synthetic lethal approach). Research over the past two decades has led to the synthesis and testing of hundreds of small inhibitors against key DDR proteins, some of which have shown antitumor activity in human cancers. In parallel, the search for synthetic lethality interaction is broadening the use of DDR inhibitors. In this review, we discuss the state-of-art of ataxia-telangiectasia mutated, ataxia-telangiectasia-and-Rad3-related protein, checkpoint kinase 1, Wee1 and Polθ inhibitors, highlighting the results obtained in the ongoing clinical trials both in monotherapy and in combination with chemotherapy and radiotherapy.
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Affiliation(s)
- Guffanti Federica
- Laboratory of Preclinical Gynecological OncologyDepartment of Experimental OncologyIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | - Chiappa Michela
- Laboratory of Preclinical Gynecological OncologyDepartment of Experimental OncologyIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
| | - Damia Giovanna
- Laboratory of Preclinical Gynecological OncologyDepartment of Experimental OncologyIstituto di Ricerche Farmacologiche Mario Negri IRCCSMilanItaly
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Kendek A, Sandron A, Lambooij JP, Colmenares S, Pociunaite S, Gooijers I, de Groot L, Karpen G, Janssen A. DNA double-strand break movement in heterochromatin depends on the histone acetyltransferase dGcn5. Nucleic Acids Res 2024; 52:11753-11767. [PMID: 39258543 PMCID: PMC11514474 DOI: 10.1093/nar/gkae775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 08/20/2024] [Accepted: 08/26/2024] [Indexed: 09/12/2024] Open
Abstract
Cells employ diverse strategies to repair double-strand breaks (DSBs), a dangerous form of DNA damage that threatens genome integrity. Eukaryotic nuclei consist of different chromatin environments, each displaying distinct molecular and biophysical properties that can significantly influence the DSB-repair process. DSBs arising in the compact and silenced heterochromatin domains have been found to move to the heterochromatin periphery in mouse and Drosophila to prevent aberrant recombination events. However, it is poorly understood how chromatin components, such as histone post-translational modifications, contribute to these DSB movements within heterochromatin. Using irradiation as well as locus-specific DSB induction in Drosophila tissues and cultured cells, we find enrichment of histone H3 lysine 9 acetylation (H3K9ac) at DSBs in heterochromatin but not euchromatin. We find this increase is mediated by the histone acetyltransferase dGcn5, which rapidly localizes to heterochromatic DSBs. Moreover, we demonstrate that in the absence of dGcn5, heterochromatic DSBs display impaired recruitment of the SUMO E3 ligase Nse2/Qjt and fail to relocate to the heterochromatin periphery to complete repair. In summary, our results reveal a previously unidentified role for dGcn5 and H3K9ac in heterochromatic DSB repair and underscore the importance of differential chromatin responses at heterochromatic and euchromatic DSBs to promote safe repair.
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Affiliation(s)
- Apfrida Kendek
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Arianna Sandron
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Jan-Paul Lambooij
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Serafin U Colmenares
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720,Berkeley, California, USA
| | - Severina M Pociunaite
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Iris Gooijers
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Lars de Groot
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
| | - Gary H Karpen
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720,Berkeley, California, USA
- Division of Biological Sciences and the Environment, Lawrence Berkeley National Laboratory, CA 94720, Berkeley, California, USA
| | - Aniek Janssen
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, the Netherlands
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Chadda R, Kaushik V, Ahmad IM, Deveryshetty J, Holehouse A, Sigurdsson S, Biswas G, Levy Y, Bothner B, Cooley R, Mehl R, Dastvan R, Origanti S, Antony E. Partial wrapping of single-stranded DNA by replication protein A and modulation through phosphorylation. Nucleic Acids Res 2024; 52:11626-11640. [PMID: 38989614 PMCID: PMC11514480 DOI: 10.1093/nar/gkae584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/30/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024] Open
Abstract
Single-stranded DNA (ssDNA) intermediates which emerge during DNA metabolic processes are shielded by replication protein A (RPA). RPA binds to ssDNA and acts as a gatekeeper to direct the ssDNA towards downstream DNA metabolic pathways with exceptional specificity. Understanding the mechanistic basis for such RPA-dependent functional specificity requires knowledge of the structural conformation of ssDNA when RPA-bound. Previous studies suggested a stretching of ssDNA by RPA. However, structural investigations uncovered a partial wrapping of ssDNA around RPA. Therefore, to reconcile the models, in this study, we measured the end-to-end distances of free ssDNA and RPA-ssDNA complexes using single-molecule FRET and double electron-electron resonance (DEER) spectroscopy and found only a small systematic increase in the end-to-end distance of ssDNA upon RPA binding. This change does not align with a linear stretching model but rather supports partial wrapping of ssDNA around the contour of DNA binding domains of RPA. Furthermore, we reveal how phosphorylation at the key Ser-384 site in the RPA70 subunit provides access to the wrapped ssDNA by remodeling the DNA-binding domains. These findings establish a precise structural model for RPA-bound ssDNA, providing valuable insights into how RPA facilitates the remodeling of ssDNA for subsequent downstream processes.
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Affiliation(s)
- Rahul Chadda
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Vikas Kaushik
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Iram Munir Ahmad
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Jaigeeth Deveryshetty
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in Saint Louis School of Medicine, St. Louis, MO 63110, USA
| | - Snorri Th Sigurdsson
- Department of Chemistry, Science Institute, University of Iceland, 107 Reykjavik, Iceland
| | - Gargi Biswas
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Brian Bothner
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Reza Dastvan
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Sofia Origanti
- Department of Biology, Saint Louis University, St. Louis, MO 63103, USA
| | - Edwin Antony
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
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Sun H, Luo M, Zhou M, Zheng L, Li H, Esworthy RS, Shen B. Structure-specific nucleases in genome dynamics and strategies for targeting cancers. J Mol Cell Biol 2024; 16:mjae019. [PMID: 38714348 PMCID: PMC11574390 DOI: 10.1093/jmcb/mjae019] [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: 12/02/2023] [Revised: 04/21/2024] [Accepted: 05/06/2024] [Indexed: 05/09/2024] Open
Abstract
Nucleases are a super family of enzymes that hydrolyze phosphodiester bonds present in genomes. They widely vary in substrates, causing differentiation in cleavage patterns and having a diversified role in maintaining genetic material. Through cellular evolution of prokaryotic to eukaryotic, nucleases become structure-specific in recognizing its own or foreign genomic DNA/RNA configurations as its substrates, including flaps, bubbles, and Holliday junctions. These special structural configurations are commonly found as intermediates in processes like DNA replication, repair, and recombination. The structure-specific nature and diversified functions make them essential to maintaining genome integrity and evolution in normal and cancer cells. In this article, we review their roles in various pathways, including Okazaki fragment maturation during DNA replication, end resection in homology-directed recombination repair of DNA double-strand breaks, DNA excision repair and apoptosis DNA fragmentation in response to exogenous DNA damage, and HIV life cycle. As the nucleases serve as key points for the DNA dynamics, cellular apoptosis, and cancer cell survival pathways, we discuss the efforts in the field in developing the therapeutic regimens, taking advantage of recently available knowledge of their diversified structures and functions.
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Affiliation(s)
- Haitao Sun
- Medicinal Plant Resources and Protection Research Center, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Megan Luo
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Hongzhi Li
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - R Steven Esworthy
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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49
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Joo YK, Ramirez C, Kabeche L. A TRilogy of ATR's Non-Canonical Roles Throughout the Cell Cycle and Its Relation to Cancer. Cancers (Basel) 2024; 16:3536. [PMID: 39456630 PMCID: PMC11506335 DOI: 10.3390/cancers16203536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 10/12/2024] [Accepted: 10/17/2024] [Indexed: 10/28/2024] Open
Abstract
Ataxia Telangiectasia and Rad3-related protein (ATR) is an apical kinase of the DNA Damage Response (DDR) pathway responsible for detecting and resolving damaged DNA. Because cancer cells depend heavily on the DNA damage checkpoint for their unchecked proliferation and propagation, ATR has gained enormous popularity as a cancer therapy target in recent decades. Yet, ATR inhibitors have not been the silver bullets as anticipated, with clinical trials demonstrating toxicity and mixed efficacy. To investigate whether the toxicity and mixed efficacy of ATR inhibitors arise from their off-target effects related to ATR's multiple roles within and outside the DDR pathway, we have analyzed recently published studies on ATR's non-canonical roles. Recent studies have elucidated that ATR plays a wide role throughout the cell cycle that is separate from its function in the DDR. This includes maintaining nuclear membrane integrity, detecting mechanical forces, and promoting faithful chromosome segregation during mitosis. In this review, we summarize the canonical, DDR-related roles of ATR and also focus on the non-canonical, multifaceted roles of ATR throughout the cell cycle and their clinical relevance. Through this summary, we also address the need for re-assessing clinical strategies targeting ATR as a cancer therapy based on these newly discovered roles for ATR.
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Affiliation(s)
- Yoon Ki Joo
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Carlos Ramirez
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
| | - Lilian Kabeche
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511, USA
- Yale Cancer Biology Institute, Yale University, West Haven, CT 06516, USA
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50
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Wensveen MR, Dixit AA, van Schendel R, Kendek A, Lambooij JP, Tijsterman M, Colmenares SU, Janssen A. Double-strand breaks in facultative heterochromatin require specific movements and chromatin changes for efficient repair. Nat Commun 2024; 15:8984. [PMID: 39419979 PMCID: PMC11487122 DOI: 10.1038/s41467-024-53313-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 10/08/2024] [Indexed: 10/19/2024] Open
Abstract
DNA double-strand breaks (DSBs) must be properly repaired within diverse chromatin domains to maintain genome stability. Whereas euchromatin has an open structure and is associated with transcription, facultative heterochromatin is essential to silence developmental genes and forms compact nuclear condensates, called polycomb bodies. Whether the specific chromatin properties of facultative heterochromatin require distinct DSB repair mechanisms remains unknown. Here, we integrate single DSB systems in euchromatin and facultative heterochromatin in Drosophila melanogaster and find that heterochromatic DSBs rapidly move outside polycomb bodies. These DSB movements coincide with a break-proximal reduction in the canonical heterochromatin mark histone H3 Lysine 27 trimethylation (H3K27me3). We demonstrate that DSB movement and loss of H3K27me3 at heterochromatic DSBs depend on the histone demethylase dUtx. Moreover, loss of dUtx specifically disrupts completion of homologous recombination at heterochromatic DSBs. We conclude that DSBs in facultative heterochromatin require dUtx-mediated loss of H3K27me3 to promote DSB movement and repair.
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Affiliation(s)
- Marieke R Wensveen
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, the Netherlands
| | - Aditya A Dixit
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, the Netherlands
| | - Robin van Schendel
- Human Genetics Department, Leiden University Medical Center, Leiden, the Netherlands
| | - Apfrida Kendek
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, the Netherlands
| | - Jan-Paul Lambooij
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, the Netherlands
| | - Marcel Tijsterman
- Human Genetics Department, Leiden University Medical Center, Leiden, the Netherlands
| | - Serafin U Colmenares
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, USA
| | - Aniek Janssen
- Center for Molecular Medicine, University Medical Center Utrecht, Universiteitsweg 100, Utrecht, the Netherlands.
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