1
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Wu CK, Shiu JL, Wu CL, Hung CF, Ho YC, Chen YT, Tung SY, Yeh CF, Shen CH, Liaw H, Su WP. APLF facilitates interstrand DNA crosslink repair and replication fork protection to confer cisplatin resistance. Nucleic Acids Res 2024; 52:5676-5697. [PMID: 38520407 PMCID: PMC11162786 DOI: 10.1093/nar/gkae211] [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: 08/06/2023] [Revised: 03/04/2024] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Replication stress converts the stalled forks into reversed forks, which is an important protection mechanism to prevent fork degradation and collapse into poisonous DNA double-strand breaks (DSBs). Paradoxically, the mechanism also acts in cancer cells to contribute to chemoresistance against various DNA-damaging agents. PARP1 binds to and is activated by stalled forks to facilitate fork reversal. Aprataxin and polynucleotide kinase/phosphatase-like factor (APLF) binds to PARP1 through the poly(ADP-ribose) zinc finger (PBZ) domain and is known to be involved in non-homologous end joining (NHEJ). Here, we identify a novel function of APLF involved in interstrand DNA crosslink (ICL) repair and fork protection. We demonstrate that PARP1 activity facilitates the APLF recruitment to stalled forks, enabling the FANCD2 recruitment to stalled forks. The depletion of APLF sensitizes cells to cisplatin, impairs ICL repair, reduces the FANCD2 recruitment to stalled forks, and results in nascent DNA degradation by MRE11 nucleases. Additionally, cisplatin-resistant cancer cells show high levels of APLF and homologous recombination-related gene expression. The depletion of APLF sensitizes cells to cisplatin and results in fork instability. Our results reveal the novel function of APLF to facilitate ICL repair and fork protection, thereby contributing to cisplatin-resistant phenotypes of cancer cells.
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Affiliation(s)
- Cheng-Kuei Wu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
| | - Jia-Lin Shiu
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City701, Taiwan
| | - Chao-Liang Wu
- Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Chi-Feng Hung
- Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi City, Taiwan
| | - Yen-Chih Ho
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City701, Taiwan
| | - Yen-Tzu Chen
- Department of Public Health & Institute of Environmental and Occupational Health Sciences, College of Public Health, National Taiwan University, Taiwan
| | - Sheng-Yung Tung
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
- Department of Urology, An Nan Hospital, China Medical University, Tainan, Taiwan
| | - Cheng-Fa Yeh
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
- Department of Internal Medicine, Chi Mei Medical Center, Tainan, Taiwan
| | - Che-Hung Shen
- National Institute of Cancer Research, National Health Research Institutes, Tainan 704, Taiwan
| | - Hungjiun Liaw
- Department of Life Sciences, National Cheng Kung University, No. 1 University Road, Tainan City701, Taiwan
| | - Wen-Pin Su
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, No. 35, Xiao-Tong Road, Tainan 704, Taiwan
- Departments of Oncology and Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Clinical Medicine Research Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 704, Taiwan
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan 701, Taiwan
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2
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Rivard RS, Chang YC, Ragland RL, Thu YM, Kassab M, Mandal RS, Van Riper SK, Kulej K, Higgins L, Markowski TM, Shang D, Hedberg J, Erber L, Garcia B, Chen Y, Bielinsky AK, Brown EJ. Improved detection of DNA replication fork-associated proteins. Cell Rep 2024; 43:114178. [PMID: 38703364 DOI: 10.1016/j.celrep.2024.114178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 03/06/2024] [Accepted: 04/16/2024] [Indexed: 05/06/2024] Open
Abstract
Innovative methods to retrieve proteins associated with actively replicating DNA have provided a glimpse into the molecular dynamics of replication fork stalling. We report that a combination of density-based replisome enrichment by isolating proteins on nascent DNA (iPOND2) and label-free quantitative mass spectrometry (iPOND2-DRIPPER) substantially increases both replication factor yields and the dynamic range of protein quantification. Replication protein abundance in retrieved nascent DNA is elevated up to 300-fold over post-replicative controls, and recruitment of replication stress factors upon fork stalling is observed at similar levels. The increased sensitivity of iPOND2-DRIPPER permits direct measurement of ubiquitination events without intervening retrieval of diglycine tryptic fragments of ubiquitin. Using this approach, we find that stalled replisomes stimulate the recruitment of a diverse cohort of DNA repair factors, including those associated with poly-K63-ubiquitination. Finally, we uncover the temporally controlled association of stalled replisomes with nuclear pore complex components and nuclear cytoskeleton networks.
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Affiliation(s)
- Rebecca S Rivard
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ya-Chu Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Ryan L Ragland
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yee-Mon Thu
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Muzaffer Kassab
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Rahul Shubhra Mandal
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Susan K Van Riper
- University of Minnesota Informatics Institute, University of Minnesota, Minneapolis, MN, USA
| | - Katarzyna Kulej
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - LeeAnn Higgins
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Todd M Markowski
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - David Shang
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Jack Hedberg
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Luke Erber
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Benjamin Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yue Chen
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Anja-Katrin Bielinsky
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA.
| | - Eric J Brown
- Department of Cancer Biology and the Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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3
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Zhang H, Zha S. The dynamics and regulation of PARP1 and PARP2 in response to DNA damage and during replication. DNA Repair (Amst) 2024; 140:103690. [PMID: 38823186 DOI: 10.1016/j.dnarep.2024.103690] [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: 01/04/2024] [Revised: 03/14/2024] [Accepted: 04/29/2024] [Indexed: 06/03/2024]
Abstract
DNA strand breaks activate Poly(ADP-ribose) polymerase (PARP) 1 and 2, which use NAD+ as the substrate to covalently conjugate ADP-ribose on themselves and other proteins (e.g., Histone) to promote chromatin relaxation and recruit additional DNA repair factors. Enzymatic inhibitors of PARP1 and PARP2 (PARPi) are promising cancer therapy agents that selectively target BRCA1- or BRCA2- deficient cancers. As immediate early responders to DNA strand breaks with robust activities, PARP1 and PARP2 normally form transient foci (<10 minutes) at the micro-irradiation-induced DNA lesions. In addition to enzymatic inhibition, PARPi also extend the presence of PARP1 and PARP2 at DNA lesions, including at replication forks, where they may post a physical block for subsequent repair and DNA replication. The dynamic nature of PARP1 and PARP2 foci made live cell imaging a unique platform to detect subtle changes and the functional interaction among PARP1, PARP2, and their regulators. Recent imaging studies have provided new understandings of the biological consequence of PARP inhibition and uncovered functional interactions between PARP1 and PARP2 and new regulators (e.g., histone poly(ADP-ribosylation) factor). Here, we review recent advances in dissecting the temporal and spatial Regulation of PARP1 and PARP2 at DNA lesions and discuss their physiological implications on both cancer and normal cells.
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Affiliation(s)
- Hanwen Zhang
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA
| | - Shan Zha
- Institute for Cancer Genetics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA; Department of Pathology and Cell Biology, Herbert Irvine Comprehensive Cancer Center, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA; Division of Hematology, Oncology and Stem Cell Transplantation, Department of Pediatrics, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA; Department of Immunology and Microbiology, Vagelos College for Physicians and Surgeons, Columbia University, New York City, NY 10032, USA.
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4
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Jurkovic CM, Raisch J, Tran S, Nguyen HD, Lévesque D, Scott MS, Campos EI, Boisvert FM. Replisome Proximal Protein Associations and Dynamic Proteomic Changes at Stalled Replication Forks. Mol Cell Proteomics 2024; 23:100767. [PMID: 38615877 PMCID: PMC11101681 DOI: 10.1016/j.mcpro.2024.100767] [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: 08/16/2023] [Revised: 03/19/2024] [Accepted: 04/11/2024] [Indexed: 04/16/2024] Open
Abstract
DNA replication is a fundamental cellular process that ensures the transfer of genetic information during cell division. Genome duplication takes place in S phase and requires a dynamic and highly coordinated recruitment of multiple proteins at replication forks. Various genotoxic stressors lead to fork instability and collapse, hence the need for DNA repair pathways. By identifying the multitude of protein interactions implicated in those events, we can better grasp the complex and dynamic molecular mechanisms that facilitate DNA replication and repair. Proximity-dependent biotin identification was used to identify associations with 17 proteins within four core replication components, namely the CDC45/MCM2-7/GINS helicase that unwinds DNA, the DNA polymerases, replication protein A subunits, and histone chaperones needed to disassemble and reassemble chromatin. We further investigated the impact of genotoxic stress on these interactions. This analysis revealed a vast proximity association network with 108 nuclear proteins further modulated in the presence of hydroxyurea; 45 being enriched and 63 depleted. Interestingly, hydroxyurea treatment also caused a redistribution of associations with 11 interactors, meaning that the replisome is dynamically reorganized when stressed. The analysis identified several poorly characterized proteins, thereby uncovering new putative players in the cellular response to DNA replication arrest. It also provides a new comprehensive proteomic framework to understand how cells respond to obstacles during DNA replication.
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Affiliation(s)
- Carla-Marie Jurkovic
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jennifer Raisch
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Stephanie Tran
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Hoang Dong Nguyen
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Dominique Lévesque
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Michelle S Scott
- Faculty of Medicine and Health Sciences, Department of Biochemistry and Functional Genomics, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Eric I Campos
- Genetics & Genome Biology Program, Department of Molecular Biology, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.
| | - François-Michel Boisvert
- Faculty of Medicine and Health Sciences, Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada.
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5
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Tian T, Chen J, Zhao H, Li Y, Xia F, Huang J, Han J, Liu T. UFL1 triggers replication fork degradation by MRE11 in BRCA1/2-deficient cells. Nat Chem Biol 2024:10.1038/s41589-024-01611-7. [PMID: 38649452 DOI: 10.1038/s41589-024-01611-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 03/26/2024] [Indexed: 04/25/2024]
Abstract
The stabilization of stalled forks has emerged as a crucial mechanism driving resistance to poly(ADP-ribose) polymerase (PARP) inhibitors in BRCA1/2-deficient tumors. Here, we identify UFL1, a UFM1-specific E3 ligase, as a pivotal regulator of fork stability and the response to PARP inhibitors in BRCA1/2-deficient cells. On replication stress, UFL1 localizes to stalled forks and catalyzes the UFMylation of PTIP, a component of the MLL3/4 methyltransferase complex, specifically at lysine 148. This modification facilitates the assembly of the PTIP-MLL3/4 complex, resulting in the enrichment of H3K4me1 and H3K4me3 at stalled forks and subsequent recruitment of the MRE11 nuclease. Consequently, loss of UFL1, disruption of PTIP UFMylation or overexpression of the UFM1 protease UFSP2 protects nascent DNA strands from extensive degradation and confers resistance to PARP inhibitors in BRCA1/2-deficient cells. These findings provide mechanistic insights into the processes underlying fork instability in BRCA1/2-deficient cells and offer potential therapeutic avenues for the treatment of BRCA1/2-deficient tumors.
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Affiliation(s)
- Tian Tian
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Junliang Chen
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
| | - Huacun Zhao
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yulin Li
- The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Feiyu Xia
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Huang
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis and Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, Shaoxing, China
- Cancer Center, Zhejiang University, Hangzhou, China
| | - Jinhua Han
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Ting Liu
- Zhejiang Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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6
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Nie L, Wang C, Huang M, Liu X, Feng X, Tang M, Li S, Hang Q, Teng H, Shen X, Ma L, Gan B, Chen J. DePARylation is critical for S phase progression and cell survival. eLife 2024; 12:RP89303. [PMID: 38578205 PMCID: PMC10997334 DOI: 10.7554/elife.89303] [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: 04/06/2024] Open
Abstract
Poly(ADP-ribose)ylation or PARylation by PAR polymerase 1 (PARP1) and dePARylation by poly(ADP-ribose) glycohydrolase (PARG) are equally important for the dynamic regulation of DNA damage response. PARG, the most active dePARylation enzyme, is recruited to sites of DNA damage via pADPr-dependent and PCNA-dependent mechanisms. Targeting dePARylation is considered an alternative strategy to overcome PARP inhibitor resistance. However, precisely how dePARylation functions in normal unperturbed cells remains elusive. To address this challenge, we conducted multiple CRISPR screens and revealed that dePARylation of S phase pADPr by PARG is essential for cell viability. Loss of dePARylation activity initially induced S-phase-specific pADPr signaling, which resulted from unligated Okazaki fragments and eventually led to uncontrolled pADPr accumulation and PARP1/2-dependent cytotoxicity. Moreover, we demonstrated that proteins involved in Okazaki fragment ligation and/or base excision repair regulate pADPr signaling and cell death induced by PARG inhibition. In addition, we determined that PARG expression is critical for cellular sensitivity to PARG inhibition. Additionally, we revealed that PARG is essential for cell survival by suppressing pADPr. Collectively, our data not only identify an essential role for PARG in normal proliferating cells but also provide a potential biomarker for the further development of PARG inhibitors in cancer therapy.
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Affiliation(s)
- Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Min Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Xiaoguang Liu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Qinglei Hang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Hongqi Teng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Xi Shen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Boyi Gan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer CenterHoustonUnited States
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7
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Jurkovic CM, Boisvert FM. Evolution of techniques and tools for replication fork proteome and protein interaction studies. Biochem Cell Biol 2024; 102:135-144. [PMID: 38113480 DOI: 10.1139/bcb-2023-0215] [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] [Indexed: 12/21/2023] Open
Abstract
Understanding the complex network of protein-protein interactions (PPI) that govern cellular functions is essential for unraveling the molecular basis of biological processes and diseases. Mass spectrometry (MS) has emerged as a powerful tool for studying protein dynamics, enabling comprehensive analysis of protein function, structure, post-translational modifications, interactions, and localization. This article provides an overview of MS techniques and their applications in proteomics studies, with a focus on the replication fork proteome. The replication fork is a multi-protein assembly involved in DNA replication, and its proper functioning is crucial for maintaining genomic integrity. By combining quantitative MS labeling techniques with various data acquisition methods, researchers have made significant strides in elucidating the complex processes and molecular mechanisms at the replication fork. Overall, MS has revolutionized our understanding of protein dynamics, offering valuable insights into cellular processes and potential targets for therapeutic interventions.
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Affiliation(s)
- Carla-Marie Jurkovic
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
| | - François-Michel Boisvert
- Department of Immunology and Cell Biology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, QC, Canada
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8
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Chen S, Pan C, Huang J, Liu T. ATR limits Rad18-mediated PCNA monoubiquitination to preserve replication fork and telomerase-independent telomere stability. EMBO J 2024; 43:1301-1324. [PMID: 38467834 PMCID: PMC10987609 DOI: 10.1038/s44318-024-00066-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 02/15/2024] [Accepted: 02/26/2024] [Indexed: 03/13/2024] Open
Abstract
Upon replication fork stalling, the RPA-coated single-stranded DNA (ssDNA) formed behind the fork activates the ataxia telangiectasia-mutated and Rad3-related (ATR) kinase, concomitantly initiating Rad18-dependent monoubiquitination of PCNA. However, whether crosstalk exists between these two events and the underlying physiological implications of this interplay remain elusive. In this study, we demonstrate that during replication stress, ATR phosphorylates human Rad18 at Ser403, an adjacent residue to a previously unidentified PIP motif (PCNA-interacting peptide) within Rad18. This phosphorylation event disrupts the interaction between Rad18 and PCNA, thereby restricting the extent of Rad18-mediated PCNA monoubiquitination. Consequently, excessive accumulation of the tumor suppressor protein SLX4, now characterized as a novel reader of ubiquitinated PCNA, at stalled forks is prevented, contributing to the prevention of stalled fork collapse. We further establish that ATR preserves telomere stability in alternative lengthening of telomere (ALT) cells by restricting Rad18-mediated PCNA monoubiquitination and excessive SLX4 accumulation at telomeres. These findings shed light on the complex interplay between ATR activation, Rad18-dependent PCNA monoubiquitination, and SLX4-associated stalled fork processing, emphasizing the critical role of ATR in preserving replication fork stability and facilitating telomerase-independent telomere maintenance.
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Affiliation(s)
- Siyuan Chen
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Chen Pan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China.
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, China.
| | - Ting Liu
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- Department of Cell Biology, and Department of General Surgery of Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
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9
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Rageul J, Lo N, Phi AL, Patel JA, Park JJ, Kim H. Poly(ADP-ribosyl)ation of TIMELESS limits DNA replication stress and promotes stalled fork protection. Cell Rep 2024; 43:113845. [PMID: 38393943 PMCID: PMC11029348 DOI: 10.1016/j.celrep.2024.113845] [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: 10/04/2023] [Revised: 01/16/2024] [Accepted: 02/06/2024] [Indexed: 02/25/2024] Open
Abstract
Poly(ADP-ribosyl)ation (PARylation), catalyzed mainly by poly(ADP-ribose) polymerase (PARP)1, is a key posttranslational modification involved in DNA replication and repair. Here, we report that TIMELESS (TIM), an essential scaffold of the replisome, is PARylated, which is linked to its proteolysis. TIM PARylation requires recognition of auto-modified PARP1 via two poly(ADP-ribose)-binding motifs, which primes TIM for proteasome-dependent degradation. Cells expressing the PARylation-refractory TIM mutant or under PARP inhibition accumulate TIM at DNA replication forks, causing replication stress and hyper-resection of stalled forks. Mechanistically, aberrant engagement of TIM with the replicative helicase impedes RAD51 loading and protection of reversed forks. Accordingly, defective TIM degradation hypersensitizes BRCA2-deficient cells to replication damage. Our study defines TIM as a substrate of PARP1 and elucidates how the control of replisome remodeling by PARylation is linked to stalled fork protection. Therefore, we propose a mechanism of PARP inhibition that impinges on the DNA replication fork instability caused by defective TIM turnover.
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Affiliation(s)
- Julie Rageul
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA.
| | - Natalie Lo
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Amy L Phi
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Jennifer J Park
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA; Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA.
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10
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Ubhi T, Zaslaver O, Quaile AT, Plenker D, Cao P, Pham NA, Békési A, Jang GH, O'Kane GM, Notta F, Moffat J, Wilson JM, Gallinger S, Vértessy BG, Tuveson DA, Röst HL, Brown GW. Cytidine deaminases APOBEC3C and APOBEC3D promote DNA replication stress resistance in pancreatic cancer cells. NATURE CANCER 2024:10.1038/s43018-024-00742-z. [PMID: 38448522 DOI: 10.1038/s43018-024-00742-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 02/09/2024] [Indexed: 03/08/2024]
Abstract
Gemcitabine is a potent inhibitor of DNA replication and is a mainstay therapeutic for diverse cancers, particularly pancreatic ductal adenocarcinoma (PDAC). However, most tumors remain refractory to gemcitabine therapies. Here, to define the cancer cell response to gemcitabine, we performed genome-scale CRISPR-Cas9 chemical-genetic screens in PDAC cells and found selective loss of cell fitness upon disruption of the cytidine deaminases APOBEC3C and APOBEC3D. Following gemcitabine treatment, APOBEC3C and APOBEC3D promote DNA replication stress resistance and cell survival by deaminating cytidines in the nuclear genome to ensure DNA replication fork restart and repair in PDAC cells. We provide evidence that the chemical-genetic interaction between APOBEC3C or APOBEC3D and gemcitabine is absent in nontransformed cells but is recapitulated across different PDAC cell lines, in PDAC organoids and in PDAC xenografts. Thus, we uncover roles for APOBEC3C and APOBEC3D in DNA replication stress resistance and offer plausible targets for improving gemcitabine-based therapies for PDAC.
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Affiliation(s)
- Tajinder Ubhi
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Olga Zaslaver
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Andrew T Quaile
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
| | - Dennis Plenker
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
- Xilis Inc., Durham, NC, USA
| | - Pinjiang Cao
- Living Biobank, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Nhu-An Pham
- Living Biobank, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Angéla Békési
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Budapest, Hungary
- Genome Metabolism Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, Budapest, Hungary
| | - Gun-Ho Jang
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Grainne M O'Kane
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Faiyaz Notta
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Division of Research, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Jason Moffat
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Julie M Wilson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Steven Gallinger
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Wallace McCain Centre for Pancreatic Cancer, Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Lunenfeld Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Ontario, Canada
- Hepatobiliary/Pancreatic Surgical Oncology Program, University Health Network, Toronto, Ontario, Canada
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Science, Faculty of Chemical Technology and Biotechnology, BME Budapest University of Technology and Economics, Budapest, Hungary
- Genome Metabolism Research Group, Institute of Molecular Life Sciences, Research Centre for Natural Sciences, Hungarian Research Network, Budapest, Hungary
| | - David A Tuveson
- Lustgarten Foundation Pancreatic Cancer Research Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Hannes L Röst
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Grant W Brown
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, Canada.
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11
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Conti BA, Ruiz PD, Broton C, Blobel NJ, Kottemann MC, Sridhar S, Lach FP, Wiley TF, Sasi NK, Carroll T, Smogorzewska A. RTF2 controls replication repriming and ribonucleotide excision at the replisome. Nat Commun 2024; 15:1943. [PMID: 38431617 PMCID: PMC10908796 DOI: 10.1038/s41467-024-45947-z] [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: 11/09/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024] Open
Abstract
DNA replication through a challenging genomic landscape is coordinated by the replisome, which must adjust to local conditions to provide appropriate replication speed and respond to lesions that hinder its progression. We have previously shown that proteasome shuttle proteins, DNA Damage Inducible 1 and 2 (DDI1/2), regulate Replication Termination Factor 2 (RTF2) levels at stalled replisomes, allowing fork stabilization and restart. Here, we show that during unperturbed replication, RTF2 regulates replisome localization of RNase H2, a heterotrimeric enzyme that removes RNA from RNA-DNA heteroduplexes. RTF2, like RNase H2, is essential for mammalian development and maintains normal replication speed. However, persistent RTF2 and RNase H2 at stalled replication forks prevent efficient replication restart, which is dependent on PRIM1, the primase component of DNA polymerase α-primase. Our data show a fundamental need for RTF2-dependent regulation of replication-coupled ribonucleotide removal and reveal the existence of PRIM1-mediated direct replication restart in mammalian cells.
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Affiliation(s)
- Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Penelope D Ruiz
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Cayla Broton
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nicolas J Blobel
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Molly C Kottemann
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Francis P Lach
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Tom F Wiley
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA
| | - Nanda K Sasi
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, 10065, USA
| | - Thomas Carroll
- Bioinformatics, The Rockefeller University, New York, NY, 10065, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, NY, 10065, USA.
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12
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Yates M, Marois I, St-Hilaire E, Ronato DA, Djerir B, Brochu C, Morin T, Hammond-Martel I, Gezzar-Dandashi S, Casimir L, Drobetsky E, Cappadocia L, Masson JY, Wurtele H, Maréchal A. SMARCAL1 ubiquitylation controls its association with RPA-coated ssDNA and promotes replication fork stability. PLoS Biol 2024; 22:e3002552. [PMID: 38502677 PMCID: PMC10950228 DOI: 10.1371/journal.pbio.3002552] [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: 04/26/2023] [Accepted: 02/19/2024] [Indexed: 03/21/2024] Open
Abstract
Impediments in replication fork progression cause genomic instability, mutagenesis, and severe pathologies. At stalled forks, RPA-coated single-stranded DNA (ssDNA) activates the ATR kinase and directs fork remodeling, 2 key early events of the replication stress response. RFWD3, a recently described Fanconi anemia (FA) ubiquitin ligase, associates with RPA and promotes its ubiquitylation, facilitating late steps of homologous recombination (HR). Intriguingly, RFWD3 also regulates fork progression, restart and stability via poorly understood mechanisms. Here, we used proteomics to identify putative RFWD3 substrates during replication stress in human cells. We show that RFWD3 interacts with and ubiquitylates the SMARCAL1 DNA translocase directly in vitro and following DNA damage in vivo. SMARCAL1 ubiquitylation does not trigger its subsequent proteasomal degradation but instead disengages it from RPA thereby regulating its function at replication forks. Proper regulation of SMARCAL1 by RFWD3 at stalled forks protects them from excessive MUS81-mediated cleavage in response to UV irradiation, thereby limiting DNA replication stress. Collectively, our results identify RFWD3-mediated SMARCAL1 ubiquitylation as a novel mechanism that modulates fork remodeling to avoid genome instability triggered by aberrant fork processing.
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Affiliation(s)
- Maïlyn Yates
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Isabelle Marois
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Edlie St-Hilaire
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
| | - Daryl A. Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Billel Djerir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Chloé Brochu
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Théo Morin
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | | | | | - Lisa Casimir
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
| | - Elliot Drobetsky
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Laurent Cappadocia
- Faculty of Sciences, Department of Chemistry, Université du Québec à Montréal, Montréal, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Canada
| | - Hugo Wurtele
- Research Center, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Medicine Department, Université de Montréal, Montréal, Canada
| | - Alexandre Maréchal
- Faculty of Sciences, Department of Biology, Université de Sherbrooke, Sherbrooke, Canada
- CHUS Research Center and Cancer Research Institute, Sherbrooke, Canada
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13
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Muñoz S, Barroso S, Badra-Fajardo N, Marqueta-Gracia JJ, García-Rubio ML, Ubieto-Capella P, Méndez J, Aguilera A. SIN3A histone deacetylase action counteracts MUS81 to promote stalled fork stability. Cell Rep 2024; 43:113778. [PMID: 38341854 PMCID: PMC10915396 DOI: 10.1016/j.celrep.2024.113778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/09/2023] [Accepted: 01/26/2024] [Indexed: 02/13/2024] Open
Abstract
During genome duplication, replication forks (RFs) can be stalled by different obstacles or by depletion of replication factors or nucleotides. A limited number of histone post-translational modifications at stalled RFs are involved in RF protection and restart. Provided the recent observation that the SIN3A histone deacetylase complex reduces transcription-replication conflicts, we explore the role of the SIN3A complex in protecting RFs under stressed conditions. We observe that Sin3A protein is enriched at replicating DNA in the presence of hydroxyurea. In this situation, Sin3A-depleted cells show increased RF stalling, H3 acetylation, and DNA breaks at stalled RFs. Under Sin3A depletion, RF recovery is impaired, and DNA damage accumulates. Importantly, these effects are partially dependent on the MUS81 endonuclease, which promotes DNA breaks and MRE11-dependent DNA degradation of such breaks. We propose that chromatin deacetylation triggered by the SIN3A complex limits MUS81 cleavage of stalled RFs, promoting genome stability when DNA replication is challenged.
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Affiliation(s)
- Sergio Muñoz
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Sonia Barroso
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Nibal Badra-Fajardo
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - José Javier Marqueta-Gracia
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - María L García-Rubio
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Patricia Ubieto-Capella
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Juan Méndez
- Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), 28029 Madrid, Spain
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa-CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, 41092 Seville, Spain; Departamento de Genética, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain.
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14
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Chen J, Wu M, Yang Y, Ruan C, Luo Y, Song L, Wu T, Huang J, Yang B, Liu T. TFIP11 promotes replication fork reversal to preserve genome stability. Nat Commun 2024; 15:1262. [PMID: 38341452 PMCID: PMC10858868 DOI: 10.1038/s41467-024-45684-3] [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: 04/28/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
Replication fork reversal, a critical protective mechanism against replication stress in higher eukaryotic cells, is orchestrated via a series of coordinated enzymatic reactions. The Bloom syndrome gene product, BLM, a member of the highly conserved RecQ helicase family, is implicated in this process, yet its precise regulation and role remain poorly understood. In this study, we demonstrate that the GCFC domain-containing protein TFIP11 forms a complex with the BLM helicase. TFIP11 exhibits a preference for binding to DNA substrates that mimic the structure generated at stalled replication forks. Loss of either TFIP11 or BLM leads to the accumulation of the other protein at stalled forks. This abnormal accumulation, in turn, impairs RAD51-mediated fork reversal and slowing, sensitizes cells to replication stress-inducing agents, and enhances chromosomal instability. These findings reveal a previously unidentified regulatory mechanism that modulates the activities of BLM and RAD51 at stalled forks, thereby impacting genome integrity.
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Affiliation(s)
- Junliang Chen
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
- Center for Life Sciences, Shaoxing Institute, Zhejiang University, 321000, Shaoxing, China
| | - Mingjie Wu
- The Trauma Center, The First Affiliated Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
| | - Yulan Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Chunyan Ruan
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Yi Luo
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Lizhi Song
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Wu
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Jun Huang
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Bing Yang
- The MOE Key Laboratory of Biosystems Homeostasis & Protection and Zhejiang Provincial Key Laboratory of Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, 310058, Hangzhou, China
| | - Ting Liu
- Zhejiang Provincial Key Laboratory of Geriatrics and Geriatrics Institute of Zhejiang Province, Affiliated Zhejiang Hospital, Zhejiang University School of Medicine, 310058, Hangzhou, China.
- Department of Cell Biology, Zhejiang University School of Medicine, 310058, Hangzhou, China.
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15
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Nie L, Wang C, Huang M, Liu X, Feng X, Tang M, Li S, Hang Q, Teng H, Shen X, Ma L, Gan B, Chen J. DePARylation is critical for S phase progression and cell survival. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.31.551317. [PMID: 37577639 PMCID: PMC10418084 DOI: 10.1101/2023.07.31.551317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Poly(ADP-ribose)ylation or PARylation by PAR polymerase 1 (PARP1) and dePARylation by poly(ADP-ribose) glycohydrolase (PARG) are equally important for the dynamic regulation of DNA damage response. PARG, the most active dePARylation enzyme, is recruited to sites of DNA damage via pADPr-dependent and PCNA-dependent mechanisms. Targeting dePARylation is considered an alternative strategy to overcome PARP inhibitor resistance. However, precisely how dePARylation functions in normal unperturbed cells remains elusive. To address this challenge, we conducted multiple CRISPR screens and revealed that dePARylation of S phase pADPr by PARG is essential for cell viability. Loss of dePARylation activity initially induced S phase-specific pADPr signaling, which resulted from unligated Okazaki fragments and eventually led to uncontrolled pADPr accumulation and PARP1/2-dependent cytotoxicity. Moreover, we demonstrated that proteins involved in Okazaki fragment ligation and/or base excision repair regulate pADPr signaling and cell death induced by PARG inhibition. In addition, we determined that PARG expression is critical for cellular sensitivity to PARG inhibition. Additionally, we revealed that PARG is essential for cell survival by suppressing pADPr. Collectively, our data not only identify an essential role for PARG in normal proliferating cells but also provide a potential biomarker for the further development of PARG inhibitors in cancer therapy.
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Affiliation(s)
- Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Min Huang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xiaoguang Liu
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Siting Li
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Qinglei Hang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Hongqi Teng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Xi Shen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Li Ma
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Boyi Gan
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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16
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Mórocz M, Qorri E, Pekker E, Tick G, Haracska L. Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools. J Biotechnol 2024; 380:1-19. [PMID: 38072328 DOI: 10.1016/j.jbiotec.2023.12.001] [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: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.
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Affiliation(s)
- Mónika Mórocz
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Erda Qorri
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged H-6720, Hungary.
| | - Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, 6720 Szeged, Hungary.
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117 Budapest, Hungary.
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17
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González-Acosta D, Lopes M. DNA replication and replication stress response in the context of nuclear architecture. Chromosoma 2024; 133:57-75. [PMID: 38055079 PMCID: PMC10904558 DOI: 10.1007/s00412-023-00813-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 10/23/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023]
Abstract
The DNA replication process needs to be coordinated with other DNA metabolism transactions and must eventually extend to the full genome, regardless of chromatin status, gene expression, secondary structures and DNA lesions. Completeness and accuracy of DNA replication are crucial to maintain genome integrity, limiting transformation in normal cells and offering targeting opportunities for proliferating cancer cells. DNA replication is thus tightly coordinated with chromatin dynamics and 3D genome architecture, and we are only beginning to understand the underlying molecular mechanisms. While much has recently been discovered on how DNA replication initiation is organised and modulated in different genomic regions and nuclear territories-the so-called "DNA replication program"-we know much less on how the elongation of ongoing replication forks and particularly the response to replication obstacles is affected by the local nuclear organisation. Also, it is still elusive how specific components of nuclear architecture participate in the replication stress response. Here, we review known mechanisms and factors orchestrating replication initiation, and replication fork progression upon stress, focusing on recent evidence linking genome organisation and nuclear architecture with the cellular responses to replication interference, and highlighting open questions and future challenges to explore this exciting new avenue of research.
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Affiliation(s)
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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18
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Lebdy R, Canut M, Patouillard J, Cadoret JC, Letessier A, Ammar J, Basbous J, Urbach S, Miotto B, Constantinou A, Abou Merhi R, Ribeyre C. The nucleolar protein GNL3 prevents resection of stalled replication forks. EMBO Rep 2023; 24:e57585. [PMID: 37965896 DOI: 10.15252/embr.202357585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/16/2023] Open
Abstract
Faithful DNA replication requires specific proteins that protect replication forks and so prevent the formation of DNA lesions that may damage the genome. Identification of new proteins involved in this process is essential to understand how DNA lesions accumulate in cancer cells and how they tolerate them. Here, we show that human GNL3/nucleostemin, a GTP-binding protein localized mostly in the nucleolus and highly expressed in cancer cells, prevents nuclease-dependent resection of nascent DNA in response to replication stress. We demonstrate that inhibiting origin firing reduces resection. This suggests that the heightened replication origin activation observed upon GNL3 depletion largely drives the observed DNA resection probably due to the exhaustion of the available RPA pool. We show that GNL3 and DNA replication initiation factor ORC2 interact in the nucleolus and that the concentration of GNL3 in the nucleolus is required to limit DNA resection. We propose that the control of origin firing by GNL3 through the sequestration of ORC2 in the nucleolus is critical to prevent nascent DNA resection in response to replication stress.
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Affiliation(s)
- Rana Lebdy
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
- Faculty of Sciences, Genomics and Surveillance Biotherapy (GSBT) Laboratory, R. Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Marine Canut
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Julie Patouillard
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | | | - Anne Letessier
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Josiane Ammar
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Jihane Basbous
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Serge Urbach
- Institut de Génomique Fonctionnelle, CNRS UMR 5203, Inserm U1191, Université de Montpellier, Montpellier Cedex 5, France
| | - Benoit Miotto
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Angelos Constantinou
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
| | - Raghida Abou Merhi
- Faculty of Sciences, Genomics and Surveillance Biotherapy (GSBT) Laboratory, R. Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Cyril Ribeyre
- Institut de Génétique Humaine (UMR9002), CNRS, Université de Montpellier, Montpellier Cedex 5, France
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19
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Leriche M, Bonnet C, Jana J, Chhetri G, Mennour S, Martineau S, Pennaneach V, Busso D, Veaute X, Bertrand P, Lambert S, Somyajit K, Uguen P, Vagner S. 53BP1 interacts with the RNA primer from Okazaki fragments to support their processing during unperturbed DNA replication. Cell Rep 2023; 42:113412. [PMID: 37963016 DOI: 10.1016/j.celrep.2023.113412] [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: 03/01/2023] [Revised: 08/03/2023] [Accepted: 10/25/2023] [Indexed: 11/16/2023] Open
Abstract
RNA-binding proteins (RBPs) are found at replication forks, but their direct interaction with DNA-embedded RNA species remains unexplored. Here, we report that p53-binding protein 1 (53BP1), involved in the DNA damage and replication stress response, is an RBP that directly interacts with Okazaki fragments in the absence of external stress. The recruitment of 53BP1 to nascent DNA shows susceptibility to in situ ribonuclease A treatment and is dependent on PRIM1, which synthesizes the RNA primer of Okazaki fragments. Conversely, depletion of FEN1, resulting in the accumulation of uncleaved RNA primers, increases 53BP1 levels at replication forks, suggesting that RNA primers contribute to the recruitment of 53BP1 at the lagging DNA strand. 53BP1 depletion induces an accumulation of S-phase poly(ADP-ribose), which constitutes a sensor of unligated Okazaki fragments. Collectively, our data indicate that 53BP1 is anchored at nascent DNA through its RNA-binding activity, highlighting the role of an RNA-protein interaction at replication forks.
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Affiliation(s)
- Melissa Leriche
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Clara Bonnet
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Jagannath Jana
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Gita Chhetri
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Sabrina Mennour
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Sylvain Martineau
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Vincent Pennaneach
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Didier Busso
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France; Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France
| | - Xavier Veaute
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France; Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France; Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, iRCM/IBFJ, 92260 Fontenay-aux-Roses, France
| | - Sarah Lambert
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Kumar Somyajit
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense, Denmark
| | - Patricia Uguen
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France
| | - Stéphan Vagner
- Institut Curie, PSL Research University, CNRS UMR 3348, INSERM U1278, Orsay, France; Université Paris-Saclay, CNRS UMR 3348, INSERM U1278, Orsay, France; Equipe labellisée Ligue contre le Cancer, Orsay, France.
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20
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Manohar S, Estrada ME, Uliana F, Vuina K, Alvarez PM, de Bruin RAM, Neurohr GE. Genome homeostasis defects drive enlarged cells into senescence. Mol Cell 2023; 83:4032-4046.e6. [PMID: 37977116 PMCID: PMC10659931 DOI: 10.1016/j.molcel.2023.10.018] [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: 09/12/2022] [Revised: 06/30/2023] [Accepted: 10/16/2023] [Indexed: 11/19/2023]
Abstract
Cellular senescence refers to an irreversible state of cell-cycle arrest and plays important roles in aging and cancer biology. Because senescence is associated with increased cell size, we used reversible cell-cycle arrests combined with growth rate modulation to study how excessive growth affects proliferation. We find that enlarged cells upregulate p21, which limits cell-cycle progression. Cells that re-enter the cell cycle encounter replication stress that is well tolerated in physiologically sized cells but causes severe DNA damage in enlarged cells, ultimately resulting in mitotic failure and permanent cell-cycle withdrawal. We demonstrate that enlarged cells fail to recruit 53BP1 and other non-homologous end joining (NHEJ) machinery to DNA damage sites and fail to robustly initiate DNA damage-dependent p53 signaling, rendering them highly sensitive to genotoxic stress. We propose that an impaired DNA damage response primes enlarged cells for persistent replication-acquired damage, ultimately leading to cell division failure and permanent cell-cycle exit.
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Affiliation(s)
- Sandhya Manohar
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Marianna E Estrada
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Federico Uliana
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Karla Vuina
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK
| | - Patricia Moyano Alvarez
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland
| | - Robertus A M de Bruin
- Laboratory for Molecular Cell Biology, University College London, London WC1E 6BT, UK; UCL Cancer Institute, University College London, London WC1E 6BT, UK
| | - Gabriel E Neurohr
- Institute for Biochemistry, Department of Biology, ETH Zürich 8093, Zürich, Zürich, Switzerland.
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21
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Gali VK, Monerawela C, Laksir Y, Hiraga SI, Donaldson AD. Checkpoint phosphorylation sites on budding yeast Rif1 protect nascent DNA from degradation by Sgs1-Dna2. PLoS Genet 2023; 19:e1011044. [PMID: 37956214 PMCID: PMC10681312 DOI: 10.1371/journal.pgen.1011044] [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: 08/05/2023] [Revised: 11/27/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
In budding yeast the Rif1 protein is important for protecting nascent DNA at blocked replication forks, but the mechanism has been unclear. Here we show that budding yeast Rif1 must interact with Protein Phosphatase 1 to protect nascent DNA. In the absence of Rif1, removal of either Dna2 or Sgs1 prevents nascent DNA degradation, implying that Rif1 protects nascent DNA by targeting Protein Phosphatase 1 to oppose degradation by the Sgs1-Dna2 nuclease-helicase complex. This functional role for Rif1 is conserved from yeast to human cells. Yeast Rif1 was previously identified as a target of phosphorylation by the Tel1/Mec1 checkpoint kinases, but the importance of this phosphorylation has been unclear. We find that nascent DNA protection depends on a cluster of Tel1/Mec1 consensus phosphorylation sites in the Rif1 protein sequence, indicating that the intra-S phase checkpoint acts to protect nascent DNA through Rif1 phosphorylation. Our observations uncover the pathway by which budding yeast Rif1 stabilises newly synthesised DNA, highlighting the crucial role Rif1 plays in maintaining genome stability from lower eukaryotes to humans.
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Affiliation(s)
- Vamsi Krishna Gali
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Chandre Monerawela
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Yassine Laksir
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Shin-Ichiro Hiraga
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Anne D Donaldson
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
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22
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Bai G, Endres T, Kühbacher U, Greer BH, Peacock EM, Crossley MP, Sathirachinda A, Cortez D, Eichman BF, Cimprich KA. HLTF Prevents G4 Accumulation and Promotes G4-induced Fork Slowing to Maintain Genome Stability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.27.563641. [PMID: 37961428 PMCID: PMC10634870 DOI: 10.1101/2023.10.27.563641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
G-quadruplexes (G4s) form throughout the genome and influence important cellular processes, but their deregulation can challenge DNA replication fork progression and threaten genome stability. Here, we demonstrate an unexpected, dual role for the dsDNA translocase HLTF in G4 metabolism. First, we find that HLTF is enriched at G4s in the human genome and suppresses G4 accumulation throughout the cell cycle using its ATPase activity. This function of HLTF affects telomere maintenance by restricting alternative lengthening of telomeres, a process stimulated by G4s. We also show that HLTF and MSH2, a mismatch repair factor that binds G4s, act in independent pathways to suppress G4s and to promote resistance to G4 stabilization. In a second, distinct role, HLTF restrains DNA synthesis upon G4 stabilization by suppressing PrimPol-dependent repriming. Together, the dual functions of HLTF in the G4 response prevent DNA damage and potentially mutagenic replication to safeguard genome stability.
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23
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Kang Z, Fu P, Ma H, Li T, Lu K, Liu J, Ginjala V, Romanienko P, Feng Z, Guan M, Ganesan S, Xia B. Distinct functions of EHMT1 and EHMT2 in cancer chemotherapy and immunotherapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560719. [PMID: 37873068 PMCID: PMC10592889 DOI: 10.1101/2023.10.03.560719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
EHTM1 (GLP) and EHMT2 (G9a) are closely related protein lysine methyltransferases often thought to function together as a heterodimer to methylate histone H3 and non-histone substrates in diverse cellular processes including transcriptional regulation, genome methylation, and DNA repair. Here we show that EHMT1/2 inhibitors cause ATM-mediated slowdown of replication fork progression, accumulation of single-stranded replication gaps, emergence of cytosolic DNA, and increased expression of STING. EHMT1/2 inhibition strongly potentiates the efficacy of alkylating chemotherapy and anti-PD-1 immunotherapy in mouse models of tripe negative breast cancer. The effects on DNA replication and alkylating agent sensitivity are largely caused by the loss of EHMT1-mediated methylation of LIG1, whereas the elevated STING expression and remarkable response to immunotherapy appear mainly elicited by the loss of EHMT2 activity. Depletion of UHRF1, a protein known to be associated with EHMT1/2 and LIG1, also induces STING expression, and depletion of either EHMT2 or UHRF1 leads to demethylation of specific CpG sites in the STING1 promoter, suggestive of a distinct EHMT2-UHRF1 axis that regulates DNA methylation and gene transcription. These results highlight distinct functions of the two EHMT paralogs and provide enlightening paradigms and corresponding molecular basis for combination therapies involving alkylating agents and immune checkpoint inhibitors.
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Affiliation(s)
- Zhihua Kang
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Pan Fu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Department of Clinical Microbiology Laboratory, Children’s Hospital of Fudan University, Shanghai, China
| | - Hui Ma
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Tao Li
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Kevin Lu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Juan Liu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Vasudeva Ginjala
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | | | - Zhaohui Feng
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Shridar Ganesan
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Medicine, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
| | - Bing Xia
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ, USA
- Department of Radiation Oncology, Rutgers Robert Wood Johnson Medical School, New Brunswick, NJ, USA
- Lead contact
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24
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Liu W, Polaczek P, Roubal I, Meng Y, Choe WC, Caron MC, Sedgeman C, Xi Y, Liu C, Wu Q, Zheng L, Masson JY, Shen B, Campbell J. FANCD2 and RAD51 recombinase directly inhibit DNA2 nuclease at stalled replication forks and FANCD2 acts as a novel RAD51 mediator in strand exchange to promote genome stability. Nucleic Acids Res 2023; 51:9144-9165. [PMID: 37526271 PMCID: PMC10516637 DOI: 10.1093/nar/gkad624] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 06/17/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023] Open
Abstract
FANCD2 protein, a key coordinator and effector of the interstrand crosslink repair pathway, is also required to prevent excessive nascent strand degradation at hydroxyurea-induced stalled forks. The RAD51 recombinase has also been implicated in regulation of resection at stalled replication forks. The mechanistic contributions of these proteins to fork protection are not well understood. Here, we used purified FANCD2 and RAD51 to study how each protein regulates DNA resection at stalled forks. We characterized three mechanisms of FANCD2-mediated fork protection: (1) The N-terminal domain of FANCD2 inhibits the essential DNA2 nuclease activity by directly binding to DNA2 accounting for over-resection in FANCD2 defective cells. (2) Independent of dimerization with FANCI, FANCD2 itself stabilizes RAD51 filaments to inhibit multiple nucleases, including DNA2, MRE11 and EXO1. (3) Unexpectedly, we uncovered a new FANCD2 function: by stabilizing RAD51 filaments, FANCD2 acts to stimulate the strand exchange activity of RAD51. Our work biochemically explains non-canonical mechanisms by which FANCD2 and RAD51 protect stalled forks. We propose a model in which the strand exchange activity of FANCD2 provides a simple molecular explanation for genetic interactions between FANCD2 and BRCA2 in the FA/BRCA fork protection pathway.
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Affiliation(s)
- Wenpeng Liu
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Piotr Polaczek
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ivan Roubal
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuan Meng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Won-chae Choe
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marie-Christine Caron
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Carl A Sedgeman
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yu Xi
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Changwei Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Qiong Wu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
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25
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Brown VE, Moore SL, Chen M, House N, Ramsden P, Wu HJ, Ribich S, Grassian AR, Choi YJ. CDK2 regulates collapsed replication fork repair in CCNE1-amplified ovarian cancer cells via homologous recombination. NAR Cancer 2023; 5:zcad039. [PMID: 37519629 PMCID: PMC10373114 DOI: 10.1093/narcan/zcad039] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 06/22/2023] [Accepted: 07/20/2023] [Indexed: 08/01/2023] Open
Abstract
CCNE1 amplification is a common alteration in high-grade serous ovarian cancer and occurs in 15-20% of these tumors. These amplifications are mutually exclusive with homologous recombination deficiency, and, as they have intact homologous recombination, are intrinsically resistant to poly (ADP-ribose) polymerase inhibitors or chemotherapy agents. Understanding the molecular mechanisms that lead to this mutual exclusivity may reveal therapeutic vulnerabilities that could be leveraged in the clinic in this still underserved patient population. Here, we demonstrate that CCNE1-amplified high-grade serous ovarian cancer cells rely on homologous recombination to repair collapsed replication forks. Cyclin-dependent kinase 2, the canonical partner of cyclin E1, uniquely regulates homologous recombination in this genetic context, and as such cyclin-dependent kinase 2 inhibition synergizes with DNA damaging agents in vitro and in vivo. We demonstrate that combining a selective cyclin-dependent kinase 2 inhibitor with a DNA damaging agent could be a powerful tool in the clinic for high-grade serous ovarian cancer.
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Affiliation(s)
- Victoria E Brown
- To whom correspondence should be addressed. Tel: +1 617 374 7580;
| | - Sydney L Moore
- Blueprint Medicines, Cambridge, MA 02139, USA
- Department of Biology, Tufts University, Medford, MA 02155, USA
| | - Maxine Chen
- Blueprint Medicines, Cambridge, MA 02139, USA
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26
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Budden AM, Eravci M, Watson AT, Campillo-Funollet E, Oliver AW, Naiman K, Carr AM. Schizosaccharomyces pombe Rtf2 is important for replication fork barrier activity of RTS1 via splicing of Rtf1. eLife 2023; 12:e78554. [PMID: 37615341 PMCID: PMC10473836 DOI: 10.7554/elife.78554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Accepted: 08/19/2023] [Indexed: 08/25/2023] Open
Abstract
Arrested replication forks, when restarted by homologous recombination, result in error-prone DNA syntheses and non-allelic homologous recombination. Fission yeast RTS1 is a model fork barrier used to probe mechanisms of recombination-dependent restart. RTS1 barrier activity is entirely dependent on the DNA binding protein Rtf1 and partially dependent on a second protein, Rtf2. Human RTF2 was recently implicated in fork restart, leading us to examine fission yeast Rtf2's role in more detail. In agreement with previous studies, we observe reduced barrier activity upon rtf2 deletion. However, we identified Rtf2 to be physically associated with mRNA processing and splicing factors and rtf2 deletion to cause increased intron retention. One of the most affected introns resided in the rtf1 transcript. Using an intronless rtf1, we observed no reduction in RFB activity in the absence of Rtf2. Thus, Rtf2 is essential for correct rtf1 splicing to allow optimal RTS1 barrier activity.
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Affiliation(s)
- Alice M Budden
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
| | - Murat Eravci
- Department of Biochemistry and Biomedicine, University of SussexBrightonUnited Kingdom
| | - Adam T Watson
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
| | | | - Antony W Oliver
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
| | - Karel Naiman
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
| | - Antony M Carr
- Genome Damage and Stability Centre, University of SussexBrightonUnited Kingdom
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27
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Berger S, Chistol G. Visualizing the dynamics of DNA replication and repair at the single-molecule level. Methods Cell Biol 2023; 182:109-165. [PMID: 38359974 DOI: 10.1016/bs.mcb.2023.07.001] [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] [Indexed: 02/17/2024]
Abstract
During cell division, the genome of each eukaryotic cell is copied by thousands of replisomes-large protein complexes consisting of several dozen proteins. Recent studies suggest that the eukaryotic replisome is much more dynamic than previously thought. To directly visualize replisome dynamics in a physiological context, we recently developed a single-molecule approach for imaging replication proteins in Xenopus egg extracts. These extracts contain all the soluble nuclear proteins and faithfully recapitulate DNA replication and repair in vitro, serving as a powerful platform for studying the mechanisms of genome maintenance. Here we present detailed protocols for conducting single-molecule experiments in nuclear egg extracts and preparing key reagents. This workflow can be easily adapted to visualize the dynamics and function of other proteins implicated in DNA replication and repair.
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Affiliation(s)
- Scott Berger
- Biophysics Program, Stanford School of Medicine, Stanford, CA, United States
| | - Gheorghe Chistol
- Biophysics Program, Stanford School of Medicine, Stanford, CA, United States; Chemical and Systems Biology Department, Cancer Biology Program, Stanford School of Medicine, Stanford, CA, United States.
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28
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Hadjicharalambous A, Whale AJ, Can G, Skehel JM, Houseley JM, Zegerman P. Checkpoint kinase interaction with DNA polymerase alpha regulates replication progression during stress. Wellcome Open Res 2023; 8:327. [PMID: 37766847 PMCID: PMC10521137 DOI: 10.12688/wellcomeopenres.19617.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 09/29/2023] Open
Abstract
Background: In eukaryotes, replication stress activates a checkpoint response, which facilitates genome duplication by stabilising the replisome. How the checkpoint kinases regulate the replisome remains poorly understood. The aim of this study is to identify new targets of checkpoint kinases within the replisome during replication stress. Methods: Here we use an unbiased biotin proximity-ligation approach in Saccharomyces cerevisiae to identify new interactors and substrates of the checkpoint kinase Rad53 in vivo. Results: From this screen, we identified the replication initiation factor Sld7 as a Rad53 substrate, and Pol1, the catalytic subunit of polymerase a, as a Rad53-interactor. We showed that CDK phosphorylation of Pol1 mediates its interaction with Rad53. Combined with other interactions between Rad53 and the replisome, this Rad53-Pol1 interaction is important for viability and replisome progression during replication stress. Conclusions: Together, we explain how the interactions of Rad53 with the replisome are controlled by both replication stress and the cell cycle, and why these interactions might be important for coordinating the stabilisation of both the leading and lagging strand machineries.
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Affiliation(s)
| | - Alex J. Whale
- Epigenetics Programme, Babraham Institute, University of Cambridge, Cambridge, England, CB22 3AT, UK
| | - Geylani Can
- Department of Biochemistry, University of Cambridge, Cambridge, England, CB2 1GA, UK
| | - J. Mark Skehel
- Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, London, England, CB2 0QH, UK
| | - Jonathan M. Houseley
- Epigenetics Programme, Babraham Institute, University of Cambridge, Cambridge, England, CB22 3AT, UK
| | - Philip Zegerman
- Department of Biochemistry, University of Cambridge, Cambridge, England, CB2 1GA, UK
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29
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Leung W, Simoneau A, Saxena S, Jackson J, Patel PS, Limbu M, Vindigni A, Zou L. ATR protects ongoing and newly assembled DNA replication forks through distinct mechanisms. Cell Rep 2023; 42:112792. [PMID: 37454295 PMCID: PMC10529362 DOI: 10.1016/j.celrep.2023.112792] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/06/2023] [Accepted: 06/27/2023] [Indexed: 07/18/2023] Open
Abstract
The ATR kinase safeguards genomic integrity during S phase, but how ATR protects DNA replication forks remains incompletely understood. Here, we combine four distinct assays to analyze ATR functions at ongoing and newly assembled replication forks upon replication inhibition by hydroxyurea. At ongoing forks, ATR inhibitor (ATRi) increases MRE11- and EXO1-mediated nascent DNA degradation from PrimPol-generated, single-stranded DNA (ssDNA) gaps. ATRi also exposes template ssDNA through fork uncoupling and nascent DNA degradation. Electron microscopy reveals that ATRi reduces reversed forks by increasing gap-dependent nascent DNA degradation. At new forks, ATRi triggers MRE11- and CtIP-initiated template DNA degradation by EXO1, exposing nascent ssDNA. Upon PARP inhibition, ATRi preferentially exacerbates gap-dependent nascent DNA degradation at ongoing forks in BRCA1/2-deficient cells and disrupts the restored gap protection in BRCA1-deficient, PARP-inhibitor-resistant cells. Thus, ATR protects ongoing and new forks through distinct mechanisms, providing an extended view of ATR's functions in stabilizing replication forks.
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Affiliation(s)
- Wendy Leung
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Antoine Simoneau
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Sneha Saxena
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Parasvi S Patel
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA
| | - Mangsi Limbu
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Lee Zou
- Massachusetts General Hospital Cancer Center, Harvard Medical School, Charlestown, MA 02129, USA; Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27708, USA.
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30
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Patel JA, Zezelic C, Rageul J, Saldanha J, Khan A, Kim H. Replisome dysfunction upon inducible TIMELESS degradation synergizes with ATR inhibition to trigger replication catastrophe. Nucleic Acids Res 2023; 51:6246-6263. [PMID: 37144518 PMCID: PMC10325925 DOI: 10.1093/nar/gkad363] [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: 01/03/2023] [Revised: 03/29/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023] Open
Abstract
The structure of DNA replication forks is preserved by TIMELESS (TIM) in the fork protection complex (FPC) to support seamless fork progression. While the scaffolding role of the FPC to couple the replisome activity is much appreciated, the detailed mechanism whereby inherent replication fork damage is sensed and counteracted during DNA replication remains largely elusive. Here, we implemented an auxin-based degron system that rapidly triggers inducible proteolysis of TIM as a source of endogenous DNA replication stress and replisome dysfunction to dissect the signaling events that unfold at stalled forks. We demonstrate that acute TIM degradation activates the ATR-CHK1 checkpoint, whose inhibition culminates in replication catastrophe by single-stranded DNA accumulation and RPA exhaustion. Mechanistically, unrestrained replisome uncoupling, excessive origin firing, and aberrant reversed fork processing account for the synergistic fork instability. Simultaneous TIM loss and ATR inactivation triggers DNA-PK-dependent CHK1 activation, which is unexpectedly necessary for promoting fork breakage by MRE11 and catastrophic cell death. We propose that acute replisome dysfunction results in a hyper-dependency on ATR to activate local and global fork stabilization mechanisms to counteract irreversible fork collapse. Our study identifies TIM as a point of replication vulnerability in cancer that can be exploited with ATR inhibitors.
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Affiliation(s)
- Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Camryn Zezelic
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Joanne Saldanha
- The Graduate program in Genetics, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Arafat Khan
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine at Stony Brook University, Stony Brook, NY 11794, USA
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31
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Saldanha J, Rageul J, Patel JA, Kim H. The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork. Int J Mol Sci 2023; 24:10488. [PMID: 37445667 PMCID: PMC10341514 DOI: 10.3390/ijms241310488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.
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Affiliation(s)
- Joanne Saldanha
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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32
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Göder A, Quinlan A, Rainey MD, Bennett D, Shamavu D, Corso J, Santocanale C. PTBP1 enforces ATR-CHK1 signaling determining the potency of CDC7 inhibitors. iScience 2023; 26:106951. [PMID: 37378325 PMCID: PMC10291475 DOI: 10.1016/j.isci.2023.106951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/27/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
CDC7 kinase is crucial for DNA replication initiation and fork processing. CDC7 inhibition mildly activates the ATR pathway, which further limits origin firing; however, to date the relationship between CDC7 and ATR remains controversial. We show that CDC7 and ATR inhibitors are either synergistic or antagonistic depending on the degree of inhibition of each individual kinase. We find that Polypyrimidine Tract Binding Protein 1 (PTBP1) is important for ATR activity in response to CDC7 inhibition and genotoxic agents. Compromised PTBP1 expression makes cells defective in RPA recruitment, genomically unstable, and resistant to CDC7 inhibitors. PTBP1 deficiency affects the expression and splicing of many genes indicating a multifactorial impact on drug response. We find that an exon skipping event in RAD51AP1 contributes to checkpoint deficiency in PTBP1-deficient cells. These results identify PTBP1 as a key factor in replication stress response and define how ATR activity modulates the activity of CDC7 inhibitors.
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Affiliation(s)
- Anja Göder
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Aisling Quinlan
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Michael D. Rainey
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Declan Bennett
- School of Mathematical & Statistical Sciences, University of Galway, Galway H91TK33, Ireland
| | - Daniel Shamavu
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Jacqueline Corso
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
| | - Corrado Santocanale
- Centre for Chromosome Biology, School of Biological and Chemical Sciences, University of Galway, Galway H91W2TY, Ireland
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33
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Liu W, Saito Y, Jackson J, Bhowmick R, Kanemaki MT, Vindigni A, Cortez D. RAD51 bypasses the CMG helicase to promote replication fork reversal. Science 2023; 380:382-387. [PMID: 37104614 PMCID: PMC10302453 DOI: 10.1126/science.add7328] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/25/2023] [Indexed: 04/29/2023]
Abstract
Replication fork reversal safeguards genome integrity as a replication stress response. DNA translocases and the RAD51 recombinase catalyze reversal. However, it remains unknown why RAD51 is required and what happens to the replication machinery during reversal. We find that RAD51 uses its strand exchange activity to circumvent the replicative helicase, which remains bound to the stalled fork. RAD51 is not required for fork reversal if the helicase is unloaded. Thus, we propose that RAD51 creates a parental DNA duplex behind the helicase that is used as a substrate by the DNA translocases for branch migration to create a reversed fork structure. Our data explain how fork reversal happens while maintaining the helicase in a position poised to restart DNA synthesis and complete genome duplication.
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Affiliation(s)
- Wenpeng Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
| | - Yuichiro Saito
- Department of Chromosome Science, National Institute of Genetics, Research Organization of Information and Systems (ROIS), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rahul Bhowmick
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
| | - Masato T. Kanemaki
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
- Department of Genetics, The Graduate University for Advanced Studies (SOKENDAI), Yata 1111, Mishima, Shizuoka, 411-8540, Japan
- Department of Biological Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, 37237 USA
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34
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Lebdy R, Patouillard J, Larroque M, Urbach S, Abou Merhi R, Larroque C, Ribeyre C. The organizer of chromatin topology RIF1 ensures cellular resilience to DNA replication stress. Life Sci Alliance 2023; 6:e202101186. [PMID: 36746532 PMCID: PMC9906048 DOI: 10.26508/lsa.202101186] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 02/08/2023] Open
Abstract
Eukaryotic genomes are duplicated from thousands of replication origins that fire sequentially forming a defined spatiotemporal pattern of replication clusters. The temporal order of DNA replication is determined by chromatin architecture and, more specifically, by chromatin contacts that are stabilized by RIF1. Here, we show that RIF1 localizes near newly synthesized DNA. In cells exposed to the DNA replication inhibitor aphidicolin, suppression of RIF1 markedly decreased the efficacy of isolation of proteins on nascent DNA, suggesting that the isolation of proteins on nascent DNA procedure is biased by chromatin topology. RIF1 was required to limit the accumulation of DNA lesions induced by aphidicolin treatment and promoted the recruitment of cohesins in the vicinity of nascent DNA. Collectively, the data suggest that the stabilization of chromatin topology by RIF1 limits replication-associated genomic instability.
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Affiliation(s)
- Rana Lebdy
- Institut de Génétique Humaine, CNRS UMR9002, Université de Montpellier, Montpellier, France
- Doctoral School of Sciences and Technology-DSST, Rafic Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Julie Patouillard
- Institut de Génétique Humaine, CNRS UMR9002, Université de Montpellier, Montpellier, France
| | | | - Serge Urbach
- Institut de Génomique Fonctionnelle, CNRS UMR5203, INSERM U1191, Université de Montpellier, Montpellier, France
| | - Raghida Abou Merhi
- Doctoral School of Sciences and Technology-DSST, Rafic Hariri Campus, Lebanese University, Hadath, Lebanon
| | - Christian Larroque
- Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France
| | - Cyril Ribeyre
- Institut de Génétique Humaine, CNRS UMR9002, Université de Montpellier, Montpellier, France
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35
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Bhandari SK, Wiest N, Sallmyr A, Du R, Ferry L, Defossez PA, Tomkinson AE. Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1. Sci Rep 2023; 13:4363. [PMID: 36928068 PMCID: PMC10020546 DOI: 10.1038/s41598-023-31367-4] [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: 12/20/2022] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
DNA ligase I (LigI), the predominant enzyme that joins Okazaki fragments, interacts with PCNA and Pol δ. LigI also interacts with UHRF1, linking Okazaki fragment joining with DNA maintenance methylation. Okazaki fragments can also be joined by a relatively poorly characterized DNA ligase IIIα (LigIIIα)-dependent backup pathway. Here we examined the effect of LigI-deficiency on proteins at the replication fork. Notably, LigI-deficiency did not alter the kinetics of association of the PCNA clamp, the leading strand polymerase Pol ε, DNA maintenance methylation proteins and core histones with newly synthesized DNA. While the absence of major changes in replication and methylation proteins is consistent with the similar proliferation rate and DNA methylation levels of the LIG1 null cells compared with the parental cells, the increased levels of LigIIIα/XRCC1 and Pol δ at the replication fork and in bulk chromatin indicate that there are subtle replication defects in the absence of LigI. Interestingly, the non-replicative histone H1 variant, H1.0, is enriched in the chromatin of LigI-deficient mouse CH12F3 and human 46BR.1G1 cells. This alteration was not corrected by expression of wild type LigI, suggesting that it is a relatively stable epigenetic change that may contribute to the immunodeficiencies linked with inherited LigI-deficiency syndrome.
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Affiliation(s)
- Seema Khattri Bhandari
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Nathaniel Wiest
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Annahita Sallmyr
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ruofei Du
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Laure Ferry
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, 750013, Paris, France
| | | | - Alan E Tomkinson
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA.
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36
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Patel JA, Kim H. The TIMELESS effort for timely DNA replication and protection. Cell Mol Life Sci 2023; 80:84. [PMID: 36892674 PMCID: PMC9998586 DOI: 10.1007/s00018-023-04738-3] [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: 01/06/2023] [Revised: 02/16/2023] [Accepted: 02/24/2023] [Indexed: 03/10/2023]
Abstract
Accurate replication of the genome is fundamental to cellular survival and tumor prevention. The DNA replication fork is vulnerable to DNA lesions and damages that impair replisome progression, and improper control over DNA replication stress inevitably causes fork stalling and collapse, a major source of genome instability that fuels tumorigenesis. The integrity of the DNA replication fork is maintained by the fork protection complex (FPC), in which TIMELESS (TIM) constitutes a key scaffold that couples the CMG helicase and replicative polymerase activities, in conjunction with its interaction with other proteins associated with the replication machinery. Loss of TIM or the FPC in general results in impaired fork progression, elevated fork stalling and breakage, and a defect in replication checkpoint activation, thus underscoring its pivotal role in protecting the integrity of both active and stalled replication forks. TIM is upregulated in multiple cancers, which may represent a replication vulnerability of cancer cells that could be exploited for new therapies. Here, we discuss recent advances on our understanding of the multifaceted roles of TIM in DNA replication and stalled fork protection, and how its complex functions are engaged in collaboration with other genome surveillance and maintenance factors.
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Affiliation(s)
- Jinal A Patel
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA
| | - Hyungjin Kim
- Department of Pharmacological Sciences, State University of New York at Stony Brook, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
- Stony Brook Cancer Center and Renaissance School of Medicine, Stony Brook University, Basic Sciences Tower 8-125, 101 Nicolls Rd, Stony Brook, NY, 11794, USA.
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37
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Kustatscher G, Hödl M, Rullmann E, Grabowski P, Fiagbedzi E, Groth A, Rappsilber J. Higher-order modular regulation of the human proteome. Mol Syst Biol 2023; 19:e9503. [PMID: 36891684 PMCID: PMC10167480 DOI: 10.15252/msb.20209503] [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: 02/06/2020] [Revised: 02/08/2023] [Accepted: 02/14/2023] [Indexed: 03/10/2023] Open
Abstract
Operons are transcriptional modules that allow bacteria to adapt to environmental changes by coordinately expressing the relevant set of genes. In humans, biological pathways and their regulation are more complex. If and how human cells coordinate the expression of entire biological processes is unclear. Here, we capture 31 higher-order co-regulation modules, which we term progulons, by help of supervised machine-learning on proteomics data. Progulons consist of dozens to hundreds of proteins that together mediate core cellular functions. They are not restricted to physical interactions or co-localisation. Progulon abundance changes are primarily controlled at the level of protein synthesis and degradation. Implemented as a web app at www.proteomehd.net/progulonFinder, our approach enables the targeted search for progulons of specific cellular processes. We use it to identify a DNA replication progulon and reveal multiple new replication factors, validated by extensive phenotyping of siRNA-induced knockdowns. Progulons provide a new entry point into the molecular understanding of biological processes.
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Affiliation(s)
- Georg Kustatscher
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Martina Hödl
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Edward Rullmann
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Piotr Grabowski
- Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Data Sciences and Artificial Intelligence, Clinical Pharmacology & Safety Sciences, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Emmanuel Fiagbedzi
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Anja Groth
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research (CPR), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Juri Rappsilber
- Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK.,Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
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38
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McMahon A, Zhao J, Yan S. APE2: catalytic function and synthetic lethality draw attention as a cancer therapy target. NAR Cancer 2023; 5:zcad006. [PMID: 36755963 PMCID: PMC9900424 DOI: 10.1093/narcan/zcad006] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/17/2023] [Accepted: 01/20/2023] [Indexed: 02/08/2023] Open
Abstract
AP endonuclease 2 (APE2, APEX2 or APN2) is an emerging critical protein involved in genome and epigenome integrity. Whereas its catalytic function as a nuclease in DNA repair is widely accepted, recent studies have elucidated the function and mechanism of APE2 in the immune response and DNA damage response. Several genome-wide screens have identified APE2 as a synthetic lethal target for deficiencies of BRCA1, BRCA2 or TDP1 in cancer cells. Due to its overexpression in several cancer types, APE2 is proposed as an oncogene and could serve as prognostic marker of overall survival of cancer treatment. However, it remains to be discovered whether and how APE2 catalytic function and synthetic lethality can be modulated and manipulated as a cancer therapy target. In this review, we provide a current understanding of alterations and expression of APE2 in cancer, the function of APE2 in the immune response, and mechanisms of APE2 in ATR/Chk1 DNA damage response. We also summarize the role of APE2 in DNA repair pathways in the removal of heterogenous and complexed 3'-termini and MMEJ. Finally, we provide an updated perspective on how APE2 may be targeted for cancer therapy and future directions of APE2 studies in cancer biology.
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Affiliation(s)
- Anne McMahon
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
| | - Jianjun Zhao
- Department of Cancer Biology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Shan Yan
- Department of Biological Sciences, University of North Carolina at Charlotte, Charlotte, NC 28223, USA
- School of Data Science, 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
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39
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Zhang W, Tang M, Wang L, Zhou H, Gao J, Chen Z, Zhao B, Zheng P. Lnc956-TRIM28-HSP90B1 complex on replication forks promotes CMG helicase retention to ensure stem cell genomic stability and embryogenesis. SCIENCE ADVANCES 2023; 9:eadf6277. [PMID: 36706191 PMCID: PMC9882984 DOI: 10.1126/sciadv.adf6277] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Replication stress is a major source of endogenous DNA damage. Despite the identification of numerous proteins on replication forks to modulate fork or replication machinery activities, it remains unexplored whether noncoding RNAs can localize on stalled forks and play critical regulatory roles. Here, we identify an uncharacterized long noncoding RNA NONMMUT028956 (Lnc956 for short) predominantly expressed in mouse embryonic stem cells. Lnc956 is accumulated on replication forks to prevent fork collapse and preserve genomic stability and is essential for mouse embryogenesis. Mechanistically, it drives assembly of the Lnc956-TRIM28-HSP90B1 complex on stalled forks in an interdependent manner downstream of ataxia telangiectasia and Rad3-related (ATR) signaling. Lnc956-TRIM28-HSP90B1 complex physically associates with minichromosome maintenance proteins 2 (MCM2) to minichromosome maintenance proteins 7 (MCM7) hexamer via TRIM28 and directly regulates the CDC45-MCM-GINS (CMG) helicase retention on chromatin. The regulation of Lnc956-TRIM28-HSP90B1 on CMG retention is mediated by HSP90B1's chaperoning function. These findings reveal a player that actively regulates replisome retention to prevent fork collapse.
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Affiliation(s)
- Weidao Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Min Tang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- University of Chinese Academy of Sciences, Beijing 101408, China
| | - Lin Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jing Gao
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
| | - Zhongliang Chen
- Key Laboratory of Adult Stem Cell Translational Research (Chinese Academy of Medical Sciences), Guizhou Medical University, Guiyang, China
- National Joint Local Engineering Laboratory for Cell Engineering and Biomedicine Technique, Guizhou Medical University, Guiyang, China
| | - Bo Zhao
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ping Zheng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- Key Laboratory of Animal Models and Human Disease Mechanisms of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
- KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
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40
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Nasioudis D, George EM, Xu H, Kim H, Simpkins F. Combination DNA Damage Response (DDR) Inhibitors to Overcome Drug Resistance in Ovarian Cancer. Cancer Treat Res 2023; 186:189-206. [PMID: 37978137 DOI: 10.1007/978-3-031-30065-3_11] [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] [Indexed: 11/19/2023]
Abstract
The DNA damage response (DDR) results in activation of a series of key target kinases that respond to different DNA damage insults. DDR inhibitors such as PARP inhibitors lead to the accumulation of DNA damage in tumor cells and ultimately apoptosis. However, responses to DDRi monotherapy in the clinic are not durable and resistance ultimately develops. DDRi-DDRi combinations such as PARPi-ATRi, PAPRi-WEE1i and PARPi-AsiDNA can overcome multiple resistance mechanisms to PARP inhibition. In addition, DDRi-DDRi combinations can provide viable treatment options for patients with platinum-resistant disease. In the present chapter we discuss rationale of DDRi-DDRi strategies that capitalize on genomic alterations found in ovarian cancer and other solid tumors and may provide in the near future new treatment options for these patients.
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Affiliation(s)
- Dimitrios Nasioudis
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Erin M George
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Haineng Xu
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Hyoung Kim
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Fiona Simpkins
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Perelman School of Medicine, Ovarian Cancer Research Center, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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41
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Böhly N, Schmidt AK, Zhang X, Slusarenko BO, Hennecke M, Kschischo M, Bastians H. Increased replication origin firing links replication stress to whole chromosomal instability in human cancer. Cell Rep 2022; 41:111836. [PMID: 36516748 DOI: 10.1016/j.celrep.2022.111836] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 09/12/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and comprises structural CIN (S-CIN) and numerical or whole chromosomal CIN (W-CIN). Recent work indicated that replication stress (RS), known to contribute to S-CIN, also affects mitotic chromosome segregation, possibly explaining the common co-existence of S-CIN and W-CIN in human cancer. Here, we show that RS-induced increased origin firing is sufficient to trigger W-CIN in human cancer cells. We discovered that overexpression of origin firing genes, including GINS1 and CDC45, correlates with W-CIN in human cancer specimens and causes W-CIN in otherwise chromosomally stable human cells. Furthermore, modulation of the ATR-CDK1-RIF1 axis increases the number of firing origins and leads to W-CIN. Importantly, chromosome missegregation upon additional origin firing is mediated by increased mitotic microtubule growth rates, a mitotic defect prevalent in chromosomally unstable cancer cells. Thus, our study identifies increased replication origin firing as a cancer-relevant trigger for chromosomal instability.
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Affiliation(s)
- Nicolas Böhly
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Ann-Kathrin Schmidt
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Xiaoxiao Zhang
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany; Technical University of Munich, Department of Informatics, 81675 Munich, Germany
| | - Benjamin O Slusarenko
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Magdalena Hennecke
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Maik Kschischo
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany
| | - Holger Bastians
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany.
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42
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Martín-Rufo R, de la Vega-Barranco G, Lecona E. Ubiquitin and SUMO as timers during DNA replication. Semin Cell Dev Biol 2022; 132:62-73. [PMID: 35210137 DOI: 10.1016/j.semcdb.2022.02.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/12/2022] [Accepted: 02/14/2022] [Indexed: 12/14/2022]
Abstract
Every time a cell copies its DNA the genetic material is exposed to the acquisition of mutations and genomic alterations that corrupt the information passed on to daughter cells. A tight temporal regulation of DNA replication is necessary to ensure the full copy of the DNA while preventing the appearance of genomic instability. Protein modification by ubiquitin and SUMO constitutes a very complex and versatile system that allows the coordinated control of protein stability, activity and interactome. In chromatin, their action is complemented by the AAA+ ATPase VCP/p97 that recognizes and removes ubiquitylated and SUMOylated factors from specific cellular compartments. The concerted action of the ubiquitin/SUMO system and VCP/p97 determines every step of DNA replication enforcing the ordered activation/inactivation, loading/unloading and stabilization/destabilization of replication factors. Here we analyze the mechanisms used by ubiquitin/SUMO and VCP/p97 to establish molecular timers throughout DNA replication and their relevance in maintaining genome stability. We propose that these PTMs are the main molecular watch of DNA replication from origin recognition to replisome disassembly.
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Affiliation(s)
- Rodrigo Martín-Rufo
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain
| | - Guillermo de la Vega-Barranco
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain
| | - Emilio Lecona
- Chromatin, Cancer and the Ubiquitin System lab, Centre for Molecular Biology Severo Ochoa (CBMSO, CSIC-UAM), Department of Genome Dynamics and Function, Madrid 28049, Spain.
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43
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Jackson LM, Moldovan GL. Mechanisms of PARP1 inhibitor resistance and their implications for cancer treatment. NAR Cancer 2022; 4:zcac042. [PMID: 36568963 PMCID: PMC9773381 DOI: 10.1093/narcan/zcac042] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 11/28/2022] [Accepted: 12/06/2022] [Indexed: 12/24/2022] Open
Abstract
The discovery of synthetic lethality as a result of the combined loss of PARP1 and BRCA has revolutionized the treatment of DNA repair-deficient cancers. With the development of PARP inhibitors, patients displaying germline or somatic mutations in BRCA1 or BRCA2 were presented with a novel therapeutic strategy. However, a large subset of patients do not respond to PARP inhibitors. Furthermore, many of those who do respond eventually acquire resistance. As such, combating de novo and acquired resistance to PARP inhibitors remains an obstacle in achieving durable responses in patients. In this review, we touch on some of the key mechanisms of PARP inhibitor resistance, including restoration of homologous recombination, replication fork stabilization and suppression of single-stranded DNA gap accumulation, as well as address novel approaches for overcoming PARP inhibitor resistance.
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Affiliation(s)
- Lindsey M Jackson
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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44
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Mosler T, Baymaz HI, Gräf JF, Mikicic I, Blattner G, Bartlett E, Ostermaier M, Piccinno R, Yang J, Voigt A, Gatti M, Pellegrino S, Altmeyer M, Luck K, Ahel I, Roukos V, Beli P. PARP1 proximity proteomics reveals interaction partners at stressed replication forks. Nucleic Acids Res 2022; 50:11600-11618. [PMID: 36350633 PMCID: PMC9723622 DOI: 10.1093/nar/gkac948] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 10/06/2022] [Accepted: 10/11/2022] [Indexed: 11/10/2022] Open
Abstract
PARP1 mediates poly-ADP-ribosylation of proteins on chromatin in response to different types of DNA lesions. PARP inhibitors are used for the treatment of BRCA1/2-deficient breast, ovarian, and prostate cancer. Loss of DNA replication fork protection is proposed as one mechanism that contributes to the vulnerability of BRCA1/2-deficient cells to PARP inhibitors. However, the mechanisms that regulate PARP1 activity at stressed replication forks remain poorly understood. Here, we performed proximity proteomics of PARP1 and isolation of proteins on stressed replication forks to map putative PARP1 regulators. We identified TPX2 as a direct PARP1-binding protein that regulates the auto-ADP-ribosylation activity of PARP1. TPX2 interacts with DNA damage response proteins and promotes homology-directed repair of DNA double-strand breaks. Moreover, TPX2 mRNA levels are increased in BRCA1/2-mutated breast and prostate cancers, and high TPX2 expression levels correlate with the sensitivity of cancer cells to PARP-trapping inhibitors. We propose that TPX2 confers a mitosis-independent function in the cellular response to replication stress by interacting with PARP1.
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Affiliation(s)
| | - H Irem Baymaz
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Justus F Gräf
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Ivan Mikicic
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | | | - Edward Bartlett
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | | | | | - Jiwen Yang
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Andrea Voigt
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Marco Gatti
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland
| | - Stefania Pellegrino
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland
| | - Matthias Altmeyer
- Department of Molecular Mechanisms of Disease, University of Zurich, Zurich CH-8057, Switzerland
| | - Katja Luck
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
| | - Ivan Ahel
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | | | - Petra Beli
- Institute of Molecular Biology (IMB), Mainz 55128, Germany
- Institute of Developmental Biology and Neurobiology (IDN), Johannes Gutenberg-Universität, Mainz, Germany
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45
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Zhu C, Iwase M, Li Z, Wang F, Quinet A, Vindigni A, Shao J. Profilin-1 regulates DNA replication forks in a context-dependent fashion by interacting with SNF2H and BOD1L. Nat Commun 2022; 13:6531. [PMID: 36319634 PMCID: PMC9626489 DOI: 10.1038/s41467-022-34310-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/21/2022] [Indexed: 12/04/2022] Open
Abstract
DNA replication forks are tightly controlled by a large protein network consisting of well-known core regulators and many accessory factors which remain functionally undefined. In this study, we report previously unknown nuclear functions of the actin-binding factor profilin-1 (PFN1) in DNA replication, which occur in a context-dependent fashion and require its binding to poly-L-proline (PLP)-containing proteins instead of actin. In unperturbed cells, PFN1 increases DNA replication initiation and accelerates fork progression by binding and stimulating the PLP-containing nucleosome remodeler SNF2H. Under replication stress, PFN1/SNF2H increases fork stalling and functionally collaborates with fork reversal enzymes to enable the over-resection of unprotected forks. In addition, PFN1 binds and functionally attenuates the PLP-containing fork protector BODL1 to increase the resection of a subset of stressed forks. Accordingly, raising nuclear PFN1 level decreases genome stability and cell survival during replication stress. Thus, PFN1 is a multi-functional regulator of DNA replication with exploitable anticancer potential.
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Affiliation(s)
- Cuige Zhu
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mari Iwase
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ziqian Li
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Faliang Wang
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Annabel Quinet
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- UMR Genetic Stability Stem Cells and Radiation, University of Paris and University of Paris-Saclay, INSERM, iRCM/IBFJ CEA, Fontenay-aux-Roses, France
| | - Alessandro Vindigni
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jieya Shao
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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46
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Lemay JF, St-Hilaire E, Ronato DA, Gao Y, Bélanger F, Gezzar-Dandashi S, Kimenyi Ishimwe AB, Sawchyn C, Lévesque D, McQuaid M, Boisvert FM, Mallette FA, Masson JY, Drobetsky EA, Wurtele H. A genome-wide screen identifies SCAI as a modulator of the UV-induced replicative stress response. PLoS Biol 2022; 20:e3001543. [PMID: 36215310 PMCID: PMC9584372 DOI: 10.1371/journal.pbio.3001543] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 10/20/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
Helix-destabilizing DNA lesions induced by environmental mutagens such as UV light cause genomic instability by strongly blocking the progression of DNA replication forks (RFs). At blocked RF, single-stranded DNA (ssDNA) accumulates and is rapidly bound by Replication Protein A (RPA) complexes. Such stretches of RPA-ssDNA constitute platforms for recruitment/activation of critical factors that promote DNA synthesis restart. However, during periods of severe replicative stress, RPA availability may become limiting due to inordinate sequestration of this multifunctional complex on ssDNA, thereby negatively impacting multiple vital RPA-dependent processes. Here, we performed a genome-wide screen to identify factors that restrict the accumulation of RPA-ssDNA during UV-induced replicative stress. While this approach revealed some expected "hits" acting in pathways such as nucleotide excision repair, translesion DNA synthesis, and the intra-S phase checkpoint, it also identified SCAI, whose role in the replicative stress response was previously unappreciated. Upon UV exposure, SCAI knock-down caused elevated accumulation of RPA-ssDNA during S phase, accompanied by reduced cell survival and compromised RF progression. These effects were independent of the previously reported role of SCAI in 53BP1-dependent DNA double-strand break repair. We also found that SCAI is recruited to UV-damaged chromatin and that its depletion promotes nascent DNA degradation at stalled RF. Finally, we (i) provide evidence that EXO1 is the major nuclease underlying ssDNA formation and DNA replication defects in SCAI knockout cells and, consistent with this, (ii) demonstrate that SCAI inhibits EXO1 activity on a ssDNA gap in vitro. Taken together, our data establish SCAI as a novel regulator of the UV-induced replicative stress response in human cells.
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Affiliation(s)
- Jean-François Lemay
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | - Edlie St-Hilaire
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | - Daryl A. Ronato
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Québec, Canada
| | - Yuandi Gao
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Québec, Canada
| | - François Bélanger
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | - Sari Gezzar-Dandashi
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montréal, Québec, Canada
| | - Aimé Boris Kimenyi Ishimwe
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Molecular Biology Program, Université de Montréal, Montréal, Québec, Canada
| | - Christina Sawchyn
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Dominique Lévesque
- Department of Immunology and Cell Biology, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Mary McQuaid
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
| | | | - Frédérick A. Mallette
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Biochemistry and Molecular Medicine, Université de Montréal, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, Oncology Division; Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Québec, Canada
| | - Elliot A. Drobetsky
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- * E-mail: (EAD); (HW)
| | - Hugo Wurtele
- Centre de recherche, de l’Hôpital Maisonneuve-Rosemont, Montréal, Québec, Canada
- Department of Medicine, Université de Montréal, Montréal, Québec, Canada
- * E-mail: (EAD); (HW)
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47
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Wardlaw CP, Petrini JHJ. ISG15 conjugation to proteins on nascent DNA mitigates DNA replication stress. Nat Commun 2022; 13:5971. [PMID: 36216822 PMCID: PMC9550767 DOI: 10.1038/s41467-022-33535-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 09/21/2022] [Indexed: 11/09/2022] Open
Abstract
The pathways involved in suppressing DNA replication stress and the associated DNA damage are critical to maintaining genome integrity. The Mre11 complex is unique among double strand break (DSB) repair proteins for its association with the DNA replication fork. Here we show that Mre11 complex inactivation causes DNA replication stress and changes in the abundance of proteins associated with nascent DNA. One of the most highly enriched proteins at the DNA replication fork upon Mre11 complex inactivation was the ubiquitin like protein ISG15. Mre11 complex deficiency and drug induced replication stress both led to the accumulation of cytoplasmic DNA and the subsequent activation of innate immune signaling via cGAS-STING-Tbk1. This led to ISG15 induction and protein ISGylation, including constituents of the replication fork. ISG15 plays a direct role in preventing replication stress. Deletion of ISG15 was associated with replication fork stalling, tonic ATR activation, genomic aberrations, and sensitivity to aphidicolin. These data reveal a previously unrecognized role for ISG15 in mitigating DNA replication stress and promoting genomic stability.
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Affiliation(s)
- Christopher P Wardlaw
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA
| | - John H J Petrini
- Molecular Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.
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48
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ASPM promotes ATR-CHK1 activation and stabilizes stalled replication forks in response to replication stress. Proc Natl Acad Sci U S A 2022; 119:e2203783119. [PMID: 36161901 PMCID: PMC9546549 DOI: 10.1073/pnas.2203783119] [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] [Indexed: 12/02/2022] Open
Abstract
ASPM (encoded by MCPH5) is a frequently mutated protein, and such mutations occur in >40% of cases of primary microcephaly (MCPH). Here, we characterize a function of ASPM in DNA replication and the replication stress response. ASPM serves as a scaffold to load stimulators required for ATR-CHK1 checkpoint signaling upon replication stress, which protects stalled replication forks from degradation. ASPM deficiency leads to genomic instability and the sensitization of cancer cells to replication stressors. ASPM is a protein encoded by primary microcephaly 5 (MCPH5) and is responsible for ensuring spindle position during mitosis and the symmetrical division of neural stem cells. We recently reported that ASPM promotes homologous recombination (HR) repair of DNA double strand breaks. However, its potential role in DNA replication and replication stress response remains elusive. Interestingly, we found that ASPM is dispensable for DNA replication under unperturbed conditions. However, ASPM is enriched at stalled replication forks in a RAD17-dependent manner in response to replication stress and promotes RAD9 and TopBP1 loading onto chromatin, facilitating ATR-CHK1 activation. ASPM depletion results in failed fork restart and nuclease MRE11-mediated nascent DNA degradation at the stalled replication fork. The overall consequence is chromosome instability and the sensitization of cancer cells to replication stressors. These data support a role for ASPM in loading RAD17-RAD9/TopBP1 onto chromatin to activate the ATR-CHK1 checkpoint and ultimately ensure genome stability.
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49
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Jeong SY, Hariharasudhan G, Kim MJ, Lim JY, Jung SM, Choi EJ, Chang IY, Kee Y, You HJ, Lee JH. SIAH2 regulates DNA end resection and replication fork recovery by promoting CtIP ubiquitination. Nucleic Acids Res 2022; 50:10469-10486. [PMID: 36155803 PMCID: PMC9561274 DOI: 10.1093/nar/gkac808] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 08/19/2022] [Accepted: 09/10/2022] [Indexed: 11/16/2022] Open
Abstract
Human CtIP maintains genomic integrity primarily by promoting 5′ DNA end resection, an initial step of the homologous recombination (HR). A few mechanisms have been suggested as to how CtIP recruitment to damage sites is controlled, but it is likely that we do not yet have full understanding of the process. Here, we provide evidence that CtIP recruitment and functioning are controlled by the SIAH2 E3 ubiquitin ligase. We found that SIAH2 interacts and ubiquitinates CtIP at its N-terminal lysine residues. Mutating the key CtIP lysine residues impaired CtIP recruitment to DSBs and stalled replication forks, DSB end resection, overall HR repair capacity of cells, and recovery of stalled replication forks, suggesting that the SIAH2-induced ubiquitination is important for relocating CtIP to sites of damage. Depleting SIAH2 consistently phenocopied these results. Overall, our work suggests that SIAH2 is a new regulator of CtIP and HR repair, and emphasizes that SIAH2-mediated recruitment of the CtIP is an important step for CtIP’s function during HR repair.
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Affiliation(s)
- Seo-Yeon Jeong
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Gurusamy Hariharasudhan
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Min-Ji Kim
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Ji-Yeon Lim
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Pharmacology, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Sung Mi Jung
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Eun-Ji Choi
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - In-Youb Chang
- Department of Anatomy, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Younghoon Kee
- Department of New Biology, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Techno-Joongang-daero, Dalseong-gun, Daegu 42988, Republic of Korea
| | - Ho Jin You
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Pharmacology, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
| | - Jung-Hee Lee
- Laboratory of Genomic Instability and Cancer therapeutics, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea.,Department of Cellular and Molecular Medicine, Chosun University School of Medicine, 309 Pilmun-daero, Dong-gu, Gwangju 61452, Republic of Korea
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Benureau Y, Pouvelle C, Dupaigne P, Baconnais S, Moreira Tavares E, Mazón G, Despras E, Le Cam E, Kannouche P. Changes in the architecture and abundance of replication intermediates delineate the chronology of DNA damage tolerance pathways at UV-stalled replication forks in human cells. Nucleic Acids Res 2022; 50:9909-9929. [PMID: 36107774 PMCID: PMC9508826 DOI: 10.1093/nar/gkac746] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 08/09/2022] [Accepted: 08/23/2022] [Indexed: 11/21/2022] Open
Abstract
DNA lesions in S phase threaten genome stability. The DNA damage tolerance (DDT) pathways overcome these obstacles and allow completion of DNA synthesis by the use of specialised translesion (TLS) DNA polymerases or through recombination-related processes. However, how these mechanisms coordinate with each other and with bulk replication remains elusive. To address these issues, we monitored the variation of replication intermediate architecture in response to ultraviolet irradiation using transmission electron microscopy. We show that the TLS polymerase η, able to accurately bypass the major UV lesion and mutated in the skin cancer-prone xeroderma pigmentosum variant (XPV) syndrome, acts at the replication fork to resolve uncoupling and prevent post-replicative gap accumulation. Repriming occurs as a compensatory mechanism when this on-the-fly mechanism cannot operate, and is therefore predominant in XPV cells. Interestingly, our data support a recombination-independent function of RAD51 at the replication fork to sustain repriming. Finally, we provide evidence for the post-replicative commitment of recombination in gap repair and for pioneering observations of in vivo recombination intermediates. Altogether, we propose a chronology of UV damage tolerance in human cells that highlights the key role of polη in shaping this response and ensuring the continuity of DNA synthesis.
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Affiliation(s)
- Yann Benureau
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Caroline Pouvelle
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- Université Paris-Saclay , France
| | - Pauline Dupaigne
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Sonia Baconnais
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Eliana Moreira Tavares
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Gerard Mazón
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Emmanuelle Despras
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- Université Paris-Saclay , France
| | - Eric Le Cam
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory DSB Repair , Replication stress and Genome Integrity, Gustave Roussy 94805 , Villejuif, France
- Université Paris-Saclay , France
| | - Patricia L Kannouche
- UMR9019 CNRS, Genome Integrity and Cancers, Laboratory Genome Integrity , Immune Response and Cancers, Equipe Labellisée La Ligue Contre Le Cancer, Gustave Roussy 94805 , Villejuif , France
- Université Paris-Saclay , France
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