1
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Dubach RA, Dubach JM. Autocorrelation analysis of a phenotypic screen reveals hidden drug activity. Sci Rep 2024; 14:10046. [PMID: 38698021 PMCID: PMC11066105 DOI: 10.1038/s41598-024-60654-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 04/25/2024] [Indexed: 05/05/2024] Open
Abstract
Phenotype based screening is a powerful tool to evaluate cellular drug response. Through high content fluorescence imaging of simple fluorescent labels and complex image analysis phenotypic measurements can identify subtle compound-induced cellular changes unique to compound mechanisms of action (MoA). Recently, a screen of 1008 compounds in three cell lines was reported where analysis detected changes in cellular phenotypes and accurately identified compound MoA for roughly half the compounds. However, we were surprised that DNA alkylating agents and other compounds known to induce or impact the DNA damage response produced no measured activity in cells with fluorescently labeled 53BP1-a canonical DNA damage marker. We hypothesized that phenotype analysis is not sensitive enough to detect small changes in 53BP1 distribution and analyzed the screen images with autocorrelation image analysis. We found that autocorrelation analysis, which quantifies fluorescently-labeled protein clustering, identified higher compound activity for compounds and MoAs known to impact the DNA damage response, suggesting altered 53BP1 recruitment to damaged DNA sites. We then performed experiments under more ideal imaging settings and found autocorrelation analysis to be a robust measure of changes to 53BP1 clustering in the DNA damage response. These results demonstrate the capacity of autocorrelation to detect otherwise undetectable compound activity and suggest that autocorrelation analysis of specific proteins could serve as a powerful screening tool.
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Affiliation(s)
| | - J Matthew Dubach
- Institute for Innovation in Imaging, Massachusetts General Hospital, Harvard Medical School, Boston, USA.
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2
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Her J, Zheng H, Bunting SF. RNF4 sustains Myc-driven tumorigenesis by facilitating DNA replication. J Clin Invest 2024; 134:e167419. [PMID: 38530355 PMCID: PMC11093604 DOI: 10.1172/jci167419] [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: 11/22/2022] [Accepted: 03/20/2024] [Indexed: 03/27/2024] Open
Abstract
The mammalian SUMO-targeted E3 ubiquitin ligase Rnf4 has been reported to act as a regulator of DNA repair, but the importance of RNF4 as a tumor suppressor has not been tested. Using a conditional-knockout mouse model, we deleted Rnf4 in the B cell lineage to test the importance of RNF4 for growth of somatic cells. Although Rnf4-conditional-knockout B cells exhibited substantial genomic instability, Rnf4 deletion caused no increase in tumor susceptibility. In contrast, Rnf4 deletion extended the healthy lifespan of mice expressing an oncogenic c-myc transgene. Rnf4 activity is essential for normal DNA replication, and in its absence, there was a failure in ATR-CHK1 signaling of replication stress. Factors that normally mediate replication fork stability, including members of the Fanconi anemia gene family and the helicases PIF1 and RECQL5, showed reduced accumulation at replication forks in the absence of RNF4. RNF4 deficiency also resulted in an accumulation of hyper-SUMOylated proteins in chromatin, including members of the SMC5/6 complex, which contributes to replication failure by a mechanism dependent on RAD51. These findings indicate that RNF4, which shows increased expression in multiple human tumor types, is a potential target for anticancer therapy, especially in tumors expressing c-myc.
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Affiliation(s)
- Joonyoung Her
- Department of Molecular Biology and Biochemistry and
| | - Haiyan Zheng
- Biological Mass Spectrometry Facility, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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3
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Chen LW, Wang SS, Chen LY, Huang HY, He SM, Hung CH, Lin CL, Chang PJ. Interaction and assembly of the DNA replication core proteins of Kaposi's sarcoma-associated herpesvirus. Microbiol Spectr 2023; 11:e0225423. [PMID: 37874136 PMCID: PMC10715029 DOI: 10.1128/spectrum.02254-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/21/2023] [Indexed: 10/25/2023] Open
Abstract
IMPORTANCE Eukaryotic DNA replication is a highly regulated process that requires multiple replication enzymes assembled onto DNA replication origins. Due to the complexity of the cell's DNA replication machinery, most of what we know about cellular DNA replication has come from the study of viral systems. Herein, we focus our study on the assembly of the Kaposi's sarcoma-associated herpesvirus core replication complex and propose a pairwise protein-protein interaction network of six highly conserved viral core replication proteins. A detailed understanding of the interaction and assembly of the viral core replication proteins may provide opportunities to develop new strategies against viral propagation.
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Affiliation(s)
- Lee-Wen Chen
- Department of Respiratory Care, Chang Gung University of Science and Technology, Chiayi, Taiwan
- Department of Pediatric Surgery, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Shie-Shan Wang
- Department of Pediatric Surgery, Chang Gung Memorial Hospital, Chiayi, Taiwan
- School of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Li-Yu Chen
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Hsiao-Yun Huang
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Si-min He
- Department of Pediatric Surgery, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Chien-Hui Hung
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chun-Liang Lin
- Department of Nephrology, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Pey-Jium Chang
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Chang Gung Memorial Hospital, Chiayi, Taiwan
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4
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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: 2] [Impact Index Per Article: 2.0] [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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5
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Wang YL, Zhao WW, Shi J, Wan XB, Zheng J, Fan XJ. Liquid-liquid phase separation in DNA double-strand breaks repair. Cell Death Dis 2023; 14:746. [PMID: 37968256 PMCID: PMC10651886 DOI: 10.1038/s41419-023-06267-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 10/23/2023] [Accepted: 11/01/2023] [Indexed: 11/17/2023]
Abstract
DNA double-strand breaks (DSBs) are the fatal type of DNA damage mostly induced by exposure genome to ionizing radiation or genotoxic chemicals. DSBs are mainly repaired by homologous recombination (HR) and nonhomologous end joining (NHEJ). To repair DSBs, a large amount of DNA repair factors was observed to be concentrated at the end of DSBs in a specific spatiotemporal manner to form a repair center. Recently, this repair center was characterized as a condensate derived from liquid-liquid phase separation (LLPS) of key DSBs repair factors. LLPS has been found to be the mechanism of membraneless organelles formation and plays key roles in a variety of biological processes. In this review, the recent advances and mechanisms of LLPS in the formation of DSBs repair-related condensates are summarized.
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Affiliation(s)
- Yun-Long Wang
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Wan-Wen Zhao
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Jie Shi
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Xiang-Bo Wan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Jian Zheng
- Department of Radiation Oncology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China
| | - Xin-Juan Fan
- Henan Provincial Key Laboratory of Radiation Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, PR China.
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, 450052, PR China.
- GuangDong Provincial Key Laboratory of Colorectal and Pelvic Floor Diseases, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China.
- Department of Pathology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, 510655, PR China.
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6
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Galhenage P, Zhou Y, Perry E, Loc B, Fietz K, Iyer S, Reinhardt F, Da Silva T, Botchkarev V, Chen J, Crum CP, Weinberg RA, Pathania S. Replication stress and defective checkpoints make fallopian tube epithelial cells putative drivers of high-grade serous ovarian cancer. Cell Rep 2023; 42:113144. [PMID: 37729060 PMCID: PMC10762650 DOI: 10.1016/j.celrep.2023.113144] [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: 09/23/2022] [Revised: 06/02/2023] [Accepted: 08/31/2023] [Indexed: 09/22/2023] Open
Abstract
Clinical and molecular evidence indicates that high-grade serous ovarian cancer (HGSOC) primarily originates from the fallopian tube, not the ovarian surface. However, the reasons for this preference remain unclear. Our study highlights significant differences between fallopian tube epithelial (FTE) and ovarian surface epithelial (OSE) cells, providing the molecular basis for FTEs as site of origin of HGSOC. FTEs, unlike OSEs, exhibit heightened replication stress (RS), impaired repair of stalled forks, ineffective G2/M checkpoint, and increased tumorigenicity. BRCA1 heterozygosity exacerbates these defects, resulting in RS suppression haploinsufficiency and an aggressive tumor phenotype. Examination of human and mouse sections reveals buildup of the RS marker 53BP1 primarily in the fallopian tubes, particularly at the fimbrial ends. Furthermore, menopausal status influences RS levels. Our study provides a mechanistic rationale for FTE as the site of origin for HGSOC, investigates the impact of BRCA1 heterozygosity, and lays the groundwork for targeting early HGSOC drivers.
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Affiliation(s)
- Pamoda Galhenage
- Center for Personalized Cancer Therapy, Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Yunlan Zhou
- Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Erica Perry
- Center for Personalized Cancer Therapy, Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Brenda Loc
- Center for Personalized Cancer Therapy, Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kelly Fietz
- Center for Personalized Cancer Therapy, Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Sonia Iyer
- Whitehead Institute for Biomedical Research, 455 Main Street, WHTH-367, Cambridge, MA 02142, USA
| | - Ferenc Reinhardt
- Whitehead Institute for Biomedical Research, 455 Main Street, WHTH-367, Cambridge, MA 02142, USA
| | - Tiego Da Silva
- Center for Personalized Cancer Therapy, Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA
| | | | - Jie Chen
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Christopher P Crum
- Department of Pathology, Division of Women's and Perinatal Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Robert A Weinberg
- Whitehead Institute for Biomedical Research, 455 Main Street, WHTH-367, Cambridge, MA 02142, USA
| | - Shailja Pathania
- Center for Personalized Cancer Therapy, Department of Biology, University of Massachusetts Boston, Boston, MA 02125, USA.
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Wang Y, Wang R, Ma H, Yang M, Li Z, Zhang L. Wnt3a signaling with serum supply induces replication stress in cultured cells. Biochem Biophys Rep 2023; 35:101499. [PMID: 37601449 PMCID: PMC10439351 DOI: 10.1016/j.bbrep.2023.101499] [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: 02/02/2023] [Revised: 06/02/2023] [Accepted: 06/05/2023] [Indexed: 08/22/2023] Open
Abstract
Wnt signaling plays a central role in tissue development and homeostasis, and its deregulation is implicated in many human diseases, including cancer. As an essential posttranslational modification, protein phosphorylation is critical in Wnt signaling and has been a focus of investigation using systematic approaches, including proteomics. Typically, studies were conducted by applying purified Wnt ligands to cells in a "starvation" condition to minimize the background noise. Despite leading to many important discoveries, such an approach may omit pivotal integrative effects of Wnt signaling in a complex physiological environment. In this study, we investigated the temporal dynamics of the phosphoproteome following treatments of Wnt3a conditioned medium (CM) with serum supply. This revealed three clusters of phosphoproteome changes with distinct temporal profiles with implications in gene expressions and chromatin organizations. Among these, we observed enhanced phosphorylation at the Thr543 residue of 53BP1, which is a key event in the cellular response to DNA damage. Functionally, it triggered the replication stress response pathway mediated by γH2AX accumulation and Chk1 activation, leading to a significant reduction of cells in the S phase of the cell cycle. Intriguingly, Wnt3a treatment in the serum-free condition did not activate 53BP1-Chk1 and replication stress response. Our study indicates the importance of noting the presence or absence of serum supply when studying the signaling pathways.
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Affiliation(s)
- Ying Wang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong, China
| | - Rui Wang
- Pingshan Translational Medicine Centre, Shenzhen Bay Laboratory, Shenzhen, 518118, PR China
| | - Haiying Ma
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong, China
- State Key Laboratory of Marine Pollution, City University of Hong Kong, Kowloon, Hong Kong
| | - Mengsu Yang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong, China
| | - Zigang Li
- Pingshan Translational Medicine Centre, Shenzhen Bay Laboratory, Shenzhen, 518118, PR China
- State Key Laboratory of Chemical Oncogenomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, PR China
| | - Liang Zhang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
- Department of Precision Diagnostic and Therapeutic Technology, City University of Hong Kong Futian Research Institute, Shenzhen, Guangdong, China
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8
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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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9
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DNA Damage Response Mechanisms in Head and Neck Cancer: Significant Implications for Therapy and Survival. Int J Mol Sci 2023; 24:ijms24032760. [PMID: 36769087 PMCID: PMC9917521 DOI: 10.3390/ijms24032760] [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: 12/28/2022] [Revised: 01/27/2023] [Accepted: 01/29/2023] [Indexed: 02/04/2023] Open
Abstract
Head and neck cancer (HNC) is a term collectively used to describe a heterogeneous group of tumors that arise in the oral cavity, larynx, nasopharynx, oropharynx, and hypopharynx, and represents the sixth most common type of malignancy worldwide. Despite advances in multimodality treatment, the disease has a recurrence rate of around 50%, and the prognosis of metastatic patients remains poor. HNCs are characterized by a high degree of genomic instability, which involves a vicious circle of accumulating DNA damage, defective DNA damage repair (DDR), and replication stress. Nonetheless, the damage that is induced on tumor cells by chemo and radiotherapy relies on defective DDR processes for a successful response to treatment, and may play an important role in the development of novel and more effective therapies. This review summarizes the current knowledge on the genes and proteins that appear to be deregulated in DDR pathways, their implication in HNC pathogenesis, and the rationale behind targeting these genes and pathways for the development of new therapies. We give particular emphasis on the therapeutic targets that have shown promising results at the pre-clinical stage and on those that have so far been associated with a therapeutic advantage in the clinical setting.
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10
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Rass E, Willaume S, Bertrand P. 53BP1: Keeping It under Control, Even at a Distance from DNA Damage. Genes (Basel) 2022; 13:genes13122390. [PMID: 36553657 PMCID: PMC9778356 DOI: 10.3390/genes13122390] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/02/2022] [Accepted: 12/07/2022] [Indexed: 12/23/2022] Open
Abstract
Double-strand breaks (DSBs) are toxic lesions that can be generated by exposure to genotoxic agents or during physiological processes, such as during V(D)J recombination. The repair of these DSBs is crucial to prevent genomic instability and to maintain cellular homeostasis. Two main pathways participate in repairing DSBs, namely, non-homologous end joining (NHEJ) and homologous recombination (HR). The P53-binding protein 1 (53BP1) plays a pivotal role in the choice of DSB repair mechanism, promotes checkpoint activation and preserves genome stability upon DSBs. By preventing DSB end resection, 53BP1 promotes NHEJ over HR. Nonetheless, the balance between DSB repair pathways remains crucial, as unscheduled NHEJ or HR events at different phases of the cell cycle may lead to genomic instability. Therefore, the recruitment of 53BP1 to chromatin is tightly regulated and has been widely studied. However, less is known about the mechanism regulating 53BP1 recruitment at a distance from the DNA damage. The present review focuses on the mechanism of 53BP1 recruitment to damage and on recent studies describing novel mechanisms keeping 53BP1 at a distance from DSBs.
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Affiliation(s)
- Emilie Rass
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Correspondence:
| | - Simon Willaume
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
| | - Pascale Bertrand
- Université Paris Cité, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
- Université Paris-Saclay, INSERM, CEA, Stabilité Génétique Cellules Souches et Radiations, LREV/iRCM/IBFJ, F-92260 Fontenay-aux-Roses, France
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11
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Le W, Zhou F, Xiang J, Weng Y, Wu D, Xu J, Zhang J. Preliminary Study on 53BP1-Mediated DNA Double-Strand Break Response in Spermatogonial Stem Cells. Reprod Sci 2022; 30:1572-1584. [PMID: 36446980 DOI: 10.1007/s43032-022-01122-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/30/2022] [Indexed: 11/30/2022]
Abstract
53BP1 mediates DNA repair process in somatic cells; however, the function of 53BP1 in germline stem cells still remains unclear. In the present study, animals and cells DNA damage repair (DDR) model was established by irradiation and HU treatment; immunofluorescence staining and laser confocal microscopy were used to detect the expression of 53BP1, p-CHK2, and p-P53 in the DDR process of mSSCs. 53BP1 knockdown expression mSSCs cell line conducted by Trp53bp1-shRNA was established and EdU staining was adopted to analyze cell cycle and cell proliferation. Moreover, NHEJ reporter vector was applied to detect the repair efficacy after Trp53bp1 knocked-down (KD) expression. Results showed that 53BP1 could form foci signals in mSSCs during DDR process both in vivo and in vitro, which was independent of γH2AX. 53BP1 downstream protein, p-P53, and p-CHK2 were involved and dynamically expressed in DDR response. Knocking down of Trp53bp1 expression in mSSCs could not dramatically inhibit cell proliferation, but may increase cell sensitivity to HU. The NHEJ repair efficacy was sharply decreased in Trp53bp-KD SSCs via flow cytometry analysis. We revealed the specific mechanism of 53BP1 in SSCs DDR process, which is expected to provide a new theoretical basis and insights for the diagnosis and treatment of male infertility.
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Affiliation(s)
- Wei Le
- Department of Urology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai, 200065, China
| | - Fang Zhou
- Department of Surgery, Tongren Hospital, Shanghai Jiaotong University School of Medicine, 1111 Xianxia Road, Shanghai, 200050, China
| | - Jun Xiang
- Department of Urology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai, 200065, China
| | - Yiming Weng
- Department of Reproductive Medicine, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai, 200065, China
| | - Denglong Wu
- Department of Urology, Tongji Hospital, Tongji University School of Medicine, 389 Xincun Road, Shanghai, 200065, China
| | - Jun Xu
- Department of Regenerative Medicine, East Hospital, Tongji University School of Medicine, 1239 Siping Road, Shanghai, 200120, China
| | - Jinfu Zhang
- Department of Reproductive Medicine, Guanghua Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, 540 Xinhua Road, Shanghai, 200052, China.
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12
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Paniagua I, Tayeh Z, Falcone M, Hernández Pérez S, Cerutti A, Jacobs JJL. MAD2L2 promotes replication fork protection and recovery in a shieldin-independent and REV3L-dependent manner. Nat Commun 2022; 13:5167. [PMID: 36075897 PMCID: PMC9458726 DOI: 10.1038/s41467-022-32861-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 08/18/2022] [Indexed: 11/10/2022] Open
Abstract
Protection of stalled replication forks is essential to prevent genome instability, a major driving force of tumorigenesis. Several key regulators of DNA double-stranded break (DSB) repair, including 53BP1 and RIF1, have been implicated in fork protection. MAD2L2, also known as REV7, plays an important role downstream of 53BP1/RIF1 by counteracting resection at DSBs in the recently discovered shieldin complex. The ability to bind and counteract resection at exposed DNA ends at DSBs makes MAD2L2/shieldin a prime candidate for also suppressing nucleolytic processing at stalled replication forks. However, the function of MAD2L2/shieldin outside of DNA repair is unknown. Here we address this by using genetic and single-molecule analyses and find that MAD2L2 is required for protecting and restarting stalled replication forks. MAD2L2 loss leads to uncontrolled MRE11-dependent resection of stalled forks and single-stranded DNA accumulation, which causes irreparable genomic damage. Unexpectedly, MAD2L2 limits resection at stalled forks independently of shieldin, since fork protection remained unaffected by shieldin loss. Instead, MAD2L2 cooperates with the DNA polymerases REV3L and REV1 to promote fork stability. Thus, MAD2L2 suppresses aberrant nucleolytic processing both at DSBs and stalled replication forks by differentially engaging shieldin and REV1/REV3L, respectively. MAD2L2 – as a member of the shieldin complex - counteracts resection during DNA repair. Here the authors demonstrate that MAD2L2 protects stalled replication forks from excessive resection, in a shieldin-independent and REV3L-dependent manner.
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Affiliation(s)
- Inés Paniagua
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Zainab Tayeh
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Mattia Falcone
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Santiago Hernández Pérez
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Aurora Cerutti
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
| | - Jacqueline J L Jacobs
- Division of Oncogenomics, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.
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13
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Sottile ML, Cuello-Carrión FD, Gómez LC, Semino S, Ibarra J, García MB, Gonzalez L, Vargas-Roig LM, Nadin SB. DNA Damage Repair Proteins, HSP27, and Phosphorylated-HSP90α as Predictive/Prognostic Biomarkers of Platinum-based Cancer Chemotherapy: An Exploratory Study. Appl Immunohistochem Mol Morphol 2022; 30:425-434. [PMID: 35639358 DOI: 10.1097/pai.0000000000001037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 04/25/2022] [Indexed: 11/27/2022]
Abstract
Platinum analogs are commonly used for cancer treatment. There is increasing interest in finding biomarkers which could predict and overcome resistance, because to date there is no reliable predictive/prognostic marker for these compounds. Here we studied the immunohistochemical expression of proteins involved in DNA damage response and repair (γH2AX, 53BP1, ERCC1, MLH1, and MSH2) in primary tumor tissues from patients treated with platinum-based chemotherapy. Levels and localization of Heat Shock Protein (HSP)27 and phospho-(Thr5/7)-HSP90α (p-HSP90α) were also determined. The implications in clinical response, disease-free survival and overall survival were analyzed. High γH2AX and 53BP1 expressions were associated with poor clinical response. Nuclear p-HSP90α, as well as nuclear absence and low cytoplasmic expression of HSP27 correlated with good response. Patients with high γH2AX and high cytoplasmic HSP27 expressions had shorter overall survival and disease-free survival. MLH1, MSH2, or ERCC1 were not associated with clinical response or survival. We report the potential utility of p-HSP90α, HSP27, γH2AX, and 53BP1 as predictive/prognostic markers for platinum-based chemotherapy. We present the first study that evaluates the predictive and prognostic value of p-HSP90α in primary tumors. Our research opens new possibilities for clinical oncology and shows the usefulness of immunohistochemistry for predicting chemotherapy response and prognosis in cancer.
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Affiliation(s)
- Mayra L Sottile
- Tumor Biology Laboratory
- Medical Sciences School, Mendoza University
| | | | - Laura C Gómez
- Tumor Biology Laboratory
- Medical Sciences School, Mendoza University
| | | | - Jorge Ibarra
- Regional Integration Cancer Center, Mendoza, Argentina
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14
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Meessen S, Najjar G, Azoitei A, Iben S, Bolenz C, Günes C. A Comparative Assessment of Replication Stress Markers in the Context of Telomerase. Cancers (Basel) 2022; 14:cancers14092205. [PMID: 35565334 PMCID: PMC9103842 DOI: 10.3390/cancers14092205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 04/26/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Genetic alterations such as oncogenic- or aneuploidy-inducing mutations can induce replication stress as a tumor protection mechansim. Previous data indicated that telomerase may ameliorate the cellular responses that induce replication stress. However, the mechanisms how this may occur are still unclear. In order to address this question, the accurate evaluation of replication stress in the presence and absence of telomerase is crucial. Therefore, we used telomerase negative normal human fibroblasts, as well as their telomerase positive counterparts to compare the suitability of three protein markers (pRPA2, γ-H2AX and 53BP1), which were previously reported to accumulate in response to harmful conditions leading to replication stress in cells. In summary, we find that pRPA2 is the most consistent and reliable marker for the detection of replication stress. Further, we demonstrated that the inhibition of the DNA-damage activated ATM and ATR kinases by specific small compounds impaired the accumulation of pRPA2 foci in the absence of telomerase. These data suggest that telomerase rescues the cells from replication stress upon supression of DNA damage induction by modulating the ATM and ATR signaling pathways, and may therefore support tumor formation of genetically unstable cells. Abstract Aberrant replication stress (RS) is a source of genome instability and has serious implications for cell survival and tumourigenesis. Therefore, the detection of RS and the identification of the underlying molecular mechanisms are crucial for the understanding of tumourigenesis. Currently, three protein markers—p33-phosphorylated replication protein A2 (pRPA2), γ-phosphorylated H2AX (γ-H2AX), and Tumor Protein P53 Binding Protein 1 (53BP1)—are frequently used to detect RS. However, to our knowledge, there is no report that compares their suitability for the detection of different sources of RS. Therefore, in this study, we evaluate the suitability of pRPA2, γ-H2AX, and 53BP1 for the detection of RS caused by different sources of RS. In addition, we examine their suitability as markers of the telomerase-mediated alleviation of RS. For these purposes, we use here telomerase-negative human fibroblasts (BJ) and their telomerase-immortalized counterparts (BJ-hTERT). Replication stress was induced by the ectopic expression of the oncogenic RAS mutant RASG12V (OI-RS), by the knockdown of ploidy-control genes ORP3 or MAD2 (AI-RS), and by treatment with hydrogen peroxide (ROS-induced RS). The level of RS was determined by immunofluorescence staining for pRPA2, γ-H2AX, and 53BP1. Evaluation of the staining results revealed that pRPA2- and γ-H2AX provide a significant and reliable assessment of OI-RS and AI-RS compared to 53BP1. On the other hand, 53BP1 and pRPA2 proved to be superior to γ-H2AX for the evaluation of ROS-induced RS. Moreover, the data showed that among the tested markers, pRPA2 is best suited to evaluate the telomerase-mediated suppression of all three types of RS. In summary, the data indicate that the choice of marker is important for the evaluation of RS activated through different conditions.
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Affiliation(s)
- Sabine Meessen
- Department of Urology, Ulm University Hospital, 89081 Ulm, Germany; (S.M.); (G.N.); (A.A.); (C.B.)
| | - Gregoire Najjar
- Department of Urology, Ulm University Hospital, 89081 Ulm, Germany; (S.M.); (G.N.); (A.A.); (C.B.)
| | - Anca Azoitei
- Department of Urology, Ulm University Hospital, 89081 Ulm, Germany; (S.M.); (G.N.); (A.A.); (C.B.)
| | - Sebastian Iben
- Department of Dermatology, Ulm University Hospital, 89081 Ulm, Germany;
| | - Christian Bolenz
- Department of Urology, Ulm University Hospital, 89081 Ulm, Germany; (S.M.); (G.N.); (A.A.); (C.B.)
| | - Cagatay Günes
- Department of Urology, Ulm University Hospital, 89081 Ulm, Germany; (S.M.); (G.N.); (A.A.); (C.B.)
- Correspondence: ; Tel.: +49-(0)731-500-58019; Fax: +49-(0)731-500-58093
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15
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Oncogenic RAS sensitizes cells to drug-induced replication stress via transcriptional silencing of P53. Oncogene 2022; 41:2719-2733. [PMID: 35393546 PMCID: PMC9076537 DOI: 10.1038/s41388-022-02291-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 03/17/2022] [Accepted: 03/21/2022] [Indexed: 11/09/2022]
Abstract
Cancer cells often experience high basal levels of DNA replication stress (RS), for example due to hyperactivation of oncoproteins like MYC or RAS. Therefore, cancer cells are considered to be sensitive to drugs that exacerbate the level of RS or block the intra S-phase checkpoint. Consequently, RS-inducing drugs including ATR and CHK1 inhibitors are used or evaluated as anti-cancer therapies. However, drug resistance and lack of biomarkers predicting therapeutic efficacy limit efficient use. This raises the question what determines sensitivity of individual cancer cells to RS. Here, we report that oncogenic RAS does not only enhance the sensitivity to ATR/CHK1 inhibitors by directly causing RS. Instead, we observed that HRASG12V dampens the activation of the P53-dependent transcriptional response to drug-induced RS, which in turn confers sensitivity to RS. We demonstrate that inducible expression of HRASG12V sensitized cells to ATR and CHK1 inhibitors. Using RNA-sequencing of FACS-sorted cells we discovered that P53 signaling is the sole transcriptional response to RS. However, oncogenic RAS attenuates the transcription of P53 and TGF-β pathway components which consequently dampens P53 target gene expression. Accordingly, live cell imaging showed that HRASG12V exacerbates RS in S/G2-phase, which could be rescued by stabilization of P53. Thus, our results demonstrate that transcriptional control of P53 target genes is the prime determinant in the response to ATR/CHK1 inhibitors and show that hyperactivation of the MAPK pathway impedes this response. Our findings suggest that the level of oncogenic MAPK signaling could predict sensitivity to intra-S-phase checkpoint inhibition in cancers with intact P53.
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16
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Jan YH, Heck DE, An Y, Laskin DL, Laskin JD. Nitrogen Mustard Alkylates and Cross-Links p53 in Human Keratinocytes. Chem Res Toxicol 2022; 35:636-650. [PMID: 35312310 PMCID: PMC9491701 DOI: 10.1021/acs.chemrestox.1c00420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cytotoxic blistering agents such as sulfur mustard and nitrogen mustard (HN2) were synthesized for chemical warfare. Toxicity is due to reactive chloroethyl side chains that modify and damage cellular macromolecules including DNA and proteins. In response to DNA damage, cells initiate a DNA damage response directed at the recruitment and activation of repair-related proteins. A central mediator of the DNA damage response is p53, a protein that plays a critical role in regulating DNA repair. We found that HN2 causes cytosolic and nuclear accumulation of p53 in HaCaT keratinocytes; HN2 also induced post-translational modifications on p53 including S15 phosphorylation and K382 acetylation, which enhance p53 stability, promote DNA repair, and mediate cellular metabolic responses to stress. HN2 also cross-linked p53, forming dimers and high-molecular-weight protein complexes in the cells. Cross-linked multimers were also modified by K48-linked ubiquitination indicating that they are targets for proteasome degradation. HN2-induced modifications transiently suppressed the transcriptional activity of p53. Using recombinant human p53, HN2 alkylation was found to be concentration- and redox status-dependent. Dithiothreitol-reduced protein was more efficiently cross-linked indicating that p53 cysteine residues play a key role in protein modification. LC-MS/MS analysis revealed that HN2 directly alkylated p53 at C124, C135, C141, C176, C182, C275, C277, H115, H178, K132, and K139, forming both monoadducts and cross-links. The formation of intermolecular complexes was a consequence of HN2 cross-linked cysteine residues between two molecules of p53. Together, these data demonstrate that p53 is a molecular target for mustard vesicants. Modification of p53 likely mediates cellular responses to HN2 including DNA repair and cell survival contributing to vesicant-induced cytotoxicity.
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Affiliation(s)
- Yi-Hua Jan
- Department of Environmental and Occupational Health and Justice, Rutgers University School of Public Health, Piscataway, New Jersey 08854, United States
| | - Diane E Heck
- Department of Environmental Health Science, New York Medical College, Valhalla, New York 10595, United States
| | - Yunqi An
- Department of Pharmacology and Toxicology, Rutgers University Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854, United States
| | - Debra L Laskin
- Department of Pharmacology and Toxicology, Rutgers University Ernest Mario School of Pharmacy, Piscataway, New Jersey 08854, United States
| | - Jeffrey D Laskin
- Department of Environmental and Occupational Health and Justice, Rutgers University School of Public Health, Piscataway, New Jersey 08854, United States
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17
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Parsa FG, Nobili S, Karimpour M, Aghdaei HA, Nazemalhosseini-Mojarad E, Mini E. Fanconi Anemia Pathway in Colorectal Cancer: A Novel Opportunity for Diagnosis, Prognosis and Therapy. J Pers Med 2022; 12:jpm12030396. [PMID: 35330396 PMCID: PMC8950345 DOI: 10.3390/jpm12030396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/01/2022] [Accepted: 03/02/2022] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is the third most commonly diagnosed malignancy and has the second highest mortality rate globally. Thanks to the advent of next-generation sequencing technologies, several novel candidate genes have been proposed for CRC susceptibility. Germline biallelic mutations in one or more of the 22 currently recognized Fanconi anemia (FA) genes have been associated with Fanconi anemia disease, while germline monoallelic mutations, somatic mutations, or the promoter hypermethylation of some FANC genes increases the risk of cancer development, including CRC. The FA pathway is a substantial part of the DNA damage response system that participates in the repair of DNA inter-strand crosslinks through homologous recombination (HR) and protects genome stability via replication fork stabilization, respectively. Recent studies revealed associations between FA gene/protein tumor expression levels (i.e., FANC genes) and CRC progression and drug resistance. Moreover, the FA pathway represents a potential target in the CRC treatment. In fact, FANC gene characteristics may contribute to chemosensitize tumor cells to DNA crosslinking agents such as oxaliplatin and cisplatin besides exploiting the synthetic lethal approach for selective targeting of tumor cells. Hence, this review summarizes the current knowledge on the function of the FA pathway in DNA repair and genomic integrity with a focus on the FANC genes as potential predisposition factors to CRC. We then introduce recent literature that highlights the importance of FANC genes in CRC as promising prognostic and predictive biomarkers for disease management and treatment. Finally, we represent a brief overview of the current knowledge around the FANC genes as synthetic lethal therapeutic targets for precision cancer medicine.
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Affiliation(s)
- Fatemeh Ghorbani Parsa
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19857-17413, Iran; (F.G.P.); (H.A.A.)
| | - Stefania Nobili
- Department of Neurosciences, Imaging and Clinical Sciences, University “G. D’Annunzio” Chieti-Pescara, 66100 Chieti, Italy;
- Center for Advanced Studies and Technology (CAST), University “G. D’Annunzio” Chieti-Pescara, 66100 Chieti, Italy
| | - Mina Karimpour
- Department of Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran 14115-154, Iran;
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19857-17413, Iran; (F.G.P.); (H.A.A.)
| | - Ehsan Nazemalhosseini-Mojarad
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran 19857-17413, Iran
- Correspondence: (E.N.-M.); (E.M.)
| | - Enrico Mini
- Department of Health Sciences, University of Florence, 50139 Florence, Italy
- DENOTHE Excellence Center, University of Florence, 50139 Florence, Italy
- Correspondence: (E.N.-M.); (E.M.)
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18
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Wu T, Jun S, Choi EJ, Sun J, Yang EB, Lee HS, Kim SY, Fahmi NA, Jiang Q, Zhang W, Yong J, Lee JH, You HJ. 53BP1-ACLY-SLBP-coordinated activation of replication-dependent histone biogenesis maintains genomic integrity. Nucleic Acids Res 2022; 50:1465-1483. [PMID: 35037047 PMCID: PMC8860602 DOI: 10.1093/nar/gkab1300] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 12/16/2021] [Accepted: 01/08/2022] [Indexed: 11/12/2022] Open
Abstract
p53-binding protein 1 (53BP1) regulates the DNA double-strand break (DSB) repair pathway and maintains genomic integrity. Here we found that 53BP1 functions as a molecular scaffold for the nucleoside diphosphate kinase-mediated phosphorylation of ATP-citrate lyase (ACLY) which enhances the ACLY activity. This functional association is critical for promoting global histone acetylation and subsequent transcriptome-wide alterations in gene expression. Specifically, expression of a replication-dependent histone biogenesis factor, stem-loop binding protein (SLBP), is dependent upon 53BP1-ACLY-controlled acetylation at the SLBP promoter. This chain of regulation events carried out by 53BP1, ACLY, and SLBP is crucial for both quantitative and qualitative histone biogenesis as well as for the preservation of genomic integrity. Collectively, our findings reveal a previously unknown role for 53BP1 in coordinating replication-dependent histone biogenesis and highlight a DNA repair-independent function in the maintenance of genomic stability through a regulatory network that includes ACLY and SLBP.
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Affiliation(s)
- TingTing Wu
- DNA Damage Response Network Center.,Department of Pharmacology
| | - Semo Jun
- DNA Damage Response Network Center.,Department of Pharmacology
| | - Eun-Ji Choi
- DNA Damage Response Network Center.,Department of Cellular and Molecular Medicine
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Eun-Bi Yang
- DNA Damage Response Network Center.,Department of Cellular and Molecular Medicine
| | | | - Sang-Yong Kim
- Division of Endocrinology, Chosun University School of medicine, 375 Seosuk-dong, Gwangju 61452, Republic of Korea
| | - Naima Ahmed Fahmi
- Division of Endocrinology, Chosun University School of medicine, 375 Seosuk-dong, Gwangju 61452, Republic of Korea
| | - Qibing Jiang
- Division of Endocrinology, Chosun University School of medicine, 375 Seosuk-dong, Gwangju 61452, Republic of Korea
| | - Wei Zhang
- Division of Endocrinology, Chosun University School of medicine, 375 Seosuk-dong, Gwangju 61452, Republic of Korea
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA
| | - Jung-Hee Lee
- DNA Damage Response Network Center.,Department of Cellular and Molecular Medicine
| | - Ho Jin You
- DNA Damage Response Network Center.,Department of Pharmacology
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19
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BRCA1/Trp53 heterozygosity and replication stress drive esophageal cancer development in a mouse model. Proc Natl Acad Sci U S A 2021; 118:2108421118. [PMID: 34607954 PMCID: PMC8521688 DOI: 10.1073/pnas.2108421118] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 12/13/2022] Open
Abstract
BRCA1 germline mutations are associated with an increased risk of breast and ovarian cancer. Recent findings of others suggest that BRCA1 mutation carriers also bear an increased risk of esophageal and gastric cancer. Here, we employ a Brca1/Trp53 mouse model to show that unresolved replication stress (RS) in BRCA1 heterozygous cells drives esophageal tumorigenesis in a model of the human equivalent. This model employs 4-nitroquinoline-1-oxide (4NQO) as an RS-inducing agent. Upon drinking 4NQO-containing water, Brca1 heterozygous mice formed squamous cell carcinomas of the distal esophagus and forestomach at a much higher frequency and speed (∼90 to 120 d) than did wild-type (WT) mice, which remained largely tumor free. Their esophageal tissue, but not that of WT control mice, revealed evidence of overt RS as reflected by intracellular CHK1 phosphorylation and 53BP1 staining. These Brca1 mutant tumors also revealed higher genome mutation rates than those of control animals; the mutational signature SBS4, which is associated with tobacco-induced tumorigenesis; and a loss of Brca1 heterozygosity (LOH). This uniquely accelerated Brca1 tumor model is also relevant to human esophageal squamous cell carcinoma, an often lethal tumor.
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20
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Uruci S, Lo CSY, Wheeler D, Taneja N. R-Loops and Its Chro-Mates: The Strange Case of Dr. Jekyll and Mr. Hyde. Int J Mol Sci 2021; 22:ijms22168850. [PMID: 34445553 PMCID: PMC8396322 DOI: 10.3390/ijms22168850] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/22/2022] Open
Abstract
Since their discovery, R-loops have been associated with both physiological and pathological functions that are conserved across species. R-loops are a source of replication stress and genome instability, as seen in neurodegenerative disorders and cancer. In response, cells have evolved pathways to prevent R-loop accumulation as well as to resolve them. A growing body of evidence correlates R-loop accumulation with changes in the epigenetic landscape. However, the role of chromatin modification and remodeling in R-loops homeostasis remains unclear. This review covers various mechanisms precluding R-loop accumulation and highlights the role of chromatin modifiers and remodelers in facilitating timely R-loop resolution. We also discuss the enigmatic role of RNA:DNA hybrids in facilitating DNA repair, epigenetic landscape and the potential role of replication fork preservation pathways, active fork stability and stalled fork protection pathways, in avoiding replication-transcription conflicts. Finally, we discuss the potential role of several Chro-Mates (chromatin modifiers and remodelers) in the likely differentiation between persistent/detrimental R-loops and transient/benign R-loops that assist in various physiological processes relevant for therapeutic interventions.
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Affiliation(s)
- Sidrit Uruci
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - Calvin Shun Yu Lo
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
| | - David Wheeler
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, NIH, Bethesda, MD 20892, USA;
| | - Nitika Taneja
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3000 CA Rotterdam, The Netherlands; (S.U.); (C.S.Y.L.)
- Correspondence:
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21
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Ihle M, Biber S, Schroeder IS, Blattner C, Deniz M, Damia G, Gottifredi V, Wiesmüller L. Impact of the interplay between stemness features, p53 and pol iota on replication pathway choices. Nucleic Acids Res 2021; 49:7457-7475. [PMID: 34165573 PMCID: PMC8287946 DOI: 10.1093/nar/gkab526] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/02/2021] [Accepted: 06/09/2021] [Indexed: 12/12/2022] Open
Abstract
Using human embryonic, adult and cancer stem cells/stem cell-like cells (SCs), we demonstrate that DNA replication speed differs in SCs and their differentiated counterparts. While SCs decelerate DNA replication, differentiated cells synthesize DNA faster and accumulate DNA damage. Notably, both replication phenotypes depend on p53 and polymerase iota (POLι). By exploring protein interactions and newly synthesized DNA, we show that SCs promote complex formation of p53 and POLι at replication sites. Intriguingly, in SCs the translocase ZRANB3 is recruited to POLι and required for slow-down of DNA replication. The known role of ZRANB3 in fork reversal suggests that the p53–POLι complex mediates slow but safe bypass of replication barriers in SCs. In differentiated cells, POLι localizes more transiently to sites of DNA synthesis and no longer interacts with p53 facilitating fast POLι-dependent DNA replication. In this alternative scenario, POLι associates with the p53 target p21, which antagonizes PCNA poly-ubiquitination and, thereby potentially disfavors the recruitment of translocases. Altogether, we provide evidence for diametrically opposed DNA replication phenotypes in SCs and their differentiated counterparts putting DNA replication-based strategies in the spotlight for the creation of therapeutic opportunities targeting SCs.
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Affiliation(s)
- Michaela Ihle
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Stephanie Biber
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Insa S Schroeder
- Department of Biophysics, GSI Helmholtz Center for Heavy Ion Research, Darmstadt 64291, Germany
| | - Christine Blattner
- Institute for Biological and Chemical Systems - Biological Information Processing, Karlsruhe Institute of Technology, Karlsruhe 76021, Germany
| | - Miriam Deniz
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
| | - Giovanna Damia
- Department of Oncology, Istituto di Ricerche Farmacologiche Mario Negri-IRCCS Milan, Milan 20156, Italy
| | - Vanesa Gottifredi
- Cell cycle and Genomic Stability Laboratory, Fundación Instituto Leloir, Buenos Aires C1405BWE, Argentina
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, Ulm 89075, Germany
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22
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Thakar T, Moldovan GL. The emerging determinants of replication fork stability. Nucleic Acids Res 2021; 49:7224-7238. [PMID: 33978751 PMCID: PMC8287955 DOI: 10.1093/nar/gkab344] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/18/2021] [Accepted: 04/20/2021] [Indexed: 12/21/2022] Open
Abstract
A universal response to replication stress is replication fork reversal, where the nascent complementary DNA strands are annealed to form a protective four-way junction allowing forks to avert DNA damage while replication stress is resolved. However, reversed forks are in turn susceptible to nucleolytic digestion of the regressed nascent DNA arms and rely on dedicated mechanisms to protect their integrity. The most well studied fork protection mechanism involves the BRCA pathway and its ability to catalyze RAD51 nucleofilament formation on the reversed arms of stalled replication forks. Importantly, the inability to prevent the degradation of reversed forks has emerged as a hallmark of BRCA deficiency and underlies genome instability and chemosensitivity in BRCA-deficient cells. In the past decade, multiple factors underlying fork stability have been discovered. These factors either cooperate with the BRCA pathway, operate independently from it to augment fork stability in its absence, or act as enablers of fork degradation. In this review, we examine these novel determinants of fork stability, explore the emergent conceptual underpinnings underlying fork protection, as well as the impact of fork protection on cellular viability and cancer therapy.
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Affiliation(s)
- Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
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23
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Clairmont CS, D'Andrea AD. REV7 directs DNA repair pathway choice. Trends Cell Biol 2021; 31:965-978. [PMID: 34147298 DOI: 10.1016/j.tcb.2021.05.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 05/18/2021] [Accepted: 05/25/2021] [Indexed: 10/21/2022]
Abstract
REV7 is a small multifunctional protein that participates in multiple DNA repair pathways, most notably translesion DNA synthesis and double-strand break (DSB) repair. While the role of REV7 in translesion synthesis has been known for several decades, its function in DSB repair is a recent discovery. Investigations into the DSB repair function of REV7 have led to the discovery of a new DNA repair complex known as Shieldin. Recent studies have also highlighted the importance of REV7's HORMA domain, an ancient structural motif, in REV7 function and have identified the HORMA regulators, TRIP13 and p31, as novel DNA repair factors. In this review, we discuss these recent findings and their implications for repair pathway choice, at both DSBs and replication forks. We suggest that REV7, in particular the activation state of its HORMA domain, can act as a critical determinant of mutagenic versus error-free repair in multiple contexts.
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Affiliation(s)
- Connor S Clairmont
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
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24
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The epigenetic regulator LSH maintains fork protection and genomic stability via MacroH2A deposition and RAD51 filament formation. Nat Commun 2021; 12:3520. [PMID: 34112784 PMCID: PMC8192551 DOI: 10.1038/s41467-021-23809-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 05/12/2021] [Indexed: 12/18/2022] Open
Abstract
The Immunodeficiency Centromeric Instability Facial Anomalies (ICF) 4 syndrome is caused by mutations in LSH/HELLS, a chromatin remodeler promoting incorporation of histone variant macroH2A. Here, we demonstrate that LSH depletion results in degradation of nascent DNA at stalled replication forks and the generation of genomic instability. The protection of stalled forks is mediated by macroH2A, whose knockdown mimics LSH depletion and whose overexpression rescues nascent DNA degradation. LSH or macroH2A deficiency leads to an impairment of RAD51 loading, a factor that prevents MRE11 and EXO1 mediated nascent DNA degradation. The defect in RAD51 loading is linked to a disbalance of BRCA1 and 53BP1 accumulation at stalled forks. This is associated with perturbed histone modifications, including abnormal H4K20 methylation that is critical for BRCA1 enrichment and 53BP1 exclusion. Altogether, our results illuminate the mechanism underlying a human syndrome and reveal a critical role of LSH mediated chromatin remodeling in genomic stability. LSH/HELLS is a chromatin remodeler promoting incorporation of histone variant macroH2A. Here the authors reveal a role for LSH in genome stability, in protecting nascent DNA at stalled forks mediated by macroH2A deposition and RAD51 filament formation.
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25
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Repair pathway choice for double-strand breaks. Essays Biochem 2021; 64:765-777. [PMID: 32648897 DOI: 10.1042/ebc20200007] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022]
Abstract
Deoxyribonucleic acid (DNA) is at a constant risk of damage from endogenous substances, environmental radiation, and chemical stressors. DNA double-strand breaks (DSBs) pose a significant threat to genomic integrity and cell survival. There are two major pathways for DSB repair: nonhomologous end-joining (NHEJ) and homologous recombination (HR). The extent of DNA end resection, which determines the length of the 3' single-stranded DNA (ssDNA) overhang, is the primary factor that determines whether repair is carried out via NHEJ or HR. NHEJ, which does not require a 3' ssDNA tail, occurs throughout the cell cycle. 53BP1 and the cofactors PTIP or RIF1-shieldin protect the broken DNA end, inhibit long-range end resection and thus promote NHEJ. In contrast, HR mainly occurs during the S/G2 phase and requires DNA end processing to create a 3' tail that can invade a homologous region, ensuring faithful gene repair. BRCA1 and the cofactors CtIP, EXO1, BLM/DNA2, and the MRE11-RAD50-NBS1 (MRN) complex promote DNA end resection and thus HR. DNA resection is influenced by the cell cycle, the chromatin environment, and the complexity of the DNA end break. Herein, we summarize the key factors involved in repair pathway selection for DSBs and discuss recent related publications.
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26
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Ashour ME, Mosammaparast N. Mechanisms of damage tolerance and repair during DNA replication. Nucleic Acids Res 2021; 49:3033-3047. [PMID: 33693881 PMCID: PMC8034635 DOI: 10.1093/nar/gkab101] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/28/2021] [Accepted: 03/02/2021] [Indexed: 01/05/2023] Open
Abstract
Accurate duplication of chromosomal DNA is essential for the transmission of genetic information. The DNA replication fork encounters template lesions, physical barriers, transcriptional machinery, and topological barriers that challenge the faithful completion of the replication process. The flexibility of replisomes coupled with tolerance and repair mechanisms counteract these replication fork obstacles. The cell possesses several universal mechanisms that may be activated in response to various replication fork impediments, but it has also evolved ways to counter specific obstacles. In this review, we will discuss these general and specific strategies to counteract different forms of replication associated damage to maintain genomic stability.
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Affiliation(s)
- Mohamed Elsaid Ashour
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
| | - Nima Mosammaparast
- Department of Pathology & Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO 63110, USA
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27
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Mirsanaye AS, Typas D, Mailand N. Ubiquitylation at Stressed Replication Forks: Mechanisms and Functions. Trends Cell Biol 2021; 31:584-597. [PMID: 33612353 DOI: 10.1016/j.tcb.2021.01.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 11/17/2022]
Abstract
Accurate duplication of chromosomal DNA is vital for faithful transmission of the genome during cell division. However, DNA replication integrity is frequently challenged by genotoxic insults that compromise the progression and stability of replication forks, posing a threat to genome stability. It is becoming clear that the organization of the replisome displays remarkable flexibility in responding to and overcoming a wide spectrum of fork-stalling insults, and that these transactions are dynamically orchestrated and regulated by protein post-translational modifications (PTMs) including ubiquitylation. In this review, we highlight and discuss important recent advances on how ubiquitin-mediated signaling at the replication fork plays a crucial multifaceted role in regulating replisome composition and remodeling its configuration upon replication stress, thereby ensuring high-fidelity duplication of the genome.
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Affiliation(s)
- Ann Schirin Mirsanaye
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Dimitris Typas
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Niels Mailand
- Protein Signaling Program, Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, DK-2200 Copenhagen, Denmark; Center for Chromosome Stability, Department of Cellular and Molecular Medicine, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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28
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Clements KE, Schleicher EM, Thakar T, Hale A, Dhoonmoon A, Tolman NJ, Sharma A, Liang X, Imamura Kawasawa Y, Nicolae CM, Wang HG, De S, Moldovan GL. Identification of regulators of poly-ADP-ribose polymerase inhibitor response through complementary CRISPR knockout and activation screens. Nat Commun 2020; 11:6118. [PMID: 33257658 PMCID: PMC7704667 DOI: 10.1038/s41467-020-19961-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 10/30/2020] [Indexed: 12/17/2022] Open
Abstract
Inhibitors of poly-ADP-ribose polymerase 1 (PARPi) are highly effective in killing cells deficient in homologous recombination (HR); thus, PARPi have been clinically utilized to successfully treat BRCA2-mutant tumors. However, positive response to PARPi is not universal, even among patients with HR-deficiency. Here, we present the results of genome-wide CRISPR knockout and activation screens which reveal genetic determinants of PARPi response in wildtype or BRCA2-knockout cells. Strikingly, we report that depletion of the ubiquitin ligase HUWE1, or the histone acetyltransferase KAT5, top hits from our screens, robustly reverses the PARPi sensitivity caused by BRCA2-deficiency. We identify distinct mechanisms of resistance, in which HUWE1 loss increases RAD51 levels to partially restore HR, whereas KAT5 depletion rewires double strand break repair by promoting 53BP1 binding to double-strand breaks. Our work provides a comprehensive set of putative biomarkers that advance understanding of PARPi response, and identifies novel pathways of PARPi resistance in BRCA2-deficient cells. Mutations in the homologous recombination proteins BRCA1 and BRCA2 can sensitize cells to treatment with inhibitors of poly-ADP-ribose polymerase 1 (PARPi), but resistance to the treatment can occur. Here the authors by genome-wide CRISPR knockout and activation screens reveal novel pathways of PARPi resistance in BRCA2-deficient cells.
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Affiliation(s)
- Kristen E Clements
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Emily M Schleicher
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Tanay Thakar
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Anastasia Hale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Ashna Dhoonmoon
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Nathanial J Tolman
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Anchal Sharma
- Rutgers Cancer Institute of New Jersey, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Xinwen Liang
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Yuka Imamura Kawasawa
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Institute for Personalized Medicine, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Hong-Gang Wang
- Department of Pediatrics, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA.,Department of Pharmacology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Subhajyoti De
- Rutgers Cancer Institute of New Jersey, Rutgers the State University of New Jersey, New Brunswick, NJ, 08901, 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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29
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Mognato M, Burdak-Rothkamm S, Rothkamm K. Interplay between DNA replication stress, chromatin dynamics and DNA-damage response for the maintenance of genome stability. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 787:108346. [PMID: 34083038 DOI: 10.1016/j.mrrev.2020.108346] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 10/02/2020] [Accepted: 11/09/2020] [Indexed: 12/17/2022]
Abstract
DNA replication stress is a major source of DNA damage, including double-stranded breaks that promote DNA damage response (DDR) signaling. Inefficient repair of such lesions can affect genome integrity. During DNA replication different factors act on chromatin remodeling in a coordinated way. While recent studies have highlighted individual molecular mechanisms of interaction, less is known about the orchestration of chromatin changes under replication stress. In this review we attempt to explore the complex relationship between DNA replication stress, DDR and genome integrity in mammalian cells, taking into account the role of chromatin disposition as an important modulator of DNA repair. Recent data on chromatin restoration and epigenetic re-establishment after DNA replication stress are reviewed.
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Affiliation(s)
| | - Susanne Burdak-Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
| | - Kai Rothkamm
- University Medical Center Hamburg-Eppendorf, Department of Radiotherapy, Laboratory of Radiobiology & Experimental Radiation Oncology, Germany.
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30
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Liu W, Krishnamoorthy A, Zhao R, Cortez D. Two replication fork remodeling pathways generate nuclease substrates for distinct fork protection factors. SCIENCE ADVANCES 2020; 6:6/46/eabc3598. [PMID: 33188024 PMCID: PMC7673757 DOI: 10.1126/sciadv.abc3598] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 09/23/2020] [Indexed: 05/11/2023]
Abstract
Fork reversal is a common response to replication stress, but it generates a DNA end that is susceptible to degradation. Many fork protection factors block degradation, but how they work remains unclear. Here, we find that 53BP1 protects forks from DNA2-mediated degradation in a cell type-specific manner. Fork protection by 53BP1 reduces S-phase DNA damage and hypersensitivity to replication stress. Unlike BRCA2, FANCD2, and ABRO1 that protect reversed forks generated by SMARCAL1, ZRANB3, and HLTF, 53BP1 protects forks remodeled by FBH1. This property is shared by the fork protection factors FANCA, FANCC, FANCG, BOD1L, and VHL. RAD51 is required to generate the resection substrate in all cases. Unexpectedly, BRCA2 is also required for fork degradation in the FBH1 pathway or when RAD51 activity is partially compromised. We conclude that there are multiple fork protection mechanisms that operate downstream of at least two RAD51-dependent fork remodeling pathways.
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Affiliation(s)
- W Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - A Krishnamoorthy
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - R Zhao
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - D Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA.
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31
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Under-Replicated DNA: The Byproduct of Large Genomes? Cancers (Basel) 2020; 12:cancers12102764. [PMID: 32992928 PMCID: PMC7601121 DOI: 10.3390/cancers12102764] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 09/21/2020] [Accepted: 09/22/2020] [Indexed: 12/28/2022] Open
Abstract
In this review, we provide an overview of how proliferating eukaryotic cells overcome one of the main threats to genome stability: incomplete genomic DNA replication during S phase. We discuss why it is currently accepted that double fork stalling (DFS) events are unavoidable events in higher eukaryotes with large genomes and which responses have evolved to cope with its main consequence: the presence of under-replicated DNA (UR-DNA) outside S phase. Particular emphasis is placed on the processes that constrain the detrimental effects of UR-DNA. We discuss how mitotic DNA synthesis (MiDAS), mitotic end joining events and 53BP1 nuclear bodies (53BP1-NBs) deal with such specific S phase DNA replication remnants during the subsequent phases of the cell cycle.
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32
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Harrision D, Gravells P, Thompson R, Bryant HE. Poly(ADP-Ribose) Glycohydrolase (PARG) vs. Poly(ADP-Ribose) Polymerase (PARP) - Function in Genome Maintenance and Relevance of Inhibitors for Anti-cancer Therapy. Front Mol Biosci 2020; 7:191. [PMID: 33005627 PMCID: PMC7485115 DOI: 10.3389/fmolb.2020.00191] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Accepted: 07/20/2020] [Indexed: 12/21/2022] Open
Abstract
Poly(ADP-ribose) polymerases (PARPs) are a family of enzymes that catalyze the addition of poly(ADP-ribose) (PAR) subunits onto themselves and other acceptor proteins. PARPs are known to function in a large range of cellular processes including DNA repair, DNA replication, transcription and modulation of chromatin structure. Inhibition of PARP holds great potential for therapy, especially in cancer. Several PARP1/2/3 inhibitors (PARPi) have had success in treating ovarian, breast and prostate tumors harboring defects in the homologous recombination (HR) DNA repair pathway, especially BRCA1/2 mutated tumors. However, treatment is limited to specific sub-groups of patients and resistance can occur, limiting the use of PARPi. Poly(ADP-ribose) glycohydrolase (PARG) reverses the action of PARP enzymes, hydrolysing the ribose-ribose bonds present in poly(ADP-ribose). Like PARPs, PARG is involved in DNA replication and repair and PARG depleted/inhibited cells show increased sensitivity to DNA damaging agents. They also display an accumulation of perturbed replication intermediates which can lead to synthetic lethality in certain contexts. In addition, PARG is thought to play an important role in preventing the accumulation of cytoplasmic PAR and therefore parthanatos, a caspase-independent PAR-mediated type of cell death. In contrast to PARP, the therapeutic potential of PARG has been largely ignored. However, several recent papers have demonstrated the exciting possibilities that inhibitors of this enzyme may have for cancer treatment, both as single agents and in combination with cytotoxic drugs and radiotherapy. This article discusses what is known about the functions of PARP and PARG and the potential future implications of pharmacological inhibition in anti-cancer therapy.
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Affiliation(s)
- Daniel Harrision
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Polly Gravells
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Ruth Thompson
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
| | - Helen E Bryant
- Academic Unit of Molecular Oncology, Sheffield Institute for Nucleic Acids (SInFoNiA), Department of Oncology and Metabolism, University of Sheffield, Sheffield, United Kingdom
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33
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Berti M, Cortez D, Lopes M. The plasticity of DNA replication forks in response to clinically relevant genotoxic stress. Nat Rev Mol Cell Biol 2020; 21:633-651. [PMID: 32612242 DOI: 10.1038/s41580-020-0257-5] [Citation(s) in RCA: 186] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/28/2022]
Abstract
Complete and accurate DNA replication requires the progression of replication forks through DNA damage, actively transcribed regions, structured DNA and compact chromatin. Recent studies have revealed a remarkable plasticity of the replication process in dealing with these obstacles, which includes modulation of replication origin firing, of the architecture of replication forks, and of the functional organization of the replication machinery in response to replication stress. However, these specialized mechanisms also expose cells to potentially dangerous transactions while replicating DNA. In this Review, we discuss how replication forks are actively stalled, remodelled, processed, protected and restarted in response to specific types of stress. We also discuss adaptations of the replication machinery and the role of chromatin modifications during these transactions. Finally, we discuss interesting recent data on the relevance of replication fork plasticity to human health, covering its role in tumorigenesis, its crosstalk with innate immunity responses and its potential as an effective cancer therapy target.
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Affiliation(s)
- Matteo Berti
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland.
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34
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Abstract
Cells confront DNA damage in every cell cycle. Among the most deleterious types of DNA damage are DNA double-strand breaks (DSBs), which can cause cell lethality if unrepaired or cancers if improperly repaired. In response to DNA DSBs, cells activate a complex DNA damage checkpoint (DDC) response that arrests the cell cycle, reprograms gene expression, and mobilizes DNA repair factors to prevent the inheritance of unrepaired and broken chromosomes. Here we examine the DDC, induced by DNA DSBs, in the budding yeast model system and in mammals.
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Affiliation(s)
- David P Waterman
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - James E Haber
- Department of Biology and Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02454, USA;
| | - Marcus B Smolka
- Department of Molecular Biology and Genetics, Weill Institute for Cell and Molecular Biology, Cornell University, Ithaca, New York 14853, USA;
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35
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West KL, Kelliher JL, Xu Z, An L, Reed MR, Eoff RL, Wang J, Huen MSY, Leung JWC. LC8/DYNLL1 is a 53BP1 effector and regulates checkpoint activation. Nucleic Acids Res 2020; 47:6236-6249. [PMID: 30982887 DOI: 10.1093/nar/gkz263] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Revised: 03/15/2019] [Accepted: 04/01/2019] [Indexed: 01/05/2023] Open
Abstract
The tumor suppressor protein 53BP1 plays key roles in response to DNA double-strand breaks (DSBs) by serving as a master scaffold at the damaged chromatin. Current evidence indicates that 53BP1 assembles a cohort of DNA damage response (DDR) factors to distinctly execute its repertoire of DSB responses, including checkpoint activation and non-homologous end joining (NHEJ) repair. Here, we have uncovered LC8 (a.k.a. DYNLL1) as an important 53BP1 effector. We found that LC8 accumulates at laser-induced DNA damage tracks in a 53BP1-dependent manner and requires the canonical H2AX-MDC1-RNF8-RNF168 signal transduction cascade. Accordingly, genetic inactivation of LC8 or its interaction with 53BP1 resulted in checkpoint defects. Importantly, loss of LC8 alleviated the hypersensitivity of BRCA1-depleted cells to ionizing radiation and PARP inhibition, highlighting the 53BP1-LC8 module in counteracting BRCA1-dependent functions in the DDR. Together, these data establish LC8 as an important mediator of a subset of 53BP1-dependent DSB responses.
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Affiliation(s)
- Kirk L West
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jessica L Kelliher
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Zhanzhan Xu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Liwei An
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Megan R Reed
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Robert L Eoff
- Department of Biochemistry and Molecular Biology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, China
| | - Michael S Y Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Justin W C Leung
- Department of Radiation Oncology, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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Mita P, Sun X, Fenyö D, Kahler DJ, Li D, Agmon N, Wudzinska A, Keegan S, Bader JS, Yun C, Boeke JD. BRCA1 and S phase DNA repair pathways restrict LINE-1 retrotransposition in human cells. Nat Struct Mol Biol 2020; 27:179-191. [PMID: 32042152 PMCID: PMC7082080 DOI: 10.1038/s41594-020-0374-z] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 01/02/2020] [Indexed: 12/30/2022]
Abstract
Long interspersed element-1 (LINE-1 or L1) is the only autonomous retrotransposon active in human cells. Different host factors have been shown to influence L1 mobility however, systematic analyses of these factors are limited. Here, we developed a high-throughput microscopy-based retrotransposition assay that identified the Double-Stranded Break (DSB) repair and Fanconi Anemia factors active in the S/G2 phase as potent inhibitors and regulators of L1 activity. In particular BRCA1, an E3 ubiquitin ligase with a key role in several DNA repair pathways, directly affects L1 retrotransposition frequency and structure and also plays a distinct role in controlling L1 ORF2 protein translation through L1 mRNA binding. These results suggest the existence of a “battleground” at the DNA replication fork between HR factors and L1 retrotransposons, and revealing a potential role for L1 in the genotypic evolution of tumors characterized by BRCA1 and HR repair deficiencies.
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Affiliation(s)
- Paolo Mita
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
| | - Xiaoji Sun
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.,Cellarity Inc., Cambridge, MA, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - David J Kahler
- High Throughput Biology Core, NYU Langone Health, New York, NY, USA.,Planet Pharma, Boston, MA, USA
| | - Donghui Li
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.,Flagship VL58, Inc., Cambridge, MA, USA
| | - Neta Agmon
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Aleksandra Wudzinska
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Sarah Keegan
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Chi Yun
- High Throughput Biology Core, NYU Langone Health, New York, NY, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York, NY, USA.
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Ardeljan D, Steranka JP, Liu C, Li Z, Taylor MS, Payer LM, Gorbounov M, Sarnecki JS, Deshpande V, Hruban RH, Boeke JD, Fenyö D, Wu PH, Smogorzewska A, Holland AJ, Burns KH. Cell fitness screens reveal a conflict between LINE-1 retrotransposition and DNA replication. Nat Struct Mol Biol 2020; 27:168-178. [PMID: 32042151 PMCID: PMC7080318 DOI: 10.1038/s41594-020-0372-1] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 12/31/2019] [Indexed: 12/18/2022]
Abstract
LINE-1 retrotransposon overexpression is a hallmark of human cancers. We identified a colorectal cancer wherein a fast-growing tumor subclone downregulated LINE-1, prompting us to examine how LINE-1 expression affects cell growth. We find that nontransformed cells undergo a TP53-dependent growth arrest and activate interferon signaling in response to LINE-1. TP53 inhibition allows LINE-1+ cells to grow, and genome-wide-knockout screens show that these cells require replication-coupled DNA-repair pathways, replication-stress signaling and replication-fork restart factors. Our findings demonstrate that LINE-1 expression creates specific molecular vulnerabilities and reveal a retrotransposition-replication conflict that may be an important determinant of cancer growth.
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Affiliation(s)
- Daniel Ardeljan
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Medical Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Jared P Steranka
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chunhong Liu
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Zhi Li
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, USA
| | - Martin S Taylor
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Lindsay M Payer
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Mikhail Gorbounov
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jacob S Sarnecki
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Vikram Deshpande
- Department of Pathology, Massachusetts General Hospital, Boston, MA, USA
| | - Ralph H Hruban
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, USA
| | - David Fenyö
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Health, New York City, NY, USA
| | - Pei-Hsun Wu
- Johns Hopkins Physical Sciences Oncology Center, Johns Hopkins University, Baltimore, MD, USA
- Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, MD, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York City, NY, USA
| | - Andrew J Holland
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kathleen H Burns
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
- Sydney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Srivastava M, Chen Z, Zhang H, Tang M, Wang C, Jung SY, Chen J. Replisome Dynamics and Their Functional Relevance upon DNA Damage through the PCNA Interactome. Cell Rep 2019; 25:3869-3883.e4. [PMID: 30590055 PMCID: PMC6364303 DOI: 10.1016/j.celrep.2018.11.099] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/09/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic cells use copious measures to ensure accurate duplication of the genome. Various genotoxic agents pose threats to the ongoing replication fork that, if not efficiently dealt with, can result in replication fork collapse. It is unknown how replication fork is precisely controlled and regulated under different conditions. Here, we examined the complexity of replication fork composition upon DNA damage by using a PCNA-based proteomic screen to uncover known and unexplored players involved in replication and replication stress response. We used camptothecin or UV radiation, which lead to fork-blocking lesions, to establish a comprehensive proteomics map of the replisome under such replication stress conditions. We identified and examined two potential candidate proteins WIZ and SALL1 for their roles in DNA replication and replication stress response. In addition, our unbiased screen uncovered many prospective candidate proteins that help fill the knowledge gap in understanding chromosomal DNA replication and DNA repair.
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Affiliation(s)
- Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- 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
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sung Yun Jung
- Department of Molecular and Cellular Biology, Baylor College of Medicine, 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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Pearson SJ, Elswood J, Barhoumi R, Ming-Whitfield B, Rijnkels M, Porter WW. Loss of SIM2s inhibits RAD51 binding and leads to unresolved replication stress. Breast Cancer Res 2019; 21:125. [PMID: 31775907 PMCID: PMC6882179 DOI: 10.1186/s13058-019-1207-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Accepted: 10/01/2019] [Indexed: 12/17/2022] Open
Abstract
Background Mutations in genes associated with homologous recombination (HR) increase an individual’s risk of developing triple-negative breast cancer (TNBC). Although known for their role in repairing dsDNA breaks, HR repair elements also stabilize and restart stalled replication forks. Essential to these functions are RAD51 and its paralogs, each of which has a unique role in preventing replication fork collapse and restart. However, progress toward understanding the regulation of these factors has been slow. With such a pivotal role in the maintenance of genomic integrity, furthering our understanding of this pathway through the discovery of new factors involved in HR is important. Recently, we showed that singleminded-2s (SIM2s) is stabilized in response to dsDNA breaks and is required for effective HR. Methods Initial analysis of the effect loss of SIM2s has on replication stress resolution was conducted using DNA combing assays in established breast cancer cell lines. Further analysis was conducted via immunostaining to determine the effect loss of SIM2s has on factor recruitment. In vivo confirmation was achieved through the use of a mammary epithelial cell conditional knockout mouse model before SIM2s’ role in RAD51 recruitment was determined by immunoblotting. Results Here, we show loss of SIM2s decreases replication fork stability, leading to fork collapse in response to genotoxic stress. Furthermore, loss of SIM2s results in aberrant separation of sister chromatids during mitosis, which has been previously shown to result in chromosomal fragmentation and aneuploidy. Interestingly, loss of SIM2s was shown to result in failure of RAD51 to localize to sites of replication stress in both breast cancer cell lines and primary mammary epithelial cells. Finally, we observed SIM2 is stabilized in response to genotoxic stress and interacts with RAD51, which is necessary for RAD51-DNA binding. Conclusions Together, these results show a role for SIM2s in the resolution of replication stress and further characterize the necessity of SIM2s for effective RAD51 loading in response to DNA damage or stress, ultimately promoting genomic integrity and thus preventing the accumulation of cancer-promoting mutations.
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Affiliation(s)
- Scott J Pearson
- Department of Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Jessica Elswood
- Department of Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Rola Barhoumi
- Department of Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Brittini Ming-Whitfield
- Department of Molecular and Cellular Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Monique Rijnkels
- Department of Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - Weston W Porter
- Department of Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA. .,Present Address: Veterinary Integrative Biosciences, Texas A&M University, College of Veterinary Medicine, College Station, TX, 77843, USA.
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40
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Entrenching role of cell cycle checkpoints and autophagy for maintenance of genomic integrity. DNA Repair (Amst) 2019; 86:102748. [PMID: 31790874 DOI: 10.1016/j.dnarep.2019.102748] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/19/2019] [Accepted: 11/08/2019] [Indexed: 12/22/2022]
Abstract
Genomic integrity of the cell is crucial for the successful transmission of genetic information to the offspring and its survival. Persistent DNA damage induced by endogenous and exogenous agents leads to various metabolic manifestations. To combat this, eukaryotes have developed complex DNA damage response (DDR) pathway which senses the DNA damage and activates an arsenal of enzymes for the repair of damaged DNA. The active pathways for DNA repair are nucleotide excision repair (NER), base excision repair (BER) and mismatch repair (MMR) for single-strand break repair whereas homologous recombination (HR) and non-homologous end-joining (NHEJ) for double-strand break repair. OGG1 is a DNA glycosylase which initiates BER while Mre11-Rad50-Nbs1 (MRN) protein complex is the primary responder to DSBs which gets localized to damage sites. DNA damage response is meticulously executed by three related kinases: ATM, ATR, and DNA-PK. ATM- and ATR-dependent phosphorylation of p53, Chk1, and Chk2 regulate the G1/S, intra-S, or G2/M checkpoints of the cell cycle, respectively. Autophagy is an evolutionarily conserved process that plays a pivotal role in the regulation of DNA repair and maintains the cellular homeostasis. Genotoxic stress-induced altered autophagy occurs in a P53 dependent manner which is also the master regulator of genotoxic stress. A plethora of proteins involved in autophagy is regulated by p53 which involve DRAM, DAPK, and AMPK. As evident, the mtDNA is more prone to damage than nuclear DNA because of its close proximity to the site of ROS generation. Depending on the extent of damage either the repair mechanism or mitophagy gets triggered. SIRT1 is the master regulator which directs the stress response to mitophagy. Nix, a LC3 adapter also participates in Parkin mediated mitophagy. This review highlights the intricate crosstalks between DNA damage and cell cycle checkpoints activation. The DNA damage mediated regulation of autophagy and mitophagy is also reviewed in detail.
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41
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Riabinska A, Lehrmann D, Jachimowicz RD, Knittel G, Fritz C, Schmitt A, Geyer A, Heneweer C, Wittersheim M, Frenzel LP, Torgovnick A, Wiederstein JL, Wunderlich CM, Ortmann M, Paillard A, Wößmann W, Borkhardt A, Burdach S, Hansmann ML, Rosenwald A, Perner S, Mall G, Klapper W, Merseburg A, Krüger M, Grüll H, Persigehl T, Wunderlich FT, Peifer M, Utermöhlen O, Büttner R, Beleggia F, Reinhardt HC. ATM activity in T cells is critical for immune surveillance of lymphoma in vivo. Leukemia 2019; 34:771-786. [PMID: 31690822 DOI: 10.1038/s41375-019-0618-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 09/25/2019] [Accepted: 10/24/2019] [Indexed: 11/09/2022]
Abstract
The proximal DNA damage response kinase ATM is frequently inactivated in human malignancies. Germline mutations in the ATM gene cause Ataxia-telangiectasia (A-T), characterized by cerebellar ataxia and cancer predisposition. Whether ATM deficiency impacts on tumor initiation or also on the maintenance of the malignant state is unclear. Here, we show that Atm reactivation in initially Atm-deficient B- and T cell lymphomas induces tumor regression. We further find a reduced T cell abundance in B cell lymphomas from Atm-defective mice and A-T patients. Using T cell-specific Atm-knockout models, as well as allogeneic transplantation experiments, we pinpoint impaired immune surveillance as a contributor to cancer predisposition and development. Moreover, we demonstrate that Atm-deficient T cells display impaired proliferation capacity upon stimulation, due to replication stress. Altogether, our data indicate that T cell-specific restoration of ATM activity or allogeneic hematopoietic stem cell transplantation may prevent lymphomagenesis in A-T patients.
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Affiliation(s)
- Arina Riabinska
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany.
| | - Daria Lehrmann
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Ron Daniel Jachimowicz
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Gero Knittel
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Christian Fritz
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Anna Schmitt
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Aenne Geyer
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Carola Heneweer
- Department of Radiology, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Maike Wittersheim
- Institute of Pathology, University Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Lukas P Frenzel
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, 50937, Germany
| | - Alessandro Torgovnick
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany.,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, 50937, Germany
| | - Janica Lea Wiederstein
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, 50937, Germany
| | | | - Monika Ortmann
- Institute of Pathology, University Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Arlette Paillard
- Intitute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, 50937, Germany
| | - Wilhelm Wößmann
- Department of Pediatric Hematology and Oncology, Justus-Liebig-University, Giessen, 35390, Germany
| | - Arndt Borkhardt
- Department of Pediatric Oncology, Hematology and Clinical Immunology, University Children's Hospital, Heinrich Heine University, Medical Faculty, Düsseldorf, 40225, Germany
| | - Stefan Burdach
- Children's Cancer Research Center and Department of Pediatrics, Rechts der Isar Hospital, Technical University of Munich and Comprehensive Cancer Center Munich, Munich, 80333, Germany
| | - Martin-Leo Hansmann
- Institute of Pathology, University of Frankfurt, Medical School, Frankfurt, 60590, Germany
| | - Andreas Rosenwald
- Institute of Pathology, University of Würzburg and Comprehensive Cancer Center Mainfranken, Würzburg, 97080, Germany
| | - Sven Perner
- Institute of Pathology, University Hospital Schleswig-Holstein, Lübeck, 23538, Germany
| | - Gita Mall
- Institute of Forensic Medicine, University Hospital Jena, Jena, 07743, Germany
| | - Wolfram Klapper
- Pathology, Hematopathology Section and Lymph Node Registry, University Hospital Schleswig-Holstein, Kiel, 24105, Germany
| | - Andrea Merseburg
- Experimental Neurophysiology, German Center for Neurodegenerative Diseases, Bonn, 53175, Germany
| | - Marcus Krüger
- Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, 50937, Germany
| | - Holger Grüll
- Department of Radiology, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Thorsten Persigehl
- Department of Radiology, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | | | - Martin Peifer
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, 50937, Germany.,Department of Translational Genomics, Cologne, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Olaf Utermöhlen
- Intitute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Cologne, 50937, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, 50937, Germany.,German Center for Infection Research (DZIF), Bonn-Cologne, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital of Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany.,Center for Molecular Medicine Cologne, University of Cologne, Cologne, 50937, Germany
| | - Filippo Beleggia
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany
| | - Hans Christian Reinhardt
- Clinic I of Internal Medicine, University Hospital Cologne, Medical Faculty, University of Cologne, Cologne, 50937, Germany. .,Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, 50937, Germany. .,Center for Molecular Medicine Cologne, University of Cologne, Cologne, 50937, Germany.
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Yan Z, Xue C, Kumar S, Crickard JB, Yu Y, Wang W, Pham N, Li Y, Niu H, Sung P, Greene EC, Ira G. Rad52 Restrains Resection at DNA Double-Strand Break Ends in Yeast. Mol Cell 2019; 76:699-711.e6. [PMID: 31542296 DOI: 10.1016/j.molcel.2019.08.017] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 12/29/2022]
Abstract
Rad52 is a key factor for homologous recombination (HR) in yeast. Rad52 helps assemble Rad51-ssDNA nucleoprotein filaments that catalyze DNA strand exchange, and it mediates single-strand DNA annealing. We find that Rad52 has an even earlier function in HR in restricting DNA double-stranded break ends resection that generates 3' single-stranded DNA (ssDNA) tails. In fission yeast, Exo1 is the primary resection nuclease, with the helicase Rqh1 playing a minor role. We demonstrate that the choice of two extensive resection pathways is regulated by Rad52. In rad52 cells, the resection rate increases from ∼3-5 kb/h up to ∼10-20 kb/h in an Rqh1-dependent manner, while Exo1 becomes dispensable. Budding yeast Rad52 similarly inhibits Sgs1-dependent resection. Single-molecule analysis with purified budding yeast proteins shows that Rad52 competes with Sgs1 for DNA end binding and inhibits Sgs1 translocation along DNA. These results identify a role for Rad52 in limiting ssDNA generated by end resection.
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Affiliation(s)
- Zhenxin Yan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chaoyou Xue
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Sandeep Kumar
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - J Brooks Crickard
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Yang Yu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Weibin Wang
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Nhung Pham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yuxi Li
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA; Department of Biochemistry and Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229 USA.
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Grzegorz Ira
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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43
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βarrestin-1 regulates DNA repair by acting as an E3-ubiquitin ligase adaptor for 53BP1. Cell Death Differ 2019; 27:1200-1213. [PMID: 31506606 PMCID: PMC7206116 DOI: 10.1038/s41418-019-0406-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2018] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 01/02/2023] Open
Abstract
Cellular DNA is constantly under threat from internal and external insults, consequently multiple pathways have evolved to maintain chromosomal fidelity. Our previous studies revealed that chronic stress, mediated by continuous stimulation of the β2-adrenergic-βarrestin-1 signaling axis suppresses activity of the tumor suppressor p53 and impairs genomic integrity. In this pathway, βarrestin-1 (βarr1) acts as a molecular scaffold to promote the binding and degradation of p53 by the E3-ubiquitin ligase, MDM2. We sought to determine whether βarr1 plays additional roles in the repair of DNA damage. Here we demonstrate that in mice βarr1 interacts with p53-binding protein 1 (53BP1) with major consequences for the repair of DNA double-strand breaks. 53BP1 is a principle component of the DNA damage response, and when recruited to the site of double-strand breaks in DNA, 53BP1 plays an important role coordinating repair of these toxic lesions. Here, we report that βarr1 directs 53BP1 degradation by acting as a scaffold for the E3-ubiquitin ligase Rad18. Consequently, knockdown of βarr1 stabilizes 53BP1 augmenting the number of 53BP1 DNA damage repair foci following exposure to ionizing radiation. Accordingly, βarr1 loss leads to a marked increase in irradiation resistance both in cells and in vivo. Thus, βarr1 is an important regulator of double strand break repair, and disruption of the βarr1/53BP1 interaction offers an attractive strategy to protect cells against high levels of exposure to ionizing radiation.
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44
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RIF1 promotes replication fork protection and efficient restart to maintain genome stability. Nat Commun 2019; 10:3287. [PMID: 31337767 PMCID: PMC6650494 DOI: 10.1038/s41467-019-11246-1] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 07/01/2019] [Indexed: 12/15/2022] Open
Abstract
Homologous recombination (HR) and Fanconi Anemia (FA) pathway proteins in addition to their DNA repair functions, limit nuclease-mediated processing of stalled replication forks. However, the mechanism by which replication fork degradation results in genome instability is poorly understood. Here, we identify RIF1, a non-homologous end joining (NHEJ) factor, to be enriched at stalled replication forks. Rif1 knockout cells are proficient for recombination, but displayed degradation of reversed forks, which depends on DNA2 nuclease activity. Notably, RIF1-mediated protection of replication forks is independent of its function in NHEJ, but depends on its interaction with Protein Phosphatase 1. RIF1 deficiency delays fork restart and results in exposure of under-replicated DNA, which is the precursor of subsequent genomic instability. Our data implicate RIF1 to be an essential factor for replication fork protection, and uncover the mechanisms by which unprotected DNA replication forks can lead to genome instability in recombination-proficient conditions. Replication fork degradation can result in genome instability. Here authors reveal a role for Rif1 protein in protecting stalled replication forks from undergoing extensive, DNA2-dependent, degradation.
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Chen BR, Quinet A, Byrum AK, Jackson J, Berti M, Thangavel S, Bredemeyer AL, Hindi I, Mosammaparast N, Tyler JK, Vindigni A, Sleckman BP. XLF and H2AX function in series to promote replication fork stability. J Cell Biol 2019; 218:2113-2123. [PMID: 31123184 PMCID: PMC6605786 DOI: 10.1083/jcb.201808134] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 04/03/2019] [Accepted: 05/03/2019] [Indexed: 12/21/2022] Open
Abstract
Chen et al. show that XLF functions to limit fork reversal during DNA replication. H2AX prevents MRE11-dependent replication stress in XLF-deficient cells, suggesting that H2AX prevents the resection of regressed arms at reversed forks. XRCC4-like factor (XLF) is a non-homologous end joining (NHEJ) DNA double strand break repair protein. However, XLF deficiency leads to phenotypes in mice and humans that are not necessarily consistent with an isolated defect in NHEJ. Here we show that XLF functions during DNA replication. XLF undergoes cell division cycle 7–dependent phosphorylation; associates with the replication factor C complex, a critical component of the replisome; and is found at replication forks. XLF deficiency leads to defects in replication fork progression and an increase in fork reversal. The additional loss of H2AX, which protects DNA ends from resection, leads to a requirement for ATR to prevent an MRE11-dependent loss of newly synthesized DNA and activation of DNA damage response. Moreover, H2ax−/−:Xlf−/− cells exhibit a marked dependence on the ATR kinase for survival. We propose that XLF and H2AX function in series to prevent replication stress induced by the MRE11-dependent resection of regressed arms at reversed replication forks.
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Affiliation(s)
- Bo-Ruei Chen
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Annabel Quinet
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Andrea K Byrum
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jessica Jackson
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Matteo Berti
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Saravanabhavan Thangavel
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Andrea L Bredemeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Issa Hindi
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Jessica K Tyler
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
| | - Alessandro Vindigni
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO
| | - Barry P Sleckman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY
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Setiaputra D, Durocher D. Shieldin - the protector of DNA ends. EMBO Rep 2019; 20:embr.201847560. [PMID: 30948458 DOI: 10.15252/embr.201847560] [Citation(s) in RCA: 143] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Revised: 01/26/2019] [Accepted: 02/06/2019] [Indexed: 12/29/2022] Open
Abstract
DNA double-strand breaks are a threat to genome integrity and cell viability. The nucleolytic processing of broken DNA ends plays a central role in dictating the repair processes that will mend these lesions. Usually, DNA end resection promotes repair by homologous recombination, whereas minimally processed ends are repaired by non-homologous end joining. Important in this process is the chromatin-binding protein 53BP1, which inhibits DNA end resection. How 53BP1 shields DNA ends from nucleases has been an enduring mystery. The recent discovery of shieldin, a four-subunit protein complex with single-stranded DNA-binding activity, illuminated a strong candidate for the ultimate effector of 53BP1-dependent end protection. Shieldin consists of REV7, a known 53BP1-pathway component, and three hitherto uncharacterized proteins: C20orf196 (SHLD1), FAM35A (SHLD2), and CTC-534A2.2 (SHLD3). Shieldin promotes many 53BP1-associated activities, such as the protection of DNA ends, non-homologous end joining, and immunoglobulin class switching. This review summarizes the identification of shieldin and the various models of shieldin action and highlights some outstanding questions requiring answers to gain a full molecular understanding of shieldin function.
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Affiliation(s)
- Dheva Setiaputra
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada
| | - Daniel Durocher
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, ON, Canada .,Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
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Functional cooperativity of p97 and histone deacetylase 6 in mediating DNA repair in mantle cell lymphoma cells. Leukemia 2019; 33:1675-1686. [PMID: 30664664 DOI: 10.1038/s41375-018-0355-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 10/15/2018] [Accepted: 11/12/2018] [Indexed: 12/29/2022]
Abstract
p97 is an ATPase that works in concert with histone deacetylase 6 (HDAC6), to facilitate the degradation of misfolded proteins by autophagosomes. p97 has also been implicated in DNA repair and maintaining genomic stability. In this study, we determined the effect of combined inhibition of p97 and HDAC6 activities in mantle cell lymphoma (MCL) cells. We report that treatment with p97 inhibitors induces dose-dependent apoptosis in MCL cells. The p97 inhibitor CB-5083 induces ER stress markers GRP78 and CHOP and results in the accumulation of polyubiquitylated proteins. Co-treatment with CB-5083 and the HDAC6 inhibitor ACY-1215 result in marked downregulation of CDK4, Cyclin D1, and BRCA1 levels without inhibiting autophagic flux. Consequently, treatment with CB-5083 accentuates DNA damage in response to treatment with ACY-1215 resulting in enhanced accumulation of H2AX-γ and synergistic apoptosis. Furthermore, ATM loss severely impairs phosphorylation of 53BP1 following co-treatment with CB-5083 and ACY-1215 in response to gamma irradiation. Finally, co-treatment CB-5083 and ACY-1215 results in reduced tumor volumes and improves survival in Z138C and Jeko-1 xenografts in NSG mice. These observations suggest that combined inhibition of p97 and HDAC6 abrogates resolution of proteotoxic stress and impairs DNA repair mechanisms in MCL cells.
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48
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53BP1: A key player of DNA damage response with critical functions in cancer. DNA Repair (Amst) 2019; 73:110-119. [DOI: 10.1016/j.dnarep.2018.11.008] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 11/18/2018] [Accepted: 11/19/2018] [Indexed: 02/06/2023]
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Bonetti D, Colombo CV, Clerici M, Longhese MP. Processing of DNA Ends in the Maintenance of Genome Stability. Front Genet 2018; 9:390. [PMID: 30258457 PMCID: PMC6143663 DOI: 10.3389/fgene.2018.00390] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 08/29/2018] [Indexed: 12/17/2022] Open
Abstract
DNA double-strand breaks (DSBs) are particularly hazardous lesions as their inappropriate repair can result in chromosome rearrangements, an important driving force of tumorigenesis. DSBs can be repaired by end joining mechanisms or by homologous recombination (HR). HR requires the action of several nucleases that preferentially remove the 5′-terminated strands at both DSB ends in a process called DNA end resection. The same nucleases are also involved in the processing of replication fork structures. Much of our understanding of these pathways has come from studies in the model organism Saccharomyces cerevisiae. Here, we review the current knowledge of the mechanism of resection at DNA DSBs and replication forks.
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Affiliation(s)
- Diego Bonetti
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | | | - Michela Clerici
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
| | - Maria Pia Longhese
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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Schmid JA, Berti M, Walser F, Raso MC, Schmid F, Krietsch J, Stoy H, Zwicky K, Ursich S, Freire R, Lopes M, Penengo L. Histone Ubiquitination by the DNA Damage Response Is Required for Efficient DNA Replication in Unperturbed S Phase. Mol Cell 2018; 71:897-910.e8. [PMID: 30122534 DOI: 10.1016/j.molcel.2018.07.011] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 06/01/2018] [Accepted: 07/11/2018] [Indexed: 01/16/2023]
Abstract
Chromatin ubiquitination by the ubiquitin ligase RNF168 is critical to regulate the DNA damage response (DDR). DDR deficiencies lead to cancer-prone syndromes, but whether this reflects DNA repair defects is still elusive. We identified key factors of the RNF168 pathway as essential mediators of efficient DNA replication in unperturbed S phase. We found that loss of RNF168 leads to reduced replication fork progression and to reversed fork accumulation, particularly evident at repetitive sequences stalling replication. Slow fork progression depends on MRE11-dependent degradation of reversed forks, implicating RNF168 in reversed fork protection and restart. Consistent with regular nucleosomal organization of reversed forks, the replication function of RNF168 requires H2A ubiquitination. As this novel function is shared with the key DDR players ATM, γH2A.X, RNF8, and 53BP1, we propose that double-stranded ends at reversed forks engage classical DDR factors, suggesting an alternative function of this pathway in preventing genome instability and human disease.
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Affiliation(s)
- Jonas Andreas Schmid
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Matteo Berti
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Franziska Walser
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Maria Chiara Raso
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Fabian Schmid
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Jana Krietsch
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Henriette Stoy
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Katharina Zwicky
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Sebastian Ursich
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Instituto de Tecnologías Biomédicas, Ofra s/n, La Cuesta, La Laguna, Tenerife 38320, Spain
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland.
| | - Lorenza Penengo
- Institute of Molecular Cancer Research, University of Zurich, Zurich 8057, Switzerland.
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