1
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Hoshii T, Kikuchi S, Kujirai T, Masuda T, Ito T, Yasuda S, Matsumoto M, Rahmutulla B, Fukuyo M, Murata T, Kurumizaka H, Kaneda A. BOD1L mediates chromatin binding and non-canonical function of H3K4 methyltransferase SETD1A. Nucleic Acids Res 2024:gkae605. [PMID: 38989615 DOI: 10.1093/nar/gkae605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 06/04/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
The H3K4 methyltransferase SETD1A plays an essential role in both development and cancer. However, essential components involved in SETD1A chromatin binding remain unclear. Here, we discovered that BOD1L exhibits the highest correlated SETD1A co-dependency in human cancer cell lines. BOD1L knockout reduces leukemia cells in vitro and in vivo, and mimics the transcriptional profiles observed in SETD1A knockout cells. The loss of BOD1L immediately reduced SETD1A distribution at transcriptional start sites (TSS), induced transcriptional elongation defect, and increased the RNA polymerase II content at TSS; however, it did not reduce H3K4me3. The Shg1 domain of BOD1L has a DNA binding ability, and a tryptophan residue (W104) in the domain recruits SETD1A to chromatin through the association with SETD1A FLOS domain. In addition, the BOD1L-SETD1A complex associates with transcriptional regulators, including E2Fs. These results reveal that BOD1L mediates chromatin and SETD1A, and regulates the non-canonical function of SETD1A in transcription.
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Affiliation(s)
- Takayuki Hoshii
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Sota Kikuchi
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Takeshi Masuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0017, Japan
| | - Tomoko Ito
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba-shi, Chiba 263-8522, Japan
| | - Makoto Matsumoto
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Bahityar Rahmutulla
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Masaki Fukuyo
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba-shi, Chiba 263-8522, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-0032, Japan
| | - Atsushi Kaneda
- Department of Molecular Oncology, Graduate School of Medicine, Chiba University, Chiba-shi, Chiba 260-8670, Japan
- Health and Disease Omics Center, Chiba University, Chiba-shi, Chiba 260-8670, Japan
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2
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Cybulla E, Wallace S, Meroni A, Jackson J, Agashe S, Tennakoon M, Limbu M, Quinet A, Lomonosova E, Noia H, Tirman S, Wood M, Lemacon D, Fuh K, Zou L, Vindigni A. A RAD18-UBC13-PALB2-RNF168 axis mediates replication fork recovery in BRCA1-deficient cancer cells. Nucleic Acids Res 2024:gkae563. [PMID: 38943334 DOI: 10.1093/nar/gkae563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/24/2024] [Accepted: 06/21/2024] [Indexed: 07/01/2024] Open
Abstract
BRCA1/2 proteins function in genome stability by promoting repair of double-stranded DNA breaks through homologous recombination and by protecting stalled replication forks from nucleolytic degradation. In BRCA1/2-deficient cancer cells, extensively degraded replication forks can be rescued through distinct fork recovery mechanisms that also promote cell survival. Here, we identified a novel pathway mediated by the E3 ubiquitin ligase RAD18, the E2-conjugating enzyme UBC13, the recombination factor PALB2, the E3 ubiquitin ligase RNF168 and PCNA ubiquitination that promotes fork recovery in BRCA1- but not BRCA2-deficient cells. We show that this pathway does not promote fork recovery by preventing replication fork reversal and degradation in BRCA1-deficient cells. We propose a mechanism whereby the RAD18-UBC13-PALB2-RNF168 axis facilitates resumption of DNA synthesis by promoting re-annealing of the complementary single-stranded template strands of the extensively degraded forks, thereby allowing re-establishment of a functional replication fork. We also provide preliminary evidence for the potential clinical relevance of this novel fork recovery pathway in BRCA1-mutated cancers, as RAD18 is over-expressed in BRCA1-deficient cancers, and RAD18 loss compromises cell viability in BRCA1-deficient cancer cells.
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Affiliation(s)
- Emily Cybulla
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Sierra Wallace
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Alice Meroni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Sumedha Agashe
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mithila Tennakoon
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Mangsi Limbu
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Annabel Quinet
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Elena Lomonosova
- Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Hollie Noia
- Department of Obstetrics and Gynecology, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Stephanie Tirman
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Matthew Wood
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
| | - Delphine Lemacon
- Edward A. Doisy Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Katherine Fuh
- Division of Gynecologic Oncology, Department of Ob/Gyn and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Lee Zou
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC 27708, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA
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3
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Qadri S, Sohail MU, Akhtar N, Pir GJ, Yousif G, Pananchikkal SV, Al-Noubi M, Choi S, Shuaib A, Haik Y, Parray A, Schmidt F. Mass spectrometry-based proteomic profiling of extracellular vesicle proteins in diabetic and non-diabetic ischemic stroke patients: a case-control study. Front Mol Biosci 2024; 11:1387859. [PMID: 38948080 PMCID: PMC11211575 DOI: 10.3389/fmolb.2024.1387859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 05/23/2024] [Indexed: 07/02/2024] Open
Abstract
Acute ischemic stroke is the most common cause of neurologic dysfunction caused by focal brain ischemia and tissue injury. Diabetes is a major risk factor of stroke, exacerbating disease management and prognosis. Therefore, discovering new diagnostic markers and therapeutic targets is critical for stroke prevention and treatment. Extracellular vesicles (EVs), with their distinctive properties, have emerged as promising candidates for biomarker discovery and therapeutic application. This case-control study utilized mass spectrometry-based proteomics to compare EVs from non-diabetic stroke (nDS = 14), diabetic stroke (DS = 13), and healthy control (HC = 12) subjects. Among 1288 identified proteins, 387 were statistically compared. Statistical comparisons using a general linear model (log2 foldchange ≥0.58 and FDR-p≤0.05) were performed for nDS vs HC, DS vs HC, and DS vs nDS. DS vs HC and DS vs nDS comparisons produced 123 and 149 differentially expressed proteins, respectively. Fibrinogen gamma chain (FIBG), Fibrinogen beta chain (FIBB), Tetratricopeptide repeat protein 16 (TTC16), Proline rich 14-like (PR14L), Inhibitor of nuclear factor kappa-B kinase subunit epsilon (IKKE), Biorientation of chromosomes in cell division protein 1-like 1 (BD1L1), and protein PR14L exhibited significant differences in the DS group. The pathway analysis revealed that the complement system pathways were activated, and blood coagulation and neuroprotection were inhibited in the DS group (z-score ≥2; p ≤ 0.05). These findings underscore the potential of EVs proteomics in identifying biomarkers for stroke management and prevention, warranting further clinical investigation.
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Affiliation(s)
- Shahnaz Qadri
- Department of Pharmaceutical Sciences, Irma Lerma Rangel School of Pharmacy, Texas A&M University, Kingsville, TX, United States
- Sustainability Division, College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Naveed Akhtar
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Ghulam Jeelani Pir
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Ghada Yousif
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Muna Al-Noubi
- Proteomics Core, Weill Cornell Medicine, Doha, Qatar
| | - Sunkyu Choi
- Proteomics Core, Weill Cornell Medicine, Doha, Qatar
| | - Ashfaq Shuaib
- Department of Medicine, University of Alberta, Edmonton, AB, Canada
| | - Yousef Haik
- Department of Mechanical and Nuclear Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Aijaz Parray
- The Neuroscience Institute, Academic Health System, Hamad Medical Corporation, Doha, Qatar
| | - Frank Schmidt
- Proteomics Core, Weill Cornell Medicine, Doha, Qatar
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Matsuzaki K, Shinohara A, Shinohara M. Human AAA+ ATPase FIGNL1 suppresses RAD51-mediated ultra-fine bridge formation. Nucleic Acids Res 2024; 52:5774-5791. [PMID: 38597669 PMCID: PMC11162793 DOI: 10.1093/nar/gkae263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 03/09/2024] [Accepted: 03/29/2024] [Indexed: 04/11/2024] Open
Abstract
RAD51 filament is crucial for the homology-dependent repair of DNA double-strand breaks and stalled DNA replication fork protection. Positive and negative regulators control RAD51 filament assembly and disassembly. RAD51 is vital for genome integrity but excessive accumulation of RAD51 on chromatin causes genome instability and growth defects. However, the detailed mechanism underlying RAD51 disassembly by negative regulators and the physiological consequence of abnormal RAD51 persistence remain largely unknown. Here, we report the role of the human AAA+ ATPase FIGNL1 in suppressing a novel type of RAD51-mediated genome instability. FIGNL1 knockout human cells were defective in RAD51 dissociation after replication fork restart and accumulated ultra-fine chromosome bridges (UFBs), whose formation depends on RAD51 rather than replication fork stalling. FIGNL1 suppresses homologous recombination intermediate-like UFBs generated between sister chromatids at genomic loci with repeated sequences such as telomeres and centromeres. These data suggest that RAD51 persistence per se induces the formation of unresolved linkage between sister chromatids resulting in catastrophic genome instability. FIGNL1 facilitates post-replicative disassembly of RAD51 filament to suppress abnormal recombination intermediates and UFBs. These findings implicate FIGNL1 as a key factor required for active RAD51 removal after processing of stalled replication forks, which is essential to maintain genome stability.
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Affiliation(s)
- Kenichiro Matsuzaki
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara 631-8505, Japan
| | - Akira Shinohara
- Laboratory of Genome and Chromosome Functions, Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Miki Shinohara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nara City, Nara 631-8505, Japan
- Agricultural Technology and Innovation Research Institute, Kindai University, Nara City, Nara 631-8505, Japan
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5
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Kuhl H, Tan WH, Klopp C, Kleiner W, Koyun B, Ciorpac M, Feron R, Knytl M, Kloas W, Schartl M, Winkler C, Stöck M. A candidate sex determination locus in amphibians which evolved by structural variation between X- and Y-chromosomes. Nat Commun 2024; 15:4781. [PMID: 38839766 PMCID: PMC11153619 DOI: 10.1038/s41467-024-49025-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 05/17/2024] [Indexed: 06/07/2024] Open
Abstract
Most vertebrates develop distinct females and males, where sex is determined by repeatedly evolved environmental or genetic triggers. Undifferentiated sex chromosomes and large genomes have caused major knowledge gaps in amphibians. Only a single master sex-determining gene, the dmrt1-paralogue (dm-w) of female-heterogametic clawed frogs (Xenopus; ZW♀/ZZ♂), is known across >8740 species of amphibians. In this study, by combining chromosome-scale female and male genomes of a non-model amphibian, the European green toad, Bufo(tes) viridis, with ddRAD- and whole genome pool-sequencing, we reveal a candidate master locus, governing a male-heterogametic system (XX♀/XY♂). Targeted sequencing across multiple taxa uncovered structural X/Y-variation in the 5'-regulatory region of the gene bod1l, where a Y-specific non-coding RNA (ncRNA-Y), only expressed in males, suggests that this locus initiates sex-specific differentiation. Developmental transcriptomes and RNA in-situ hybridization show timely and spatially relevant sex-specific ncRNA-Y and bod1l-gene expression in primordial gonads. This coincided with differential H3K4me-methylation in pre-granulosa/pre-Sertoli cells, pointing to a specific mechanism of amphibian sex determination.
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Affiliation(s)
- Heiner Kuhl
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
| | - Wen Hui Tan
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Block S1A, Level 6, Singapore, 117543, Singapore
| | - Christophe Klopp
- SIGENAE, Plate-forme Bio-informatique Genotoul, Mathématiques et Informatique Appliquées de Toulouse, INRAe, 31326, Castanet-Tolosan, France
| | - Wibke Kleiner
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
| | - Baturalp Koyun
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
- Department of Molecular Biology and Genetics, Genetics, Faculty of Science, Bilkent University, SB Building, Ankara, 06800, Turkey
| | - Mitica Ciorpac
- Danube Delta National Institute for Research and Development, Tulcea, 820112, Romania
- Advanced Research and Development Center for Experimental Medicine-CEMEX, "Grigore T. Popa", University of Medicine and Pharmacy, Mihail Kogălniceanu Street 9-13, Iasi, 700259, Romania
| | - Romain Feron
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Martin Knytl
- Department of Cell Biology, Faculty of Science, Charles University, Viničná 7, Prague, 12843, Czech Republic
- Department of Biology, McMaster University, 1280 Main Street West, Hamilton, L8S 4K1, Ontario, ON, Canada
| | - Werner Kloas
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany
| | - Manfred Schartl
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Am Hubland, 97074, Wuerzburg, Germany
- The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX, 78666, USA
| | - Christoph Winkler
- Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, 14 Science Drive 4, Block S1A, Level 6, Singapore, 117543, Singapore.
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Müggelseedamm 301 & 310, 12587, Berlin, Germany.
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Kong L, Cheng C, Cheruiyot A, Yuan J, Yang Y, Hwang S, Foust D, Tsao N, Wilkerson E, Mosammaparast N, Major MB, Piston DW, Li S, You Z. TCAF1 promotes TRPV2-mediated Ca 2+ release in response to cytosolic DNA to protect stressed replication forks. Nat Commun 2024; 15:4609. [PMID: 38816425 PMCID: PMC11139906 DOI: 10.1038/s41467-024-48988-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 05/21/2024] [Indexed: 06/01/2024] Open
Abstract
The protection of the replication fork structure under stress conditions is essential for genome maintenance and cancer prevention. A key signaling pathway for fork protection involves TRPV2-mediated Ca2+ release from the ER, which is triggered after the generation of cytosolic DNA and the activation of cGAS/STING. This results in CaMKK2/AMPK activation and subsequent Exo1 phosphorylation, which prevent aberrant fork processing, thereby ensuring genome stability. However, it remains poorly understood how the TRPV2 channel is activated by the presence of cytosolic DNA. Here, through a genome-wide CRISPR-based screen, we identify TRPM8 channel-associated factor 1 (TCAF1) as a key factor promoting TRPV2-mediated Ca2+ release under replication stress or other conditions that activate cGAS/STING. Mechanistically, TCAF1 assists Ca2+ release by facilitating the dissociation of STING from TRPV2, thereby relieving TRPV2 repression. Consistent with this function, TCAF1 is required for fork protection, chromosomal stability, and cell survival after replication stress.
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Affiliation(s)
- Lingzhen Kong
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Chen Cheng
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Abigael Cheruiyot
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jiayi Yuan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Yichan Yang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Sydney Hwang
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Daniel Foust
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Ning Tsao
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Emily Wilkerson
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Nima Mosammaparast
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, St. Louis, MO, 63110, USA
| | - Michael B Major
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - David W Piston
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Shan Li
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
- Zhejiang Provincial Key Laboratory of Pancreatic Disease in the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, 310029, China.
- Cancer Center, Zhejiang University, Hangzhou, Zhejiang, 310029, China.
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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7
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Schreuder A, Wendel TJ, Dorresteijn CGV, Noordermeer SM. (Single-stranded DNA) gaps in understanding BRCAness. Trends Genet 2024:S0168-9525(24)00100-8. [PMID: 38789375 DOI: 10.1016/j.tig.2024.04.013] [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: 02/02/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/26/2024]
Abstract
The tumour-suppressive roles of BRCA1 and 2 have been attributed to three seemingly distinct functions - homologous recombination, replication fork protection, and single-stranded (ss)DNA gap suppression - and their relative importance is under debate. In this review, we examine the origin and resolution of ssDNA gaps and discuss the recent advances in understanding the role of BRCA1/2 in gap suppression. There are ample data showing that gap accumulation in BRCA1/2-deficient cells is linked to genomic instability and chemosensitivity. However, it remains unclear whether there is a causative role and the function of BRCA1/2 in gap suppression cannot unambiguously be dissected from their other functions. We therefore conclude that the three functions of BRCA1 and 2 are closely intertwined and not mutually exclusive.
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Affiliation(s)
- Anne Schreuder
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Tiemen J Wendel
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands
| | - Carlo G V Dorresteijn
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands
| | - Sylvie M Noordermeer
- Leiden University Medical Center, Department of Human Genetics, Leiden, The Netherlands; Oncode Institute, Utrecht, The Netherlands.
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8
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Fancy NN, Smith AM, Caramello A, Tsartsalis S, Davey K, Muirhead RCJ, McGarry A, Jenkyns MH, Schneegans E, Chau V, Thomas M, Boulger S, Cheung TKD, Adair E, Papageorgopoulou M, Willumsen N, Khozoie C, Gomez-Nicola D, Jackson JS, Matthews PM. Characterisation of premature cell senescence in Alzheimer's disease using single nuclear transcriptomics. Acta Neuropathol 2024; 147:78. [PMID: 38695952 PMCID: PMC11065703 DOI: 10.1007/s00401-024-02727-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/11/2024] [Accepted: 03/28/2024] [Indexed: 05/05/2024]
Abstract
Aging is associated with cell senescence and is the major risk factor for AD. We characterized premature cell senescence in postmortem brains from non-diseased controls (NDC) and donors with Alzheimer's disease (AD) using imaging mass cytometry (IMC) and single nuclear RNA (snRNA) sequencing (> 200,000 nuclei). We found increases in numbers of glia immunostaining for galactosidase beta (> fourfold) and p16INK4A (up to twofold) with AD relative to NDC. Increased glial expression of genes related to senescence was associated with greater β-amyloid load. Prematurely senescent microglia downregulated phagocytic pathways suggesting reduced capacity for β-amyloid clearance. Gene set enrichment and pseudo-time trajectories described extensive DNA double-strand breaks (DSBs), mitochondrial dysfunction and ER stress associated with increased β-amyloid leading to premature senescence in microglia. We replicated these observations with independent AD snRNA-seq datasets. Our results describe a burden of senescent glia with AD that is sufficiently high to contribute to disease progression. These findings support the hypothesis that microglia are a primary target for senolytic treatments in AD.
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Affiliation(s)
- Nurun N Fancy
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Amy M Smith
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- Centre for Brain Research and Department of Pharmacology and Clinical Pharmacology, University of Auckland, Auckland, New Zealand
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Alessia Caramello
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Stergios Tsartsalis
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- Department of Psychiatry, University of Geneva, Geneva, Switzerland
| | - Karen Davey
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- UK Dementia Research Institute Centre, King's College London, London, UK
| | - Robert C J Muirhead
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- UK Dementia Research Institute Centre, King's College London, London, UK
| | - Aisling McGarry
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Marion H Jenkyns
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
| | - Eleonore Schneegans
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Vicky Chau
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Michael Thomas
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Sam Boulger
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - To Ka Dorcas Cheung
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Emily Adair
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Marianna Papageorgopoulou
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Nanet Willumsen
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Combiz Khozoie
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Diego Gomez-Nicola
- School of Biological Sciences, University of Southampton, Southampton, UK
| | - Johanna S Jackson
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK
- UK Dementia Research Institute Centre, Imperial College London, London, UK
| | - Paul M Matthews
- Department of Brain Sciences, Imperial College London, Hammersmith Hospital, Du Cane Road, London, W12 0NN, UK.
- UK Dementia Research Institute Centre, Imperial College London, London, UK.
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9
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Kucharski TJ, Vlasac IM, Higgs MR, Christensen BC, Bechstedt S, Compton DA. An Aurora kinase A-BOD1L1-PP2A B56 Axis promotes chromosome segregation fidelity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.08.06.552174. [PMID: 37609141 PMCID: PMC10441337 DOI: 10.1101/2023.08.06.552174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Cancer cells are often aneuploid and frequently display elevated rates of chromosome missegregation in a phenomenon called chromosomal instability (CIN). CIN is commonly caused by hyperstable kinetochore-microtubule (K-MT) attachments that reduces the efficiency of correction of erroneous K-MT attachments. We recently showed that UMK57, a chemical agonist of MCAK (alias KIF2C) improves chromosome segregation fidelity in CIN cancer cells although cells rapidly develop adaptive resistance. To determine the mechanism of resistance we performed unbiased proteomic screens which revealed increased phosphorylation in cells adapted to UMK57 at two Aurora kinase A phosphoacceptor sites on BOD1L1 (alias FAM44A). BOD1L1 depletion or Aurora kinase A inhibition eliminated resistance to UMK57 in CIN cancer cells. BOD1L1 localizes to spindles/kinetochores during mitosis, interacts with the PP2A phosphatase, and regulates phosphorylation levels of kinetochore proteins, chromosome alignment, mitotic progression and fidelity. Moreover, the BOD1L1 gene is mutated in a subset of human cancers, and BOD1L1 depletion reduces cell growth in combination with clinically relevant doses of taxol or Aurora kinase A inhibitor. Thus, an Aurora kinase A -BOD1L1-PP2A axis promotes faithful chromosome segregation during mitosis.
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Affiliation(s)
- Thomas J. Kucharski
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth
- Department of Anatomy and Cell Biology, McGill University, Montréal, Canada, H3A 0C7
| | - Irma M. Vlasac
- Department of Epidemiology, Geisel School of Medicine at Dartmouth
| | - Martin R. Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Brock C. Christensen
- Department of Epidemiology, Geisel School of Medicine at Dartmouth
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth
- Dartmouth Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, NH
| | - Susanne Bechstedt
- Department of Anatomy and Cell Biology, McGill University, Montréal, Canada, H3A 0C7
| | - Duane A. Compton
- Department of Biochemistry and Cell Biology, Geisel School of Medicine at Dartmouth
- Department of Community and Family Medicine, Geisel School of Medicine at Dartmouth
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10
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Mórocz M, Qorri E, Pekker E, Tick G, Haracska L. Exploring RAD18-dependent replication of damaged DNA and discontinuities: A collection of advanced tools. J Biotechnol 2024; 380:1-19. [PMID: 38072328 DOI: 10.1016/j.jbiotec.2023.12.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/01/2023] [Accepted: 12/03/2023] [Indexed: 12/21/2023]
Abstract
DNA damage tolerance (DDT) pathways mitigate the effects of DNA damage during replication by rescuing the replication fork stalled at a DNA lesion or other barriers and also repair discontinuities left in the newly replicated DNA. From yeast to mammalian cells, RAD18-regulated translesion synthesis (TLS) and template switching (TS) represent the dominant pathways of DDT. Monoubiquitylation of the polymerase sliding clamp PCNA by HRAD6A-B/RAD18, an E2/E3 protein pair, enables the recruitment of specialized TLS polymerases that can insert nucleotides opposite damaged template bases. Alternatively, the subsequent polyubiquitylation of monoubiquitin-PCNA by Ubc13-Mms2 (E2) and HLTF or SHPRH (E3) can lead to the switching of the synthesis from the damaged template to the undamaged newly synthesized sister strand to facilitate synthesis past the lesion. When immediate TLS or TS cannot occur, gaps may remain in the newly synthesized strand, partly due to the repriming activity of the PRIMPOL primase, which can be filled during the later phases of the cell cycle. The first part of this review will summarize the current knowledge about RAD18-dependent DDT pathways, while the second part will offer a molecular toolkit for the identification and characterization of the cellular functions of a DDT protein. In particular, we will focus on advanced techniques that can reveal single-stranded and double-stranded DNA gaps and their repair at the single-cell level as well as monitor the progression of single replication forks, such as the specific versions of the DNA fiber and comet assays. This collection of methods may serve as a powerful molecular toolkit to monitor the metabolism of gaps, detect the contribution of relevant pathways and molecular players, as well as characterize the effectiveness of potential inhibitors.
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Affiliation(s)
- Mónika Mórocz
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Erda Qorri
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Faculty of Science and Informatics, Doctoral School of Biology, University of Szeged, Szeged H-6720, Hungary.
| | - Emese Pekker
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; Doctoral School of Interdisciplinary Medicine, University of Szeged, Korányi fasor 10, 6720 Szeged, Hungary.
| | - Gabriella Tick
- Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary.
| | - Lajos Haracska
- HCEMM-HUN-REN BRC Mutagenesis and Carcinogenesis Research Group, HUN-REN Biological Research Centre, Szeged H-6726, Hungary; National Laboratory for Drug Research and Development, Magyar tudósok krt. 2. H-1117 Budapest, Hungary.
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11
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Xu MJ, Jordan PW. SMC5/6 Promotes Replication Fork Stability via Negative Regulation of the COP9 Signalosome. Int J Mol Sci 2024; 25:952. [PMID: 38256025 PMCID: PMC10815603 DOI: 10.3390/ijms25020952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/06/2024] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
It is widely accepted that DNA replication fork stalling is a common occurrence during cell proliferation, but there are robust mechanisms to alleviate this and ensure DNA replication is completed prior to chromosome segregation. The SMC5/6 complex has consistently been implicated in the maintenance of replication fork integrity. However, the essential role of the SMC5/6 complex during DNA replication in mammalian cells has not been elucidated. In this study, we investigate the molecular consequences of SMC5/6 loss at the replication fork in mouse embryonic stem cells (mESCs), employing the auxin-inducible degron (AID) system to deplete SMC5 acutely and reversibly in the defined cellular contexts of replication fork stall and restart. In SMC5-depleted cells, we identify a defect in the restart of stalled replication forks, underpinned by excess MRE11-mediated fork resection and a perturbed localization of fork protection factors to the stalled fork. Previously, we demonstrated a physical and functional interaction of SMC5/6 with the COP9 signalosome (CSN), a cullin deneddylase that enzymatically regulates cullin ring ligase (CRL) activity. Employing a combination of DNA fiber techniques, the AID system, small-molecule inhibition assays, and immunofluorescence microscopy analyses, we show that SMC5/6 promotes the localization of fork protection factors to stalled replication forks by negatively modulating the COP9 signalosome (CSN). We propose that the SMC5/6-mediated modulation of the CSN ensures that CRL activity and their roles in DNA replication fork stabilization are maintained to allow for efficient replication fork restart when a replication fork stall is alleviated.
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Affiliation(s)
- Michelle J. Xu
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Philip W. Jordan
- Department of Biochemistry and Molecular Biology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA
- Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, MD 20814, USA
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12
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Mellor C, Nassar J, Šviković S, Sale J. PRIMPOL ensures robust handoff between on-the-fly and post-replicative DNA lesion bypass. Nucleic Acids Res 2024; 52:243-258. [PMID: 37971291 PMCID: PMC10783524 DOI: 10.1093/nar/gkad1054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 10/17/2023] [Accepted: 10/24/2023] [Indexed: 11/19/2023] Open
Abstract
The primase/polymerase PRIMPOL restarts DNA synthesis when replication is arrested by template impediments. However, we do not have a comprehensive view of how PRIMPOL-dependent repriming integrates with the main pathways of damage tolerance, REV1-dependent 'on-the-fly' lesion bypass at the fork and PCNA ubiquitination-dependent post-replicative gap filling. Guided by genome-wide CRISPR/Cas9 screens to survey the genetic interactions of PRIMPOL in a non-transformed and p53-proficient human cell line, we find that PRIMPOL is needed for cell survival following loss of the Y-family polymerases REV1 and POLη in a lesion-dependent manner, while it plays a broader role in promoting survival of cells lacking PCNA K164-dependent post-replicative gap filling. Thus, while REV1- and PCNA K164R-bypass provide two layers of protection to ensure effective damage tolerance, PRIMPOL is required to maximise the effectiveness of the interaction between them. We propose this is through the restriction of post-replicative gap length provided by PRIMPOL-dependent repriming.
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Affiliation(s)
- Christopher Mellor
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Joelle Nassar
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Saša Šviković
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Julian E Sale
- Division of Protein & Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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13
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Yu G, Xiong Y, Xu Z, Zhang L, Zhou XA, Nie C, Li S, Wang W, Li X, Wang J. MBD1 protects replication fork stability by recruiting PARP1 and controlling transcription-replication conflicts. Cancer Gene Ther 2024; 31:94-107. [PMID: 37949945 DOI: 10.1038/s41417-023-00685-0] [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: 05/30/2023] [Revised: 10/16/2023] [Accepted: 10/31/2023] [Indexed: 11/12/2023]
Abstract
The replication-stress response is essential to ensure the faithful transmission of genetic information to daughter cells. Although several stress-resolution pathways have been identified to deal with replication stress, the precise regulatory mechanisms for replication fork stability are not fully understood. Our study identified Methyl-CpG Binding Domain 1 (MBD1) as essential for the maintaining genomic stability and protecting stalled replication forks in mammalian cells. Depletion of MBD1 increases DNA lesions and sensitivity to replication stress. Mechanistically, we found that loss of MBD1 leads to the dissociation of Poly(ADP-ribose) polymerase 1 (PARP1) from the replication fork, potentially accelerating fork progression and resulting in higher levels of transcription-replication conflicts (T-R conflicts). Using a proximity ligation assay combined with 5-ethynyl-2'-deoxyuridine, we revealed that the MBD1 and PARP1 proteins were recruited to stalled forks under hydroxyurea (HU) treatment. In addition, our study showed that the level of R-loops also increased in MBD1-delated cells. Without MBD1, stalled replication forks resulting from T-R conflicts were primarily degraded by the DNA2 nuclease. Our findings shed light on a new aspect of MBD1 in maintaining genome stability and providing insights into the mechanisms underlying replication stress response.
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Affiliation(s)
- Guihui Yu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Yundong Xiong
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Zhanzhan Xu
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Lei Zhang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Chen Nie
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Shiwei Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China
| | - Weibin Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China.
| | - Xiaoman Li
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China.
| | - Jiadong Wang
- Department of Radiation Medicine, School of Basic Medical Sciences, Peking University International Cancer Institute, Beijing Key Laboratory of Tumor Systems Biology, Peking University Health Science Center, Beijing, 100191, China.
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14
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Zhao Y, Hou K, Li Y, Hao S, Liu Y, Na Y, Li C, Cui J, Xu X, Wu X, Wang H. Human HELQ regulates DNA end resection at DNA double-strand breaks and stalled replication forks. Nucleic Acids Res 2023; 51:12207-12223. [PMID: 37897354 PMCID: PMC10711563 DOI: 10.1093/nar/gkad940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/15/2023] [Accepted: 10/11/2023] [Indexed: 10/30/2023] Open
Abstract
Following a DNA double strand break (DSB), several nucleases and helicases coordinate to generate single-stranded DNA (ssDNA) with 3' free ends, facilitating precise DNA repair by homologous recombination (HR). The same nucleases can act on stalled replication forks, promoting nascent DNA degradation and fork instability. Interestingly, some HR factors, such as CtIP and BRCA1, have opposite regulatory effects on the two processes, promoting end resection at DSB but inhibiting the degradation of nascent DNA on stalled forks. However, the reason why nuclease actions are regulated by different mechanisms in two DNA metabolism is poorly understood. We show that human HELQ acts as a DNA end resection regulator, with opposing activities on DNA end resection at DSBs and on stalled forks as seen for other regulators. Mechanistically, HELQ helicase activity is required for EXO1-mediated DSB end resection, while ssDNA-binding capacity of HELQ is required for its recruitment to stalled forks, facilitating fork protection and preventing chromosome aberrations caused by replication stress. Here, HELQ synergizes with CtIP but not BRCA1 or BRCA2 to protect stalled forks. These findings reveal an unanticipated role of HELQ in regulating DNA end resection at DSB and stalled forks, which is important for maintaining genome stability.
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Affiliation(s)
- Yuqin Zhao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Kaiping Hou
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Youhang Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Shuailin Hao
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yu Liu
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Yinan Na
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Chao Li
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Jian Cui
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
| | - Xingzhi Xu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Carson International Cancer Center, Marshall Laboratory of Biomedical Engineering, China Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xiaohua Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Hailong Wang
- Beijing Key Laboratory of DNA Damage Response and College of Life Sciences, Capital Normal University, Beijing 100048, China
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15
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Gali VK, Monerawela C, Laksir Y, Hiraga SI, Donaldson AD. Checkpoint phosphorylation sites on budding yeast Rif1 protect nascent DNA from degradation by Sgs1-Dna2. PLoS Genet 2023; 19:e1011044. [PMID: 37956214 PMCID: PMC10681312 DOI: 10.1371/journal.pgen.1011044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 11/27/2023] [Accepted: 10/31/2023] [Indexed: 11/15/2023] Open
Abstract
In budding yeast the Rif1 protein is important for protecting nascent DNA at blocked replication forks, but the mechanism has been unclear. Here we show that budding yeast Rif1 must interact with Protein Phosphatase 1 to protect nascent DNA. In the absence of Rif1, removal of either Dna2 or Sgs1 prevents nascent DNA degradation, implying that Rif1 protects nascent DNA by targeting Protein Phosphatase 1 to oppose degradation by the Sgs1-Dna2 nuclease-helicase complex. This functional role for Rif1 is conserved from yeast to human cells. Yeast Rif1 was previously identified as a target of phosphorylation by the Tel1/Mec1 checkpoint kinases, but the importance of this phosphorylation has been unclear. We find that nascent DNA protection depends on a cluster of Tel1/Mec1 consensus phosphorylation sites in the Rif1 protein sequence, indicating that the intra-S phase checkpoint acts to protect nascent DNA through Rif1 phosphorylation. Our observations uncover the pathway by which budding yeast Rif1 stabilises newly synthesised DNA, highlighting the crucial role Rif1 plays in maintaining genome stability from lower eukaryotes to humans.
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Affiliation(s)
- Vamsi Krishna Gali
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Chandre Monerawela
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Yassine Laksir
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Shin-Ichiro Hiraga
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
| | - Anne D Donaldson
- Chromosome & Cellular Dynamics Section, Institute of Medical Sciences, University of Aberdeen, Aberdeen, Scotland, United Kingdom
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16
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Liu W, Polaczek P, Roubal I, Meng Y, Choe WC, Caron MC, Sedgeman C, Xi Y, Liu C, Wu Q, Zheng L, Masson JY, Shen B, Campbell J. FANCD2 and RAD51 recombinase directly inhibit DNA2 nuclease at stalled replication forks and FANCD2 acts as a novel RAD51 mediator in strand exchange to promote genome stability. Nucleic Acids Res 2023; 51:9144-9165. [PMID: 37526271 PMCID: PMC10516637 DOI: 10.1093/nar/gkad624] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 06/17/2023] [Accepted: 07/28/2023] [Indexed: 08/02/2023] Open
Abstract
FANCD2 protein, a key coordinator and effector of the interstrand crosslink repair pathway, is also required to prevent excessive nascent strand degradation at hydroxyurea-induced stalled forks. The RAD51 recombinase has also been implicated in regulation of resection at stalled replication forks. The mechanistic contributions of these proteins to fork protection are not well understood. Here, we used purified FANCD2 and RAD51 to study how each protein regulates DNA resection at stalled forks. We characterized three mechanisms of FANCD2-mediated fork protection: (1) The N-terminal domain of FANCD2 inhibits the essential DNA2 nuclease activity by directly binding to DNA2 accounting for over-resection in FANCD2 defective cells. (2) Independent of dimerization with FANCI, FANCD2 itself stabilizes RAD51 filaments to inhibit multiple nucleases, including DNA2, MRE11 and EXO1. (3) Unexpectedly, we uncovered a new FANCD2 function: by stabilizing RAD51 filaments, FANCD2 acts to stimulate the strand exchange activity of RAD51. Our work biochemically explains non-canonical mechanisms by which FANCD2 and RAD51 protect stalled forks. We propose a model in which the strand exchange activity of FANCD2 provides a simple molecular explanation for genetic interactions between FANCD2 and BRCA2 in the FA/BRCA fork protection pathway.
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Affiliation(s)
- Wenpeng Liu
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Piotr Polaczek
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ivan Roubal
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yuan Meng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Won-chae Choe
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Marie-Christine Caron
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada
| | - Carl A Sedgeman
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Yu Xi
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Changwei Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China
| | - Qiong Wu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, 9 McMahon, Québec City, QC G1R 3S3, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, QC G1V 0A6, Canada
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute, City of Hope, 1500 East Duarte Road, Duarte, CA 91010-3000, USA
| | - Judith L Campbell
- Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
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17
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Watson AJ, Shaffer ML, Bouley RA, Petreaca RC. F-box DNA Helicase 1 (FBH1) Contributes to the Destabilization of DNA Damage Repair Machinery in Human Cancers. Cancers (Basel) 2023; 15:4439. [PMID: 37760409 PMCID: PMC10526855 DOI: 10.3390/cancers15184439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/01/2023] [Accepted: 09/03/2023] [Indexed: 09/29/2023] Open
Abstract
Homologous recombination (HR) is the major mechanism of rescue of stalled replication forks or repair of DNA double-strand breaks (DSBs) during S phase or mitosis. In human cells, HR is facilitated by the BRCA2-BRCA1-PALB2 module, which loads the RAD51 recombinase onto a resected single-stranded DNA end to initiate repair. Although the process is essential for error-free repair, unrestrained HR can cause chromosomal rearrangements and genome instability. F-box DNA Helicase 1 (FBH1) antagonizes the role of BRCA2-BRCA1-PALB2 to restrict hyper-recombination and prevent genome instability. Here, we analyzed reported FBH1 mutations in cancer cells using the Catalogue of Somatic Mutations in Cancers (COSMIC) to understand how they interact with the BRCA2-BRCA1-PALB2. Consistent with previous results from yeast, we find that FBH1 mutations co-occur with BRCA2 mutations and to some degree BRCA1 and PALB2. We also describe some co-occurring mutations with RAD52, the accessory RAD51 loader and facilitator of single-strand annealing, which is independent of RAD51. In silico modeling was used to investigate the role of key FBH1 mutations on protein function, and a Q650K mutation was found to destabilize the protein structure. Taken together, this work highlights how mutations in several DNA damage repair genes contribute to cellular transformation and immortalization.
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Affiliation(s)
- Alizhah J. Watson
- Biology Program, The Ohio State University, Marion, OH 433023, USA; (A.J.W.); (M.L.S.)
| | - Michaela L. Shaffer
- Biology Program, The Ohio State University, Marion, OH 433023, USA; (A.J.W.); (M.L.S.)
| | - Renee A. Bouley
- Department of Chemistry and Biochemistry, The Ohio State University, Marion, OH 43302, USA
| | - Ruben C. Petreaca
- Department of Molecular Genetics, The Ohio State University, Marion, OH 43302, USA
- Cancer Biology Program, James Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210, USA
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18
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Sharma AB, Ramlee MK, Kosmin J, Higgs MR, Wolstenholme A, Ronson GE, Jones D, Ebner D, Shamkhi N, Sims D, Wijnhoven PWG, Forment JV, Gibbs-Seymour I, Lakin ND. C16orf72/HAPSTR1/TAPR1 functions with BRCA1/Senataxin to modulate replication-associated R-loops and confer resistance to PARP disruption. Nat Commun 2023; 14:5003. [PMID: 37591890 PMCID: PMC10435583 DOI: 10.1038/s41467-023-40779-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 08/10/2023] [Indexed: 08/19/2023] Open
Abstract
While the toxicity of PARP inhibitors to cells with defects in homologous recombination (HR) is well established, other synthetic lethal interactions with PARP1/PARP2 disruption are poorly defined. To inform on these mechanisms we conducted a genome-wide screen for genes that are synthetic lethal with PARP1/2 gene disruption and identified C16orf72/HAPSTR1/TAPR1 as a novel modulator of replication-associated R-loops. C16orf72 is critical to facilitate replication fork restart, suppress DNA damage and maintain genome stability in response to replication stress. Importantly, C16orf72 and PARP1/2 function in parallel pathways to suppress DNA:RNA hybrids that accumulate at stalled replication forks. Mechanistically, this is achieved through an interaction of C16orf72 with BRCA1 and the RNA/DNA helicase Senataxin to facilitate their recruitment to RNA:DNA hybrids and confer resistance to PARP inhibitors. Together, this identifies a C16orf72/Senataxin/BRCA1-dependent pathway to suppress replication-associated R-loop accumulation, maintain genome stability and confer resistance to PARP inhibitors.
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Affiliation(s)
| | | | - Joel Kosmin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Amy Wolstenholme
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - George E Ronson
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Dylan Jones
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daniel Ebner
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Noor Shamkhi
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - David Sims
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Paul W G Wijnhoven
- Early Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA, UK
| | - Josep V Forment
- Early Oncology R&D, AstraZeneca, 1 Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge, CB2 0AA, UK
| | - Ian Gibbs-Seymour
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Nicholas D Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK.
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19
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Xu W, Yang Y, Yu Y, Wen C, Zhao S, Cao L, Zhao S, Qin Y, Chen ZJ. FAAP100 is required for the resolution of transcription-replication conflicts in primordial germ cells. BMC Biol 2023; 21:174. [PMID: 37580696 PMCID: PMC10426154 DOI: 10.1186/s12915-023-01676-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 08/03/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND The maintenance of genome stability in primordial germ cells (PGCs) is crucial for the faithful transmission of genetic information and the establishment of reproductive reserve. Numerous studies in recent decades have linked the Fanconi anemia (FA) pathway with fertility, particularly PGC development. However, the role of FAAP100, an essential component of the FA core complex, in germ cell development is unexplored. RESULTS We find that FAAP100 plays an essential role in R-loop resolution and replication fork protection to counteract transcription-replication conflicts (TRCs) during mouse PGC proliferation. FAAP100 deletion leads to FA pathway inactivation, increases TRCs as well as cotranscriptional R-loops, and contributes to the collapse of replication forks and the generation of DNA damage. Then, the activated p53 signaling pathway triggers PGC proliferation defects, ultimately resulting in insufficient establishment of reproductive reserve in both sexes of mice. CONCLUSIONS Our findings suggest that FAAP100 is required for the resolution of TRCs in PGCs to safeguard their genome stability.
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Affiliation(s)
- Weiwei Xu
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Yajuan Yang
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Yongze Yu
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Canxin Wen
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Simin Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Lili Cao
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, 250012, Shandong, China
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Shidou Zhao
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China.
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.
| | - Yingying Qin
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China.
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.
| | - Zi-Jiang Chen
- Center for Reproductive Medicine, Shandong University, Jinan, 250012, Shandong, China.
- State Key Laboratory of Reproductive Medicine and Offspring Health, Shandong University, Jinan, 250012, Shandong, China.
- Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.
- Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.
- Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.
- Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.
- National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.
- Research Unit of Gametogenesis and Health of ART-Offspring, Chinese Academy of Medical Sciences (No.2021RU001), Jinan, 250012, Shandong, China.
- Shanghai Key Laboratory for Assisted Reproduction and Reproductive Genetics, Shanghai, 200135, China.
- Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200135, China.
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20
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Nieminuszczy J, Martin PR, Broderick R, Krwawicz J, Kanellou A, Mocanu C, Bousgouni V, Smith C, Wen KK, Woodward B, Bakal C, Shackley F, Aguilera A, Stewart G, Vyas Y, Niedzwiedz W. Actin nucleators safeguard replication forks by limiting nascent strand degradation. Nucleic Acids Res 2023; 51:6337-6354. [PMID: 37224534 PMCID: PMC10325910 DOI: 10.1093/nar/gkad369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 04/17/2023] [Accepted: 05/11/2023] [Indexed: 05/26/2023] Open
Abstract
Accurate genome replication is essential for all life and a key mechanism of disease prevention, underpinned by the ability of cells to respond to replicative stress (RS) and protect replication forks. These responses rely on the formation of Replication Protein A (RPA)-single stranded (ss) DNA complexes, yet this process remains largely uncharacterized. Here, we establish that actin nucleation-promoting factors (NPFs) associate with replication forks, promote efficient DNA replication and facilitate association of RPA with ssDNA at sites of RS. Accordingly, their loss leads to deprotection of ssDNA at perturbed forks, impaired ATR activation, global replication defects and fork collapse. Supplying an excess of RPA restores RPA foci formation and fork protection, suggesting a chaperoning role for actin nucleators (ANs) (i.e. Arp2/3, DIAPH1) and NPFs (i.e, WASp, N-WASp) in regulating RPA availability upon RS. We also discover that β-actin interacts with RPA directly in vitro, and in vivo a hyper-depolymerizing β-actin mutant displays a heightened association with RPA and the same dysfunctional replication phenotypes as loss of ANs/NPFs, which contrasts with the phenotype of a hyper-polymerizing β-actin mutant. Thus, we identify components of actin polymerization pathways that are essential for preventing ectopic nucleolytic degradation of perturbed forks by modulating RPA activity.
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Affiliation(s)
- Jadwiga Nieminuszczy
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Peter R Martin
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Ronan Broderick
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Joanna Krwawicz
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Alexandra Kanellou
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Camelia Mocanu
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Vicky Bousgouni
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Charlotte Smith
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Kuo-Kuang Wen
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, Penn State College of Medicine, Penn State Health Children's Hospital, Hershey, PA 17033, USA
| | - Beth L Woodward
- Genome Stability and Human Disease Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Chris Bakal
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
| | - Fiona Shackley
- Paediatric Immunology, Allergy and Infectious Diseases, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Andrés Aguilera
- Centro Andaluz de Biología Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Grant S Stewart
- Genome Stability and Human Disease Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Yatin M Vyas
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, Penn State College of Medicine, Penn State Health Children's Hospital, Hershey, PA 17033, USA
| | - Wojciech Niedzwiedz
- Division of Cancer Biology, The Institute of Cancer Research, London SW3 6JB, UK
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21
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Saldanha J, Rageul J, Patel JA, Kim H. The Adaptive Mechanisms and Checkpoint Responses to a Stressed DNA Replication Fork. Int J Mol Sci 2023; 24:10488. [PMID: 37445667 PMCID: PMC10341514 DOI: 10.3390/ijms241310488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/13/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
DNA replication is a tightly controlled process that ensures the faithful duplication of the genome. However, DNA damage arising from both endogenous and exogenous assaults gives rise to DNA replication stress associated with replication fork slowing or stalling. Therefore, protecting the stressed fork while prompting its recovery to complete DNA replication is critical for safeguarding genomic integrity and cell survival. Specifically, the plasticity of the replication fork in engaging distinct DNA damage tolerance mechanisms, including fork reversal, repriming, and translesion DNA synthesis, enables cells to overcome a variety of replication obstacles. Furthermore, stretches of single-stranded DNA generated upon fork stalling trigger the activation of the ATR kinase, which coordinates the cellular responses to replication stress by stabilizing the replication fork, promoting DNA repair, and controlling cell cycle and replication origin firing. Deregulation of the ATR checkpoint and aberrant levels of chronic replication stress is a common characteristic of cancer and a point of vulnerability being exploited in cancer therapy. Here, we discuss the various adaptive responses of a replication fork to replication stress and the roles of ATR signaling that bring fork stabilization mechanisms together. We also review how this knowledge is being harnessed for the development of checkpoint inhibitors to trigger the replication catastrophe of cancer cells.
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Affiliation(s)
- Joanne Saldanha
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Julie Rageul
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jinal A Patel
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
| | - Hyungjin Kim
- The Graduate Program in Genetics, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Pharmacological Sciences, Stony Brook University, Stony Brook, NY 11794, USA
- Stony Brook Cancer Center, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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22
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Fletcher SC, Hall C, Kennedy TJ, Pajusalu S, Wojcik MH, Boora U, Li C, Oja KT, Hendrix E, Westrip CA, Andrijes R, Piasecka SK, Singh M, El-Asrag ME, Ptasinska A, Tillmann V, Higgs MR, Carere DA, Beggs AD, Pappas J, Rabin R, Smerdon SJ, Stewart GS, Õunap K, Coleman ML. Impaired protein hydroxylase activity causes replication stress and developmental abnormalities in humans. J Clin Invest 2023; 133:e152784. [PMID: 36795492 PMCID: PMC10065073 DOI: 10.1172/jci152784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Although protein hydroxylation is a relatively poorly characterized posttranslational modification, it has received significant recent attention following seminal work uncovering its role in oxygen sensing and hypoxia biology. Although the fundamental importance of protein hydroxylases in biology is becoming clear, the biochemical targets and cellular functions often remain enigmatic. JMJD5 is a "JmjC-only" protein hydroxylase that is essential for murine embryonic development and viability. However, no germline variants in JmjC-only hydroxylases, including JMJD5, have yet been described that are associated with any human pathology. Here we demonstrate that biallelic germline JMJD5 pathogenic variants are deleterious to JMJD5 mRNA splicing, protein stability, and hydroxylase activity, resulting in a human developmental disorder characterized by severe failure to thrive, intellectual disability, and facial dysmorphism. We show that the underlying cellular phenotype is associated with increased DNA replication stress and that this is critically dependent on the protein hydroxylase activity of JMJD5. This work contributes to our growing understanding of the role and importance of protein hydroxylases in human development and disease.
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Affiliation(s)
- Sally C. Fletcher
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Charlotte Hall
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Tristan J. Kennedy
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sander Pajusalu
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Monica H. Wojcik
- Center for Mendelian Genomics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Divisions of Newborn Medicine and Genetics and Genomics, Department of Pediatrics, Boston Children’s Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Uncaar Boora
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Chan Li
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Kaisa Teele Oja
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Eline Hendrix
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Christian A.E. Westrip
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Regina Andrijes
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sonia K. Piasecka
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mansi Singh
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Mohammed E. El-Asrag
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
- Faculty of Science, Benha University, Benha, Egypt
| | - Anetta Ptasinska
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Vallo Tillmann
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Children’s Clinic, Tartu University Hospital, Tartu, Estonia
| | - Martin R. Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | | | - Andrew D. Beggs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - John Pappas
- Clinical Genetic Services, Department of Pediatrics, NYU Langone Medical Center, New York, New York, USA
| | - Rachel Rabin
- Clinical Genetic Services, Department of Pediatrics, NYU Langone Medical Center, New York, New York, USA
| | - Stephen J. Smerdon
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Grant S. Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Katrin Õunap
- Department of Clinical Genetics, Genetics and Personalized Medicine Clinic, Tartu University Hospital, Tartu, Estonia
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Mathew L. Coleman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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23
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Debaugnies M, Rodríguez-Acebes S, Blondeau J, Parent MA, Zocco M, Song Y, de Maertelaer V, Moers V, Latil M, Dubois C, Coulonval K, Impens F, Van Haver D, Dufour S, Uemura A, Sotiropoulou PA, Méndez J, Blanpain C. RHOJ controls EMT-associated resistance to chemotherapy. Nature 2023; 616:168-175. [PMID: 36949199 PMCID: PMC10076223 DOI: 10.1038/s41586-023-05838-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 49.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 02/14/2023] [Indexed: 03/24/2023]
Abstract
The resistance of cancer cells to therapy is responsible for the death of most patients with cancer1. Epithelial-to-mesenchymal transition (EMT) has been associated with resistance to therapy in different cancer cells2,3. However, the mechanisms by which EMT mediates resistance to therapy remain poorly understood. Here, using a mouse model of skin squamous cell carcinoma undergoing spontaneous EMT during tumorigenesis, we found that EMT tumour cells are highly resistant to a wide range of anti-cancer therapies both in vivo and in vitro. Using gain and loss of function studies in vitro and in vivo, we found that RHOJ-a small GTPase that is preferentially expressed in EMT cancer cells-controls resistance to therapy. Using genome-wide transcriptomic and proteomic profiling, we found that RHOJ regulates EMT-associated resistance to chemotherapy by enhancing the response to replicative stress and activating the DNA-damage response, enabling tumour cells to rapidly repair DNA lesions induced by chemotherapy. RHOJ interacts with proteins that regulate nuclear actin, and inhibition of actin polymerization sensitizes EMT tumour cells to chemotherapy-induced cell death in a RHOJ-dependent manner. Together, our study uncovers the role and the mechanisms through which RHOJ acts as a key regulator of EMT-associated resistance to chemotherapy.
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Affiliation(s)
- Maud Debaugnies
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
- CHU Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Sara Rodríguez-Acebes
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Jeremy Blondeau
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Marie-Astrid Parent
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Manuel Zocco
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Yura Song
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Viviane de Maertelaer
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Virginie Moers
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Mathilde Latil
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Christine Dubois
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium
| | - Katia Coulonval
- Institute of Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles (ULB), Brussels, Belgium
- ULB-Cancer Research Center (U-crc), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Francis Impens
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Delphi Van Haver
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Sara Dufour
- VIB Center for Medical Biotechnology, VIB Proteomics Core, Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Akiyoshi Uemura
- Department of Retinal Vascular Biology, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | | | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre, Madrid, Spain
| | - Cédric Blanpain
- Laboratory of Stem Cells and Cancer, Université Libre de Buxelles (ULB), Brussels, Belgium.
- WELBIO, Université Libre de Bruxelles (ULB), Brussels, Belgium.
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24
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Nieminuszczy J, Martin PR, Broderick R, Krwawicz J, Kanellou A, Mocanu C, Bousgouni V, Smith C, Wen KK, Woodward BL, Bakal C, Shackley F, Aguilera A, Stewart GS, Vyas YM, Niedzwiedz W. Actin nucleators safeguard replication forks by limiting nascent strand degradation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523639. [PMID: 36711944 PMCID: PMC9882250 DOI: 10.1101/2023.01.12.523639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Accurate genome replication is essential for all life and a key mechanism of disease prevention, underpinned by the ability of cells to respond to replicative stress (RS) and protect replication forks. These responses rely on the formation of Replication Protein A (RPA)-single stranded (ss) DNA complexes, yet this process remains largely uncharacterized. Here we establish that actin nucleation-promoting factors (NPFs) associate with replication forks, promote efficient DNA replication and facilitate association of RPA with ssDNA at sites of RS. Accordingly, their loss leads to deprotection of ssDNA at perturbed forks, impaired ATR activation, global replication defects and fork collapse. Supplying an excess of RPA restores RPA foci formation and fork protection, suggesting a chaperoning role for actin nucleators (ANs) (i.e., Arp2/3, DIAPH1) and NPFs (i.e, WASp, N-WASp) in regulating RPA availability upon RS. We also discover that β-actin interacts with RPA directly in vitro , and in vivo a hyper-depolymerizing β-actin mutant displays a heightened association with RPA and the same dysfunctional replication phenotypes as loss of ANs/NPFs, which contrasts with the phenotype of a hyper-polymerizing β-actin mutant. Thus, we identify components of actin polymerization pathways that are essential for preventing ectopic nucleolytic degradation of perturbed forks by modulating RPA activity.
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Affiliation(s)
| | - Peter R. Martin
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Ronan Broderick
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Joanna Krwawicz
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | | | - Camelia Mocanu
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Vicky Bousgouni
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Charlotte Smith
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Kuo-Kuang Wen
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, PennState College of Medicine, PennState Health Children’s Hospital, Hershey, Pennsylvania 17033, USA
| | - Beth L. Woodward
- Genome Stability and Human Disease Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Chris Bakal
- Cancer Biology, The Institute of Cancer Research, London, SW3 6JB, UK
| | - Fiona Shackley
- Paediatric Immunology, Allergy and Infectious Diseases, Sheffield Children's Hospital NHS Foundation Trust, Sheffield, UK
| | - Andres Aguilera
- Centro Andaluz de Biologia Molecular y Medicina Regenerativa CABIMER, Universidad de Sevilla-CSIC-Universidad Pablo de Olavide, Seville, Spain
| | - Grant S. Stewart
- Genome Stability and Human Disease Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Yatin M. Vyas
- Department of Pediatrics, Division of Pediatric Hematology-Oncology, PennState College of Medicine, PennState Health Children’s Hospital, Hershey, Pennsylvania 17033, USA
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25
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Gospodinov A, Dzhokova S, Petrova M, Ugrinova I. Chromatin regulators in DNA replication and genome stability maintenance during S-phase. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 135:243-280. [PMID: 37061334 DOI: 10.1016/bs.apcsb.2023.02.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
The duplication of genetic information is central to life. The replication of genetic information is strictly controlled to ensure that each piece of genomic DNA is copied only once during a cell cycle. Factors that slow or stop replication forks cause replication stress. Replication stress is a major source of genome instability in cancer cells. Multiple control mechanisms facilitate the unimpeded fork progression, prevent fork collapse and coordinate fork repair. Chromatin alterations, caused by histone post-translational modifications and chromatin remodeling, have critical roles in normal replication and in avoiding replication stress and its consequences. This text reviews the chromatin regulators that ensure DNA replication and the proper response to replication stress. We also briefly touch on exploiting replication stress in therapeutic strategies. As chromatin regulators are frequently mutated in cancer, manipulating their activity could provide many possibilities for personalized treatment.
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Affiliation(s)
- Anastas Gospodinov
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria.
| | - Stefka Dzhokova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Maria Petrova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Iva Ugrinova
- Roumen Tsanev Institute of Molecular Biology, Bulgarian Academy of Sciences, Sofia, Bulgaria
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26
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Kavlashvili T, Liu W, Mohamed TM, Cortez D, Dewar JM. Replication fork uncoupling causes nascent strand degradation and fork reversal. Nat Struct Mol Biol 2023; 30:115-124. [PMID: 36593312 PMCID: PMC9868089 DOI: 10.1038/s41594-022-00871-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 10/14/2022] [Indexed: 01/03/2023]
Abstract
Genotoxins cause nascent strand degradation (NSD) and fork reversal during DNA replication. NSD and fork reversal are crucial for genome stability and are exploited by chemotherapeutic approaches. However, it is unclear how NSD and fork reversal are triggered. Additionally, the fate of the replicative helicase during these processes is unknown. We developed a biochemical approach to study synchronous, localized NSD and fork reversal using Xenopus egg extracts and validated this approach with experiments in human cells. We show that replication fork uncoupling stimulates NSD of both nascent strands and progressive conversion of uncoupled forks to reversed forks. Notably, the replicative helicase remains bound during NSD and fork reversal. Unexpectedly, NSD occurs before and after fork reversal, indicating that multiple degradation steps take place. Overall, our data show that uncoupling causes NSD and fork reversal and elucidate key events that precede fork reversal.
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Affiliation(s)
- Tamar Kavlashvili
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Wenpeng Liu
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Taha M Mohamed
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - James M Dewar
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.
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27
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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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28
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Zhu C, Iwase M, Li Z, Wang F, Quinet A, Vindigni A, Shao J. Profilin-1 regulates DNA replication forks in a context-dependent fashion by interacting with SNF2H and BOD1L. Nat Commun 2022; 13:6531. [PMID: 36319634 PMCID: PMC9626489 DOI: 10.1038/s41467-022-34310-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 10/21/2022] [Indexed: 12/04/2022] Open
Abstract
DNA replication forks are tightly controlled by a large protein network consisting of well-known core regulators and many accessory factors which remain functionally undefined. In this study, we report previously unknown nuclear functions of the actin-binding factor profilin-1 (PFN1) in DNA replication, which occur in a context-dependent fashion and require its binding to poly-L-proline (PLP)-containing proteins instead of actin. In unperturbed cells, PFN1 increases DNA replication initiation and accelerates fork progression by binding and stimulating the PLP-containing nucleosome remodeler SNF2H. Under replication stress, PFN1/SNF2H increases fork stalling and functionally collaborates with fork reversal enzymes to enable the over-resection of unprotected forks. In addition, PFN1 binds and functionally attenuates the PLP-containing fork protector BODL1 to increase the resection of a subset of stressed forks. Accordingly, raising nuclear PFN1 level decreases genome stability and cell survival during replication stress. Thus, PFN1 is a multi-functional regulator of DNA replication with exploitable anticancer potential.
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Affiliation(s)
- Cuige Zhu
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Mari Iwase
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Ziqian Li
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Department of Microbial and Biochemical Pharmacy, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Faliang Wang
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
| | - Annabel Quinet
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- UMR Genetic Stability Stem Cells and Radiation, University of Paris and University of Paris-Saclay, INSERM, iRCM/IBFJ CEA, Fontenay-aux-Roses, France
| | - Alessandro Vindigni
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jieya Shao
- Divison of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA.
- Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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29
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Identification of Gene Coexpression Modules and Prognostic Genes Associated with Papillary Thyroid Cancer. JOURNAL OF ONCOLOGY 2022; 2022:9025198. [PMID: 36245994 PMCID: PMC9553521 DOI: 10.1155/2022/9025198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/21/2022] [Accepted: 09/02/2022] [Indexed: 11/17/2022]
Abstract
Thyroid cancer is a great part of the endocrine tumor with an increasing incidence. Papillary thyroid carcinoma (PTC) is the most common subtype. With the enormous pace taken in the microarray technology, bioinformatics is applied in data mining more frequently. Weighted gene coexpression network analysis (WGCNA) can perform analysis combining clinic information. We performed WGCNA for prognostic genes associated with PTC. From the GEO profile, we got ten modules. We identified a key module that was closest to patients’ survival time. Then, we screened five hub genes (ATRX, BOD1L1, CEP290, DCAF16, and NEK1) from the key module based on the clinical information from TCGA. These five genes not only significantly differ between the normal and tumor groups but have prognostic value. The receiver operating characteristic (ROC) curve indicated that they had the potential to serve as prognostic genes. We performed next-generation sequencing using the PTC tissue to get more convincing evidence. Besides, we established a new signature and verified it through K-M plots and ROC. The signature could be an independent factor for the prognosis of PTC, and we built a nomogram to carry out a quantitative study. In a word, the hub genes we explored in the study deserved more basic and clinical research.
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30
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Role of Cockayne Syndrome Group B Protein in Replication Stress: Implications for Cancer Therapy. Int J Mol Sci 2022; 23:ijms231810212. [PMID: 36142121 PMCID: PMC9499456 DOI: 10.3390/ijms231810212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/01/2022] [Accepted: 09/03/2022] [Indexed: 12/01/2022] Open
Abstract
A variety of endogenous and exogenous insults are capable of impeding replication fork progression, leading to replication stress. Several SNF2 fork remodelers have been shown to play critical roles in resolving this replication stress, utilizing different pathways dependent upon the nature of the DNA lesion, location on the DNA, and the stage of the cell cycle, to complete DNA replication in a manner preserving genetic integrity. Under certain conditions, however, the attempted repair may lead to additional genetic instability. Cockayne syndrome group B (CSB) protein, a SNF2 chromatin remodeler best known for its role in transcription-coupled nucleotide excision repair, has recently been shown to catalyze fork reversal, a pathway that can provide stability of stalled forks and allow resumption of DNA synthesis without chromosome breakage. Prolonged stalling of replication forks may collapse to give rise to DNA double-strand breaks, which are preferentially repaired by homology-directed recombination. CSB plays a role in repairing collapsed forks by promoting break-induced replication in S phase and early mitosis. In this review, we discuss roles of CSB in regulating the sources of replication stress, replication stress response, as well as the implications of CSB for cancer therapy.
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31
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Halder S, Sanchez A, Ranjha L, Reginato G, Ceppi I, Acharya A, Anand R, Cejka P. Double-stranded DNA binding function of RAD51 in DNA protection and its regulation by BRCA2. Mol Cell 2022; 82:3553-3565.e5. [PMID: 36070766 DOI: 10.1016/j.molcel.2022.08.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 06/16/2022] [Accepted: 08/10/2022] [Indexed: 11/26/2022]
Abstract
RAD51 and the breast cancer suppressor BRCA2 have critical functions in DNA double-strand (dsDNA) break repair by homologous recombination and the protection of newly replicated DNA from nucleolytic degradation. The recombination function of RAD51 requires its binding to single-stranded DNA (ssDNA), whereas binding to dsDNA is inhibitory. Using reconstituted MRE11-, EXO1-, and DNA2-dependent nuclease reactions, we show that the protective function of RAD51 unexpectedly depends on its binding to dsDNA. The BRC4 repeat of BRCA2 abrogates RAD51 binding to dsDNA and accordingly impairs the function of RAD51 in protection. The BRCA2 C-terminal RAD51-binding segment (TR2) acts in a dominant manner to overcome the effect of BRC4. Mechanistically, TR2 stabilizes RAD51 binding to dsDNA, even in the presence of BRC4, promoting DNA protection. Our data suggest that RAD51's dsDNA-binding capacity may have evolved together with its function in replication fork protection and provide a mechanistic basis for the DNA-protection function of BRCA2.
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Affiliation(s)
- Swagata Halder
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Aurore Sanchez
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Lepakshi Ranjha
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Giordano Reginato
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Ilaria Ceppi
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Ananya Acharya
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland
| | - Roopesh Anand
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland
| | - Petr Cejka
- Institute for Research in Biomedicine, Università della Svizzera italiana (USI), Faculty of Biomedical Sciences, 6500 Bellinzona, Switzerland; Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH), 8049 Zürich, Switzerland.
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32
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Clarke TL, Mostoslavsky R. DNA repair as a shared hallmark in cancer and ageing. Mol Oncol 2022; 16:3352-3379. [PMID: 35834102 PMCID: PMC9490147 DOI: 10.1002/1878-0261.13285] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/23/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
Increasing evidence demonstrates that DNA damage and genome instability play a crucial role in ageing. Mammalian cells have developed a wide range of complex and well‐orchestrated DNA repair pathways to respond to and resolve many different types of DNA lesions that occur from exogenous and endogenous sources. Defects in these repair pathways lead to accelerated or premature ageing syndromes and increase the likelihood of cancer development. Understanding the fundamental mechanisms of DNA repair will help develop novel strategies to treat ageing‐related diseases. Here, we revisit the processes involved in DNA damage repair and how these can contribute to diseases, including ageing and cancer. We also review recent mechanistic insights into DNA repair and discuss how these insights are being used to develop novel therapeutic strategies for treating human disease. We discuss the use of PARP inhibitors in the clinic for the treatment of breast and ovarian cancer and the challenges associated with acquired drug resistance. Finally, we discuss how DNA repair pathway‐targeted therapeutics are moving beyond PARP inhibition in the search for ever more innovative and efficacious cancer therapies.
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Affiliation(s)
- Thomas L Clarke
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
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33
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Yang Z, Lemacon DS, Li S, Cheruiyot A, Kong L, Tan K, Cheng C, Turkay E, He D, You Z. Context-dependent pro- and anti-resection roles of ZKSCAN3 in the regulation of fork processing during replication stress. J Biol Chem 2022; 298:102215. [PMID: 35779634 PMCID: PMC9352557 DOI: 10.1016/j.jbc.2022.102215] [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: 05/18/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 11/26/2022] Open
Abstract
Uncontrolled resection of replication forks under stress can cause genomic instability and influence cancer formation. Extensive fork resection has also been implicated in the chemosensitivity of “BReast CAncer gene” BRCA-deficient cancers. However, how fork resection is controlled in different genetic contexts and how it affects chromosomal stability and cell survival remains incompletely understood. Here, we report a novel function of the transcription repressor ZKSCAN3 in fork protection and chromosomal stability maintenance under replication stress. We show disruption of ZKSCAN3 function causes excessive resection of replication forks by the exonuclease Exo1 and homologous DNA recombination/repair protein Mre11 following fork reversal. Interestingly, in BRCA1-deficient cells, we found ZKSCAN3 actually promotes fork resection upon replication stress. We demonstrate these anti- and pro-resection roles of ZKSCAN3, consisting of a SCAN box, Kruppel-associated box, and zinc finger domain, are mediated by its SCAN box domain and do not require the Kruppel-associated box or zinc finger domains, suggesting that the transcriptional function of ZKSCAN3 is not involved. Furthermore, despite the severe impact on fork structure and chromosomal stability, depletion of ZKSCAN3 did not affect the short-term survival of BRCA1-proficient or BRCA1-deficient cells after treatment with cancer drugs hydroxyurea, PARPi, or cisplatin. Our findings reveal a unique relationship between ZKSCAN3 and BRCA1 in fork protection and add to our understanding of the relationships between replication fork protection, chromosomal instability, and chemosensitivity.
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Affiliation(s)
- Zheng Yang
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061 China; Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Delphine Sangotokun Lemacon
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Shan Li
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Abigael Cheruiyot
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Lingzhen Kong
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ke Tan
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Chen Cheng
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Ecenur Turkay
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dalin He
- Department of Urology, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi 710061 China
| | - Zhongsheng You
- Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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34
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Bayley R, Borel V, Moss RJ, Sweatman E, Ruis P, Ormrod A, Goula A, Mottram RMA, Stanage T, Hewitt G, Saponaro M, Stewart GS, Boulton SJ, Higgs MR. H3K4 methylation by SETD1A/BOD1L facilitates RIF1-dependent NHEJ. Mol Cell 2022; 82:1924-1939.e10. [PMID: 35439434 PMCID: PMC9616806 DOI: 10.1016/j.molcel.2022.03.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 12/14/2021] [Accepted: 03/23/2022] [Indexed: 12/14/2022]
Abstract
The 53BP1-RIF1-shieldin pathway maintains genome stability by suppressing nucleolytic degradation of DNA ends at double-strand breaks (DSBs). Although RIF1 interacts with damaged chromatin via phospho-53BP1 and facilitates recruitment of the shieldin complex to DSBs, it is unclear whether other regulatory cues contribute to this response. Here, we implicate methylation of histone H3 at lysine 4 by SETD1A-BOD1L in the recruitment of RIF1 to DSBs. Compromising SETD1A or BOD1L expression or deregulating H3K4 methylation allows uncontrolled resection of DNA ends, impairs end-joining of dysfunctional telomeres, and abrogates class switch recombination. Moreover, defects in RIF1 localization to DSBs are evident in patient cells bearing loss-of-function mutations in SETD1A. Loss of SETD1A-dependent RIF1 recruitment in BRCA1-deficient cells restores homologous recombination and leads to resistance to poly(ADP-ribose)polymerase inhibition, reinforcing the clinical relevance of these observations. Mechanistically, RIF1 binds directly to methylated H3K4, facilitating its recruitment to, or stabilization at, DSBs.
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Affiliation(s)
- Rachel Bayley
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Valerie Borel
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Rhiannon J Moss
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Ellie Sweatman
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Philip Ruis
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Alice Ormrod
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Amalia Goula
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Rachel M A Mottram
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Tyler Stanage
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Graeme Hewitt
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK
| | - Marco Saponaro
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK
| | - Grant S Stewart
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Simon J Boulton
- DSB Repair Metabolism Laboratory, The Francis Crick Institute, Midland Road, London, UK.
| | - Martin R Higgs
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK.
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35
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Gorsi B, Hernandez E, Moore MB, Moriwaki M, Chow CY, Coelho E, Taylor E, Lu C, Walker A, Touraine P, Nelson LM, Cooper AR, Mardis ER, Rajkovic A, Yandell M, Welt CK. Causal and Candidate Gene Variants in a Large Cohort of Women With Primary Ovarian Insufficiency. J Clin Endocrinol Metab 2022; 107:685-714. [PMID: 34718612 PMCID: PMC9006976 DOI: 10.1210/clinem/dgab775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT A genetic etiology likely accounts for the majority of unexplained primary ovarian insufficiency (POI). OBJECTIVE We hypothesized that heterozygous rare variants and variants in enhanced categories are associated with POI. DESIGN The study was an observational study. SETTING Subjects were recruited at academic institutions. PATIENTS Subjects from Boston (n = 98), the National Institutes of Health and Washington University (n = 98), Pittsburgh (n = 20), Italy (n = 43), and France (n = 32) were diagnosed with POI (amenorrhea with an elevated follicle-stimulating hormone level). Controls were recruited for health in old age or were from the 1000 Genomes Project (total n = 233). INTERVENTION We performed whole exome sequencing (WES), and data were analyzed using a rare variant scoring method and a Bayes factor-based framework for identifying genes harboring pathogenic variants. We performed functional studies on identified genes that were not previously implicated in POI in a D. melanogaster model. MAIN OUTCOME Genes with rare pathogenic variants and gene sets with increased burden of deleterious variants were identified. RESULTS Candidate heterozygous variants were identified in known genes and genes with functional evidence. Gene sets with increased burden of deleterious alleles included the categories transcription and translation, DNA damage and repair, meiosis and cell division. Variants were found in novel genes from the enhanced categories. Functional evidence supported 7 new risk genes for POI (USP36, VCP, WDR33, PIWIL3, NPM2, LLGL1, and BOD1L1). CONCLUSIONS Candidate causative variants were identified through WES in women with POI. Aggregating clinical data and genetic risk with a categorical approach may expand the genetic architecture of heterozygous rare gene variants causing risk for POI.
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Affiliation(s)
- Bushra Gorsi
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Edgar Hernandez
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Marvin Barry Moore
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Mika Moriwaki
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, UT, USA
| | - Clement Y Chow
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Emily Coelho
- Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Elaine Taylor
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Claire Lu
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Amanda Walker
- University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Philippe Touraine
- Sorbonne Universite, Hôpital Universitaire Pitié Salpêtrière-Charles Foix, Service d’Endocrinologie et Médecine de la Reproduction, Centre de Maladies Endocriniennes Rares de la Croissance et du Développement, Centre de Pathologies Gynécologiques Rares, Paris, France
| | | | | | - Elaine R Mardis
- Institute for Genomic Medicine, Nationwide Children’s Hospital, Ohio State University College of Medicine, Columbus, OH, USA
| | - Aleksander Rajkovic
- Department of Pathology, University of California San Francisco School of Medicine, San Francisco, CA, USA
| | - Mark Yandell
- Utah Center for Genetic Discovery, Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Corrine K Welt
- Division of Endocrinology, Metabolism and Diabetes, University of Utah, Salt Lake City, UT, USA
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Elbæk CR, Petrosius V, Benada J, Erichsen L, Damgaard RB, Sørensen CS. WEE1 kinase protects the stability of stalled DNA replication forks by limiting CDK2 activity. Cell Rep 2022; 38:110261. [PMID: 35045293 DOI: 10.1016/j.celrep.2021.110261] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 10/15/2021] [Accepted: 12/21/2021] [Indexed: 12/26/2022] Open
Abstract
Cellular feedback systems ensure genome maintenance during DNA replication. When replication forks stall, newly replicated DNA is protected by pathways that limit excessive DNA nuclease attacks. Here we show that WEE1 activity guards against nascent DNA degradation at stalled forks. Furthermore, we identify WEE1-dependent suppression of cyclin-dependent kinase 2 (CDK2) as a major activity counteracting fork degradation. We establish DNA2 as the nuclease responsible for excessive fork degradation in WEE1-inhibited cells. In addition, WEE1 appears to be unique among CDK activity suppressors in S phase because neither CHK1 nor p21 promote fork protection as WEE1 does. Our results identify a key role of WEE1 in protecting stalled forks, which is separate from its established role in safeguarding DNA replication initiation. Our findings highlight how WEE1 inhibition evokes massive genome challenges during DNA replication, and this knowledge may improve therapeutic strategies to specifically eradicate cancer cells that frequently harbor elevated DNA replication stress.
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Affiliation(s)
- Camilla Reiter Elbæk
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløesvej 5, Copenhagen N 2200, Denmark; Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark
| | - Valdemaras Petrosius
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløesvej 5, Copenhagen N 2200, Denmark
| | - Jan Benada
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløesvej 5, Copenhagen N 2200, Denmark
| | - Louisa Erichsen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløesvej 5, Copenhagen N 2200, Denmark
| | - Rune Busk Damgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Søltofts Plads, Kongens Lyngby 2800, Denmark
| | - Claus Storgaard Sørensen
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Ole Maaløesvej 5, Copenhagen N 2200, Denmark.
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37
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Abu-Libdeh B, Jhujh SS, Dhar S, Sommers JA, Datta A, Longo GM, Grange LJ, Reynolds JJ, Cooke SL, McNee GS, Hollingworth R, Woodward BL, Ganesh AN, Smerdon SJ, Nicolae CM, Durlacher-Betzer K, Molho-Pessach V, Abu-Libdeh A, Meiner V, Moldovan GL, Roukos V, Harel T, Brosh RM, Stewart GS. RECON syndrome is a genome instability disorder caused by mutations in the DNA helicase RECQL1. J Clin Invest 2022; 132:147301. [PMID: 35025765 PMCID: PMC8884905 DOI: 10.1172/jci147301] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 01/11/2022] [Indexed: 11/17/2022] Open
Abstract
Despite being the first homolog of the bacterial RecQ helicase to be identified in humans, the function of RECQL1 remains poorly characterized. Furthermore, unlike other members of the human RECQ family of helicases, mutations in RECQL1 have not been associated with a genetic disease. Here, we identify 2 families with a genome instability disorder that we have named RECON (RECql ONe) syndrome, caused by biallelic mutations in the RECQL gene. The affected individuals had short stature, progeroid facial features, a hypoplastic nose, xeroderma, and skin photosensitivity and were homozygous for the same missense mutation in RECQL1 (p.Ala459Ser), located within its zinc binding domain. Biochemical analysis of the mutant RECQL1 protein revealed that the p.A459S missense mutation compromised its ATPase, helicase, and fork restoration activity, while its capacity to promote single-strand DNA annealing was largely unaffected. At the cellular level, this mutation in RECQL1 gave rise to a defect in the ability to repair DNA damage induced by exposure to topoisomerase poisons and a failure of DNA replication to progress efficiently in the presence of abortive topoisomerase lesions. Taken together, RECQL1 is the fourth member of the RecQ family of helicases to be associated with a human genome instability disorder.
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Affiliation(s)
- Bassam Abu-Libdeh
- Department of Pediatrics & Genetics, Makassed Hospital & Al-Quds Medical School, Jerusalem, Israel
| | - Satpal S Jhujh
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Srijita Dhar
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Canada
| | - Joshua A Sommers
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Canada
| | - Arindam Datta
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Canada
| | - Gabriel Mc Longo
- Institute of Molecular Biology, Institute of Molecular Biology, Mainz, Germany
| | - Laura J Grange
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - John J Reynolds
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sophie L Cooke
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Gavin S McNee
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Robert Hollingworth
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Beth L Woodward
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Anil N Ganesh
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Stephen J Smerdon
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, United States of America
| | | | - Vered Molho-Pessach
- Department of Dermatology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Abdulsalam Abu-Libdeh
- Department of Pediatrics & Genetics, Makassed Hospital & Al-Quds Medical School, Jerusalem, Israel
| | - Vardiella Meiner
- Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, United States of America
| | - Vassilis Roukos
- Institute of Molecular Biology, Institute of Molecular Biology, Mainz, Germany
| | - Tamar Harel
- Faculty of Medicine, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Robert M Brosh
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Canada
| | - Grant S Stewart
- Institute for Cancer and Genomic Sciences, University of Birmingham, Birmingham, United Kingdom
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38
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Lappin KM, Barros EM, Jhujh SS, Irwin GW, McMillan H, Liberante FG, Latimer C, LaBonte MJ, Mills KI, Harkin DP, Stewart GS, Savage KI. CANCER-ASSOCIATED SF3B1 MUTATIONS CONFER A BRCA-LIKE CELLULAR PHENOTYPE AND SYNTHETIC LETHALITY TO PARP INHIBITORS. Cancer Res 2022; 82:819-830. [DOI: 10.1158/0008-5472.can-21-1843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/12/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022]
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Yamindago A, Lee N, Lee N, Jo Y, Woo S, Yum S. Fluoxetine in the environment may interfere with the neurotransmission or endocrine systems of aquatic animals. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 227:112931. [PMID: 34715500 DOI: 10.1016/j.ecoenv.2021.112931] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/28/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Antidepressants are extensively used to treat the symptoms of depression in humans, and the environmentally discharged drugs potentially threaten aquatic organisms. In this study, the acute toxic effects of fluoxetine (FLX) were investigated in two aquatic organisms, the freshwater polyp (Hydra magnipapillata) and Javanese medaka (Oryzias javanicus). The median lethal concentration (LC50) of FLX in H. magnipapillata was 3.678, 3.082, and 2.901 mg/L after 24, 48, and 72 h, respectively. Morphological observations of the FLX-exposed H. magnipapillata showed that 1.5 mg/L FLX induced the contraction of the tentacles and body column. The LC50 of FLX in O. javanicus was 2.046, 1.936, 1.532, and 1.237 mg/L after 24, 48, 72, and 96 h, respectively. Observation of the behavior of the FLX-exposed fish showed that FLX reduced their swimming performance at a minimum concentration of 10 µg/L. The half-maximal effective concentration (EC50) of FLX for swimming behavior in O. javanicus was 0.135, 0.108, and 0.011 mg/L after 12, 24, and 96 h, respectively. Transcriptomic analyses indicated that FLX affects various physiological and metabolic processes in both species. FLX exposure induced oxidative stress, reproductive deficiency, abnormal pattern formation, DNA damage, and neurotransmission disturbance in H. magnipapillata, whereas it adversely affected O. javanicus by inducing oxidative stress, DNA damage, endoplasmic reticulum stress, and mRNA instability. Neurotransmission-based behavioral changes and endocrine disruption were strongly suspected in the FLX-exposed fish. These results suggest that FLX affects the behavior and metabolic regulation of aquatic organisms.
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Affiliation(s)
- Ade Yamindago
- CORECT Research Group, Faculty of Fisheries and Marine Science, Universitas Brawijaya, Malang 65145, Indonesia; Study Program of Marine Science, Faculty of Fisheries and Marine Science, Universitas Brawijaya, Malang 65145, Indonesia.
| | - Nayun Lee
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
| | - Nayoung Lee
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
| | - Yejin Jo
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea
| | - Seonock Woo
- Marine Biotechnology Research Center, Korea Institute of Ocean Science and Technology, Busan 49111, Republic of Korea
| | - Seungshic Yum
- Ecological Risk Research Division, Korea Institute of Ocean Science and Technology, Geoje 53201, Republic of Korea; KIOST School, University of Science and Technology, Geoje 53201, Republic of Korea.
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40
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Batenburg NL, Mersaoui SY, Walker JR, Coulombe Y, Hammond-Martel I, Wurtele H, Masson JY, Zhu XD. Cockayne syndrome group B protein regulates fork restart, fork progression and MRE11-dependent fork degradation in BRCA1/2-deficient cells. Nucleic Acids Res 2021; 49:12836-12854. [PMID: 34871413 PMCID: PMC8682776 DOI: 10.1093/nar/gkab1173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 11/08/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
Cockayne syndrome group B (CSB) protein has been implicated in the repair of a variety of DNA lesions that induce replication stress. However, little is known about its role at stalled replication forks. Here, we report that CSB is recruited to stalled forks in a manner dependent upon its T1031 phosphorylation by CDK. While dispensable for MRE11 association with stalled forks in wild-type cells, CSB is required for further accumulation of MRE11 at stalled forks in BRCA1/2-deficient cells. CSB promotes MRE11-mediated fork degradation in BRCA1/2-deficient cells. CSB possesses an intrinsic ATP-dependent fork reversal activity in vitro, which is activated upon removal of its N-terminal region that is known to autoinhibit CSB’s ATPase domain. CSB functions similarly to fork reversal factors SMARCAL1, ZRANB3 and HLTF to regulate slowdown in fork progression upon exposure to replication stress, indicative of a role of CSB in fork reversal in vivo. Furthermore, CSB not only acts epistatically with MRE11 to facilitate fork restart but also promotes RAD52-mediated break-induced replication repair of double-strand breaks arising from cleavage of stalled forks by MUS81 in BRCA1/2-deficient cells. Loss of CSB exacerbates chemosensitivity in BRCA1/2-deficient cells, underscoring an important role of CSB in the treatment of cancer lacking functional BRCA1/2.
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Affiliation(s)
- Nicole L Batenburg
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Sofiane Y Mersaoui
- CHU de Québec-Université Laval, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - John R Walker
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
| | - Yan Coulombe
- CHU de Québec-Université Laval, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - Ian Hammond-Martel
- Centre de recherche, de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, Québec H1T 2M4, Canada
| | - Hugo Wurtele
- Centre de recherche, de l'Hôpital Maisonneuve-Rosemont, 5415 boulevard de l'Assomption, Montréal, Québec H1T 2M4, Canada.,Department of Medicine, Université de Montréal, Montréal, Québec H3T 1J4, Canada
| | - Jean-Yves Masson
- CHU de Québec-Université Laval, Oncology Division, Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, 9 McMahon, Québec City, Québec G1R 3S3, Canada
| | - Xu-Dong Zhu
- Department of Biology, McMaster University, Hamilton, Ontario L8S 4K1, Canada
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Abstract
DNA double-strand breaks (DSBs) are cytotoxic lesions that threaten genome integrity and cell viability. Typically, cells repair DSBs by either nonhomologous end joining (NHEJ) or homologous recombination (HR). The relative use of these two pathways depends on many factors, including cell cycle stage and the nature of the DNA ends. A critical determinant of repair pathway selection is the initiation of 5'→3' nucleolytic degradation of DNA ends, a process referred to as DNA end resection. End resection is essential to create single-stranded DNA overhangs, which serve as the substrate for the Rad51 recombinase to initiate HR and are refractory to NHEJ repair. Here, we review recent insights into the mechanisms of end resection, how it is regulated, and the pathological consequences of its dysregulation.
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Affiliation(s)
- Petr Cejka
- Faculty of Biomedical Sciences, Institute for Research in Biomedicine, Università della Svizzera italiana (USI), 6500 Bellinzona, Switzerland; .,Department of Biology, Institute of Biochemistry, Eidgenössische Technische Hochschule (ETH) Zürich, 8093 Zürich, Switzerland
| | - Lorraine S Symington
- Department of Microbiology & Immunology, Columbia University Irving Medical Center, New York, NY 10032, USA; .,Department of Genetics & Development, Columbia University Irving Medical Center, New York, NY 10032, USA
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42
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Datta A, Biswas K, Sommers JA, Thompson H, Awate S, Nicolae CM, Thakar T, Moldovan GL, Shoemaker RH, Sharan SK, Brosh RM. WRN helicase safeguards deprotected replication forks in BRCA2-mutated cancer cells. Nat Commun 2021; 12:6561. [PMID: 34772932 PMCID: PMC8590011 DOI: 10.1038/s41467-021-26811-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 10/20/2021] [Indexed: 11/08/2022] Open
Abstract
The tumor suppressor BRCA2 protects stalled forks from degradation to maintain genome stability. However, the molecular mechanism(s) whereby unprotected forks are stabilized remains to be fully characterized. Here, we demonstrate that WRN helicase ensures efficient restart and limits excessive degradation of stalled forks in BRCA2-deficient cancer cells. In vitro, WRN ATPase/helicase catalyzes fork restoration and curtails MRE11 nuclease activity on regressed forks. We show that WRN helicase inhibitor traps WRN on chromatin leading to rapid fork stalling and nucleolytic degradation of unprotected forks by MRE11, resulting in MUS81-dependent double-strand breaks, elevated non-homologous end-joining and chromosomal instability. WRN helicase inhibition reduces viability of BRCA2-deficient cells and potentiates cytotoxicity of a poly (ADP)ribose polymerase (PARP) inhibitor. Furthermore, BRCA2-deficient xenograft tumors in mice exhibited increased DNA damage and growth inhibition when treated with WRN helicase inhibitor. This work provides mechanistic insight into stalled fork stabilization by WRN helicase when BRCA2 is deficient.
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Affiliation(s)
- Arindam Datta
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Kajal Biswas
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Joshua A Sommers
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Haley Thompson
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Sanket Awate
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA
| | - Claudia M Nicolae
- 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
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA, 17033, USA
| | - Robert H Shoemaker
- Chemopreventive Agent Development Research Group, Division of Cancer Prevention, National Cancer Institute, NIH, Rockville, MD, 20850, USA
| | - Shyam K Sharan
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, NIH, Frederick, MD, 21702, USA
| | - Robert M Brosh
- Translational Gerontology Branch, National Institute on Aging, NIH, Baltimore, MD, 21224, USA.
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43
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Russi M, Marson D, Fermeglia A, Aulic S, Fermeglia M, Laurini E, Pricl S. The fellowship of the RING: BRCA1, its partner BARD1 and their liaison in DNA repair and cancer. Pharmacol Ther 2021; 232:108009. [PMID: 34619284 DOI: 10.1016/j.pharmthera.2021.108009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
The breast cancer type 1 susceptibility protein (BRCA1) and its partner - the BRCA1-associated RING domain protein 1 (BARD1) - are key players in a plethora of fundamental biological functions including, among others, DNA repair, replication fork protection, cell cycle progression, telomere maintenance, chromatin remodeling, apoptosis and tumor suppression. However, mutations in their encoding genes transform them into dangerous threats, and substantially increase the risk of developing cancer and other malignancies during the lifetime of the affected individuals. Understanding how BRCA1 and BARD1 perform their biological activities therefore not only provides a powerful mean to prevent such fatal occurrences but can also pave the way to the development of new targeted therapeutics. Thus, through this review work we aim at presenting the major efforts focused on the functional characterization and structural insights of BRCA1 and BARD1, per se and in combination with all their principal mediators and regulators, and on the multifaceted roles these proteins play in the maintenance of human genome integrity.
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Affiliation(s)
- Maria Russi
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Domenico Marson
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Alice Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Suzana Aulic
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Maurizio Fermeglia
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Erik Laurini
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy
| | - Sabrina Pricl
- Molecular Biology and Nanotechnology Laboratory (MolBNL@UniTs), DEA, University of Trieste, Trieste, Italy; Department of General Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland.
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44
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Tamura Y, Ohhata T, Niida H, Sakai S, Uchida C, Masumoto K, Katou F, Wutz A, Kitagawa M. Homologous recombination is reduced in female embryonic stem cells by two active X chromosomes. EMBO Rep 2021; 22:e52190. [PMID: 34309165 DOI: 10.15252/embr.202052190] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
The reactivation of X-linked genes is observed in some primary breast tumors. Two active X chromosomes are also observed in female embryonic stem cells (ESCs), but whether double doses of X-linked genes affect DNA repair efficiency remains unclear. Here, we establish isogenic female/male ESCs and show that the female ESCs are more sensitive to camptothecin and have lower gene targeting efficiency than male ESCs, suggesting that homologous recombination (HR) efficiency is reduced in female ESCs. We also generate Xist-inducible female ESCs and show that the lower HR efficiency is restored when X chromosome inactivation is induced. Finally, we assess the X-linked genes with a role in DNA repair and find that Brcc3 is one of the genes involved in a network promoting proper HR. Our findings link the double doses of X-linked genes with lower DNA repair activity, and this may have relevance for common diseases in female patients, such as breast cancer.
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Affiliation(s)
- Yuka Tamura
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan.,Department of Oral and Maxillofacial Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Tatsuya Ohhata
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hiroyuki Niida
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Satoshi Sakai
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Chiharu Uchida
- Advanced Research Facilities & Services, Preeminent Medical Photonics Education & Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Kazuma Masumoto
- Department of Oral and Maxillofacial Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Fuminori Katou
- Department of Oral and Maxillofacial Surgery, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Anton Wutz
- Institute of Molecular Health Sciences, ETH Zürich, Zurich, Switzerland
| | - Masatoshi Kitagawa
- Department of Molecular Biology, Hamamatsu University School of Medicine, Hamamatsu, Japan
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45
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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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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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Krishnamoorthy A, Jackson J, Mohamed T, Adolph M, Vindigni A, Cortez D. RADX prevents genome instability by confining replication fork reversal to stalled forks. Mol Cell 2021; 81:3007-3017.e5. [PMID: 34107305 DOI: 10.1016/j.molcel.2021.05.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 04/02/2021] [Accepted: 05/10/2021] [Indexed: 12/16/2022]
Abstract
RAD51 facilitates replication fork reversal and protects reversed forks from nuclease degradation. Although potentially a useful replication stress response mechanism, unregulated fork reversal can cause genome instability. Here we show that RADX, a single-strand DNA binding protein that binds to and destabilizes RAD51 nucleofilaments, can either inhibit or promote fork reversal depending on replication stress levels. RADX inhibits fork reversal at elongating forks, thereby preventing fork slowing and collapse. Paradoxically, in the presence of persistent replication stress, RADX localizes to stalled forks to generate reversed fork structures. Consequently, inactivating RADX prevents fork-reversal-dependent telomere dysfunction in the absence of RTEL1 and blocks nascent strand degradation when fork protection factors are inactivated. Addition of RADX increases SMARCAL1-dependent fork reversal in conditions in which pre-binding RAD51 to a model fork substrate is inhibitory. Thus, RADX directly interacts with RAD51 and single-strand DNA to confine fork reversal to persistently stalled forks.
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Affiliation(s)
- Archana Krishnamoorthy
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Jessica Jackson
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Taha Mohamed
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Madison Adolph
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA
| | - Alessandro Vindigni
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN 37237, USA.
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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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49
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Qiu S, Jiang G, Cao L, Huang J. Replication Fork Reversal and Protection. Front Cell Dev Biol 2021; 9:670392. [PMID: 34041245 PMCID: PMC8141627 DOI: 10.3389/fcell.2021.670392] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 04/19/2021] [Indexed: 12/12/2022] Open
Abstract
During genome replication, replication forks often encounter obstacles that impede their progression. Arrested forks are unstable structures that can give rise to collapse and rearrange if they are not properly processed and restarted. Replication fork reversal is a critical protective mechanism in higher eukaryotic cells in response to replication stress, in which forks reverse their direction to form a Holliday junction-like structure. The reversed replication forks are protected from nuclease degradation by DNA damage repair proteins, such as BRCA1, BRCA2, and RAD51. Some of these molecules work cooperatively, while others have unique functions. Once the stress is resolved, the replication forks can restart with the help of enzymes, including human RECQ1 helicase, but restart will not be considered here. Here, we review research on the key factors and mechanisms required for the remodeling and protection of stalled replication forks in mammalian cells.
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Affiliation(s)
- Shan Qiu
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China.,Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Zhejiang University, Haining, China
| | - Guixing Jiang
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liping Cao
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Huang
- Department of General Surgery, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China.,The MOE Key Laboratory of Biosystems Homeostasis and Protection, Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, China
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Tye S, Ronson GE, Morris JR. A fork in the road: Where homologous recombination and stalled replication fork protection part ways. Semin Cell Dev Biol 2021; 113:14-26. [PMID: 32653304 PMCID: PMC8082280 DOI: 10.1016/j.semcdb.2020.07.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 07/06/2020] [Accepted: 07/06/2020] [Indexed: 12/14/2022]
Abstract
In response to replication hindrances, DNA replication forks frequently stall and are remodelled into a four-way junction. In such a structure the annealed nascent strand is thought to resemble a DNA double-strand break and remodelled forks are vulnerable to nuclease attack by MRE11 and DNA2. Proteins that promote the recruitment, loading and stabilisation of RAD51 onto single-stranded DNA for homology search and strand exchange in homologous recombination (HR) repair and inter-strand cross-link repair also act to set up RAD51-mediated protection of nascent DNA at stalled replication forks. However, despite the similarities of these pathways, several lines of evidence indicate that fork protection is not simply analogous to the RAD51 loading step of HR. Protection of stalled forks not only requires separate functions of a number of recombination proteins, but also utilises nucleases important for the resection steps of HR in alternative ways. Here we discuss how fork protection arises and how its differences with HR give insights into the differing contexts of these two pathways.
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Affiliation(s)
- Stephanie Tye
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, London, SW7 2AZ, UK
| | - George E Ronson
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK
| | - Joanna R Morris
- University of Birmingham, College of Medical Dental Schools, Institute of Cancer and Genomics Sciences, Birmingham Centre for Genome Biology, Vincent Drive, Edgbaston, Birmingham, B15 2TT, UK.
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