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Talibova G, Bilmez Y, Tire B, Ozturk S. The DNA double-strand break repair proteins γH2AX, RAD51, BRCA1, RPA70, KU80, and XRCC4 exhibit follicle-specific expression differences in the postnatal mouse ovaries from early to older ages. J Assist Reprod Genet 2024; 41:2419-2439. [PMID: 39023827 PMCID: PMC11405603 DOI: 10.1007/s10815-024-03189-4] [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: 02/05/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024] Open
Abstract
PURPOSE Ovarian aging is closely related to a decrease in follicular reserve and oocyte quality. The precise molecular mechanisms underlying these reductions have yet to be fully elucidated. Herein, we examine spatiotemporal distribution of key proteins responsible for DNA double-strand break (DSB) repair in ovaries from early to older ages. Functional studies have shown that the γH2AX, RAD51, BRCA1, and RPA70 proteins play indispensable roles in HR-based repair pathway, while the KU80 and XRCC4 proteins are essential for successfully operating cNHEJ pathway. METHODS Female Balb/C mice were divided into five groups as follows: Prepuberty (3 weeks old; n = 6), puberty (7 weeks old; n = 7), postpuberty (18 weeks old; n = 7), early aged (52 weeks old; n = 7), and late aged (60 weeks old; n = 7). The expression of DSB repair proteins, cellular senescence (β-GAL) and apoptosis (cCASP3) markers was evaluated in the ovaries using immunohistochemistry. RESULT β-GAL and cCASP3 levels progressively increased from prepuberty to aged groups (P < 0.05). Notably, γH2AX levels varied in preantral and antral follicles among the groups (P < 0.05). In aged groups, RAD51, BRCA1, KU80, and XRCC4 levels increased (P < 0.05), while RPA70 levels decreased (P < 0.05) compared to the other groups. CONCLUSIONS The observed alterations were primarily attributed to altered expression in oocytes and granulosa cells of the follicles and other ovarian cells. As a result, the findings indicate that these DSB repair proteins may play a role in the repair processes and even other related cellular events in ovarian cells from early to older ages.
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Affiliation(s)
- Gunel Talibova
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Yesim Bilmez
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Betul Tire
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey
| | - Saffet Ozturk
- Department of Histology and Embryology, Akdeniz University School of Medicine, Campus, 07070, Antalya, Turkey.
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2
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Sharma R, Oak N, Chen W, Gogal R, Kirschner M, Beier F, Schnieders MJ, Spies M, Nichols KE, Wlodarski M. Germline landscape of RPA1, RPA2 and RPA3 variants in pediatric malignancies: identification of RPA1 as a novel cancer predisposition candidate gene. Front Oncol 2023; 13:1229507. [PMID: 37869077 PMCID: PMC10588448 DOI: 10.3389/fonc.2023.1229507] [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: 05/26/2023] [Accepted: 09/18/2023] [Indexed: 10/24/2023] Open
Abstract
Replication Protein A (RPA) is single-strand DNA binding protein that plays a key role in the replication and repair of DNA. RPA is a heterotrimer made of 3 subunits - RPA1, RPA2, and RPA3. Germline pathogenic variants affecting RPA1 were recently described in patients with Telomere Biology Disorders (TBD), also known as dyskeratosis congenita or short telomere syndrome. Premature telomere shortening is a hallmark of TBD and results in bone marrow failure and predisposition to hematologic malignancies. Building on the finding that somatic mutations in RPA subunit genes occur in ~1% of cancers, we hypothesized that germline RPA alterations might be enriched in human cancers. Because germline RPA1 mutations are linked to early onset TBD with predisposition to myelodysplastic syndromes, we interrogated pediatric cancer cohorts to define the prevalence and spectrum of rare/novel and putative damaging germline RPA1, RPA2, and RPA3 variants. In this study of 5,993 children with cancer, 75 (1.25%) harbored heterozygous rare (non-cancer population allele frequency (AF) < 0.1%) variants in the RPA heterotrimer genes, of which 51 cases (0.85%) had ultra-rare (AF < 0.005%) or novel variants. Compared with Genome Aggregation Database (gnomAD) non-cancer controls, there was significant enrichment of ultra-rare and novel RPA1, but not RPA2 or RPA3, germline variants in our cohort (adjusted p-value < 0.05). Taken together, these findings suggest that germline putative damaging variants affecting RPA1 are found in excess in children with cancer, warranting further investigation into the functional role of these variants in oncogenesis.
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Affiliation(s)
- Richa Sharma
- Department of Hematology, St. Jude Children´s Research Hospital, Memphis, TN, United States
| | - Ninad Oak
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Wenan Chen
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Rose Gogal
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Martin Kirschner
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Bonn, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Bonn, Germany
| | - Michael J. Schnieders
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Maria Spies
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Kim E. Nichols
- Department of Oncology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Marcin Wlodarski
- Department of Hematology, St. Jude Children´s Research Hospital, Memphis, TN, United States
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3
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Miao X, Guo R, Williams A, Lee C, Ma J, Wang PJ, Cui W. Replication Protein A1 is essential for DNA damage repair during mammalian oogenesis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.04.547725. [PMID: 37461444 PMCID: PMC10349974 DOI: 10.1101/2023.07.04.547725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Persistence of unrepaired DNA damage in oocytes is detrimental and may cause genetic aberrations, miscarriage, and infertility. RPA, an ssDNA-binding complex, is essential for various DNA-related processes. Here we report that RPA plays a novel role in DNA damage repair during postnatal oocyte development after meiotic recombination. To investigate the role of RPA during oogenesis, we inactivated RPA1 (replication protein A1), the largest subunit of the heterotrimeric RPA complex, specifically in oocytes using two germline-specific Cre drivers (Ddx4-Cre and Zp3-Cre). We find that depletion of RPA1 leads to the disassembly of the RPA complex, as evidenced by the absence of RPA2 and RPA3 in RPA1-deficient oocytes. Strikingly, severe DNA damage occurs in RPA1-deficient GV-stage oocytes. Loss of RPA in oocytes triggered the canonical DNA damage response mechanisms and pathways, such as activation of ATM, ATR, DNA-PK, and p53. In addition, the RPA deficiency causes chromosome misalignment at metaphase I and metaphase II stages of oocytes, which is consistent with altered transcript levels of genes involved in cytoskeleton organization in RPA1-deficient oocytes. Absence of the RPA complex in oocytes severely impairs folliculogenesis and leads to a significant reduction in oocyte number and female infertility. Our results demonstrate that RPA plays an unexpected role in DNA damage repair during mammalian folliculogenesis.
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Affiliation(s)
- Xiaosu Miao
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Rui Guo
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract, Anhui Medical University, Hefei, Anhui, China
| | - Andrea Williams
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Catherine Lee
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
| | - Jun Ma
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - P. Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, PA, USA
| | - Wei Cui
- Department of Veterinary and Animal Sciences, University of Massachusetts, Amherst, MA, USA
- Animal Models Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts, Amherst, MA, USA
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4
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Algethami M, Toss MS, Woodcock CL, Jaipal C, Brownlie J, Shoqafi A, Alblihy A, Mesquita KA, Green AR, Mongan NP, Jeyapalan JN, Rakha EA, Madhusudan S. Unravelling the clinicopathological and functional significance of replication protein A (RPA) heterotrimeric complex in breast cancers. NPJ Breast Cancer 2023; 9:18. [PMID: 36997566 PMCID: PMC10063624 DOI: 10.1038/s41523-023-00524-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
Abstract
Replication Protein A (RPA), a heterotrimeric complex consisting of RPA1, 2, and 3 subunits, is a single-stranded DNA (ssDNA)-binding protein that is critically involved in replication, checkpoint regulation and DNA repair. Here we have evaluated RPA in 776 pure ductal carcinomas in situ (DCIS), 239 DCIS that co-exist with invasive breast cancer (IBC), 50 normal breast tissue and 4221 IBC. Transcriptomic [METABRIC cohort (n = 1980)] and genomic [TCGA cohort (n = 1090)] evaluations were completed. Preclinically, RPA deficient cells were tested for cisplatin sensitivity and Olaparib induced synthetic lethality. Low RPA linked to aggressive DCIS, aggressive IBC, and shorter survival outcomes. At the transcriptomic level, low RPA tumours overexpress pseudogene/lncRNA as well as genes involved in chemical carcinogenesis, and drug metabolism. Low RPA remains linked with poor outcome. RPA deficient cells are sensitive to cisplatin and Olaparib induced synthetic lethality. We conclude that RPA directed precision oncology strategy is feasible in breast cancers.
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Affiliation(s)
- Mashael Algethami
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Michael S Toss
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Department of Pathology, Nottingham University Hospital, City Campus, Hucknall Road, Nottingham, NG51PB, UK
| | - Corinne L Woodcock
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Faculty of Medicine and Health Sciences, Centre for Cancer Sciences, University of Nottingham, Sutton Bonington Campus, Sutton Bonington, Leicestershire, LE12 5RD, UK
| | - Chandar Jaipal
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Juliette Brownlie
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Ahmed Shoqafi
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Adel Alblihy
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Medical Center, King Fahad Security College (KFSC), Riyadh, 11461, Saudi Arabia
| | - Katia A Mesquita
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Andrew R Green
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
| | - Nigel P Mongan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Department of Pharmacology, Weill Cornell Medicine, New York, NY, 10065, USA
| | - Jennie N Jeyapalan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Department of Pathology, Nottingham University Hospital, City Campus, Hucknall Road, Nottingham, NG51PB, UK
| | - Emad A Rakha
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK
- Medical Center, King Fahad Security College (KFSC), Riyadh, 11461, Saudi Arabia
| | - Srinivasan Madhusudan
- Nottingham Biodiscovery Institute, School of Medicine, University of Nottingham, University Park, Nottingham, NG7 3RD, UK.
- Department of Oncology, Nottingham University Hospitals, Nottingham, NG51PB, UK.
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5
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Lee SHT, Kim JY, Kim P, Dong Z, Su CY, Ahn EH. Changes of Mutations and Copy-Number and Enhanced Cell Migration during Breast Tumorigenesis. Adv Biol (Weinh) 2023; 7:e2200072. [PMID: 36449747 PMCID: PMC10836759 DOI: 10.1002/adbi.202200072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 11/14/2022] [Indexed: 12/02/2022]
Abstract
Although cancer stem cells (CSCs) play a major role in tumorigenesis and metastasis, the role of genetic alterations in invasiveness of CSCs is still unclear. Tumor microenvironment signals, such as extracellular matrix (ECM) composition, significantly influence cell behaviors. Unfortunately, these signals are often lost in in vitro cell culture. This study determines putative CSC populations, examines genetic changes during tumorigenesis of human breast epithelial stem cells, and investigates single-cell migration properties on ECM-mimetic platforms. Whole exome sequencing data indicate that tumorigenic cells have a higher somatic mutation burden than non-tumorigenic cells, and that mutations exclusive to tumorigenic cells exhibit higher predictive deleterious scores. Tumorigenic cells exhibit distinct somatic copy number variations (CNVs) including gain of duplications in chromosomes 5 and 8. ECM-mimetic topography selectively enhances migration speed of tumorigenic cells, but not of non-tumorigenic cells, and results in a wide distribution of tumorigenic single-cell migration speeds, suggesting heterogeneity in cellular sensing of contact guidance cues. This study identifies mutations and CNVs acquired during breast tumorigenesis, which can be associated with enhanced migration of breast tumorigenic cells, and demonstrates that a nanotopographically-defined platform can be applied to recapitulate an ECM structure for investigating cellular migration in the simulated tumor microenvironment.
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Affiliation(s)
- Seung Hyuk T. Lee
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Joon Yup Kim
- Department of Pathology, University of Washington, Seattle,
WA 98195, USA
| | - Peter Kim
- Department of Bioengineering, University of Washington,
Seattle, WA 98195, USA
| | - Zhipeng Dong
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Chia-Yi Su
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
| | - Eun Hyun Ahn
- Department of Biomedical Engineering, Johns Hopkins
University, Baltimore, MD 21205, USA
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6
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The Roles of EXO1 and RPA1 Polymorphisms in Prognosis of Lung Cancer Patients Treated with Platinum-Based Chemotherapy. DISEASE MARKERS 2022; 2022:3306189. [PMID: 36277983 PMCID: PMC9584701 DOI: 10.1155/2022/3306189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 09/29/2022] [Indexed: 12/24/2022]
Abstract
Background. Lung cancer is one of the major causes of cancer-related mortality worldwide. DNA repair and damage response contribute to genomic instability that accompanies tumor progression. In this study, we focus on evaluating association between DNA repair polymorphisms of EXO1, RPA1, and prognosis in lung cancer patients whom received platinum-based chemotherapy. Methods. 593 lung cancer patients were recruited in this study. We performed genotyping of 19 single nucleotide polymorphisms (SNPs) by Sequenom MassARRAY. Cox regression analysis was used to assess overall survival (OS) and progression-free survival (PFS) among SNP genotypes. Results. Significant differences in PFS and OS were observed in RPA1 rs5030740, EXO1 rs1776148, and rs1047840. Results showed that patients with CC genotype in rs5030740 (recessive model:
) had a better PFS. Patients with AA or/and AG genotypes in rs1776148 (additive model:
; dominant model:
) and AA genotype in rs1047840 (recessive model:
) had longer OS. We also demonstrated differences in subgroup analysis between rs5030740, rs1776148, rs1047840, and prognosis. Conclusions. Our results indicated that EXO1 rs1776148, rs1047840, and RPA1 rs5030740 were significantly associated with prognosis of lung cancer. Rs1776148, rs1047840, and rs5030740 may act as prognosis markers in lung cancer patients with platinum-based chemotherapy.
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7
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Guo JT, Malik F. Single-Stranded DNA Binding Proteins and Their Identification Using Machine Learning-Based Approaches. Biomolecules 2022; 12:biom12091187. [PMID: 36139026 PMCID: PMC9496475 DOI: 10.3390/biom12091187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/11/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022] Open
Abstract
Single-stranded DNA (ssDNA) binding proteins (SSBs) are critical in maintaining genome stability by protecting the transient existence of ssDNA from damage during essential biological processes, such as DNA replication and gene transcription. The single-stranded region of telomeres also requires protection by ssDNA binding proteins from being attacked in case it is wrongly recognized as an anomaly. In addition to their critical roles in genome stability and integrity, it has been demonstrated that ssDNA and SSB-ssDNA interactions play critical roles in transcriptional regulation in all three domains of life and viruses. In this review, we present our current knowledge of the structure and function of SSBs and the structural features for SSB binding specificity. We then discuss the machine learning-based approaches that have been developed for the prediction of SSBs from double-stranded DNA (dsDNA) binding proteins (DSBs).
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8
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RPA1 controls chromatin architecture and maintains lipid metabolic homeostasis. Cell Rep 2022; 40:111071. [PMID: 35830798 DOI: 10.1016/j.celrep.2022.111071] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/24/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease, with a prevalence of 25% worldwide. However, the underlying molecular mechanism involved in the development and progression of the NAFLD spectrum remains unclear. Single-stranded DNA-binding protein replication protein A1 (RPA1) participates in DNA replication, recombination, and damage repair. Here, we show that Rpa1+/- mice develop fatty liver disease during aging and in response to a high-fat diet. Liver-specific deletion of Rpa1 results in downregulation of genes related to fatty acid oxidation and impaired fatty acid oxidation, which leads to hepatic steatosis and hepatocellular carcinoma. Mechanistically, RPA1 binds gene regulatory regions, chromatin-remodeling factors, and HNF4A and remodels chromatin architecture, through which RPA1 promotes HNF4A transcriptional activity and fatty acid β oxidation. Collectively, our data demonstrate that RPA1 is an important regulator of NAFLD through controlling chromatin accessibility.
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WASp modulates RPA function on single-stranded DNA in response to replication stress and DNA damage. Nat Commun 2022; 13:3743. [PMID: 35768435 PMCID: PMC9243104 DOI: 10.1038/s41467-022-31415-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 06/08/2022] [Indexed: 02/07/2023] Open
Abstract
Perturbation in the replication-stress response (RSR) and DNA-damage response (DDR) causes genomic instability. Genomic instability occurs in Wiskott-Aldrich syndrome (WAS), a primary immunodeficiency disorder, yet the mechanism remains largely uncharacterized. Replication protein A (RPA), a single-strand DNA (ssDNA) binding protein, has key roles in the RSR and DDR. Here we show that human WAS-protein (WASp) modulates RPA functions at perturbed replication forks (RFs). Following genotoxic insult, WASp accumulates at RFs, associates with RPA, and promotes RPA:ssDNA complexation. WASp deficiency in human lymphocytes destabilizes RPA:ssDNA-complexes, impairs accumulation of RPA, ATR, ETAA1, and TOPBP1 at genotoxin-perturbed RFs, decreases CHK1 activation, and provokes global RF dysfunction. las17 (yeast WAS-homolog)-deficient S. cerevisiae also show decreased ScRPA accumulation at perturbed RFs, impaired DNA recombination, and increased frequency of DNA double-strand break (DSB)-induced single-strand annealing (SSA). Consequently, WASp (or Las17)-deficient cells show increased frequency of DSBs upon genotoxic insult. Our study reveals an evolutionarily conserved, essential role of WASp in the DNA stress-resolution pathway, such that WASp deficiency provokes RPA dysfunction-coupled genomic instability. Cancer develops in Wiskott-Aldrich syndrome (WAS). Here the authors identify a role for WAS-protein (WASp) in the DNA stress-resolution pathway by promoting the function of Replication Protein A at replication forks after DNA damage.
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10
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Chanihoon GQ, Afridi HI, Talpur FN, Kazi TG, Baig JA. Interaction Between Essential (Zn) and Toxic (Cd) Elements in Different Stages of Female Breast Cancer Patients, Resident in Different Cities of Sindh, Pakistan. Biol Trace Elem Res 2022; 200:1117-1126. [PMID: 34057654 DOI: 10.1007/s12011-021-02757-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 05/20/2021] [Indexed: 11/29/2022]
Abstract
Breast cancer is the most familiar solid tumor analyzed in women. Trace elements have critical roles in cancer biology. In this research, the relationship between carcinogenic element, cadmium (Cd), and anti-carcinogenic elements, zinc (Zn), in the scalp hair and blood samples of four stages of female breast cancer patients was studied. We have determined the essential trace (Zn) and toxic (Cd) elements, in biological samples (scalp hair and blood) of female breast cancer (n = 96 age ranging 22-35 years), residents of various cities of Pakistan. For comparative study, the biological samples of age-matched healthy (referent) subjects (n = 115) were also analyzed for selected metals. The validity and accuracy of the methodology were checked by using certified reference materials of biological referent materials (human hair (BCR 397) and ClinCheck lyophilized blood). The mean concentrations of Cd were found to be 3- to fourfold significantly higher in the scalp hair and blood samples of female breast patients as compared to referents, while reverse results were obtained in the case of Zn (p > 0.001). The observed data shows the significant effect of carcinogenic (Cd) and their balance towards the anti-carcinogenic (Zn) in humans.
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Affiliation(s)
- Ghulam Qadir Chanihoon
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro, 76080, Pakistan
| | - Hassan Imran Afridi
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro, 76080, Pakistan.
| | - Farah Naz Talpur
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro, 76080, Pakistan
| | - Tasneen Gul Kazi
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro, 76080, Pakistan
| | - Jameel Ahmed Baig
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro, 76080, Pakistan
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11
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Bao K, Zhang Q, Liu S, Song N, Guo Q, Liu L, Tian S, Hao J, Zhu Y, Zhang K, Ai D, Yang J, Yao Z, Foisner R, Shi L. LAP2α preserves genome integrity through assisting RPA deposition on damaged chromatin. Genome Biol 2022; 23:64. [PMID: 35227284 PMCID: PMC8883701 DOI: 10.1186/s13059-022-02638-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 02/17/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Single-stranded DNA (ssDNA) coated with replication protein A (RPA) acts as a key platform for the recruitment and exchange of genome maintenance factors in DNA damage response. Yet, how the formation of the ssDNA-RPA intermediate is regulated remains elusive. RESULTS Here, we report that the lamin-associated protein LAP2α is physically associated with RPA, and LAP2α preferentially facilitates RPA deposition on damaged chromatin via physical contacts between LAP2α and RPA1. Importantly, LAP2α-promoted RPA binding to ssDNA plays a critical role in protection of replication forks, activation of ATR, and repair of damaged DNA. We further demonstrate that the preference of LAP2α-promoted RPA loading on damaged chromatin depends on poly ADP-ribose polymerase PARP1, but not poly(ADP-ribosyl)ation. CONCLUSIONS Our study provides mechanistic insight into RPA deposition in response to DNA damage and reveals a genome protection role of LAP2α.
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Affiliation(s)
- Kaiwen Bao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Qi Zhang
- Department of Clinical Laboratory, First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Shuai Liu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Nan Song
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Qiushi Guo
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Ling Liu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Shanshan Tian
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jihui Hao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Yi Zhu
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Kai Zhang
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Ding Ai
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Jie Yang
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Zhi Yao
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China
| | - Roland Foisner
- Max Perutz Laboratories, Center of Medical Biochemistry, Medical University of Vienna, Vienna Biocenter (VBC), Vienna, Austria
| | - Lei Shi
- State Key Laboratory of Experimental Hematology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University General Hospital, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
- Department of Biochemistry and Molecular Biology, Tianjin Medical University, 22 Qixiangtai Road, Tianjin, 300070, China.
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12
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Lynch-like Syndrome: Potential Mechanisms and Management. Cancers (Basel) 2022; 14:cancers14051115. [PMID: 35267422 PMCID: PMC8909420 DOI: 10.3390/cancers14051115] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 02/05/2023] Open
Abstract
Simple Summary Lynch-like syndrome (LLS) is defined as colorectal cancer cases with microsatellite instability (MSI) and loss of expression of MLH1, MSH2, MSH6, or PMS2 by immunohistochemistry (IHC) in the absence of a germline mutation in these genes that cannot be explained by BRAF mutation or MLH1 hypermethylation. The application of the universal strategy for the diagnosis of Lynch syndrome (LS) in all CRCs is leading to an increase in the incidence of cases of LLS. It has been described that risk of cancer in relatives of LLS patients is in between of that found in Lynch syndrome families and sporadic cases. That makes LLS patients and their families a challenging group for which the origin of CRC is unknown, being a mixture between unidentified hereditary CRC and sporadic cases. The potential causes of LLS are discussed in this review, as well as methods for identification of truly hereditary cases. Abstract Lynch syndrome is an autosomal dominant disorder caused by germline mutations in DNA mismatch repair (MMR) system genes, such as MLH1, MSH2, MSH6, or PMS2. It is the most common hereditary colorectal cancer syndrome. Screening is regularly performed by using microsatellite instability (MSI) or immunohistochemistry for the MMR proteins in tumor samples. However, in a proportion of cases, MSI is found or MMR immunohistochemistry is impaired in the absence of a germline mutation in MMR genes, BRAF mutation, or MLH1 hypermethylation. These cases are defined as Lynch-like syndrome. Patients with Lynch-like syndrome represent a mixture of truly hereditary and sporadic cases, with a risk of colorectal cancer in first-degree relatives that is between the risk of Lynch syndrome in families and relatives of sporadic colon cancer cases. Although multiple approaches have been suggested to distinguish between hereditary and sporadic cases, a homogeneous testing protocol and consensus on the adequate classification of these patients is still lacking. For this reason, management of Lynch-like syndrome and prevention of cancer in these families is clinically challenging. This review explains the concept of Lynch-like syndrome, potential mechanisms for its development, and methods for adequately distinguishing between sporadic and hereditary cases of this entity.
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Sharma R, Sahoo SS, Honda M, Granger SL, Goodings C, Sanchez L, Künstner A, Busch H, Beier F, Pruett-Miller SM, Valentine MB, Fernandez AG, Chang TC, Géli V, Churikov D, Hirschi S, Pastor VB, Boerries M, Lauten M, Kelaidi C, Cooper MA, Nicholas S, Rosenfeld JA, Polychronopoulou S, Kannengiesser C, Saintomé C, Niemeyer CM, Revy P, Wold MS, Spies M, Erlacher M, Coulon S, Wlodarski MW. Gain-of-function mutations in RPA1 cause a syndrome with short telomeres and somatic genetic rescue. Blood 2022; 139:1039-1051. [PMID: 34767620 PMCID: PMC8854676 DOI: 10.1182/blood.2021011980] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 10/15/2021] [Indexed: 11/20/2022] Open
Abstract
Human telomere biology disorders (TBD)/short telomere syndromes (STS) are heterogeneous disorders caused by inherited loss-of-function mutations in telomere-associated genes. Here, we identify 3 germline heterozygous missense variants in the RPA1 gene in 4 unrelated probands presenting with short telomeres and varying clinical features of TBD/STS, including bone marrow failure, myelodysplastic syndrome, T- and B-cell lymphopenia, pulmonary fibrosis, or skin manifestations. All variants cluster to DNA-binding domain A of RPA1 protein. RPA1 is a single-strand DNA-binding protein required for DNA replication and repair and involved in telomere maintenance. We showed that RPA1E240K and RPA1V227A proteins exhibit increased binding to single-strand and telomeric DNA, implying a gain in DNA-binding function, whereas RPA1T270A has binding properties similar to wild-type protein. To study the mutational effect in a cellular system, CRISPR/Cas9 was used to knock-in the RPA1E240K mutation into healthy inducible pluripotent stem cells. This resulted in severe telomere shortening and impaired hematopoietic differentiation. Furthermore, in patients with RPA1E240K, we discovered somatic genetic rescue in hematopoietic cells due to an acquired truncating cis RPA1 mutation or a uniparental isodisomy 17p with loss of mutant allele, coinciding with stabilized blood counts. Using single-cell sequencing, the 2 somatic genetic rescue events were proven to be independently acquired in hematopoietic stem cells. In summary, we describe the first human disease caused by germline RPA1 variants in individuals with TBD/STS.
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Affiliation(s)
- Richa Sharma
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN
| | - Sushree S Sahoo
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN
| | - Masayoshi Honda
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Sophie L Granger
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Charnise Goodings
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN
| | - Louis Sanchez
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7196, INSERM Unité1154, Paris, France
| | - Axel Künstner
- Lübeck Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Hauke Busch
- Lübeck Institute of Experimental Dermatology and Institute of Cardiogenetics, University of Lübeck, Lübeck, Germany
- University Cancer Center Schleswig-Holstein, University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Fabian Beier
- Department of Hematology, Oncology, Hemostaseology and Stem Cell Transplantation, Medical Faculty, RWTH Aachen University, Aachen, Germany
| | | | | | | | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN
| | - Vincent Géli
- Marseille Cancer Research Centre, Unité1068 INSERM, UMR 7258 CNRS, Aix-Marseille University (UM 105), Institut Paoli-Calmettes, Equipe Labellisée par la Ligue Nationale contre le Cancer, Marseille, France
| | - Dmitri Churikov
- Marseille Cancer Research Centre, Unité1068 INSERM, UMR 7258 CNRS, Aix-Marseille University (UM 105), Institut Paoli-Calmettes, Equipe Labellisée par la Ligue Nationale contre le Cancer, Marseille, France
| | - Sandrine Hirschi
- Department of Respiratory Medicine and Rare Pulmonary Diseases, Strasbourg University Hospital, Strasbourg, France
| | - Victor B Pastor
- Center for Applied Bioinformatics, St Jude Children's Research Hospital, Memphis, TN
| | - Melanie Boerries
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK), Freiburg, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Melchior Lauten
- University Hospital Schleswig-Holstein, Department of Pediatrics, University of Lübeck, Lübeck, Germany
| | - Charikleia Kelaidi
- Department of Pediatric Hematology/Oncology, Aghia Sophia Children's Hospital, Athens, Greece
| | - Megan A Cooper
- Department of Pediatrics, Washington University School of Medicine, St Louis, MO
| | | | - Jill A Rosenfeld
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX
| | - Sophia Polychronopoulou
- Department of Pediatric Hematology/Oncology, Aghia Sophia Children's Hospital, Athens, Greece
| | - Caroline Kannengiesser
- Department of Genetics, Bichat Hospital, Assistance Publique-Hôpitaux de Paris, Paris University, INSERM U1152, Paris, France
| | - Carole Saintomé
- Structure et Instabilité des Génomes, Muséum National d'Histoire Naturelle, Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR) 7196, INSERM Unité1154, Paris, France
- Sorbonne Université, Education and Research Unit for Life Sciences (UFR 927), Paris, France
| | - Charlotte M Niemeyer
- German Cancer Consortium (DKTK), Freiburg, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Freiburg, Germany; and
| | - Patrick Revy
- Université de Paris, Imagine Institute, Laboratory of Genome Dynamics in the Immune System, Laboratoire Labellisé Ligue, INSERM UMR 1163, Paris, France
| | - Marc S Wold
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Maria Spies
- Department of Biochemistry and Molecular Biology, Carver College of Medicine, University of Iowa, Iowa City, IA
| | - Miriam Erlacher
- German Cancer Consortium (DKTK), Freiburg, Germany, and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Freiburg, Germany; and
| | - Stéphane Coulon
- Marseille Cancer Research Centre, Unité1068 INSERM, UMR 7258 CNRS, Aix-Marseille University (UM 105), Institut Paoli-Calmettes, Equipe Labellisée par la Ligue Nationale contre le Cancer, Marseille, France
| | - Marcin W Wlodarski
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN
- Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, University of Freiburg, Freiburg, Germany; and
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14
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Telomere biology disorders gain a family member. Blood 2022; 139:957-959. [PMID: 35175322 DOI: 10.1182/blood.2021014533] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 11/09/2021] [Indexed: 12/27/2022] Open
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15
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RPA phosphorylation facilitates RAD52 dependent homologous recombination in BRCA-deficient cells. Mol Cell Biol 2021; 42:e0052421. [PMID: 34928169 DOI: 10.1128/mcb.00524-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Loss of RAD52 is synthetically lethal in BRCA-deficient cells, owing to its role in backup homologous recombination (HR) repair of DNA double-strand breaks (DSBs). In HR in mammalian cells, DSBs are processed to single-stranded DNA (ssDNA) overhangs, which are then bound by Replication Protein A(RPA). RPA is exchanged for RAD51 by mediator proteins: in mammals BRCA2 is the primary mediator, however, RAD52 provides an alternative mediator pathway in BRCA-deficient cells. RAD51 stimulates strand exchange between homologous DNA duplexes, a critical step in HR. RPA phosphorylation and de-phosphorylation are important for HR, but its effect on RAD52 mediator function is unknown. Here, we show that RPA phosphorylation is required for RAD52 to salvage HR in BRCA-deficient cells. Using BRCA2-depleted human cells, in which the only available mediator pathway is RAD52-dependent, the expression of phosphorylation-deficient RPA mutant reduced HR. Furthermore, RPA-phospho-mutant cells showed reduced association of RAD52 with RAD51. Interestingly, there was no effect of RPA phosphorylation on RAD52 recruitment to repair foci. Finally, we show that RPA phosphorylation does not affect RAD52-dependent ssDNA annealing. Thus, although RAD52 can be recruited independently of RPA's phosphorylation status, RPA phosphorylation is required for RAD52's association with RAD51, and its subsequent promotion of RAD52-mediated HR.
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16
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Depletion of NK6 Homeobox 3 (NKX6.3) causes gastric carcinogenesis through copy number alterations by inducing impairment of DNA replication and repair regulation. Oncogenesis 2021; 10:85. [PMID: 34893582 PMCID: PMC8664813 DOI: 10.1038/s41389-021-00365-4] [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: 06/15/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 11/21/2022] Open
Abstract
Genomic stability maintenance requires correct DNA replication, chromosome segregation, and DNA repair, while defects of these processes result in tumor development or cell death. Although abnormalities in DNA replication and repair regulation are proposed as underlying causes for genomic instability, the detailed mechanism remains unclear. Here, we investigated whether NKX6.3 plays a role in the maintenance of genomic stability in gastric epithelial cells. NKX6.3 functioned as a transcription factor for CDT1 and RPA1, and its depletion increased replication fork rate, and fork asymmetry. Notably, we showed that abnormal DNA replication by the depletion of NKX6.3 caused DNA damage and induced homologous recombination inhibition. Depletion of NKX6.3 also caused copy number alterations of various genes in the vast chromosomal region. Hence, our findings underscore NKX6.3 might be a crucial factor of DNA replication and repair regulation from genomic instability in gastric epithelial cells.
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17
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Matos-Rodrigues GE, Martins RAP. An Eye in the Replication Stress Response: Lessons From Tissue-Specific Studies in vivo. Front Cell Dev Biol 2021; 9:731308. [PMID: 34805142 PMCID: PMC8599991 DOI: 10.3389/fcell.2021.731308] [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: 06/26/2021] [Accepted: 09/21/2021] [Indexed: 11/29/2022] Open
Abstract
Several inherited human syndromes that severely affect organogenesis and other developmental processes are caused by mutations in replication stress response (RSR) genes. Although the molecular machinery of RSR is conserved, disease-causing mutations in RSR-genes may have distinct tissue-specific outcomes, indicating that progenitor cells may differ in their responses to RSR inactivation. Therefore, understanding how different cell types respond to replication stress is crucial to uncover the mechanisms of RSR-related human syndromes. Here, we review the ocular manifestations in RSR-related human syndromes and summarize recent findings investigating the mechanisms of RSR during eye development in vivo. We highlight a remarkable heterogeneity of progenitor cells responses to RSR inactivation and discuss its implications for RSR-related human syndromes.
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Affiliation(s)
- Gabriel E Matos-Rodrigues
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Rodrigo A P Martins
- Programa de Biologia Celular e do Desenvolvimento, Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
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18
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Miao Y, Shi W, Wang H, Xue Z, You H, Zhang F, Du G, Tang D, Li Y, Shen Y, Cheng Z. Replication protein A large subunit (RPA1a) limits chiasma formation during rice meiosis. PLANT PHYSIOLOGY 2021; 187:1605-1618. [PMID: 34618076 PMCID: PMC8566244 DOI: 10.1093/plphys/kiab365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/06/2021] [Indexed: 05/06/2023]
Abstract
Replication protein A (RPA), a single-stranded DNA-binding protein, plays essential role in homologous recombination. However, because deletion of RPA causes embryonic lethality in mammals, the exact function of RPA in meiosis remains unclear. In this study, we generated an rpa1a mutant using CRISPR/Cas9 technology and explored its function in rice (Oryza sativa) meiosis. In rpa1a, 12 bivalents were formed at metaphase I, just like in wild-type, but chromosome fragmentations were consistently observed at anaphase I. Fluorescence in situ hybridization assays indicated that these fragmentations were due to the failure of the recombination intermediates to resolve. Importantly, the mutant had a highly elevated chiasma number, and loss of RPA1a could completely restore the 12 bivalent formations in the zmm (for ZIP1-4, MSH4/5, and MER3) mutant background. Protein-protein interaction assays showed that RPA1a formed a complex with the methyl methansulfonate and UV sensitive 81 (and the Fanconi anemia complementation group M-Bloom syndrome protein homologs (RECQ4A)-Topoisomerase3α-RecQ-mediated genome instability 1 complex to regulate chiasma formation and processing of the recombination intermediates. Thus, our data establish a pivotal role for RPA1a in promoting the accurate resolution of recombination intermediates and in limiting redundant chiasma formation during rice meiosis.
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Affiliation(s)
- Yongjie Miao
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wenqing Shi
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Hongjun Wang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhihui Xue
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Hanli You
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fanfan Zhang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Guijie Du
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Ding Tang
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yafei Li
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yi Shen
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhukuan Cheng
- State Key Lab of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, 225009, China
- Author for Communication:
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19
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Coupled protein synthesis and ribosome-guided piRNA processing on mRNAs. Nat Commun 2021; 12:5970. [PMID: 34645830 PMCID: PMC8514520 DOI: 10.1038/s41467-021-26233-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/17/2021] [Indexed: 12/16/2022] Open
Abstract
PIWI-interacting small RNAs (piRNAs) protect the germline genome and are essential for fertility. piRNAs originate from transposable element (TE) RNAs, long non-coding RNAs, or 3´ untranslated regions (3´UTRs) of protein-coding messenger genes, with the last being the least characterized of the three piRNA classes. Here, we demonstrate that the precursors of 3´UTR piRNAs are full-length mRNAs and that post-termination 80S ribosomes guide piRNA production on 3´UTRs in mice and chickens. At the pachytene stage, when other co-translational RNA surveillance pathways are sequestered, piRNA biogenesis degrades mRNAs right after pioneer rounds of translation and fine-tunes protein production from mRNAs. Although 3´UTR piRNA precursor mRNAs code for distinct proteins in mice and chickens, they all harbor embedded TEs and produce piRNAs that cleave TEs. Altogether, we discover a function of the piRNA pathway in fine-tuning protein production and reveal a conserved piRNA biogenesis mechanism that recognizes translating RNAs in amniotes.
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20
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Chanihoon GQ, Afridi HI, Kazi TG, Talpur FN, Baig JA. Evaluation of zinc and cadmium levels in the biological samples of Ewing sarcomas patients and healthy subjects. Clin Chim Acta 2021; 522:1-7. [PMID: 34364855 DOI: 10.1016/j.cca.2021.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 07/27/2021] [Accepted: 08/03/2021] [Indexed: 11/18/2022]
Abstract
BACKGROUND Ewing's sarcoma is a very rare type of cancerous tumor that grows in bones or the soft tissue around the bones, such as cartilage or the nerves. It frequently affects the people at the age of 10 to 20 years and has elevated rate of being cured. METHODS Assessment of essential trace [zinc (Zn)] and toxic [cadmium (Cd)] elements in biological samples (scalp hair and blood) of Ewing sarcoma patients (n = 87 age ranging 07-19 years) residents of various cities of Pakistan was done. For comparative study, the biological samples of age matched healthy (referent) subjects (n = 62) were also analyzed for selected metals. The matrices of biological samples was oxidized with the help of HNO3 (65%) and H2O2 (30%) mixture at the ratio of 2:1 with the aid of microwave oven. The oxidized biological samples were subjected to atomic absorption spectrometry for their determination. RESULT The Zn contents in the scalp hair and blood samples of different types of Ewing sarcoma patients were found to be lower, in the range of (45.9-141.2 µg/g) and (0.65-3.12 mg/l), respectively than the biological samples of referent subjects (246-265 µg/g) and (6.40-7.25 mg/l), respectively. Whilst, the Cd concentrations in the scalp hair and blood samples of different types of Ewing sarcoma patients were found to be higher, in the range of (2.70-5.60 µg/g) and (2.46-5.64 µg/l), respectively than the biological samples of controls (1.49-1.79 µg/g) and (1.52-1.90 µg/l), respectively. The biochemical parameters including hemoglobin% and RBC counts were significantly lower in patients than referents (p < 0.001), whereas WBC counts was alarmingly higher in patients than referents (p < 0.001). CONCLUSION The resulted data will be helpful to treat patients of Ewing sarcoma with mineral supplement contains essential trace element (Zn) in recommended dose to further increase their survival rate.
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Affiliation(s)
- Ghulam Qadir Chanihoon
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro Postal Code 76080, Pakistan.
| | - Hassan Imran Afridi
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro Postal Code 76080, Pakistan.
| | - Tasneem Gul Kazi
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro Postal Code 76080, Pakistan.
| | - Farah Naz Talpur
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro Postal Code 76080, Pakistan.
| | - Jameel Ahmed Baig
- National Centre of Excellence in Analytical Chemistry, University of Sindh, Jamshoro Postal Code 76080, Pakistan.
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21
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Huang C, Guo T, Qin Y. Meiotic Recombination Defects and Premature Ovarian Insufficiency. Front Cell Dev Biol 2021; 9:652407. [PMID: 33763429 PMCID: PMC7982532 DOI: 10.3389/fcell.2021.652407] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 02/05/2021] [Indexed: 12/12/2022] Open
Abstract
Premature ovarian insufficiency (POI) is the depletion of ovarian function before 40 years of age due to insufficient oocyte formation or accelerated follicle atresia. Approximately 1–5% of women below 40 years old are affected by POI. The etiology of POI is heterogeneous, including genetic disorders, autoimmune diseases, infection, iatrogenic factors, and environmental toxins. Genetic factors account for 20–25% of patients. However, more than half of the patients were idiopathic. With the widespread application of next-generation sequencing (NGS), the genetic spectrum of POI has been expanded, especially the latest identification in meiosis and DNA repair-related genes. During meiotic prophase I, the key processes include DNA double-strand break (DSB) formation and subsequent homologous recombination (HR), which are essential for chromosome segregation at the first meiotic division and genome diversity of oocytes. Many animal models with defective meiotic recombination present with meiotic arrest, DSB accumulation, and oocyte apoptosis, which are similar to human POI phenotype. In the article, based on different stages of meiotic recombination, including DSB formation, DSB end processing, single-strand invasion, intermediate processing, recombination, and resolution and essential proteins involved in synaptonemal complex (SC), cohesion complex, and fanconi anemia (FA) pathway, we reviewed the individual gene mutations identified in POI patients and the potential candidate genes for POI pathogenesis, which will shed new light on the genetic architecture of POI and facilitate risk prediction, ovarian protection, and early intervention for POI women.
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Affiliation(s)
- Chengzi Huang
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, China
| | - Ting Guo
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, China
| | - Yingying Qin
- Center for Reproductive Medicine, Cheeloo College of Medicine, Shandong University, Jinan, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, China.,Shandong Provincial Clinical Medicine Research Center for Reproductive Health, Shandong University, Jinan, China
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22
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Liu XY, Fan Q, Wang J, Li R, Xu Y, Guo J, Wang YZ, Zeng YH, Ding CH, Cai B, Zhou CQ, Xu YW. Higher chromosomal abnormality rate in blastocysts from young patients with idiopathic recurrent pregnancy loss. Fertil Steril 2020; 113:853-864. [PMID: 32228881 DOI: 10.1016/j.fertnstert.2019.11.016] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 11/10/2019] [Accepted: 11/12/2019] [Indexed: 12/21/2022]
Abstract
OBJECTIVE To determine whether the incidence of chromosomal abnormalities in blastocysts is higher in patients with idiopathic recurrent pregnancy loss (iRPL) who underwent preimplantation genetic testing for aneuploidy (PGT-A) than in those who underwent preimplantation genetic testing for monogenic defects (PGT-M). DESIGN Retrospective cohort study. SETTING University-affiliated reproductive center. PATIENT(S) A total of 62 patients with iRPL underwent 101 PGT-A cycles (iRPL group), and 212 patients underwent 311 PGT-M cycles (control group). INTERVENTIONS(S) Blastocyst biopsy and comprehensive chromosome screening technologies, including single-nucleotide polymorphism microarrays and next-generation sequencing. MAIN OUTCOME MEASURE(S) Incidence of chromosomal abnormalities in blastocysts and clinical miscarriage (CM) rate. RESULT(S) Stratification analysis by maternal age showed an increased incidence of chromosomal abnormalities in the iRPL group aged ≤35 years (48.9% vs. 36.9%), whereas no significant increase was found in the iRPL group aged >35 years (66.9% vs. 61.4%). After transfer of euploid embryos, women aged ≤35 years with iRPL exhibited an increased CM rate compared with the control group (26.1% vs. 3.1%). CONCLUSION(S) Young patients with iRPL have a significantly higher rate of chromosomal abnormalities in blastocysts compared with patients with no or sporadic CM. Although euploid embryos were transferred after PGT-A, young patients with iRPL had a higher CM rate, which may indicate that chromosomal abnormalities might not be the only causal factor for iRPL. Therefore, the role of PGT-A in iRPL still needs to be clarified.
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Affiliation(s)
- Xin-Yan Liu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Qi Fan
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Jing Wang
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Rong Li
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yan Xu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Jing Guo
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yi-Zi Wang
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yan-Hong Zeng
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Chen-Hui Ding
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Bing Cai
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Can-Quan Zhou
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China
| | - Yan-Wen Xu
- Guangdong Provincial Key Laboratory of Reproductive Medicine, First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong, People's Republic of China.
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23
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Dueva R, Iliakis G. Replication protein A: a multifunctional protein with roles in DNA replication, repair and beyond. NAR Cancer 2020; 2:zcaa022. [PMID: 34316690 PMCID: PMC8210275 DOI: 10.1093/narcan/zcaa022] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 08/23/2020] [Accepted: 08/27/2020] [Indexed: 02/07/2023] Open
Abstract
Single-stranded DNA (ssDNA) forms continuously during DNA replication and is an important intermediate during recombination-mediated repair of damaged DNA. Replication protein A (RPA) is the major eukaryotic ssDNA-binding protein. As such, RPA protects the transiently formed ssDNA from nucleolytic degradation and serves as a physical platform for the recruitment of DNA damage response factors. Prominent and well-studied RPA-interacting partners are the tumor suppressor protein p53, the RAD51 recombinase and the ATR-interacting proteins ATRIP and ETAA1. RPA interactions are also documented with the helicases BLM, WRN and SMARCAL1/HARP, as well as the nucleotide excision repair proteins XPA, XPG and XPF–ERCC1. Besides its well-studied roles in DNA replication (restart) and repair, accumulating evidence shows that RPA is engaged in DNA activities in a broader biological context, including nucleosome assembly on nascent chromatin, regulation of gene expression, telomere maintenance and numerous other aspects of nucleic acid metabolism. In addition, novel RPA inhibitors show promising effects in cancer treatment, as single agents or in combination with chemotherapeutics. Since the biochemical properties of RPA and its roles in DNA repair have been extensively reviewed, here we focus on recent discoveries describing several non-canonical functions.
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Affiliation(s)
- Rositsa Dueva
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, 45122 Essen, Germany
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24
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Velegzhaninov IO, Belykh ES, Rasova EE, Pylina YI, Shadrin DM, Klokov DY. Radioresistance, DNA Damage and DNA Repair in Cells With Moderate Overexpression of RPA1. Front Genet 2020; 11:855. [PMID: 32849834 PMCID: PMC7411226 DOI: 10.3389/fgene.2020.00855] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 07/13/2020] [Indexed: 12/02/2022] Open
Abstract
Molecular responses to genotoxic stress, such as ionizing radiation, are intricately complex and involve hundreds of genes. Whether targeted overexpression of an endogenous gene can enhance resistance to ionizing radiation remains to be explored. In the present study we take an advantage of the CRISPR/dCas9 technology to moderately overexpress the RPA1 gene that encodes a key functional subunit of the replication protein A (RPA). RPA is a highly conserved heterotrimeric single-stranded DNA-binding protein complex involved in DNA replication, recombination, and repair. Dysfunction of RPA1 is detrimental for cells and organisms and can lead to diminished resistance to many stress factors. We demonstrate that HEK293T cells overexpressing RPA1 exhibit enhanced resistance to cell killing by gamma-radiation. Using the alkali comet assay, we show a remarkable acceleration of DNA breaks rejoining after gamma-irradiation in RPA1 overexpressing cells. However, the spontaneous rate of DNA damage was also higher in the presence of RPA1 overexpression, suggesting alterations in the processing of replication errors due to elevated activity of the RPA protein. Additionally, the analysis of the distributions of cells with different levels of DNA damage showed a link between the RPA1 overexpression and the kinetics of DNA repair within differentially damaged cell subpopulations. Our results provide knew knowledge on DNA damage stress responses and indicate that the concept of enhancing radioresistance by targeted alteration of the expression of a single gene is feasible, however undesired consequences should be considered and evaluated.
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Affiliation(s)
- Ilya O Velegzhaninov
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Elena S Belykh
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Elena E Rasova
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Yana I Pylina
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Dmitry M Shadrin
- Institute of Biology of Komi Scientific Centre of the Ural Branch of the Russian Academy of Sciences, Syktyvkar, Russia
| | - Dmitry Yu Klokov
- Institut de Radioprotection et de Sureté Nucléaire, PSE-SANTE, SESANE, LRTOX, Fontenay-aux-Roses, France.,Department of Biochemistry, Microbiology, and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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25
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Kafer GR, Cesare AJ. A Survey of Essential Genome Stability Genes Reveals That Replication Stress Mitigation Is Critical for Peri-Implantation Embryogenesis. Front Cell Dev Biol 2020; 8:416. [PMID: 32548123 PMCID: PMC7274024 DOI: 10.3389/fcell.2020.00416] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/05/2020] [Indexed: 12/16/2022] Open
Abstract
Murine development demands that pluripotent epiblast stem cells in the peri-implantation embryo increase from approximately 120 to 14,000 cells between embryonic days (E) 4.5 and E7.5. This is possible because epiblast stem cells can complete cell cycles in under 3 h in vivo. To ensure conceptus fitness, epiblast cells must undertake this proliferative feat while maintaining genome integrity. How epiblast cells maintain genome health under such an immense proliferation demand remains unclear. To illuminate the contribution of genome stability pathways to early mammalian development we systematically reviewed knockout mouse data from 347 DDR and repair associated genes. Cumulatively, the data indicate that while many DNA repair functions are dispensable in embryogenesis, genes encoding replication stress response and homology directed repair factors are essential specifically during the peri-implantation stage of early development. We discuss the significance of these findings in the context of the unique proliferative demands placed on pluripotent epiblast stem cells.
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Affiliation(s)
| | - Anthony J. Cesare
- Genome Integrity Unit, Children’s Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
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26
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Guo Y, Chen J, Feng Y, Chua MLK, Zeng Y, Hui EP, Chan AKC, Tang L, Wang L, Cui Q, Han H, Luo C, Lin G, Liang Y, Liu Y, He Z, Liu Y, Wei P, Liu C, Peng W, Han B, Zuo X, Ong EHW, Yeo ELL, Low KP, Tan GS, Lim TKH, Hwang JSG, Li B, Feng Q, Xia X, Xia Y, Ko J, Dai W, Lung ML, Chan ATC, Lo DYM, Zeng M, Mai H, Liu J, Zeng Y, Bei J. Germline Polymorphisms and Length of Survival of Nasopharyngeal Carcinoma: An Exome-Wide Association Study in Multiple Cohorts. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:1903727. [PMID: 32440486 PMCID: PMC7237860 DOI: 10.1002/advs.201903727] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 02/14/2020] [Accepted: 02/17/2020] [Indexed: 06/11/2023]
Abstract
Germline polymorphisms are linked with differential survival outcomes in cancers but are not well studied in nasopharyngeal carcinoma (NPC). Here, a two-phase association study is conducted to discover germline polymorphisms that are associated with the prognosis of NPC. The discovery phase includes two consecutive hospital cohorts of patients with NPC from Southern China. Exome-wide genotypes at 246 173 single nucleotide polymorphisms (SNPs) are determined, followed by survival analysis for each SNP under Cox proportional hazard regression model. Candidate SNP is replicated in another two independent cohorts from Southern China and Singapore. Meta-analysis of all samples (n = 5553) confirms that the presence of rs1131636-T, located in the 3'-UTR of RPA1, confers an inferior overall survival (HR = 1.33, 95% CI = 1.20-1.47, P = 6.31 × 10-8). Bioinformatics and biological assays show that rs1131636 has regulatory effects on upstream RPA1. Functional studies further demonstrate that RPA1 promotes the growth, invasion, migration, and radioresistance of NPC cells. Additionally, miR-1253 is identified as a suppressor for RPA1 expression, likely through regulation of its binding affinity to rs1131636 locus. Collectively, these findings provide a promising biomarker aiding in stratifying patients with poor survival, as well as a potential drug target for NPC.
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27
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Apostolou Z, Chatzinikolaou G, Stratigi K, Garinis GA. Nucleotide Excision Repair and Transcription-Associated Genome Instability. Bioessays 2019; 41:e1800201. [PMID: 30919497 DOI: 10.1002/bies.201800201] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 12/10/2018] [Indexed: 12/12/2022]
Abstract
Transcription is a potential threat to genome integrity, and transcription-associated DNA damage must be repaired for proper messenger RNA (mRNA) synthesis and for cells to transmit their genome intact into progeny. For a wide range of structurally diverse DNA lesions, cells employ the highly conserved nucleotide excision repair (NER) pathway to restore their genome back to its native form. Recent evidence suggests that NER factors function, in addition to the canonical DNA repair mechanism, in processes that facilitate mRNA synthesis or shape the 3D chromatin architecture. Here, these findings are critically discussed and a working model that explains the puzzling clinical heterogeneity of NER syndromes highlighting the relevance of physiological, transcription-associated DNA damage to mammalian development and disease is proposed.
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Affiliation(s)
- Zivkos Apostolou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece.,Department of Biology, University of Crete, Vassilika Vouton, Heraklion GR71409, Crete, Greece
| | - Georgia Chatzinikolaou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece
| | - Kalliopi Stratigi
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece
| | - George A Garinis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, Heraklion 70013, Crete, Greece.,Department of Biology, University of Crete, Vassilika Vouton, Heraklion GR71409, Crete, Greece
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28
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Meng Y, Liu C, Shen L, Zhou M, Liu W, Kowolik C, Campbell JL, Zheng L, Shen B. TRAF6 mediates human DNA2 polyubiquitination and nuclear localization to maintain nuclear genome integrity. Nucleic Acids Res 2019; 47:7564-7579. [PMID: 31216032 PMCID: PMC6698806 DOI: 10.1093/nar/gkz537] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 05/29/2019] [Accepted: 06/07/2019] [Indexed: 12/14/2022] Open
Abstract
The multifunctional human DNA2 (hDNA2) nuclease/helicase is required to process DNA ends for homology-directed recombination repair (HDR) and to counteract replication stress. To participate in these processes, hDNA2 must localize to the nucleus and be recruited to the replication or repair sites. However, because hDNA2 lacks the nuclear localization signal that is found in its yeast homolog, it is unclear how its migration into the nucleus is regulated during replication or in response to DNA damage. Here, we report that the E3 ligase TRAF6 binds to and mediates the K63-linked polyubiquitination of hDNA2, increasing the stability of hDNA2 and promoting its nuclear localization. Inhibiting TRAF6-mediated polyubiquitination abolishes the nuclear localization of hDNA2, consequently impairing DNA end resection and HDR. Thus, the current study reveals a mechanism for the regulation of hDNA2 localization and establishes that TRAF6-mediated hDNA2 ubiquitination activates DNA repair pathways to maintain nuclear genome integrity.
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Affiliation(s)
- Yuan Meng
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China.,Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Changwei Liu
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Lei Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Mian Zhou
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Wenpeng Liu
- Colleges of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310027, China.,Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Claudia Kowolik
- Department of Molecular Medicine, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Judith L Campbell
- Division of Chemistry and Chemical Engineering, Braun Laboratories, California Institute of Technology, Pasadena, CA 91125, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, Beckman Research Institute of City of Hope, 1500 East Duarte Road, Duarte, CA 91010, USA
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29
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De Los Santos H, Bennett KP, Hurley JM. ENCORE: A Visualization Tool for Insight into Circadian Omics. ACM-BCB ... ... : THE ... ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE. ACM CONFERENCE ON BIOINFORMATICS, COMPUTATIONAL BIOLOGY AND BIOMEDICINE 2019; 2019:5-14. [PMID: 31754663 PMCID: PMC6868525 DOI: 10.1145/3307339.3342137] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Circadian rhythms are 24-hour biological cycles that control daily molecular rhythms in many organisms. The cellular elements that fall under the regulation of the clock are often studied through the use of omics-scale data sets gathered over time to determine how circadian regulation impacts cellular physiology. Previously, we created the ECHO (Extended Circadian Harmonic Oscillator) tool to identify rhythms in these data sets. Using ECHO, we found that circadian oscillations widely undergo a change in amplitude over time and that these amplitude changes have a biological function in the cell. However, ECHO does not align gene ontologies with the identified oscillating genes to give functional context. Thus, we created ENCORE (ECHO Native Circadian Ontological Rhythmicity Explorer), a novel visualization tool which combines the disparate databases of Gene Ontologies, protein-protein interactions, and auxiliary information to uncover the meaning of circadianly-regulated genes. This freely-available tool performs automatic enrichment and creates publication-worthy visualizations which we used to extend previously-gathered data on circadian regulation of physiology from published omics-scale studies in three circadian model organisms: mouse, fruit fly, and Neurospora crassa.
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Affiliation(s)
- Hannah De Los Santos
- Institute for Data Exploration and Applications/Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY
| | - Kristin P Bennett
- Institute for Data Exploration and Applications/Department of Computer Science, Rensselaer Polytechnic Institute, Troy, NY
| | - Jennifer M Hurley
- Department of Biological Sciences/Center for Biotechnology and Interdisciplinary Sciences, Rensselaer Polytechnic Institute, Troy, NY
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30
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Xavier A, Olsen MF, Lavik LA, Johansen J, Singh AK, Sjursen W, Scott RJ, Talseth‐Palmer BA. Comprehensive mismatch repair gene panel identifies variants in patients with Lynch-like syndrome. Mol Genet Genomic Med 2019; 7:e850. [PMID: 31297992 PMCID: PMC6687620 DOI: 10.1002/mgg3.850] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 12/14/2022] Open
Abstract
Background Lynch‐like syndrome (LLS) represents around 50% of the patients fulfilling the Amsterdam Criteria II/revised Bethesda Guidelines, characterized by a strong family history of Lynch Syndrome (LS) associated cancer, where a causative variant was not identified during genetic testing for LS. Methods Using data extracted from a larger gene panel, we have analyzed next‐generation sequencing data from 22 mismatch repair (MMR) genes (MSH3, PMS1, MLH3, EXO1, POLD1, POLD3 RFC1, RFC2, RFC3, RFC4, RFC5, PCNA, LIG1, RPA1, RPA2, RPA3, POLD2, POLD4, MLH1, MSH2, MSH6, and PMS2) in 274 LLS patients. Detected variants were annotated and filtered using ANNOVAR and FILTUS software. Results Thirteen variants were revealed in MLH1, MSH2, and MSH6, all genes previously linked to LS. Five additional genes (EXO1, POLD1, RFC1, RPA1, and MLH3) were found to harbor 11 variants of unknown significance in our sample cohort, two of them being frameshift variants. Conclusion We have shown that other genes associated with the process of DNA MMR have a high probability of being associated with LLS families. These findings indicate that the spectrum of genes that should be tested when considering an entity like Lynch‐like syndrome should be expanded so that a more inclusive definition of this entity can be developed.
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Affiliation(s)
- Alexandre Xavier
- University of Newcastle Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
| | - Maren Fridtjofsen Olsen
- Faculty of Medicine and Health Sciences, Department of Clinical and Molecular MedicineNorwegian University of Science and TechnologyTrondheimNorway
- Department of Medical GeneticsSaint Olavs Hospital University HospitalTrondheimNorway
| | - Liss A. Lavik
- Department of Medical GeneticsSaint Olavs Hospital University HospitalTrondheimNorway
| | - Jostein Johansen
- Faculty of Medicine and Health Sciences, Department of Clinical and Molecular MedicineNorwegian University of Science and TechnologyTrondheimNorway
| | - Ashish Kumar Singh
- Department of Medical GeneticsSaint Olavs Hospital University HospitalTrondheimNorway
| | - Wenche Sjursen
- Faculty of Medicine and Health Sciences, Department of Clinical and Molecular MedicineNorwegian University of Science and TechnologyTrondheimNorway
- Department of Medical GeneticsSaint Olavs Hospital University HospitalTrondheimNorway
| | - Rodney J. Scott
- University of Newcastle Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- Pathology NorthHunter New England HealthNewcastleNew South WalesAustralia
| | - Bente A. Talseth‐Palmer
- University of Newcastle Hunter Medical Research InstituteNew Lambton HeightsNew South WalesAustralia
- Møre and Romsdal Hospital Trust, Clinic Research and DevelopmentMoldeNorway
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31
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Shi B, Xue J, Yin H, Guo R, Luo M, Ye L, Shi Q, Huang X, Liu M, Sha J, Wang PJ. Dual functions for the ssDNA-binding protein RPA in meiotic recombination. PLoS Genet 2019; 15:e1007952. [PMID: 30716097 PMCID: PMC6375638 DOI: 10.1371/journal.pgen.1007952] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/14/2019] [Accepted: 01/09/2019] [Indexed: 01/08/2023] Open
Abstract
Meiotic recombination permits exchange of genetic material between homologous chromosomes. The replication protein A (RPA) complex, the predominant ssDNA-binding complex, is required for nearly all aspects of DNA metabolism, but its role in mammalian meiotic recombination remains unknown due to the embryonic lethality of RPA mutant mice. RPA is a heterotrimer of RPA1, RPA2, and RPA3. We find that loss of RPA1, the largest subunit, leads to disappearance of RPA2 and RPA3, resulting in the absence of the RPA complex. Using an inducible germline-specific inactivation strategy, we find that loss of RPA completely abrogates loading of RAD51/DMC1 recombinases to programmed meiotic DNA double strand breaks, thus blocking strand invasion required for chromosome pairing and synapsis. Surprisingly, loading of MEIOB, SPATA22, and ATR to DNA double strand breaks is RPA-independent and does not promote RAD51/DMC1 recruitment in the absence of RPA. Finally, inactivation of RPA reduces crossover formation. Our results demonstrate that RPA plays two distinct roles in meiotic recombination: an essential role in recombinase recruitment at early stages and an important role in promoting crossover formation at later stages.
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Affiliation(s)
- Baolu Shi
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Jiangyang Xue
- Center for Reproduction and Genetics, Nanjing Medical University Affiliated Suzhou Hospital, Suzhou, Jiangsu, China
| | - Hao Yin
- USTC-SJH Joint Center for Human Reproduction and Genetics, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Rui Guo
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
| | - Mengcheng Luo
- Department of Tissue and Embryology, Hubei Provincial Key Laboratory of Developmentally Originated Disease, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Lan Ye
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Qinghua Shi
- USTC-SJH Joint Center for Human Reproduction and Genetics, School of Life Sciences, University of Science and Technology of China, Hefei, China
| | - Xiaoyan Huang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Mingxi Liu
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - P. Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, United States of America
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32
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Wang L, Valiskova B, Forejt J. Cisplatin-induced DNA double-strand breaks promote meiotic chromosome synapsis in PRDM9-controlled mouse hybrid sterility. eLife 2018; 7:e42511. [PMID: 30592461 PMCID: PMC6324875 DOI: 10.7554/elife.42511] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 12/27/2018] [Indexed: 01/08/2023] Open
Abstract
PR domain containing 9 (Prdm9) is specifying hotspots of meiotic recombination but in hybrids between two mouse subspecies Prdm9 controls failure of meiotic chromosome synapsis and hybrid male sterility. We have previously reported that Prdm9-controlled asynapsis and meiotic arrest are conditioned by the inter-subspecific heterozygosity of the hybrid genome and we presumed that the insufficient number of properly repaired PRDM9-dependent DNA double-strand breaks (DSBs) causes asynapsis of chromosomes and meiotic arrest (Gregorova et al., 2018). We now extend the evidence for the lack of properly processed DSBs by improving meiotic chromosome synapsis with exogenous DSBs. A single injection of chemotherapeutic drug cisplatin increased frequency of RPA and DMC1 foci at the zygotene stage of sterile hybrids, enhanced homolog recognition and increased the proportion of spermatocytes with fully synapsed homologs at pachytene. The results bring a new evidence for a DSB-dependent mechanism of synapsis failure and infertility of intersubspecific hybrids.
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Affiliation(s)
- Liu Wang
- BIOCEV DivisionInstitute of Molecular Genetics, Czech Academy of SciencesVestecCzech Republic
| | - Barbora Valiskova
- BIOCEV DivisionInstitute of Molecular Genetics, Czech Academy of SciencesVestecCzech Republic
- Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Jiri Forejt
- BIOCEV DivisionInstitute of Molecular Genetics, Czech Academy of SciencesVestecCzech Republic
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Human Exonuclease 1 (EXO1) Regulatory Functions in DNA Replication with Putative Roles in Cancer. Int J Mol Sci 2018; 20:ijms20010074. [PMID: 30585186 PMCID: PMC6337416 DOI: 10.3390/ijms20010074] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 12/12/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022] Open
Abstract
Human exonuclease 1 (EXO1), a 5'→3' exonuclease, contributes to the regulation of the cell cycle checkpoints, replication fork maintenance, and post replicative DNA repair pathways. These processes are required for the resolution of stalled or blocked DNA replication that can lead to replication stress and potential collapse of the replication fork. Failure to restart the DNA replication process can result in double-strand breaks, cell-cycle arrest, cell death, or cellular transformation. In this review, we summarize the involvement of EXO1 in the replication, DNA repair pathways, cell cycle checkpoints, and the link between EXO1 and cancer.
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Byrne BM, Oakley GG. Replication protein A, the laxative that keeps DNA regular: The importance of RPA phosphorylation in maintaining genome stability. Semin Cell Dev Biol 2018; 86:112-120. [PMID: 29665433 DOI: 10.1016/j.semcdb.2018.04.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 03/30/2018] [Accepted: 04/06/2018] [Indexed: 11/25/2022]
Abstract
The eukaryotic ssDNA-binding protein, Replication protein A (RPA), was first discovered almost three decades ago. Since then, much progress has been made to elucidate the critical roles for RPA in DNA metabolic pathways that help promote genomic stability. The canonical RPA heterotrimer (RPA1-3) is an essential coordinator of DNA metabolism that interacts with ssDNA and numerous protein partners to coordinate its roles in DNA replication, repair, recombination and telomere maintenance. An alternative form of RPA, termed aRPA, is formed by a complex of RPA4 with RPA1 and RPA3. aRPA is expressed differentially in cells compared to canonical RPA and has been shown to inhibit canonical RPA function while allowing for regular maintenance of cell viability. Interestingly, while aRPA is defective in DNA replication and cell cycle progression, it was shown to play a supporting role in nucleotide excision repair and recombination. The binding domains of canonical RPA interact with a growing number of partners involved in numerous genome maintenance processes. The protein interactions of the RPA-ssDNA complex are not only governed by competition between the binding proteins but also by post-translation modifications such as phosphorylation. Phosphorylation of RPA2 is an important post-translational modification of the RPA complex, and is essential for directing context-specific functions of the RPA complex in the DNA damage response. Due to the importance of RPA in cellular metabolism, it was identified as an appealing target for chemotherapeutic drug development that could be used in future cancer treatment regimens.
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Affiliation(s)
- Brendan M Byrne
- University of Nebraska Medical Center Department of Oral Biology, Lincoln NE, USA.
| | - Gregory G Oakley
- University of Nebraska Medical Center Department of Oral Biology, Lincoln NE, USA; Eppley Cancer Center, Omaha NE, USA.
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In silico identification of inhibitors targeting N-Terminal domain of human Replication Protein A. J Mol Graph Model 2018; 86:149-159. [PMID: 30366191 DOI: 10.1016/j.jmgm.2018.10.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 10/08/2018] [Accepted: 10/09/2018] [Indexed: 12/29/2022]
Abstract
Replication Protein A (RPA) mediates DNA Damage Response (DDR) pathways through protein-protein interactions (PPIs). Targeting the PPIs formed between RPA and other DNA Damage Response (DDR) mediators has become an intriguing area of research for cancer drug discovery. A number of studies applied different methods ranging from high throughput screening approaches to fragment-based drug design tools to discover RPA inhibitors. Although these methods are robust, virtual screening approaches may be allocated as an alternative to such experimental methods, especially for screening of large libraries. Here we report the comprehensive screening of the large database, ZINC15 composed of ∼750 M compounds and the comparison of the identified ligands with the previously known inhibitors by means of binding affinity and drug-likeness. Initially, a ligand library sharing similarity with a promising inhibitor of the N-terminal domain of the RPA70 subunit (RPA70N) was generated by screening of the ZINC15 library. 46,999 ligands were collected and screened by LeDock which produced a satisfactory correlation with the experimental values (R2 = 0.77). 10 of the top-scoring ligands in LeDock were directly progressed to molecular dynamics (MD) simulations, while 10 additional ligands were also selected based on their LeDock scores and the presence of a functional group that could interact with the key amino acids in the RPA70N cleft. MD simulations were used to predict the binding free energy of the ligands by the MM-PBSA method which produced a high level of agreement with the experiments (R2 = 0.85). Binding free energy predictions pointed out 2 ligands with higher binding affinity than any of the reference inhibitors. Particularly the ligand ZINC000753854163 exhibited superior drug-likeness features than any of the known inhibitors. Overall, this study reports ZINC000753854163 as a possible inhibitor of RPA70N, reflecting its possible use in RPA70N targeted cancer therapy.
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Xu Y, Greenberg RA, Schonbrunn E, Wang PJ. Meiosis-specific proteins MEIOB and SPATA22 cooperatively associate with the single-stranded DNA-binding replication protein A complex and DNA double-strand breaks. Biol Reprod 2018; 96:1096-1104. [PMID: 28453612 DOI: 10.1093/biolre/iox040] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/26/2017] [Indexed: 12/27/2022] Open
Abstract
Meiotic recombination ensures faithful segregation of homologous chromosomes during meiosis and generates genetic diversity in gametes. MEIOB (meiosis specific with OB domains), a meiosis-specific single-stranded DNA-binding homolog of replication protein A1 (RPA1), is essential for meiotic recombination. Here, we investigated the molecular mechanisms of MEIOB by characterizing its binding partners spermatogenesis associated 22 (SPATA22) and RPA. We find that MEIOB and SPATA22 form an obligate complex and contain defined interaction domains. The interaction between these two proteins is unusual in that nearly any deletion in the binding domains abolishes the interaction. Strikingly, a single residue D383 in MEIOB is indispensable for the interaction. The MEIOB/SPATA22 complex interacts with the RPA heterotrimeric complex in a collaborative manner. Furthermore, MEIOB and SPATA22 are recruited to induced DNA double-strand breaks (DSBs) together but not alone. These results demonstrate the cooperative property of the MEIOB-SPATA22 complex in its interaction with RPA and recruitment to DSBs.
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Affiliation(s)
- Yang Xu
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
| | - Roger A Greenberg
- Departments of Cancer Biology and Pathology, Abramson Family Cancer Research Institute, Basser Research Center for BRCA, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ernst Schonbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida, USA
| | - P Jeremy Wang
- Department of Biomedical Sciences, University of Pennsylvania School of Veterinary Medicine, Philadelphia, Pennsylvania, USA
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Repair of exogenous DNA double-strand breaks promotes chromosome synapsis in SPO11-mutant mouse meiocytes, and is altered in the absence of HORMAD1. DNA Repair (Amst) 2018; 63:25-38. [PMID: 29414051 DOI: 10.1016/j.dnarep.2018.01.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 01/16/2018] [Accepted: 01/17/2018] [Indexed: 11/22/2022]
Abstract
Repair of SPO11-dependent DNA double-strand breaks (DSBs) via homologous recombination (HR) is essential for stable homologous chromosome pairing and synapsis during meiotic prophase. Here, we induced radiation-induced DSBs to study meiotic recombination and homologous chromosome pairing in mouse meiocytes in the absence of SPO11 activity (Spo11YF/YF model), and in the absence of both SPO11 and HORMAD1 (Spo11/Hormad1 dko). Within 30 min after 5 Gy irradiation of Spo11YF/YF mice, 140-160 DSB repair foci were detected, which specifically localized to the synaptonemal complex axes. Repair of radiation-induced DSBs was incomplete in Spo11YF/YF compared to Spo11+/YF meiocytes. Still, repair of exogenous DSBs promoted partial recovery of chromosome pairing and synapsis in Spo11YF/YF meiocytes. This indicates that at least part of the exogenous DSBs can be processed in an interhomolog recombination repair pathway. Interestingly, in a seperate experiment, using 3 Gy of irradiation, we observed that Spo11/Hormad1 dko spermatocytes contained fewer remaining DSB repair foci at 48 h after irradiation compared to irradiated Spo11 knockout spermatocytes. Together, these results show that recruitment of exogenous DSBs to the synaptonemal complex, in conjunction with repair of exogenous DSBs via the homologous chromosome, contributes to homology recognition. In addition, the data suggest a role for HORMAD1 in DNA repair pathway choice in mouse meiocytes.
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Winship AL, Stringer JM, Liew SH, Hutt KJ. The importance of DNA repair for maintaining oocyte quality in response to anti-cancer treatments, environmental toxins and maternal ageing. Hum Reprod Update 2018; 24:119-134. [PMID: 29377997 DOI: 10.1093/humupd/dmy002] [Citation(s) in RCA: 92] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Revised: 12/05/2017] [Accepted: 01/14/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Within the ovary, oocytes are stored in long-lived structures called primordial follicles, each comprising a meiotically arrested oocyte, surrounded by somatic granulosa cells. It is essential that their genetic integrity is maintained throughout life to ensure that high quality oocytes are available for ovulation. Of all the possible types of DNA damage, DNA double-strand breaks (DSBs) are considered to be the most severe. Recent studies have shown that DNA DSBs can accumulate in oocytes in primordial follicles during reproductive ageing, and are readily induced by exogenous factors such as γ-irradiation, chemotherapy and environmental toxicants. DSBs can induce oocyte death or, alternatively, activate a program of DNA repair in order to restore genetic integrity and promote survival. The repair of DSBs has been intensively studied in the context of meiotic recombination, and in recent years more detail is becoming available regarding the repair capabilities of primordial follicle oocytes. OBJECTIVE AND RATIONALE This review discusses the induction and repair of DNA DSBs in primordial follicle oocytes. SEARCH METHODS PubMed (Medline) and Google Scholar searches were performed using the key words: primordial follicle oocyte, DNA repair, double-strand break, DNA damage, chemotherapy, radiotherapy, ageing, environmental toxicant. The literature was restricted to papers in the English language and limited to reports in animals and humans dated from 1964 until 2017. The references within these articles were also manually searched. OUTCOMES Recent experiments in animal models and humans have provided compelling evidence that primordial follicle oocytes can efficiently repair DNA DSBs arising from diverse origins, but this capacity may decline with increasing age. WIDER IMPLICATIONS Primordial follicle oocytes are vulnerable to DNA DSBs emanating from endogenous and exogenous sources. The ability to repair this damage is essential for female fertility. In the long term, augmenting DNA repair in primordial follicle oocytes has implications for the development of novel fertility preservation agents for female cancer patients and for the management of maternal ageing. However, further work is required to fully characterize the specific proteins involved and to develop strategies to bolster their activity.
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Affiliation(s)
- Amy L Winship
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Jessica M Stringer
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Seng H Liew
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
| | - Karla J Hutt
- Ovarian Biology Laboratory, Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia
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Pathways and Mechanisms that Prevent Genome Instability in Saccharomyces cerevisiae. Genetics 2017; 206:1187-1225. [PMID: 28684602 PMCID: PMC5500125 DOI: 10.1534/genetics.112.145805] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 04/26/2017] [Indexed: 12/13/2022] Open
Abstract
Genome rearrangements result in mutations that underlie many human diseases, and ongoing genome instability likely contributes to the development of many cancers. The tools for studying genome instability in mammalian cells are limited, whereas model organisms such as Saccharomyces cerevisiae are more amenable to these studies. Here, we discuss the many genetic assays developed to measure the rate of occurrence of Gross Chromosomal Rearrangements (called GCRs) in S. cerevisiae. These genetic assays have been used to identify many types of GCRs, including translocations, interstitial deletions, and broken chromosomes healed by de novo telomere addition, and have identified genes that act in the suppression and formation of GCRs. Insights from these studies have contributed to the understanding of pathways and mechanisms that suppress genome instability and how these pathways cooperate with each other. Integrated models for the formation and suppression of GCRs are discussed.
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40
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Zhao M, Geng R, Guo X, Yuan R, Zhou X, Zhong Y, Huo Y, Zhou M, Shen Q, Li Y, Zhu W, Wang J. PCAF/GCN5-Mediated Acetylation of RPA1 Promotes Nucleotide Excision Repair. Cell Rep 2017; 20:1997-2009. [DOI: 10.1016/j.celrep.2017.08.015] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 06/21/2017] [Accepted: 07/14/2017] [Indexed: 12/14/2022] Open
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Systems-guided forward genetic screen reveals a critical role of the replication stress response protein ETAA1 in T cell clonal expansion. Proc Natl Acad Sci U S A 2017; 114:E5216-E5225. [PMID: 28607084 DOI: 10.1073/pnas.1705795114] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
T-cell immunity requires extremely rapid clonal proliferation of rare, antigen-specific T lymphocytes to form effector cells. Here we identify a critical role for ETAA1 in this process by surveying random germ line mutations in mice using exome sequencing and bioinformatic annotation to prioritize mutations in genes of unknown function with potential effects on the immune system, followed by breeding to homozygosity and testing for immune system phenotypes. Effector CD8+ and CD4+ T-cell formation following immunization, lymphocytic choriomeningitis virus (LCMV) infection, or herpes simplex virus 1 (HSV1) infection was profoundly decreased despite normal immune cell development in adult mice homozygous for two different Etaa1 mutations: an exon 2 skipping allele that deletes Gly78-Leu119, and a Cys166Stop truncating allele that eliminates most of the 877-aa protein. ETAA1 deficiency decreased clonal expansion cell autonomously within the responding T cells, causing no decrease in their division rate but increasing TP53-induced mRNAs and phosphorylation of H2AX, a marker of DNA replication stress induced by the ATM and ATR kinases. Homozygous ETAA1-deficient adult mice were otherwise normal, healthy, and fertile, although slightly smaller, and homozygotes were born at lower frequency than expected, consistent with partial lethality after embryonic day 12. Taken together with recently reported evidence in human cancer cell lines that ETAA1 activates ATR kinase through an exon 2-encoded domain, these findings reveal a surprisingly specific requirement for this ATR activator in adult mice restricted to rapidly dividing effector T cells. This specific requirement may provide new ways to suppress pathological T-cell responses in transplantation or autoimmunity.
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Interactive Roles of DNA Helicases and Translocases with the Single-Stranded DNA Binding Protein RPA in Nucleic Acid Metabolism. Int J Mol Sci 2017; 18:ijms18061233. [PMID: 28594346 PMCID: PMC5486056 DOI: 10.3390/ijms18061233] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 05/30/2017] [Accepted: 06/01/2017] [Indexed: 01/05/2023] Open
Abstract
Helicases and translocases use the energy of nucleoside triphosphate binding and hydrolysis to unwind/resolve structured nucleic acids or move along a single-stranded or double-stranded polynucleotide chain, respectively. These molecular motors facilitate a variety of transactions including replication, DNA repair, recombination, and transcription. A key partner of eukaryotic DNA helicases/translocases is the single-stranded DNA binding protein Replication Protein A (RPA). Biochemical, genetic, and cell biological assays have demonstrated that RPA interacts with these human molecular motors physically and functionally, and their association is enriched in cells undergoing replication stress. The roles of DNA helicases/translocases are orchestrated with RPA in pathways of nucleic acid metabolism. RPA stimulates helicase-catalyzed DNA unwinding, enlists translocases to sites of action, and modulates their activities in DNA repair, fork remodeling, checkpoint activation, and telomere maintenance. The dynamic interplay between DNA helicases/translocases and RPA is just beginning to be understood at the molecular and cellular levels, and there is still much to be learned, which may inform potential therapeutic strategies.
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43
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Lan Y, Sun J, Tian R, Bartlett DH, Li R, Wong YH, Zhang W, Qiu JW, Xu T, He LS, Tabata HG, Qian PY. Molecular adaptation in the world's deepest-living animal: Insights from transcriptome sequencing of the hadal amphipod Hirondellea gigas. Mol Ecol 2017; 26:3732-3743. [PMID: 28429829 DOI: 10.1111/mec.14149] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 03/30/2017] [Accepted: 04/05/2017] [Indexed: 12/17/2022]
Abstract
The Challenger Deep in the Mariana Trench is the deepest point in the oceans of our planet. Understanding how animals adapt to this harsh environment characterized by high hydrostatic pressure, food limitation, dark and cold is of great scientific interest. Of the animals dwelling in the Challenger Deep, amphipods have been captured using baited traps. In this study, we sequenced the transcriptome of the amphipod Hirondellea gigas collected at a depth of 10,929 m from the East Pond of the Challenger Deep. Assembly of these sequences resulted in 133,041 contigs and 22,046 translated proteins. Functional annotation of these contigs was made using the go and kegg databases. Comparison of these translated proteins with those of four shallow-water amphipods revealed 10,731 gene families, of which 5659 were single-copy orthologs. Base substitution analysis on these single-copy orthologs showed that 62 genes are positively selected in H. gigas, including genes related to β-alanine biosynthesis, energy metabolism and genetic information processing. For multiple-copy orthologous genes, gene family expansion analysis revealed that cold-inducible proteins (i.e., transcription factors II A and transcription elongation factor 1) as well as zinc finger domains are expanded in H. gigas. Overall, our results indicate that genetic adaptation to the hadal environment by H. gigas may be mediated by both gene family expansion and amino acid substitutions of specific proteins.
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Affiliation(s)
- Yi Lan
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jin Sun
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Renmao Tian
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Douglas H Bartlett
- Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA
| | - Runsheng Li
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Yue Him Wong
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Weipeng Zhang
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Jian-Wen Qiu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Ting Xu
- Department of Biology, Hong Kong Baptist University, Hong Kong, China
| | - Li-Sheng He
- Institute of Deep Sea Science and Engineering, Chinese Academy of Sciences, Sanya, Hainan, China
| | - Harry G Tabata
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
| | - Pei-Yuan Qian
- Division of Life Science, Hong Kong University of Science and Technology, Kowloon, Hong Kong, China
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DNA damage repair in breast cancer and its therapeutic implications. Pathology 2016; 49:156-165. [PMID: 28034453 DOI: 10.1016/j.pathol.2016.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Revised: 10/06/2016] [Accepted: 11/02/2016] [Indexed: 11/23/2022]
Abstract
The DNA damage response (DDR) involves the activation of numerous cellular activities that repair DNA lesions and maintain genomic integrity, and is critical in preventing tumorigenesis. Inherited or acquired mutations in specific genes involved in the DNA damage response, for example the breast cancer susceptibility genes 1/2 (BRCA1/2), phosphatase and tensin homolog (PTEN) and P53 are associated with various subtypes of breast cancer. Such changes can render breast cancer cells particularly sensitive to specific DNA damage response inhibitors, for example BRCA1/2 germline mutated cells are sensitive to poly (ADP-ribose) polymerase (PARP) inhibitors. The aims of this review are to discuss specific DNA damage response defects in breast cancer and to present the current stage of development of various DDR inhibitors (namely PARP, ATM/ATR, DNA-PK, PARG, RECQL5, FEN1 and APE1) for breast cancer mono- and combination therapy.
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Irianto J, Xia Y, Pfeifer CR, Athirasala A, Ji J, Alvey C, Tewari M, Bennett RR, Harding SM, Liu AJ, Greenberg RA, Discher DE. DNA Damage Follows Repair Factor Depletion and Portends Genome Variation in Cancer Cells after Pore Migration. Curr Biol 2016; 27:210-223. [PMID: 27989676 DOI: 10.1016/j.cub.2016.11.049] [Citation(s) in RCA: 194] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2016] [Revised: 11/11/2016] [Accepted: 11/23/2016] [Indexed: 11/25/2022]
Abstract
Migration through micron-size constrictions has been seen to rupture the nucleus, release nuclear-localized GFP, and cause localized accumulations of ectopic 53BP1-a DNA repair protein. Here, constricted migration of two human cancer cell types and primary mesenchymal stem cells (MSCs) increases DNA breaks throughout the nucleoplasm as assessed by endogenous damage markers and by electrophoretic "comet" measurements. Migration also causes multiple DNA repair proteins to segregate away from DNA, with cytoplasmic mis-localization sustained for many hours as is relevant to delayed repair. Partial knockdown of repair factors that also regulate chromosome copy numbers is seen to increase DNA breaks in U2OS osteosarcoma cells without affecting migration and with nucleoplasmic patterns of damage similar to constricted migration. Such depletion also causes aberrant levels of DNA. Migration-induced nuclear damage is nonetheless reversible for wild-type and sub-cloned U2OS cells, except for lasting genomic differences between stable clones as revealed by DNA arrays and sequencing. Gains and losses of hundreds of megabases in many chromosomes are typical of the changes and heterogeneity in bone cancer. Phenotypic differences that arise from constricted migration of U2OS clones are further illustrated by a clone with a highly elongated and stable MSC-like shape that depends on microtubule assembly downstream of the transcription factor GATA4. Such changes are consistent with reversion to a more stem-like state upstream of cancerous osteoblastic cells. Migration-induced genomic instability can thus associate with heritable changes.
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Affiliation(s)
- Jerome Irianto
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yuntao Xia
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte R Pfeifer
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group, Department of Physics and Astronomy, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Avathamsa Athirasala
- Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jiazheng Ji
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cory Alvey
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Manu Tewari
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rachel R Bennett
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group, Department of Physics and Astronomy, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Shane M Harding
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Andrea J Liu
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group, Department of Physics and Astronomy, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Roger A Greenberg
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Cancer Biology, Abramson Family Cancer Research Institute, Perelman School of Medicine, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Dennis E Discher
- Physical Sciences Oncology Center at Penn (PSOC@Penn), 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Molecular and Cell Biophysics Lab, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group, Department of Physics and Astronomy, 129 Towne Building, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Ma CJ, Gibb B, Kwon Y, Sung P, Greene EC. Protein dynamics of human RPA and RAD51 on ssDNA during assembly and disassembly of the RAD51 filament. Nucleic Acids Res 2016; 45:749-761. [PMID: 27903895 PMCID: PMC5314761 DOI: 10.1093/nar/gkw1125] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 10/21/2016] [Accepted: 10/27/2016] [Indexed: 12/31/2022] Open
Abstract
Homologous recombination (HR) is a crucial pathway for double-stranded DNA break (DSB) repair. During the early stages of HR, the newly generated DSB ends are processed to yield long single-stranded DNA (ssDNA) overhangs, which are quickly bound by replication protein A (RPA). RPA is then replaced by the DNA recombinase Rad51, which forms extended helical filaments on the ssDNA. The resulting nucleoprotein filament, known as the presynaptic complex, is responsible for pairing the ssDNA with homologous double-stranded DNA (dsDNA), which serves as the template to guide DSB repair. Here, we use single-molecule imaging to visualize the interplay between human RPA (hRPA) and human RAD51 during presynaptic complex assembly and disassembly. We demonstrate that ssDNA-bound hRPA can undergo facilitated exchange, enabling hRPA to undergo rapid exchange between free and ssDNA-bound states only when free hRPA is present in solution. Our results also indicate that the presence of free hRPA inhibits RAD51 filament nucleation, but has a lesser impact upon filament elongation. This finding suggests that hRPA exerts important regulatory influence over RAD51 and may in turn affect the properties of the assembled RAD51 filament. These experiments provide an important basis for further investigations into the regulation of human presynaptic complex assembly.
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Affiliation(s)
- Chu Jian Ma
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Bryan Gibb
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - YoungHo Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Eric C Greene
- Department of Biochemistry & Molecular Biophysics, Columbia University, New York, NY 10032, USA
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Keijzers G, Liu D, Rasmussen LJ. Exonuclease 1 and its versatile roles in DNA repair. Crit Rev Biochem Mol Biol 2016; 51:440-451. [PMID: 27494243 DOI: 10.1080/10409238.2016.1215407] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Exonuclease 1 (EXO1) is a multifunctional 5' → 3' exonuclease and a DNA structure-specific DNA endonuclease. EXO1 plays roles in DNA replication, DNA mismatch repair (MMR) and DNA double-stranded break repair (DSBR) in lower and higher eukaryotes and contributes to meiosis, immunoglobulin maturation, and micro-mediated end-joining in higher eukaryotes. In human cells, EXO1 is also thought to play a role in telomere maintenance. Mutations in the human EXO1 gene correlate with increased susceptibility to some cancers. This review summarizes recent studies on the enzymatic functions and biological roles of EXO1, its possible protective role against cancer and aging, and regulation of EXO1 by posttranslational modification.
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Affiliation(s)
- Guido Keijzers
- a Department of Cellular and Molecular Medicine , Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark
| | - Dekang Liu
- a Department of Cellular and Molecular Medicine , Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark
| | - Lene Juel Rasmussen
- a Department of Cellular and Molecular Medicine , Center for Healthy Aging, University of Copenhagen , Copenhagen , Denmark
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48
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Jang SW, Jung JK, Kim JM. Replication Protein A (RPA) deficiency activates the Fanconi anemia DNA repair pathway. Cell Cycle 2016; 15:2336-45. [PMID: 27398742 DOI: 10.1080/15384101.2016.1201621] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The Fanconi anemia (FA) pathway regulates DNA inter-strand crosslink (ICL) repair. Despite our greater understanding of the role of FA in ICL repair, its function in the preventing spontaneous genome instability is not well understood. Here, we show that depletion of replication protein A (RPA) activates the FA pathway. RPA1 deficiency increases chromatin recruitment of FA core complex, leading to FANCD2 monoubiquitination (FANCD2-Ub) and foci formation in the absence of DNA damaging agents. Importantly, ATR depletion, but not ATM, abolished RPA1 depletion-induced FANCD2-Ub, suggesting that ATR activation mediated FANCD2-Ub. Interestingly, we found that depletion of hSSB1/2-INTS3, a single-stranded DNA-binding protein complex, induces FANCD2-Ub, like RPA1 depletion. More interestingly, depletion of either RPA1 or INTS3 caused increased accumulation of DNA damage in FA pathway deficient cell lines. Taken together, these results indicate that RPA deficiency induces activation of the FA pathway in an ATR-dependent manner, which may play a role in the genome maintenance.
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Affiliation(s)
- Seok-Won Jang
- a Department of Pharmacology , Medical Research Center for Gene Regulation, Chonnam National University Medical School , Gwangju , Korea
| | - Jin Ki Jung
- a Department of Pharmacology , Medical Research Center for Gene Regulation, Chonnam National University Medical School , Gwangju , Korea
| | - Jung Min Kim
- a Department of Pharmacology , Medical Research Center for Gene Regulation, Chonnam National University Medical School , Gwangju , Korea
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Wu Y, Lu J, Kang T. Human single-stranded DNA binding proteins: guardians of genome stability. Acta Biochim Biophys Sin (Shanghai) 2016; 48:671-7. [PMID: 27217471 DOI: 10.1093/abbs/gmw044] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/15/2016] [Indexed: 01/03/2023] Open
Abstract
Single-stranded DNA-binding proteins (SSBs) are essential for maintaining the integrity of the genome in all organisms. All processes related to DNA, such as replication, excision, repair, and recombination, require the participation of SSBs whose oligonucleotide/oligosaccharide-binding (OB)-fold domain is responsible for the interaction with single-stranded DNA (ssDNA). For a long time, the heterotrimeric replication protein A (RPA) complex was believed to be the only nuclear SSB in eukaryotes to participate in ssDNA processing, while mitochondrial SSBs that are conserved with prokaryotic SSBs were shown to be essential for maintaining genome stability in eukaryotic mitochondria. In recent years, two new proteins, hSSB1 and hSSB2 (human SSBs 1/2), were identified and have better sequence similarity to bacterial and archaeal SSBs than RPA. This review summarizes the current understanding of these human SSBs in DNA damage repair and in cell-cycle checkpoint activation following DNA damage, as well as their relationships with cancer.
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Affiliation(s)
- Yuanzhong Wu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Jinping Lu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Tiebang Kang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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The FEN1 L209P mutation interferes with long-patch base excision repair and induces cellular transformation. Oncogene 2016; 36:194-207. [PMID: 27270424 PMCID: PMC5140775 DOI: 10.1038/onc.2016.188] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2015] [Revised: 04/12/2016] [Accepted: 04/12/2016] [Indexed: 12/20/2022]
Abstract
Flap endonuclease-1 (FEN1) is a multifunctional, structure-specific nuclease that has a critical role in maintaining human genome stability. FEN1 mutations have been detected in human cancer specimens and have been suggested to cause genomic instability and cancer predisposition. However, the exact relationship between FEN1 deficiency and cancer susceptibility remains unclear. In the current work, we report a novel colorectal cancer-associated FEN1 mutation, L209P. This mutant protein lacks the FEN, exonuclease (EXO) and gap endonuclease (GEN) activities of FEN1 but retains DNA-binding affinity. The L209P FEN1 variant interferes with the function of the wild-type FEN1 enzyme in a dominant-negative manner and impairs long-patch base excision repair in vitro and in vivo. Expression of L209P FEN1 sensitizes cells to DNA damage, resulting in endogenous genomic instability and cellular transformation, as well as tumor growth in a mouse xenograft model. These data indicate that human cancer-associated genetic alterations in the FEN1 gene can contribute substantially to cancer development.
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