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Bader AS, Bushell M. iMUT-seq: high-resolution DSB-induced mutation profiling reveals prevalent homologous-recombination dependent mutagenesis. Nat Commun 2023; 14:8419. [PMID: 38110444 PMCID: PMC10728174 DOI: 10.1038/s41467-023-44167-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 12/04/2023] [Indexed: 12/20/2023] Open
Abstract
DNA double-strand breaks (DSBs) are the most mutagenic form of DNA damage, and play a significant role in cancer biology, neurodegeneration and aging. However, studying DSB-induced mutagenesis is limited by our current approaches. Here, we describe iMUT-seq, a technique that profiles DSB-induced mutations at high-sensitivity and single-nucleotide resolution around endogenous DSBs. By depleting or inhibiting 20 DSB-repair factors we define their mutational signatures in detail, revealing insights into the mechanisms of DSB-induced mutagenesis. Notably, we find that homologous-recombination (HR) is more mutagenic than previously thought, inducing prevalent base substitutions and mononucleotide deletions at distance from the break due to DNA-polymerase errors. Simultaneously, HR reduces translocations, suggesting a primary role of HR is specifically the prevention of genomic rearrangements. The results presented here offer fundamental insights into DSB-induced mutagenesis and have significant implications for our understanding of cancer biology and the development of DDR-targeting chemotherapeutics.
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Affiliation(s)
- Aldo S Bader
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK.
- Cancer Research UK/CI, University of Cambridge, Li Ka Shing Centre, Cambridge, CB2 0RE, UK.
- The Gurdon Institute, University of Cambridge, Biochemistry, Cambridge, UK.
| | - Martin Bushell
- Cancer Research UK Beatson Institute, Glasgow, G61 1BD, UK.
- Institute of Cancer Sciences, University of Glasgow, Glasgow, G61 1QH, UK.
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2
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Hammarsten O, Lyytikäinen A, Thunström S, Ek T, Fasth A, Ekwall O, Cajander S, Borgström EW, Smith CIE, Johansson P. Clinical measurement of cellular DNA damage hypersensitivity in patients with DNA repair defects. Orphanet J Rare Dis 2022; 17:50. [PMID: 35164800 PMCID: PMC8842932 DOI: 10.1186/s13023-022-02199-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 01/30/2022] [Indexed: 11/18/2022] Open
Abstract
Background DNA repair deficiency disorders are rare inherited diseases arising from pathogenic (disease-causing) variants in genes involved in DNA repair. There are no standardized diagnostic assays for the investigation of pathological significance of unknown variants in DNA repair genes. We hypothesized that our assays for measuring in vitro patient blood cell hypersensitivity to DNA-damaging agents can be used to establish the pathological significance of unknown variants in DNA repair genes. Six patients with variants in the DNA repair genes PRKDC (two siblings), DCLRE1C (two siblings), NBN, and MSH6 were included. Here, we used the cell division assay (CDA) and the γ-H2AX assay, which were both developed and clinically validated by us, to measure patient cell hypersensitivity in response to ionizing radiation, mitomycin C, cytarabine and doxorubicin. Results Radiation hypersensitivity was detected in the two patients with variants in the PRKDC gene (p < 0.0001 for both at 3.5 Gy), and the two patients with DCLRE1C variants (p < 0.0001 at 3.5 Gy for sibling 1 and p < 0.0001 at 1 Gy for sibling 2). The cells from the patients with the PRKDC variant were also deficient in removing γ-H2AX (p < 0.001). The cells from the patient with variants in the NBN gene were hypersensitive to mitomycin C (p = 0.0008) and deficient in both induction and removal of γ-H2AX in response to radiation. Conclusions The combination of the CDA and the γ-H2AX assay is useful in investigating the significance of unknown variants in some DNA repair genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13023-022-02199-8.
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3
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Liu D, Lieber MR. The mechanisms of human lymphoid chromosomal translocations and their medical relevance. Crit Rev Biochem Mol Biol 2021; 57:227-243. [PMID: 34875186 DOI: 10.1080/10409238.2021.2004576] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The most common human lymphoid chromosomal translocations involve concurrent failures of the recombination activating gene (RAG) complex and Activation-Induced Deaminase (AID). These are two enzymes that are normally expressed for purposes of the two site-specific DNA recombination processes: V(D)J recombination and class switch recombination (CSR). First, though it is rare, a low level of expression of AID can introduce long-lived T:G mismatch lesions at 20-600 bp fragile zones. Second, the V(D)J recombination process can occasionally fail to rejoin coding ends, and this failure may permit an opportunity for Artemis:DNA-dependent kinase catalytic subunit (DNA-PKcs) to convert the T:G mismatch sites at the fragile zones into double-strand breaks. The 20-600 bp fragile zones must be, at least transiently, in a single-stranded DNA (ssDNA) state for the first step to occur, because AID only acts on ssDNA. Here we discuss the key DNA sequence features that lead to AID action at a fragile zone, which are (a) the proximity and density of strings of cytosine nucleotides (C-strings) that cause a B/A-intermediate DNA conformation; (b) overlapping AID hotspots that contain a methyl CpG (WRCG), which AID converts to a long-lived T:G mismatch; and (c) transcription, which, though not essential, favors increased ssDNA in the fragile zone. We also summarize chromosomal features of the focal fragile zones in lymphoid malignancies and discuss the clinical relevance of understanding the translocation mechanisms. Many of the key principles covered here are also relevant to chromosomal translocations in non-lymphoid somatic cells as well.
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Affiliation(s)
- Di Liu
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Michael R Lieber
- Department of Pathology & Laboratory Medicine, Department of Biochemistry & Molecular Biology, Department of Molecular Microbiology and Immunology, and Section of Computational Biology in the Department of Biological Sciences, USC Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
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4
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Zhang W, Gou P, Dupret JM, Chomienne C, Rodrigues-Lima F. Etoposide, an anticancer drug involved in therapy-related secondary leukemia: Enzymes at play. Transl Oncol 2021; 14:101169. [PMID: 34243013 PMCID: PMC8273223 DOI: 10.1016/j.tranon.2021.101169] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 01/13/2023] Open
Abstract
Etoposide is a semi-synthetic glycoside derivative of podophyllotoxin, also known as VP-16. It is a widely used anticancer medicine in clinics. Unfortunately, high doses or long-term etoposide treatment can induce therapy-related leukemia. The mechanism by which etoposide induces secondary hematopoietic malignancies is still unclear. In this article, we review the potential mechanisms of etoposide induced therapy-related leukemia. Etoposide related leukemogenesis is known to depend on reactive oxidative metabolites of etoposide, notably etoposide quinone, which interacts with cellular proteins such as topoisomerases II (TOP2), CREB-binding protein (CREBBP), and T-Cell Protein Tyrosine Phosphatase (TCPTP). CYP3A4 and CYP3A5 metabolize etoposide to etoposide catechol, which readily oxidizes to etoposide quinone. As a poison of TOP2 enzymes, etoposide and its metabolites induce DNA double-stranded breaks (DSB), and the accumulation of DSB triggers cell apoptosis. If the cell survives, the DSB gives rise to the likelihood of faulty DNA repair events. The gene translocation could occur in mixed-lineage leukemia (MLL) gene, which is well-known in leukemogenesis. Recently, studies have revealed that etoposide metabolites, especially etoposide quinone, can covalently bind to cysteines residues of CREBBP and TCPTP enzymes, . This leads to enzyme inhibition and further affects histone acetylation and phosphorylation of the JAK-STAT pathway, thus putatively altering the proliferation and differentiation of hematopoietic stem cells (HSC). In brief, current studies suggest that etoposide and its metabolites contribute to etoposide therapy-related leukemia through TOP2 mediated DSB and impairs specific enzyme activity, such as CREBBP and TCPTP.
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Affiliation(s)
- Wenchao Zhang
- Université de Paris, BFA, UMR 8251, CNRS, Paris F-75013, France.
| | - Panhong Gou
- Inserm UMR-S1131, Université de Paris, IRSL, Hôpital Saint-Louis, Paris, France
| | | | - Christine Chomienne
- Inserm UMR-S1131, Université de Paris, IRSL, Hôpital Saint-Louis, Paris, France; Service de Biologie Cellulaire, Assistance Publique des Hôpitaux de Paris (AP-HP), Hôpital Saint Louis, Paris, France
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5
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Zhao X, Kumari D, Miller CJ, Kim GY, Hayward B, Vitalo AG, Pinto RM, Usdin K. Modifiers of Somatic Repeat Instability in Mouse Models of Friedreich Ataxia and the Fragile X-Related Disorders: Implications for the Mechanism of Somatic Expansion in Huntington's Disease. J Huntingtons Dis 2021; 10:149-163. [PMID: 33579860 PMCID: PMC7990428 DOI: 10.3233/jhd-200423] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Huntington's disease (HD) is one of a large group of human disorders that are caused by expanded DNA repeats. These repeat expansion disorders can have repeat units of different size and sequence that can be located in any part of the gene and, while the pathological consequences of the expansion can differ widely, there is evidence to suggest that the underlying mutational mechanism may be similar. In the case of HD, the expanded repeat unit is a CAG trinucleotide located in exon 1 of the huntingtin (HTT) gene, resulting in an expanded polyglutamine tract in the huntingtin protein. Expansion results in neuronal cell death, particularly in the striatum. Emerging evidence suggests that somatic CAG expansion, specifically expansion occurring in the brain during the lifetime of an individual, contributes to an earlier disease onset and increased severity. In this review we will discuss mouse models of two non-CAG repeat expansion diseases, specifically the Fragile X-related disorders (FXDs) and Friedreich ataxia (FRDA). We will compare and contrast these models with mouse and patient-derived cell models of various other repeat expansion disorders and the relevance of these findings for somatic expansion in HD. We will also describe additional genetic factors and pathways that modify somatic expansion in the FXD mouse model for which no comparable data yet exists in HD mice or humans. These additional factors expand the potential druggable space for diseases like HD where somatic expansion is a significant contributor to disease impact.
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Affiliation(s)
- Xiaonan Zhao
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Daman Kumari
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Carson J Miller
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Geum-Yi Kim
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Bruce Hayward
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Antonia G Vitalo
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA
| | - Ricardo Mouro Pinto
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.,Department of Neurology, Harvard Medical School, Boston, MA, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Karen Usdin
- Laboratory of Cell and Molecular Biology, National Institutes of Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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6
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Pan H, Yu W, Zhang M. Homology-directed repair in mouse cells increased by CasRx-mediated knockdown or co-expressing Kaposi's sarcoma-associated herpesvirus ORF52. Biosci Rep 2019; 39:BSR20191914. [PMID: 31519773 PMCID: PMC6822532 DOI: 10.1042/bsr20191914] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/03/2019] [Accepted: 09/11/2019] [Indexed: 12/28/2022] Open
Abstract
Precise genome editing with directed base insertion or targeted point mutations can be achieved by CRISPR/Cas9-mediated homology-directed repair (HDR) and is of great significance in clinical disease therapy. However, HDR efficiency, compared with non-homologous end-joining (NHEJ), is inherently low. To enhance HDR, enabling the insertion of precise genetic modifications, we compared two strategies during surrogate reporter assays in mouse N2A cells: the suppression of DNA ligase IV, a key molecule in NHEJ, using the CasRx (Ruminococcus flavefaciens Cas13d) system, and co-expression of Kaposi's sarcoma-associated herpesvirus (KSHV) ORF52 proteins. We found that suppression of DNA ligase IV promotes HDR efficiency by 1.4-fold. When co-expressed with the Cas9 system, ORF52 improved HDR efficiency by up to 2.1-fold. In addition, we used ORF52 co-expression to modify the ACTB and Tubb3 genes of mouse N2A and E14 cells, which further increased HDR efficiency by approximately two- to four-fold. In conclusion, our data suggest that ORF52 co-expression is effective for enhancing CRISPR/Cas9-mediated HDR, which may be useful for future studies involving precise genome editing.
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Affiliation(s)
- Hong Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
| | - Weina Yu
- Department of Assisted Reproduction, Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, China
| | - Ming Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
- College of Animal Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, Guangxi, China
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Hu X, Wu X, Liu H, Cheng Z, Zhao Z, Xiang C, Feng X, Takeda S, Qing Y. Genistein-induced DNA damage is repaired by nonhomologous end joining and homologous recombination in TK6 cells. J Cell Physiol 2018; 234:2683-2692. [PMID: 30070703 DOI: 10.1002/jcp.27082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/28/2018] [Indexed: 02/05/2023]
Abstract
Genistein (GES), a phytoestrogen, has potential chemopreventive and chemotherapeutic effects on cancer. The anticancer mechanism of GES may be related with topoisomerase II associated DNA double-strand breaks (DSBs). However, the precise molecular mechanism remains elusive. Here, we performed genetic analyses using human lymphoblastoid TK6 cell lines to investigate whether non-homologous DNA end joining (NHEJ) and homologous recombination (HR), the two major repair pathways of DSBs, were involved in repairing GES-induced DNA damage. Our results showed that GES induced DSBs in TK6 cells. Cells lacking Ligase4, an NHEJ enzyme, are hypersensitive to GES. Furthermore, the sensitivity of Ligase4-/- cells was associated with enhanced DNA damage when comparing the accumulation of γ-H2AX foci and number of chromosomal aberrations (CAs) with WT cells. In addition, cells lacking Rad54, a HR enzyme, also presented hypersensitivity and increased DNA damages in response to GES. Meanwhile, Treatment of GES-lacking enhanced the accumulation of Rad51, an HR factor, in TK6 cells, especially in Ligase4-/- . These results provided direct evidence that GES induced DSBs in TK6 cells and clarified that both NHEJ and HR were involved in the repair of GES-induced DNA damage, suggesting that GES in combination with inhibition of NHEJ or HR would provide a potential anticancer strategy.
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Affiliation(s)
- Xiaoqing Hu
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xiaohua Wu
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Hao Liu
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Ziyuan Cheng
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Zilu Zhao
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Cuifang Xiang
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Xiaoyu Feng
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
| | - Shunichi Takeda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yong Qing
- State Key Laboratory of Biotherapy, West China Hospital, and Department of Pharmacology, West China School of Pharmacy, Sichuan University, Chengdu, Sichuan, China
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8
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HuR silencing elicits oxidative stress and DNA damage and sensitizes human triple-negative breast cancer cells to radiotherapy. Oncotarget 2018; 7:64820-64835. [PMID: 27588488 PMCID: PMC5323119 DOI: 10.18632/oncotarget.11706] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022] Open
Abstract
HuR is an mRNA-binding protein whose overexpression in cancer cells has been associated with poor prognosis and resistance to therapy. While reports on HuR overexpression contributing to chemoresistance exist, limited information is available on HuR and radioresistance especially in triple-negative breast cancer (TNBC). In this study we investigated the role of HuR in radiation resistance in three TNBC (MDA-MB-231, MDA-MB-468 and Hs578t) cell lines. Endogenous HuR expression was higher in TNBC cells compared to normal cells. siRNA mediated knockdown of HuR (siHuR) markedly reduced HuR mRNA and protein levels compared to scrambled siRNA (siScr) treatment. Further, siHuR treatment sensitized TNBC cells to ionizing radiation at 2 Gy compared to siScr treatment as evidenced by the significant reduction in clonogenic cell survival from 59%, 49%, and 65% in siScr-treated cells to 40%, 33%, and 46% in siHuR-treated MDA-MB-231, MDA-MB-468 and Hs578t cells, respectively. Molecular studies showed increased ROS production and inhibition of thioredoxin reductase (TrxR) in HuR knockdown cells contributed to radiosensitization. Associated with increased ROS production was evidence of increased DNA damage, demonstrated by a significant increase (p < 0.05) in γ-H2AX foci that persisted for up to 24 h in siHuR plus radiation treated cells compared to control cells. Further, comet assay revealed that HuR-silenced cells had larger and longer-lasting tails than control cells, indicating higher levels of DNA damage. In conclusion, our studies demonstrate that HuR knockdown in TNBC cells elicits oxidative stress and DNA damage resulting in radiosensitization.
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Abstract
Bacteria of the order Actinomycetales are one of the most important sources of bioactive natural products, which are the source of many drugs. However, many of them still lack efficient genome editing methods, some strains even cannot be manipulated at all. This restricts systematic metabolic engineering approaches for boosting known and discovering novel natural products. In order to facilitate the genome editing for actinomycetes, we developed a CRISPR-Cas9 toolkit with high efficiency for actinomyces genome editing. This basic toolkit includes a software for spacer (sgRNA) identification, a system for in-frame gene/gene cluster knockout, a system for gene loss-of-function study, a system for generating a random size deletion library, and a system for gene knockdown. For the latter, a uracil-specific excision reagent (USER) cloning technology was adapted to simplify the CRISPR vector construction process. The application of this toolkit was successfully demonstrated by perturbation of genomes of Streptomyces coelicolor A3(2) and Streptomyces collinus Tü 365. The CRISPR-Cas9 toolkit and related protocol described here can be widely used for metabolic engineering of actinomycetes.
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Affiliation(s)
- Yaojun Tong
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Helene Lunde Robertsen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Kai Blin
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark
| | - Tilmann Weber
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.
| | - Sang Yup Lee
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs. Lyngby, 2800, Denmark.
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Plus Program), Center for Systems and Synthetic Biotechnology, Institute for the BioCentury, BioInformatics Research Center, and BioProcess Engineering Research Center, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea.
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Yang H, Ahn C, Shin EK, Lee JS, An BS, Jeung EB. NCKX3 was compensated by calcium transporting genes and bone resorption in a NCKX3 KO mouse model. Mol Cell Endocrinol 2017; 454:93-102. [PMID: 28602864 DOI: 10.1016/j.mce.2017.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 05/18/2017] [Accepted: 06/06/2017] [Indexed: 01/10/2023]
Abstract
Gene knockout is the most powerful tool for determination of gene function or permanent modification of the phenotypic characteristics of an animal. Existing methods for gene disruption are limited by their efficiency, time required for completion and potential for confounding off-target effects. In this study, a rapid single-step approach to knockout of a targeted gene in mice using zinc-finger nucleases (ZFNs) was demonstrated for generation of mutant (knockout; KO) alleles. Specifically, ZFNs to target the sodium/calcium/potassium exchanger3 (NCKX3) gene in C57bl/6j were designed using the concept of this approach. NCKX3 KO mice were generated and the phenotypic characterization and molecular regulation of active calcium transporting genes was assessed when mice were fed different calcium diets during growth. General phenotypes such as body weight and plasma ion level showed no distinct abnormalities. Thus, the potassium/sodium/calcium exchanger of NCKX3 KO mice proceeded normally in this study. As a result, the compensatory molecular regulation of this mechanism was elucidated. Renal TRPV5 mRNA of NCKX3 KO mice increased in both male and female mice. Expression of TRPV6 mRNA was only down-regulated in the duodenum of male KO mice. Renal- and duodenal expression of PTHR and VDR were not changed; however, GR mRNA expression was increased in the kidney of NCKX3 KO mice. Depletion of the NCKX3 gene in a KO mouse model showed loss of bone mineral contents and increased plasma parathyroid hormone, suggesting that NCKX3 may play a role in regulating calcium homeostasis.
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Affiliation(s)
- Hyun Yang
- Laboratory of Veterinary Biochemistry and Molecular Biology, Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea; Korean Medicine Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, Republic of Korea
| | - Changhwan Ahn
- Laboratory of Veterinary Biochemistry and Molecular Biology, Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Eun-Kyeong Shin
- Laboratory of Veterinary Biochemistry and Molecular Biology, Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Ji-Sun Lee
- Laboratory of Veterinary Biochemistry and Molecular Biology, Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea
| | - Beum-Soo An
- Department of Biomaterials Science, College of National Resources & Life Science, Pusan National University, Miryang, Gyeongsangnam-do 627-706, Republic of Korea
| | - Eui-Bae Jeung
- Laboratory of Veterinary Biochemistry and Molecular Biology, Veterinary Medical Center and College of Veterinary Medicine, Chungbuk National University, Cheongju, Chungbuk 28644, Republic of Korea.
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Kanungo J. DNA-PK and P38 MAPK: A Kinase Collusion in Alzheimer's Disease? BRAIN DISORDERS & THERAPY 2017; 6:232. [PMID: 28706768 PMCID: PMC5504707 DOI: 10.4172/2168-975x.1000232] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The pathogenesis of Alzheimer's disease (AD), characterized by prevalent neuronal death and extracellular deposit of amyloid plaques, is poorly understood. DNA lesions downstream of reduced DNA repair ability have been reported in AD brains. Neurons predominantly use a mechanism to repair double-strand DNA breaks (DSB), which is non-homologous end joining (NHEJ). NHEJ requires DNA-dependent protein kinase (DNA-PK) activity. DNA-PK is a holoenzyme comprising the p460 kD catalytic subunit (DNA-PKcs) and its activator Ku, a heterodimer of p86 and p70 subunits. Ku first binds and then recruits DNA-PKcs to double-stranded DNA ends before NHEJ process begins. Studies have shown reduced NHEJ activity as well as DNA-PKcs and Ku protein levels in AD brains suggesting possible contribution of unrepaired DSB to AD development. However, normal aging brains also show reduced DNA-PKcs and Ku levels thus challenging the notion of any direct link between NHEJ and AD. Another kinase, p38 MAPK is induced by various DNA damaging agents and DSB itself. Increased DNA damage with aging could induce p38 MAPK and its induction may be sustained when DNA repair is compromised in the brain with reduced DNA-PK activity. Combined, these two events may potentially set the stage for an awry nervous system approaching AD.
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Affiliation(s)
- Jyotshna Kanungo
- Division of Neurotoxicology, National Center for Toxicological Research, US Food and Drug Administration, USA
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12
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The potential impact of new generation transgenic methods on creating rabbit models of cardiac diseases. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 121:123-30. [DOI: 10.1016/j.pbiomolbio.2016.05.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/01/2016] [Indexed: 12/11/2022]
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He M, Hu X, Chen L, Cao AY, Yu KD, Shi TY, Kuang XY, Shi WB, Ling H, Li S, Qiao F, Yao L, Wei Q, Di GH, Shao ZM. A recessive variant of XRCC4 predisposes to non- BRCA1/2 breast cancer in chinese women and impairs the DNA damage response via dysregulated nuclear localization. Oncotarget 2015; 5:12218-32. [PMID: 25360583 PMCID: PMC4322983 DOI: 10.18632/oncotarget.2623] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2014] [Accepted: 10/22/2014] [Indexed: 11/25/2022] Open
Abstract
XRCC4 plays a crucial role in the non-homologous end joining pathway that maintains genome stability. In this two-stage case-control study with 1,764 non-BRCA1/2 breast cancer patients and 1,623 cancer-free controls, we investigated the contribution of genetic variants of XRCC4 to breast cancer susceptibility in Chinese women. We identified a recessive missense variant, rs3734091 (c.739G>T, p.Ala247Ser), of XRCC4 that was significantly associated with an increased risk of breast cancer (odds ratio [OR] = 3.92, P = 0.007), particularly with the risk of developing triple-negative breast cancer (OR = 18.65, P < 0.0001). This p.Ala247Ser variant disturbed the nuclear localization of XRCC4 in cells homozygous for the rs3734091-T allele but not in heterozygous cells at both the cellular and tissue levels. In heterozygous cells, wild-type XRCC4 facilitated the nuclear localization of the XRCC4A247S mutant, thus compensating for the impaired localization of XRCC4A247S. This provided a biological mechanism by which rs3734091 conferred an increased susceptibility to non-BRCA1/2 breast cancer exclusively under a recessive model. Further functional analyses revealed that p.Ala247Ser impaired the DNA damage repair capacity and ultimately perturbed genomic stability. Taken together, our findings document the role of XRCC4 in non-BRCA1/2 breast cancer predisposition and reveal its underlying biological mechanism of action.
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Affiliation(s)
- Min He
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China. Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xin Hu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Li Chen
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China. Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - A-Yong Cao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ke-Da Yu
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ting-Yan Shi
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Xia-Ying Kuang
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China. Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Wen-Biao Shi
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Hong Ling
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Shan Li
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Feng Qiao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Ling Yao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Qingyi Wei
- Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China. Duke Cancer Institute, Duke University Medical Center, Durham, NC, United States of America
| | - Gen-Hong Di
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China. Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhi-Ming Shao
- Department of Breast Surgery, Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Shanghai, China. Cancer Institute, Fudan University Shanghai Cancer Center, Shanghai, China. Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
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14
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Bachu R, Bergareche I, Chasin LA. CRISPR-Cas targeted plasmid integration into mammalian cells via non-homologous end joining. Biotechnol Bioeng 2015; 112:2154-62. [PMID: 25943095 DOI: 10.1002/bit.25629] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 04/27/2015] [Indexed: 12/20/2022]
Abstract
Mammalian cells are widely used for the production of therapeutic recombinant proteins, as these cells facilitate accurate folding and post-translational modifications often essential for optimum activity. Targeted insertion of a plasmid harboring a gene of interest into the genome of mammalian cells for the expression of a desired protein is a key step in production of such biologics. Here we show that a site specific double strand break (DSB) generated both in the genome and the donor plasmid using the CRISPR-Cas9 system can be efficiently used to target ∼5 kb plasmids into mammalian genomes via nonhomologous end joining (NHEJ). We were able to achieve efficiencies of up to 0.17% in HEK293 cells and 0.45% in CHO cells. This technique holds promise for quick and efficient insertion of a large foreign DNA sequence into a predetermined genomic site in mammalian cells.
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Affiliation(s)
- Ravichandra Bachu
- Department of Biological Sciences, Columbia University, New York, New York, 10027
| | - Iñigo Bergareche
- Department of Biological Sciences, Columbia University, New York, New York, 10027
| | - Lawrence A Chasin
- Department of Biological Sciences, Columbia University, New York, New York, 10027.
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15
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Efficient creation of an APOE knockout rabbit. Transgenic Res 2014; 24:227-35. [PMID: 25216764 DOI: 10.1007/s11248-014-9834-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 09/04/2014] [Indexed: 10/24/2022]
Abstract
The rabbit is a preferred model system for diverse areas of human disease research, such as hypertension and atherosclerosis, for its close resemblance to human physiology. Its larger size than that of rodents allows for more convenient physiological and surgical manipulations as well as imaging. The rapid development of nuclease technologies enables the rabbit genome to be engineered as readily as that of rats and mice, offering rabbit models a chance to make their due impact on medical research. Here, we report the efficient creation of an APOE knockout rabbit by using zinc finger nucleases. The knockout rabbits had drastically elevated cholesterol and moderately increased triglyceride levels, mimicking symptoms in human heart disease. So far the rabbit genome has been successfully modified with three nuclease technologies. With a gestation period only days longer than those of rodents, we hope additional reports on their creation and characterization will help encourage the use of rabbit models where they are most relevant to human conditions.
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16
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Wierstra I. The transcription factor FOXM1 (Forkhead box M1): proliferation-specific expression, transcription factor function, target genes, mouse models, and normal biological roles. Adv Cancer Res 2013; 118:97-398. [PMID: 23768511 DOI: 10.1016/b978-0-12-407173-5.00004-2] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
FOXM1 (Forkhead box M1) is a typical proliferation-associated transcription factor, which stimulates cell proliferation and exhibits a proliferation-specific expression pattern. Accordingly, both the expression and the transcriptional activity of FOXM1 are increased by proliferation signals, but decreased by antiproliferation signals, including the positive and negative regulation by protooncoproteins or tumor suppressors, respectively. FOXM1 stimulates cell cycle progression by promoting the entry into S-phase and M-phase. Moreover, FOXM1 is required for proper execution of mitosis. Accordingly, FOXM1 regulates the expression of genes, whose products control G1/S-transition, S-phase progression, G2/M-transition, and M-phase progression. Additionally, FOXM1 target genes encode proteins with functions in the execution of DNA replication and mitosis. FOXM1 is a transcriptional activator with a forkhead domain as DNA binding domain and with a very strong acidic transactivation domain. However, wild-type FOXM1 is (almost) inactive because the transactivation domain is repressed by three inhibitory domains. Inactive FOXM1 can be converted into a very potent transactivator by activating signals, which release the transactivation domain from its inhibition by the inhibitory domains. FOXM1 is essential for embryonic development and the foxm1 knockout is embryonically lethal. In adults, FOXM1 is important for tissue repair after injury. FOXM1 prevents premature senescence and interferes with contact inhibition. FOXM1 plays a role for maintenance of stem cell pluripotency and for self-renewal capacity of stem cells. The functions of FOXM1 in prevention of polyploidy and aneuploidy and in homologous recombination repair of DNA-double-strand breaks suggest an importance of FOXM1 for the maintenance of genomic stability and chromosomal integrity.
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17
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da Silva ALG, da Rosa HT, Karnopp TE, Charlier CF, Ellwanger JH, Moura DJ, Possuelo LG, Valim ARDM, Guecheva TN, Henriques JAP. Evaluation of DNA damage in COPD patients and its correlation with polymorphisms in repair genes. BMC MEDICAL GENETICS 2013; 14:93. [PMID: 24053728 PMCID: PMC3848611 DOI: 10.1186/1471-2350-14-93] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/17/2013] [Accepted: 09/11/2013] [Indexed: 02/07/2023]
Abstract
BACKGROUND We investigated a potential link between genetic polymorphisms in genes XRCC1 (Arg399Gln), OGG1 (Ser326Cys), XRCC3 (Thr241Met), and XRCC4 (Ile401Thr) with the level of DNA damage and repair, accessed by comet and micronucleus test, in 51 COPD patients and 51 controls. METHODS Peripheral blood was used to perform the alkaline and neutral comet assay; and genetic polymorphisms by PCR/RFLP. To assess the susceptibility to exogenous DNA damage, the cells were treated with methyl methanesulphonate for 1-h or 3-h. After 3-h treatment the % residual damage was calculated assuming the value of 1-h treatment as 100%. The cytogenetic damage was evaluated by buccal micronucleus cytome assay (BMCyt). RESULTS COPD patients with the risk allele XRCC1 (Arg399Gln) and XRCC3 (Thr241Met) showed higher DNA damage by comet assay. The residual damage was higher for COPD with risk allele in the four genes. In COPD patients was showed negative correlation between BMCyt (binucleated, nuclear bud, condensed chromatin and karyorrhexic cells) with pulmonary function and some variant genotypes. CONCLUSION Our results suggest a possible association between variant genotypes in XRCC1 (Arg399Gln), OGG1 (Ser326Cys), XRCC3 (Thr241Met), and XRCC4 (Ile401Thr), DNA damage and progression of COPD.
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Affiliation(s)
- Andréa Lúcia Gonçalves da Silva
- Santa Cruz Hospital and Department of Health and Physical Education, University of Santa Cruz do Sul - UNISC, Avenida Independência, 2293, Bloco 42, Bairro Universitário, Santa Cruz do Sul, RS, Brazil.
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18
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Qiu Z, Liu M, Chen Z, Shao Y, Pan H, Wei G, Yu C, Zhang L, Li X, Wang P, Fan HY, Du B, Liu B, Liu M, Li D. High-efficiency and heritable gene targeting in mouse by transcription activator-like effector nucleases. Nucleic Acids Res 2013; 41:e120. [PMID: 23630316 PMCID: PMC3675477 DOI: 10.1093/nar/gkt258] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Transcription activator-like effector nucleases (TALENs) are a powerful new approach for targeted gene disruption in various animal models, but little is known about their activities in Mus musculus, the widely used mammalian model organism. Here, we report that direct injection of in vitro transcribed messenger RNA of TALEN pairs into mouse zygotes induced somatic mutations, which were stably passed to the next generation through germ-line transmission. With one TALEN pair constructed for each of 10 target genes, mutant F0 mice for each gene were obtained with the mutation rate ranged from 13 to 67% and an average of ∼40% of total healthy newborns with no significant differences between C57BL/6 and FVB/N genetic background. One TALEN pair with single mismatch to their intended target sequence in each side failed to yield any mutation. Furthermore, highly efficient germ-line transmission was obtained, as all the F0 founders tested transmitted the mutations to F1 mice. In addition, we also observed that one bi-allele mutant founder of Lepr gene, encoding Leptin receptor, had similar diabetic phenotype as db/db mouse. Together, our results suggest that TALENs are an effective genetic tool for rapid gene disruption with high efficiency and heritability in mouse with distinct genetic background.
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Affiliation(s)
- Zhongwei Qiu
- Shanghai Key Laboratory of Regulatory Biology, Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai 200241, China
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19
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Kanungo J. DNA-dependent protein kinase and DNA repair: relevance to Alzheimer's disease. ALZHEIMERS RESEARCH & THERAPY 2013; 5:13. [PMID: 23566654 PMCID: PMC3706827 DOI: 10.1186/alzrt167] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The pathological hallmark of Alzheimer's disease (AD), the leading cause of senile dementia, involves region-specific neuronal death and an accumulation of neuronal and extracellular lesions termed neurofibrillary tangles and senile plaques, respectively. One of the biochemical abnormalities observed in AD is reduced DNA end-joining activity. The reduced capacity of post-mitotic neurons for some types of DNA repair is further compromised by aging. The predominant mechanism to repair double-strand DNA (dsDNA) breaks (DSB) is non-homologous end joining (NHEJ), which requires DNA-dependent protein kinase (DNA-PK) activity. DNA-PK is a holoenzyme comprising the p460 kDa DNA-PK catalytic subunit (DNA-PKcs) and the Ku heterodimer consisting of p86 (Ku 80) and p70 (Ku 70) subunits. Ku binds to DNA ends first and then recruits DNA-PKcs during NHEJ. However, in AD brains, reduced NHEJ activity has been reported along with reduced levels of DNA-PKcs and the Ku proteins, indicating a potential link between AD and dsDNA damage. Since age-matched control brains also show a reduction in these protein levels, whether there is a direct link between NHEJ ability and AD remains unknown. Possible mechanisms involving the role of DNA-PK in neurodegeneration, a benchmark of AD, are the focus of this review.
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Affiliation(s)
- Jyotshna Kanungo
- Division of Neurotoxicology, National Center for Toxicological Research, US Food and Drug Administration, 3900 NCTR Road, Jefferson, AR 72079, USA
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20
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Oxidative DNA damage in neurons: implication of ku in neuronal homeostasis and survival. Int J Cell Biol 2012; 2012:752420. [PMID: 22737170 PMCID: PMC3378965 DOI: 10.1155/2012/752420] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/05/2012] [Indexed: 12/30/2022] Open
Abstract
Oxidative DNA damage is produced by reactive oxygen species (ROS) which are generated by exogenous and endogenous sources and continuously challenge the cell. One of the most severe DNA lesions is the double-strand break (DSB), which is mainly repaired by nonhomologous end joining (NHEJ) pathway in mammals. NHEJ directly joins the broken ends, without using the homologous template. Ku70/86 heterodimer, also known as Ku, is the first component of NHEJ as it directly binds DNA and recruits other NHEJ factors to promote the repair of the broken ends. Neurons are particularly metabolically active, displaying high rates of transcription and translation, which are associated with high metabolic and mitochondrial activity as well as oxygen consumption. In such a way, excessive oxygen radicals can be generated and constantly attack DNA, thereby producing several lesions. This condition, together with defective DNA repair systems, can lead to a high accumulation of DNA damage resulting in neurodegenerative processes and defects in neurodevelopment. In light of recent findings, in this paper, we will discuss the possible implication of Ku in neurodevelopment and in mediating the DNA repair dysfunction observed in certain neurodegenerations.
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21
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Meussen BJ, de Graaff LH, Sanders JPM, Weusthuis RA. Metabolic engineering of Rhizopus oryzae for the production of platform chemicals. Appl Microbiol Biotechnol 2012; 94:875-86. [PMID: 22526790 PMCID: PMC3339055 DOI: 10.1007/s00253-012-4033-0] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Revised: 03/14/2012] [Accepted: 03/15/2012] [Indexed: 11/28/2022]
Abstract
Rhizopus oryzae is a filamentous fungus belonging to the Zygomycetes. It is among others known for its ability to produce the sustainable platform chemicals L: -(+)-lactic acid, fumaric acid, and ethanol. During glycolysis, all fermentable carbon sources are metabolized to pyruvate and subsequently distributed over the pathways leading to the formation of these products. These platform chemicals are produced in high yields on a wide range of carbon sources. The yields are in excess of 85 % of the theoretical yield for L: -(+)-lactic acid and ethanol and over 65 % for fumaric acid. The study and optimization of the metabolic pathways involved in the production of these compounds requires well-developed metabolic engineering tools and knowledge of the genetic makeup of this organism. This review focuses on the current metabolic engineering techniques available for R. oryzae and their application on the metabolic pathways of the main fermentation products.
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Affiliation(s)
- Bas J Meussen
- Fungal Systems Biology, Laboratory of Systems and Synthetic Biology, Wageningen University, Dreijenplein 10, Wageningen, The Netherlands
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22
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Duranthon V, Beaujean N, Brunner M, Odening KE, Santos AN, Kacskovics I, Hiripi L, Weinstein EJ, Bosze Z. On the emerging role of rabbit as human disease model and the instrumental role of novel transgenic tools. Transgenic Res 2012; 21:699-713. [PMID: 22382461 DOI: 10.1007/s11248-012-9599-x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Accepted: 02/04/2012] [Indexed: 12/19/2022]
Abstract
The laboratory rabbit (Oryctolagus cuniculus) is widely used as a model for human diseases, because of its size, which permits non-lethal monitoring of physiological changes and similar disease characteristics. Novel transgenic tools such as, the zinc finger nuclease method and the sleeping beauty transposon mediated or BAC transgenesis were recently adapted to the laboratory rabbit and opened new opportunities in precise tissue and developmental stage specific gene expression/silencing, coupled with increased transgenic efficiencies. Many facets of human development and diseases cannot be investigated in rodents. This is especially true for early prenatal development, its long-lasting effects on health and complex disorders, and some economically important diseases such as atherosclerosis or cardiovascular diseases. The first transgenic rabbits models of arrhythmogenesis mimic human cardiac diseases much better than transgenic mice and hereby underline the importance of non-mouse models. Another emerging field is epigenetic reprogramming and pathogenic mechanisms in diabetic pregnancy, where rabbit models are indispensable. Beyond that rabbit is used for decades as major source of polyclonal antibodies and recently in monoclonal antibody production. Alteration of its genome to increase the efficiency and value of the antibodies by humanization of the immunoglobulin genes, or by increasing the expression of a special receptor (Fc receptor) that augments humoral immune response is a current demand.
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Affiliation(s)
- V Duranthon
- INRA, UMR 1198 Biologie du Développement et Reproduction, 78350 Jouy en Josas, France
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Chayot R, Montagne B, Ricchetti M. DNA polymerase μ is a global player in the repair of non-homologous end-joining substrates. DNA Repair (Amst) 2012; 11:22-34. [DOI: 10.1016/j.dnarep.2011.09.016] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 09/23/2011] [Accepted: 09/27/2011] [Indexed: 12/25/2022]
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Mannuss A, Trapp O, Puchta H. Gene regulation in response to DNA damage. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:154-65. [PMID: 21867786 DOI: 10.1016/j.bbagrm.2011.08.003] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 07/25/2011] [Accepted: 08/04/2011] [Indexed: 11/17/2022]
Abstract
To deal with different kinds of DNA damages, there are a number of repair pathways that must be carefully orchestrated to guarantee genomic stability. Many proteins that play a role in DNA repair are involved in multiple pathways and need to be tightly regulated to conduct the functions required for efficient repair of different DNA damage types, such as double strand breaks or DNA crosslinks caused by radiation or genotoxins. While most of the factors involved in DNA repair are conserved throughout the different kingdoms, recent results have shown that the regulation of their expression is variable between different organisms. In the following paper, we give an overview of what is currently known about regulating factors and gene expression in response to DNA damage and put this knowledge in context with the different DNA repair pathways in plants. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.
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Affiliation(s)
- Anja Mannuss
- Botanical Institute II, Karlsruhe Institute of Technology, Karlsruhe, Germany
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25
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Datta K, Purkayastha S, Neumann RD, Pastwa E, Winters TA. Base damage immediately upstream from double-strand break ends is a more severe impediment to nonhomologous end joining than blocked 3'-termini. Radiat Res 2011; 175:97-112. [PMID: 21175352 PMCID: PMC3518376 DOI: 10.1667/rr2332.1] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Radiation-induced DNA double-strand breaks (DSBs) are critical cytotoxic lesions that are typically repaired by nonhomologous end joining (NHEJ) in human cells. Our previous work indicated that the highly cytotoxic DSBs formed by (125)I decay possess base damage clustered within 8 to 10 bases of the break and 3'-phosphate (P) and 3'-OH ends. This study examined the effect of such structures on NHEJ in in vitro assays employing either (125)I decay-induced DSB linearized plasmid DNA or structurally defined duplex oligonucleotides. Duplex oligonucleotides that possess either a 3'-P or 3'-phosphoglycolate (PG) or a ligatable 3'-OH end with either an AP site or an 8-oxo-dG 1 nucleotide upstream (-1n) from the 3'-terminus have been examined for reparability. Moderate to severe end-joining inhibition was observed for modified DSB ends or 8-oxo-dG upstream from a 3'-OH end. In contrast, abolition of end joining was observed with duplexes possessing an AP site upstream from a ligatable 3'-OH end or for a lesion combination involving 3'-P plus an upstream 8-oxo-dG. In addition, base mismatches at the -1n position were also strong inhibitors of NHEJ in this system, suggesting that destabilization of the DSB terminus as a result of base loss or improper base pairing may play a role in the inhibitory effects of these structures. Furthermore, we provide data indicating that DSB end joining is likely to occur prior to removal or repair of base lesions proximal to the DSB terminus. Our results show that base damage or base loss near a DSB end may be a severe block to NHEJ and that complex combinations of lesions presented in the context of a DSB may be more inhibitory than the individual lesions alone. In contrast, blocked DSB 3'-ends alone are only modestly inhibitory to NHEJ. Finally, DNA ligase activity is implicated as being responsible for these effects.
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Affiliation(s)
- Kamal Datta
- Nuclear Medicine Department, Warren Grant Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892
| | - Shubhadeep Purkayastha
- Nuclear Medicine Department, Warren Grant Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892
| | - Ronald D. Neumann
- Nuclear Medicine Department, Warren Grant Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892
| | - Elzbieta Pastwa
- Department of Medicinal Chemistry, Medical University of Lodz, Lodz, Poland 92-215
| | - Thomas A. Winters
- Nuclear Medicine Department, Warren Grant Magnuson Clinical Center, National Institutes of Health, Bethesda, MD 20892
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26
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Targeted integration in rat and mouse embryos with zinc-finger nucleases. Nat Biotechnol 2010; 29:64-7. [PMID: 21151125 DOI: 10.1038/nbt.1731] [Citation(s) in RCA: 245] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2010] [Accepted: 11/10/2010] [Indexed: 11/09/2022]
Abstract
Gene targeting is indispensible for reverse genetics and the generation of animal models of disease. The mouse has become the most commonly used animal model system owing to the success of embryonic stem cell-based targeting technology, whereas other mammalian species lack convenient tools for genome modification. Recently, microinjection of engineered zinc-finger nucleases (ZFNs) in embryos was used to generate gene knockouts in the rat and the mouse by introducing nonhomologous end joining (NHEJ)-mediated deletions or insertions at the target site. Here we use ZFN technology in embryos to introduce sequence-specific modifications (knock-ins) by means of homologous recombination in Sprague Dawley and Long-Evans hooded rats and FVB mice. This approach enables precise genome engineering to generate modifications such as point mutations, accurate insertions and deletions, and conditional knockouts and knock-ins. The same strategy can potentially be applied to many other species for which genetic engineering tools are needed.
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27
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Chayot R, Danckaert A, Montagne B, Ricchetti M. Lack of DNA polymerase μ affects the kinetics of DNA double-strand break repair and impacts on cellular senescence. DNA Repair (Amst) 2010; 9:1187-99. [DOI: 10.1016/j.dnarep.2010.09.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2010] [Revised: 07/28/2010] [Accepted: 09/02/2010] [Indexed: 01/06/2023]
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28
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Wang YK, Chang WC, Liu PF, Hsiao MK, Lin CT, Lin SM, Pan RL. Ovate family protein 1 as a plant Ku70 interacting protein involving in DNA double-strand break repair. PLANT MOLECULAR BIOLOGY 2010; 74:453-66. [PMID: 20844935 DOI: 10.1007/s11103-010-9685-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2010] [Accepted: 08/26/2010] [Indexed: 05/22/2023]
Abstract
The Ku heterodimer, a DNA repair protein complex consisting of 70- and 80-kDa subunits, is involved in the non-homologous end-joining (NHEJ) pathway. Plants are thought to use the NHEJ pathway primarily for the repair of DNA double-strand breaks (DSBs). The Ku70/80 protein has been identified in many plants and been shown to possess several similar functions to its counter protein complex in mammals. In the present study, ovate family protein 1 (AtOFP1) was demonstrated to be a plant Ku-interacting protein by yeast two-hybrid screening and the GST pull-down assay. Truncation analysis revealed that the C-terminal domain of AtKu70 contains interacting sites for AtOFP1. The electrophoretic mobility shift assay (EMSA) indicated that AtOFP1 is also a DNA binding protein with its binding domain at the N-terminus. In 3-week-old seedlings, expression of the AtOFP1 gene increased after exposure to DNA-damaging agents (such as methyl methanesulfonate (MMS) and menadione) in a time dependent manner. Seedlings lacking the AtOFP1 protein were more sensitive to MMS and menadione as compared with wild-type. Furthermore, similar to AtKu70(-/-) and AtKu80(-/-), the AtOFP1(-/-) mutant showed relatively lower NHEJ activity in vivo. Taken together, these results suggest that AtOFP1 may play a role in DNA repair through the NHEJ pathway accompanying with the AtKu protein.
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Affiliation(s)
- Yung-Kai Wang
- Institute of Bioinformatics and Structural Biology, College of Life Science, National Tsing Hua University, Hsin-Chu, 30013, Taiwan, ROC
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Abstract
Homologous recombination-based gene targeting using Mus musculus embryonic stem cells has greatly impacted biomedical research. This study presents a powerful new technology for more efficient and less time-consuming gene targeting in mice using embryonic injection of zinc-finger nucleases (ZFNs), which generate site-specific double strand breaks, leading to insertions or deletions via DNA repair by the nonhomologous end joining pathway. Three individual genes, multidrug resistant 1a (Mdr1a), jagged 1 (Jag1), and notch homolog 3 (Notch3), were targeted in FVB/N and C57BL/6 mice. Injection of ZFNs resulted in a range of specific gene deletions, from several nucleotides to >1000 bp in length, among 20-75% of live births. Modified alleles were efficiently transmitted through the germline, and animals homozygous for targeted modifications were obtained in as little as 4 months. In addition, the technology can be adapted to any genetic background, eliminating the need for generations of backcrossing to achieve congenic animals. We also validated the functional disruption of Mdr1a and demonstrated that the ZFN-mediated modifications lead to true knockouts. We conclude that ZFN technology is an efficient and convenient alternative to conventional gene targeting and will greatly facilitate the rapid creation of mouse models and functional genomics research.
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Kurosawa A, Adachi N. Functions and regulation of Artemis: a goddess in the maintenance of genome integrity. JOURNAL OF RADIATION RESEARCH 2010; 51:503-509. [PMID: 20543526 DOI: 10.1269/jrr.10017] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Artemis is a structure-specific endonuclease when associated with and phosphorylated by DNA-dependent protein kinase catalytic subunit. This structure-specific endonuclease is responsible for the resolution of hairpin coding ends in V(D)J recombination. In DNA double-strand break repair, Artemis is implicated in the end-processing step of the non-homologous end-joining (NHEJ) pathway. Recently, we have demonstrated that the involvement of Artemis in NHEJ depends on the type of DNA damage. Interestingly, recent evidence suggests that the end-processing activity is not the only function of Artemis. Indeed, Artemis is rapidly phosphorylated by ataxia telangiectasia mutated in response to DNA damage, and such phosphorylation of Artemis appears to be involved in the regulation of cell cycle checkpoints. These findings suggest that Artemis is a multifunctional protein participating in the maintenance of genome integrity at two distinct levels; one at the end processing step of NHEJ, and the other at the signaling pathway of cell cycle regulation. Therefore, understanding Artemis function may give us profound insights into the DNA repair network. In this review, we summarize the functions and regulation of Artemis.
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Affiliation(s)
- Aya Kurosawa
- Graduate School of Nanobioscience, Yokohama City University, Yokohama, Japan.
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31
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Stavnezer J, Björkman A, Du L, Cagigi A, Pan-Hammarström Q. Mapping of Switch Recombination Junctions, a Tool for Studying DNA Repair Pathways during Immunoglobulin Class Switching. Adv Immunol 2010; 108:45-109. [DOI: 10.1016/b978-0-12-380995-7.00003-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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Heisig P. Type II topoisomerases--inhibitors, repair mechanisms and mutations. Mutagenesis 2009; 24:465-9. [PMID: 19762349 DOI: 10.1093/mutage/gep035] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Type II topoisomerases are ubiquitous enzymes that play an essential role in the control of replicative DNA synthesis and share structural and functional homology among different prokaryotic and eukaryotic organisms. Antibacterial fluoroquinolones target prokaryotic topoisomerases at concentrations 100- to 1000-fold lower than mammalian enzymes, the preferred targets of anticancer drugs such as etoposide. The mechanisms of action of both of these types of inhibitors involve the fixation of an intermediate reaction step, where the enzyme is covalently bound to an enzyme-mediated DNA double-strand break (DSB). The resulting ternary drug-enzyme-DNA complexes can then be converted to cleavage complexes that block further movement of the DNA replication fork, subsequently inducing stress responses. In haploid prokaryotic cells, stress responses include error-free and error-prone DNA damage repair pathways, such as homologous recombination and translesion synthesis, respectively. The latter can result in the acquisition of point mutations. Diploid mammalian cells are assumed to preferentially use recombination mechanisms for the repair of DSBs, an example of which, non-homologous end joining, is a major error-prone repair mechanism associated with an increased frequency of detectable small deletions, insertions and translocations. However, results obtained from safety testing of novel fluoroquinolones at high concentrations indicate that point mutations may also occur in mammalian cells. Recent data provide evidence for translesion synthesis catalysed by error-prone repair polymerases as a damage-tolerance repair mechanism of DSBs in eukaryotic cells. This paper discusses possible roles of different mechanisms for the repair of DSBs operating in both eukaryotic and prokaryotic cells that result in recombinational rearrangements, deletions/insertions as well as point mutations.
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Affiliation(s)
- Peter Heisig
- Pharmaceutical Biology and Microbiology, Department of Chemistry, University of Hamburg, Bundesstrasse 45, 20146 Hamburg, Germany.
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Kotnis A, Du L, Liu C, Popov SW, Pan-Hammarström Q. Non-homologous end joining in class switch recombination: the beginning of the end. Philos Trans R Soc Lond B Biol Sci 2009; 364:653-65. [PMID: 19008195 PMCID: PMC2660918 DOI: 10.1098/rstb.2008.0196] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Immunoglobulin class switch recombination (CSR) is initiated by a B-cell-specific factor, activation-induced deaminase, probably through deamination of deoxycytidine residues within the switch (S) regions. The initial lesions in the S regions are subsequently processed, resulting in the production of DNA double-strand breaks (DSBs). These breaks will then be recognized, edited and repaired, finally leading to the recombination of the two S regions. Two major repair pathways have been implicated in CSR, the predominant non-homologous end joining (NHEJ) and the alternative end-joining (A-EJ) pathways. The former requires not only components of the ‘classical’ NHEJ machinery, i.e. Ku70/Ku80, DNA-dependent protein kinase catalytic subunit, DNA ligase IV and XRCC4, but also a number of DNA-damage sensors or adaptors, such as ataxia–telangiectasia mutated, γH2AX, 53BP1, MDC1, the Mre11–Rad50–NBS1 complex and the ataxia telangiectasia and Rad3-related protein (ATR). The latter pathway is not well characterized yet and probably requires microhomologies. In this review, we will focus on the current knowledge of the predominant NHEJ pathway in CSR and will also give a perspective on the A-EJ pathway.
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Affiliation(s)
- Ashwin Kotnis
- Division of Clinical Immunology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital Huddinge, 14186 Stockholm, Sweden
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34
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Abstract
Critically shortened telomeres can be subjected to DNA repair events that generate end-to-end chromosome fusions. The resulting dicentric chromosomes can enter breakage-fusion-bridge cycles, thereby impeding elucidation of the structures of the initial fusion events and a mechanistic understanding of their genesis. Current models for the molecular basis of fusion of critically shortened, uncapped telomeres rely on PCR assays that typically capture fusion breakpoints created by direct ligation of chromosome ends. Here we use independent approaches that rely on distinctive features of Caenorhabditis elegans to study the frequency of direct end-to-end chromosome fusion in telomerase mutants: (1) holocentric chromosomes that allow for genetic isolation of stable end-to-end fusions and (2) unique subtelomeric sequences that allow for thorough PCR analysis of samples of genomic DNA harboring multiple end-to-end fusions. Surprisingly, only a minority of end-to-end fusion events resulted from direct end joining with no additional genome rearrangements. We also demonstrate that deficiency for the C. elegans Ku DNA repair heterodimer does not affect telomere length or cause synthetic effects in the absence of telomerase.
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Toyoda E, Kagaya S, Cowell IG, Kurosawa A, Kamoshita K, Nishikawa K, Iiizumi S, Koyama H, Austin CA, Adachi N. NK314, a topoisomerase II inhibitor that specifically targets the alpha isoform. J Biol Chem 2008; 283:23711-20. [PMID: 18596031 PMCID: PMC3259784 DOI: 10.1074/jbc.m803936200] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2008] [Revised: 06/27/2008] [Indexed: 11/06/2022] Open
Abstract
Topoisomerase II (Top2) is a ubiquitous nuclear enzyme that relieves torsional stress in chromosomal DNA during various cellular processes. Agents that target Top2, involving etoposide, doxorubicin, and mitoxantrone, are among the most effective anticancer drugs used in the clinic. Mammalian cells possess two genetically distinct Top2 isoforms, both of which are the target of these agents. Top2alpha is essential for cell proliferation and is highly expressed in vigorously growing cells, whereas Top2beta is nonessential for growth and has recently been implicated in treatment-associated secondary malignancies, highlighting the validity of a Top2alpha-specific drug for future cancer treatment; however, no such agent has been hitherto reported. Here we show that NK314, a novel synthetic benzo[c]phenanthridine alkaloid, targets Top2alpha and not Top2beta in vivo. Unlike other Top2 inhibitors, NK314 induces Top2-DNA complexes and double-strand breaks (DSBs) in an alpha isoform-specific manner. Heterozygous disruption of the human TOP2alpha gene confers increased NK314 resistance, whereas TOP2beta homozygous knock-out cells display increased NK314 sensitivity, indicating that the alpha isoform is the cellular target. We further show that the absence of Top2beta does not alleviate NK314 hypersensitivity of cells deficient in non-homologous end-joining, a critical pathway for repairing Top2-mediated DSBs. Our results indicate that NK314 acts as a Top2alpha-specific poison in mammalian cells, with excellent potential as an efficacious and safe chemotherapeutic agent. We also suggest that a series of human knock-out cell lines are useful in assessing DNA damage and repair induced by potential topoisomerase-targeting agents.
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Affiliation(s)
- Eriko Toyoda
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
| | - Shigehide Kagaya
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
| | - Ian G. Cowell
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
| | - Aya Kurosawa
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
| | - Keiichi Kamoshita
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
| | - Kiyohiro Nishikawa
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
| | - Susumu Iiizumi
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
| | - Hideki Koyama
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
| | - Caroline A. Austin
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
| | - Noritaka Adachi
- International Graduate School of Arts and
Sciences, Yokohama City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027,
Japan, the Pharmaceutical Research Laboratories,
Nippon Kayaku Co., Ltd., 31-12, Shimo 3-chome, Kita-ku, Tokyo 115-8588, Japan,
and the Institute for Cell and Molecular
Biosciences, The Medical School, Newcastle University, Newcastle-upon-Tyne,
NE2 4HH United Kingdom
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36
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DNA-PKcs and ATM influence generation of ionizing radiation-induced bystander signals. Oncogene 2008; 27:6761-9. [DOI: 10.1038/onc.2008.276] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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37
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Abe T, Ishiai M, Hosono Y, Yoshimura A, Tada S, Adachi N, Koyama H, Takata M, Takeda S, Enomoto T, Seki M. KU70/80, DNA-PKcs, and Artemis are essential for the rapid induction of apoptosis after massive DSB formation. Cell Signal 2008; 20:1978-85. [PMID: 18674614 DOI: 10.1016/j.cellsig.2008.07.006] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Revised: 07/05/2008] [Accepted: 07/07/2008] [Indexed: 02/06/2023]
Abstract
KU70(-/-) and DNA-PKcs(-/-/-)chicken DT40 cells are reportedly highly sensitive to the DNA topoisomerase II inhibitor etoposide. Here we report that KU70 and DNA-PKcs unexpectedly function together during the induction of apoptosis after exposure to high levels of etoposide. In the presence of 100 microM etoposide, apoptosis was induced within 1 h in wild type DT40 cells but not in KU70(-/-) and DNA-PKcs(-/-/-) cells. In addition, the DNA-PK inhibitors NU7026 and wortmannin, as well as the caspase inhibitor Z-VAD-FMK, inhibited etoposide-induced apoptosis in wild type cells. Although Artemis(-/-) cells also showed defects in the etoposide-induced apoptosis, the other mutants defective in nonhomologous end-joining (NHEJ), LIG4(-/-), XRCC4(-), and XLF(-/-) cells were capable to induce apoptosis. When cells were treated with high doses of etoposide, the chromatin binding of DNA-PKcs was impaired by deletion of KU70 but not of Artemis, suggesting that KU70 acts upstream of DNA-PKcs and Artemis acts downstream of DNA-PKcs in the apoptotic pathway like the NHEJ pathway. These results suggest that the proteins involved in the early stage of NHEJ pathway including Artemis but not the downstream factors decide the cell fate by selecting apoptosis or DNA repair according to the degree of DNA damage.
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Affiliation(s)
- Takuya Abe
- Molecular Cell Biology Laboratory, Graduate School of Pharmaceutical Sciences, Tohoku University, Aoba 6-3, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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Friesen C, Uhl M, Pannicke U, Schwarz K, Miltner E, Debatin KM. DNA-ligase IV and DNA-protein kinase play a critical role in deficient caspases activation in apoptosis-resistant cancer cells by using doxorubicin. Mol Biol Cell 2008; 19:3283-9. [PMID: 18508926 DOI: 10.1091/mbc.e08-03-0306] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Resistance toward cytotoxic drugs is one of the primary causes for therapeutic failure in cancer therapy. DNA repair mechanisms as well as deficient caspases activation play a critical role in apoptosis resistance of tumor cells toward anticancer drug treatment. Here, we discovered that deficient caspases activation in apoptosis-resistant cancer cells depends on DNA-ligase IV and DNA-protein kinase (DNA-PK), playing crucial roles in the nonhomologous end joining (NHEJ) pathway, which is the predominant pathway for DNA double-strand break repair (DNA-DSB-repair) in mammalian cells. DNA-PK(+/+) as well as DNA-ligase IV (+/+) cancer cells were apoptosis resistant and deficient in activation of caspase-3, caspase-9, and caspase-8 and in cleavage of poly(ADP-ribose) polymerase after doxorubicin treatment. Inhibition of NHEJ by knocking out DNA-PK or DNA-ligase IV restored caspases activation and apoptosis sensitivity after doxorubicin treatment. In addition, inhibition of caspases activation prevented doxorubicin-induced apoptosis but could not prevent doxorubicin-induced DNA damage, indicating that induction of DNA damage is independent of caspases activation. However, caspases activation depends on induction of DNA damage left unrepaired by NHEJ-DNA-DSB-repair. We conclude that DNA damage left unrepaired by DNA-ligase IV or DNA-PK might be the initiator for caspases activation by doxorubicin in cancer cells. Failure in caspases activation using doxorubicin depends on loss of DNA damage and is due to higher rates of NHEJ-DNA-DBS-repair.
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Affiliation(s)
- Claudia Friesen
- Institute of Legal Medicine, University of Ulm, 89075 Ulm, Germany.
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39
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Abstract
The DNA-dependent protein kinase (DNA-PK) is central to the process of nonhomologous end joining because it recognizes and then binds double strand breaks initiating repair. It has long been appreciated that DNA-PK protects DNA ends to promote end joining. Here we review recent work from our laboratories and others demonstrating that DNA-PK can regulate end access both positively and negatively. This is accomplished via distinct autophosphorylation events that result in opposing effects on DNA end access. Additional autophosphorylations that are both physically and functionally distinct serve to regulate kinase activity and complex dissociation. Finally, DNA-PK both positively and negatively regulates DNA end access to repair via the homologous recombination pathway. This has particularly important implications in human cells because of DNA-PK's cellular abundance.
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Affiliation(s)
- Katheryn Meek
- College of Veterinary Medicine, Michigan State University, East Lansing, Michigan, USA
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40
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Ishiguro A, Aruga J. Functional role of Zic2 phosphorylation in transcriptional regulation. FEBS Lett 2007; 582:154-8. [PMID: 18068128 DOI: 10.1016/j.febslet.2007.11.080] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2007] [Revised: 11/05/2007] [Accepted: 11/15/2007] [Indexed: 11/19/2022]
Abstract
Zic2 is a transcriptional activator that plays a crucial role in mammalian forebrain development. It activates the transcription of target genes by DNA binding and recruitment of RNA helicase A (RHA). We recently reported that the Zic2-RHA interaction is decreased by phosphatase treatment in vitro. We have now identified the phosphorylation site (serine 200) in mouse Zic2. Zic2S200A was defective in RHA-binding, and its transcriptional activation ability was diminished. These data indicate that Zic2S200 is a target for phosphorylation by DNA-dependent protein kinase, regulating Zic2-mediated transcriptional activation.
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Affiliation(s)
- Akira Ishiguro
- Laboratory for Comparative Neurogenesis, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan.
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41
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Kosmider B, Wells RD. Fragile X repeats are potent inducers of complex, multiple site rearrangements in flanking sequences in Escherichia coli. DNA Repair (Amst) 2007; 6:1850-63. [PMID: 17851139 DOI: 10.1016/j.dnarep.2007.07.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2006] [Revised: 06/27/2007] [Accepted: 07/12/2007] [Indexed: 01/02/2023]
Abstract
(CGG.CCG)n repeats induce the formation of complex, multiple site rearrangements and/or gross deletions in flanking DNA sequences in Escherichia coli plasmids. DNA sequence analyses of mutant clones revealed the influence of (a) the length (24, 44 or 73 repeats), (b) the orientation of the CGG.CCG region relative to the unidirectional origin, and (c) its transcription status. Complex rearrangements had occurred in the mutant clones since some products contained deletions, inversions and insertions and some products had only gross deletions. Furthermore, the CGG.CCG repeats repeatedly induced, up to 22 times, the formation of identical (to the bp) mutagenic products indicating the powerful nature of the complex processes involved. Also, the mutations were bidirectional from the CGG.CCG tract. The healed junctions had CG-rich microhomologies of 1-6bp, CG-rich regions and putative cruciforms and slipped structures. Hence, the fragile X syndrome mutagenic spectrum has been found, at least in part, in our model system.
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Affiliation(s)
- Beata Kosmider
- Center for Genome Research, Institute of Biosciences and Technology, Texas A&M University System Health Science Center, Texas Medical Center, 2121 W. Holcombe Blvd., Houston, TX 77030-3303, USA
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42
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Abstract
DNA is a precious molecule. It encodes vital information about cellular content and function. There are only two copies of each chromosome in the cell, and once the sequence is lost no replacement is possible. The irreplaceable nature of the DNA sets it apart from other cellular molecules, and makes it a critical target for age-related deterioration. To prevent DNA damage cells have evolved elaborate DNA repair machinery. Paradoxically, DNA repair can itself be subject to age-related changes and deterioration. In this review we will discuss the changes in efficiency of mismatch repair (MMR), base excision repair (BER), nucleotide excision repair (NER) and double-strand break (DSB) repair systems during aging, and potential changes in DSB repair pathway usage that occur with age. Mutations in DNA repair genes and premature aging phenotypes they cause have been reviewed extensively elsewhere, therefore the focus of this review is on the comparison of DNA repair mechanisms in young versus old.
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Affiliation(s)
- Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA.
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43
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Lee K, Lee SE. Saccharomyces cerevisiae Sae2- and Tel1-dependent single-strand DNA formation at DNA break promotes microhomology-mediated end joining. Genetics 2007; 176:2003-14. [PMID: 17565964 PMCID: PMC1950609 DOI: 10.1534/genetics.107.076539] [Citation(s) in RCA: 128] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ) joins DNA ends via short stretches [5-20 nucleotides (nt)] of direct repeat sequences, yielding deletions of intervening sequences. Non-homologous end joining (NHEJ) and single-strand annealing (SSA) are other error prone processes that anneal single-stranded DNA (ssDNA) via a few bases (<5 nt) or extensive direct repeat homologies (>20 nt). Although the genetic components involved in MMEJ are largely unknown, those in NHEJ and SSA are characterized in some detail. Here, we surveyed the role of NHEJ or SSA factors in joining of double-strand breaks (DSBs) with no complementary DNA ends that rely primarily on MMEJ repair. We found that MMEJ requires the nuclease activity of Mre11/Rad50/Xrs2, 3' flap removal by Rad1/Rad10, Nej1, and DNA synthesis by multiple polymerases including Pol4, Rad30, Rev3, and Pol32. The mismatch repair proteins, Rad52 group genes, and Rad27 are dispensable for MMEJ. Sae2 and Tel1 promote MMEJ but inhibit NHEJ, likely by regulating Mre11-dependent ssDNA accumulation at DNA break. Our data support the role of Sae2 and Tel1 in MMEJ and genome integrity.
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Affiliation(s)
- Kihoon Lee
- Department of Molecular Medicine and Institute of Biotechnology, University of Texas Health Science Center at San Antonio, 15355 Lambda Drive, San Antonio, TX 78245, USA.
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Ishiguro A, Ideta M, Mikoshiba K, Chen DJ, Aruga J. ZIC2-dependent Transcriptional Regulation Is Mediated by DNA-dependent Protein Kinase, Poly(ADP-ribose) Polymerase, and RNA Helicase A. J Biol Chem 2007; 282:9983-9995. [PMID: 17251188 DOI: 10.1074/jbc.m610821200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The Zic family of zinc finger proteins is essential for animal development, as demonstrated by the holoprosencephaly caused by mammalian Zic2 mutation. To determine the molecular mechanism of Zic-mediated developmental control, we characterized two types of high molecular weight complexes, including Zic2. Complex I was composed of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), Ku70/80, and poly(ADP-ribose) polymerase; complex II contained Ku70/80 and RNA helicase A; all the components interacted directly with Zic2 protein. Immunoprecipitation, subnuclear localization, and in vitro phosphorylation analyses revealed that the DNA-PKcs in complex I played an essential role in the assembly of complex II. Stepwise exchange from complex I to complex II depended on phosphorylation of Zic2 by DNA-PK and poly-(ADP-ribose) polymerase. Phosphorylated Zic2 protein made a stable complex with RNA helicase A, and complex II could interact with RNA polymerase II. Phosphorylation-dependent transformation of Zic2-containing molecular complexes may occur in transcriptional regulation.
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Affiliation(s)
- Akira Ishiguro
- Laboratory for Comparative Neurogenesis, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan.
| | - Maki Ideta
- Laboratory for Comparative Neurogenesis, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan
| | - Katsuhiko Mikoshiba
- Laboratory of Developmental Neurobiology, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan
| | - David J Chen
- Department of Radiation Oncology, University of Texas Southwestern Medical Center, Dallas, Texas 75390
| | - Jun Aruga
- Laboratory for Comparative Neurogenesis, RIKEN Brain Science Institute, Wako-shi, Saitama 351-0198, Japan.
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45
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Pedraza-Alva G, Koulnis M, Charland C, Thornton T, Clements JL, Schlissel MS, Rincón M. Activation of p38 MAP kinase by DNA double-strand breaks in V(D)J recombination induces a G2/M cell cycle checkpoint. EMBO J 2006; 25:763-73. [PMID: 16456545 PMCID: PMC1383553 DOI: 10.1038/sj.emboj.7600972] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2005] [Accepted: 01/02/2006] [Indexed: 11/09/2022] Open
Abstract
Delay of cell cycle progression in response to double-strand DNA breaks (DSBs) is critical to allow time for DNA repair and prevent cellular transformation. Here, we show that the p38 mitogen-activated protein (MAP) kinase signaling pathway is activated in immature thymocytes along with TcRbeta gene V(D)J recombination. Active p38 MAP kinase promotes a G2/M cell cycle checkpoint through the phosphorylation and activation of p53 in these cells in vivo. Inactivation of p38 MAP kinase and p53 is required for DN3 thymocytes to exit the G2/M checkpoint, progress through mitosis and further differentiate. We propose that p38 MAP kinase is activated by V(D)J-mediated DSBs and induces a p53-mediated G2/M checkpoint to allow DNA repair and prevent cellular transformation.
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Affiliation(s)
- Gustavo Pedraza-Alva
- Department of Medicine/Immunobiology Program, University of Vermont, Burlington, VT, USA
- Instituto de Biotecnología, Universidad Nacional Autónoma de México. Cuernavaca, Mor., México
| | - Miroslav Koulnis
- Department of Medicine/Immunobiology Program, University of Vermont, Burlington, VT, USA
| | - Colette Charland
- Department of Medicine/Immunobiology Program, University of Vermont, Burlington, VT, USA
| | - Tina Thornton
- Department of Medicine/Immunobiology Program, University of Vermont, Burlington, VT, USA
| | - James L Clements
- Department of Immunology, Cancer Cell Center, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Mark S Schlissel
- Department of Molecular & Cell Biology, University of California-Berkeley, Berkeley, CA, USA
| | - Mercedes Rincón
- Department of Medicine/Immunobiology Program, University of Vermont, Burlington, VT, USA
- Department of Medicine/Immunobiology Program, Given Medical Building D-305, University of Vermont, 89 Beaumont Avenue, Burlington, VT 05405, USA. Tel.: +1 802 656 0937; Fax: +1 802 656 3854; E-mail:
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46
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Munshi A, Kurland JF, Nishikawa T, Tanaka T, Hobbs ML, Tucker SL, Ismail S, Stevens C, Meyn RE. Histone deacetylase inhibitors radiosensitize human melanoma cells by suppressing DNA repair activity. Clin Cancer Res 2005; 11:4912-22. [PMID: 16000590 DOI: 10.1158/1078-0432.ccr-04-2088] [Citation(s) in RCA: 262] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Histone deacetylase (HDAC) inhibitors have emerged recently as promising anticancer agents. They arrest cells in the cell cycle and induce differentiation and cell death. The antitumor activity of HDAC inhibitors has been linked to their ability to induce gene expression through acetylation of histone and nonhistone proteins. However, it has recently been suggested that HDAC inhibitors may also enhance the activity of other cancer therapeutics, including radiotherapy. The purpose of this study was to evaluate the ability of HDAC inhibitors to radiosensitize human melanoma cells in vitro. EXPERIMENTAL DESIGN A panel of HDAC inhibitors that included sodium butyrate (NaB), phenylbutyrate, tributyrin, and trichostatin A were tested for their ability to radiosensitize two human melanoma cell lines (A375 and MeWo) using clonogenic cell survival assays. Apoptosis and DNA repair were measured by standard assays. RESULTS NaB induced hyperacetylation of histone H4 in the two melanoma cell lines and the normal human fibroblasts. NaB radiosensitized both the A375 and MeWo melanoma cell lines, substantially reducing the surviving fraction at 2 Gy (SF2), whereas it had no effect on the normal human fibroblasts. The other HDAC inhibitors, phenylbutyrate, tributyrin, and trichostatin A had significant radiosensitizing effects on both melanoma cell lines tested. NaB modestly enhanced radiation-induced apoptosis that did not correlate with survival but did correlate with functional impairment of DNA repair as determined based on the host cell reactivation assay. Moreover, NaB significantly reduced the expression of the repair-related genes Ku70 and Ku86 and DNA-dependent protein kinase catalytic subunit in melanoma cells at the protein and mRNA levels. Normal human fibroblasts showed no change in DNA repair capacity or levels of DNA repair proteins following NaB treatment. We also examined gamma-H2AX phosphorylation as a marker of radiation response to NaB and observed that compared with controls, gamma-H2AX foci persisted long after ionizing exposure in the NaB-treated cells. CONCLUSIONS HDAC inhibitors radiosensitize human tumor cells by affecting their ability to repair the DNA damage induced by ionizing radiation and that gamma-H2AX phosphorylation can be used as a predictive marker of radioresponse.
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Affiliation(s)
- Anupama Munshi
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030, USA.
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Adachi N, Iiizumi S, Koyama H. Evidence for a role of vertebrate Rad52 in the repair of topoisomerase II-mediated DNA damage. DNA Cell Biol 2005; 24:388-93. [PMID: 15941391 DOI: 10.1089/dna.2005.24.388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
DNA topoisomerase II (Top2) inhibitors are useful as anticancer agents, mostly by virtue of their ability to induce DNA double-strand breaks (DSBs). These DSBs are repaired almost exclusively by Rad52-dependent homologous recombination (HR) in yeast. However, we have recently shown that in vertebrate cells such lesions are primarily repaired by nonhomologous end-joining, but not HR. This finding, taken together with previous observations that disruption of RAD52 does not severely affect HR in vertebrate cells, makes it highly unlikely that Rad52 contributes to the repair of Top2-mediated DNA damage. However, in this paper we show that chicken cells lacking Rad52 do exhibit increased sensitivity to the Top2 inhibitor VP-16. Remarkably, the level of hypersensitivity of RAD52-null cells was comparable to that of RAD54-null cells, albeit only at high doses. Our data thus provide the first demonstration of a major repair defect associated with loss of Rad52 in vertebrate cells.
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Affiliation(s)
- Noritaka Adachi
- Kihara Institute for Biological Research, Graduate School of Integrated Science, Yokohama City University, Yokohama, Japan.
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48
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Skory CD. Inhibition of non-homologous end joining and integration of DNA upon transformation of Rhizopus oryzae. Mol Genet Genomics 2005; 274:373-83. [PMID: 16133163 DOI: 10.1007/s00438-005-0028-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2004] [Accepted: 06/27/2005] [Indexed: 01/12/2023]
Abstract
Site-directed integration of DNA in the fungus Rhizopus has long been problematic because linearized plasmids used for transformation tend to replicate in high-molecular-weight concatenated structures, and rarely integrate into the chromosome. This work examines the methods that might interfere with the multimerization process, select against plasmids that had recircularized, and encourage strand invasion, hopefully leading to plasmid integration. In vitro methods were used to determine if the structure of the double-strand break had any effect on the ability to rejoin plasmid ends. In cell-free extracts, little difference in end-joining activity was found between linearized plasmids with 5' overhangs, 3' overhangs, or blunt ends. In addition, dephosphorylation of ends had no effect. Transformation of plasmids prepared in the same ways confirmed that they were easily religated in vivo, with almost all prototrophic isolates retaining autonomously replicated plasmids. It was possible to block religation by modifying the free ends of the linearized plasmids using oligonucleotide adapters which were blocked at the 3'-OH position and contained phosphorothioate nucleotides to make them nuclease-resistant. However, gene replacement, with repair of the auxotrophic mutation in the host chromosome, was the predominant event observed upon the transformation of these plasmids. The highest rates of integration were obtained with a plasmid containing a truncated, non-functional pyrG gene. Autonomous replication of this plasmid did not support prototrophic growth, but homologous recombination into the chromosome restored the function of the endogenous pyrG gene. All of the transformants obtained with this selective construct were found to have integrated the plasmid, with multicopy insertion being common.
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Affiliation(s)
- Christopher D Skory
- Bioproducts and Biocatalysis Research Unit, USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, 1815 N. University Street, Peoria, IL 61604, USA
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Raghavan SC, Hsieh CL, Lieber MR. Both V(D)J coding ends but neither signal end can recombine at the bcl-2 major breakpoint region, and the rejoining is ligase IV dependent. Mol Cell Biol 2005; 25:6475-84. [PMID: 16024785 PMCID: PMC1190333 DOI: 10.1128/mcb.25.15.6475-6484.2005] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 03/31/2005] [Accepted: 04/13/2005] [Indexed: 12/22/2022] Open
Abstract
The t(14;18) chromosomal translocation is the most common translocation in human cancer, and it occurs in all follicular lymphomas. The 150-bp bcl-2 major breakpoint region (Mbr) on chromosome 18 is a fragile site, because it adopts a non-B DNA conformation that can be cleaved by the RAG complex. The non-B DNA structure and the chromosomal translocation can be recapitulated on intracellular human minichromosomes where immunoglobulin 12- and 23-signals are positioned downstream of the bcl-2 Mbr. Here we show that either of the two coding ends in these V(D)J recombination reactions can recombine with either of the two broken ends of the bcl-2 Mbr but that neither signal end can recombine with the Mbr. Moreover, we show that the rejoining is fully dependent on DNA ligase IV, indicating that the rejoining phase relies on the nonhomologous DNA end-joining pathway. These results permit us to formulate a complete model for the order and types of cleavage and rejoining events in the t(14;18) translocation.
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Affiliation(s)
- Sathees C Raghavan
- USC Norris Comprehensive Cancer Ctr., Rm. 5428, 1441 Eastlake Ave., Los Angeles, CA 90089-9176, USA
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Dmitrieva NI, Celeste A, Nussenzweig A, Burg MB. Ku86 preserves chromatin integrity in cells adapted to high NaCl. Proc Natl Acad Sci U S A 2005; 102:10730-5. [PMID: 16027367 PMCID: PMC1180807 DOI: 10.1073/pnas.0504870102] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cells adapted to high NaCl have many DNA breaks both in cell culture and in the renal inner medulla in vivo; yet they survive, function, and even proliferate. Here, we show that Ku86 is important for maintaining chromosomal integrity despite the continued presence of DNA breaks. The Ku heterodimer is part of DNA-dependent PK (DNA-PK), a complex that contributes by nonhomologous end joining to repair of double-strand breaks. We demonstrate that cells deficient in Ku86, but not cells deficient in DNA-PKcs (the catalytic subunit of DNA-PK), are hypersensitive to high NaCl as manifested by profound inhibition of proliferation, aberrant mitosis, and increased chromosomal fragmentation. Lower eukaryotes, including the soil nematode Caenorhabditis elegans, lack a DNA-PKcs homologue but are able to adapt to high NaCl. We show that cells of C. elegans adapted to high NaCl have many DNA breaks, similar to the mammalian cells adapted to high NaCl. Ku86 mutant C. elegans as well as C. elegans fed with cku86 dsRNA also display hypersensitivity to high NaCl, characterized by a reduced number of progeny and prolonged generation time in high NaCl. We propose that Ku86 ameliorates the effects of high NaCl-induced DNA breaks in adapted cells by supporting alignment of the broken ends of the DNA and thus maintaining integrity of the fragmented chromatin.
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Affiliation(s)
- Natalia I Dmitrieva
- Laboratory of Kidney and Electrolyte Metabolism, National Heart, Lung, and Blood Institute, and Experimental Immunology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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