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Dendritic cells induce Th2-mediated airway inflammatory responses to house dust mite via DNA-dependent protein kinase. Nat Commun 2015; 6:6224. [PMID: 25692509 PMCID: PMC4333735 DOI: 10.1038/ncomms7224] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 01/07/2015] [Indexed: 11/09/2022] Open
Abstract
DNA-dependent protein kinase (DNA-PK) mediates double-stranded DNA break repair, V(D)J recombination and immunoglobulin class switch recombination, as well as innate immune and pro-inflammatory responses. However, there is limited information regarding the role of DNA-PK in adaptive immunity mediated by dendritic cells (DCs), which are the primary antigen-presenting cells in allergic asthma. Here we show that house dust mite induces DNA-PK phosphorylation, which is a marker of DNA-PK activation, in DCs via the generation of intracellular reactive oxygen species. We also demonstrate that pharmacological inhibition of DNA-PK, as well as the specific deletion of DNA-PK in DCs, attenuates the induction of allergic sensitization and Th2 immunity via a mechanism that involves the impaired presentation of mite antigens. Furthermore, pharmacological inhibition of DNA-PK following antigen priming similarly reduces the manifestations of mite-induced airway disease. Collectively, these findings suggest that DNA-PK may be a potential target for treatment of allergic asthma.
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Belov OV, Krasavin EA, Lyashko MS, Batmunkh M, Sweilam NH. A quantitative model of the major pathways for radiation-induced DNA double-strand break repair. J Theor Biol 2015; 366:115-30. [DOI: 10.1016/j.jtbi.2014.09.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 09/11/2014] [Accepted: 09/17/2014] [Indexed: 12/11/2022]
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53
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Barnum KJ, O'Connell MJ. Molecular mechanisms involved in initiation of the DNA damage response. Mol Cell Oncol 2015; 2:e970065. [PMID: 27308403 PMCID: PMC4905235 DOI: 10.4161/23723548.2014.970065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Revised: 09/04/2014] [Accepted: 09/06/2014] [Indexed: 11/19/2022]
Abstract
DNA is subject to a wide variety of damage. In order to maintain genomic integrity, cells must respond to this damage by activating repair and cell cycle checkpoint pathways. The initiating events in the DNA damage response entail recognition of the lesion and the assembly of DNA damage response complexes at the DNA. Here, we review what is known about these processes for various DNA damage pathways.
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Affiliation(s)
- Kevin J Barnum
- Department of Oncological Sciences and the Graduate School of Biomedical Sciences; Icahn School of Medicine at Mount Sinai ; New York, NY USA
| | - Matthew J O'Connell
- Department of Oncological Sciences and the Graduate School of Biomedical Sciences; Icahn School of Medicine at Mount Sinai ; New York, NY USA
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The DNA-dependent protein kinase: A multifunctional protein kinase with roles in DNA double strand break repair and mitosis. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2014; 117:194-205. [PMID: 25550082 DOI: 10.1016/j.pbiomolbio.2014.12.003] [Citation(s) in RCA: 198] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/16/2014] [Accepted: 12/19/2014] [Indexed: 11/21/2022]
Abstract
The DNA-dependent protein kinase (DNA-PK) is a serine/threonine protein kinase composed of a large catalytic subunit (DNA-PKcs) and the Ku70/80 heterodimer. Over the past two decades, significant progress has been made in elucidating the role of DNA-PK in non-homologous end joining (NHEJ), the major pathway for repair of ionizing radiation-induced DNA double strand breaks in human cells and recently, additional roles for DNA-PK have been reported. In this review, we will describe the biochemistry, structure and function of DNA-PK, its roles in DNA double strand break repair and its newly described roles in mitosis and other cellular processes.
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Sowd GA, Mody D, Eggold J, Cortez D, Friedman KL, Fanning E. SV40 utilizes ATM kinase activity to prevent non-homologous end joining of broken viral DNA replication products. PLoS Pathog 2014; 10:e1004536. [PMID: 25474690 PMCID: PMC4256475 DOI: 10.1371/journal.ppat.1004536] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Accepted: 10/23/2014] [Indexed: 11/18/2022] Open
Abstract
Simian virus 40 (SV40) and cellular DNA replication rely on host ATM and ATR DNA damage signaling kinases to facilitate DNA repair and elicit cell cycle arrest following DNA damage. During SV40 DNA replication, ATM kinase activity prevents concatemerization of the viral genome whereas ATR activity prevents accumulation of aberrant genomes resulting from breakage of a moving replication fork as it converges with a stalled fork. However, the repair pathways that ATM and ATR orchestrate to prevent these aberrant SV40 DNA replication products are unclear. Using two-dimensional gel electrophoresis and Southern blotting, we show that ATR kinase activity, but not DNA-PKcs kinase activity, facilitates some aspects of double strand break (DSB) repair when ATM is inhibited during SV40 infection. To clarify which repair factors associate with viral DNA replication centers, we examined the localization of DSB repair proteins in response to SV40 infection. Under normal conditions, viral replication centers exclusively associate with homology-directed repair (HDR) and do not colocalize with non-homologous end joining (NHEJ) factors. Following ATM inhibition, but not ATR inhibition, activated DNA-PKcs and KU70/80 accumulate at the viral replication centers while CtIP and BLM, proteins that initiate 5′ to 3′ end resection during HDR, become undetectable. Similar to what has been observed during cellular DSB repair in S phase, these data suggest that ATM kinase influences DSB repair pathway choice by preventing the recruitment of NHEJ factors to replicating viral DNA. These data may explain how ATM prevents concatemerization of the viral genome and promotes viral propagation. We suggest that inhibitors of DNA damage signaling and DNA repair could be used during infection to disrupt productive viral DNA replication. Viruses from both Polyomaviridae and Papillomaviridae families share several characteristics. These include common modes of DNA replication and an accumulation of DNA damage signaling and repair proteins at replicating viral DNA. Several DNA repair proteins, with unknown functions during viral DNA replication, associate with the viral replication centers of the polyomavirus simian virus 40 (SV40). In this study we examined the mechanisms that regulate and recruit DNA repair machinery to replicating viral DNA during permissive SV40 infection. We found that the virus deploys DNA repair to broken viral DNA using cellular DNA damage signaling pathways. Our results shed light on why both Polyomaviridae and Papillomaviridae DNA replication elicits DNA damage signaling and repair. As no effective treatments currently exist for the Polyomaviridae family, our data identify pathways that might be therapeutically targeted to inhibit productive viral replication. Additionally, we categorize distinct functions for DNA repair and damage signaling pathways during viral replication. The results provide insights into how viruses exploit cellular processes to overwhelm the cell and propagate.
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Affiliation(s)
- Gregory A. Sowd
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (GAS); (KLF)
| | - Dviti Mody
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Joshua Eggold
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
| | - David Cortez
- Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
| | - Katherine L. Friedman
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail: (GAS); (KLF)
| | - Ellen Fanning
- Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee, United States of America
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Abdel-Fatah TMA, Arora A, Moseley P, Coveney C, Perry C, Johnson K, Kent C, Ball G, Chan S, Madhusudan S. ATM, ATR and DNA-PKcs expressions correlate to adverse clinical outcomes in epithelial ovarian cancers. BBA CLINICAL 2014; 2:10-7. [PMID: 26674120 PMCID: PMC4633921 DOI: 10.1016/j.bbacli.2014.08.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 07/29/2014] [Accepted: 08/01/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND Ataxia-telangiectasia mutated (ATM), ataxia-telangiectasia mutated and rad3 related (ATR) and DNA-dependent protein kinase catalytic sub-unit (DNA-PKcs) play critical roles in DNA damage response (DDR) by linking DNA damage sensing to DDR effectors that regulate cell cycle progression and DNA repair. Our objective was to evaluate if ATM, ATR and DNA-PKcs expressions could predict response to therapy and clinical outcome in epithelial ovarian cancers. METHODS We investigated ATM, ATR, and DNA-PKcs expressions in ovarian epithelial cancers [protein expression (n = 194 patients), mRNA expression (n = 156 patients)] and correlated to clinicopathological outcomes as well as expression of X-ray repair cross-complementing protein 1 (XRCC1), cell division cycle-45 (CDC45), cyclin-dependent kinase 1(CDK1) and Ki-67 in tumours. RESULTS High ATM protein expression was associated with serous cystadenocarcinomas (p = 0.021) and platinum resistance (p = 0.017). High DNA-PKcs protein expression was associated with serous cystadenocarcinomas (p = 0.006) and advanced stage tumours (p = 0.018). High ATM protein (p = 0.001), high ATM mRNA (p = 0.018), high DNA-PKcs protein (p = 0.002), high DNA-PKcs mRNA (p = 0.044) and high ATR protein (p = 0.001) expressions are correlated with poor ovarian cancer specific survival (OCSS). In multivariate Cox model, high DNA-PKcs (p = 0.006) and high ATR (p = 0.043) protein expressions remain independently associated with poor OCSS. CONCLUSIONS ATM, ATR and DNA-PKcs expressions may have prognostic and predictive significances in epithelial ovarian cancer. GENERAL SIGNIFICANCE The data presented here provides evidence that ATM, ATR and DNA-PKcs involved in DDR are not only promising biomarkers but are also rational targets for personalized therapy in ovarian cancer.
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Affiliation(s)
| | - Arvind Arora
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Paul Moseley
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Clare Coveney
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK
| | - Christina Perry
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK ; Laboratory of Molecular Oncology, Division of Oncology, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Kerstie Johnson
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Christopher Kent
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Graham Ball
- School of Science and Technology, Nottingham Trent University, Clifton Campus, Nottingham NG11 8NS, UK
| | - Stephen Chan
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK
| | - Srinivasan Madhusudan
- Department of Oncology, Nottingham University Hospitals, Nottingham NG5 1PB, UK ; Laboratory of Molecular Oncology, Division of Oncology, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham NG5 1PB, UK
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Abstract
UNLABELLED The DNA-dependent protein kinase (DNA-PK) is a pivotal component of the DNA repair machinery that governs the response to DNA damage, serving to maintain genome integrity. However, the DNA-PK kinase component was initially isolated with transcriptional complexes, and recent findings have illuminated the impact of DNA-PK-mediated transcriptional regulation on tumor progression and therapeutic response. DNA-PK expression has also been correlated with poor outcome in selected tumor types, further underscoring the importance of understanding its role in disease. Herein, the molecular and cellular consequences of DNA-PK are considered, with an eye toward discerning the rationale for therapeutic targeting of DNA-PK. SIGNIFICANCE Although DNA-PK is classically considered a component of damage response, recent findings illuminate damage-independent functions of DNA-PK that affect multiple tumor-associated pathways and provide a rationale for the development of novel therapeutic strategies.
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Affiliation(s)
- Jonathan F Goodwin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Department of Urology, Thomas Jefferson University, Philadelphia, Pennsylvania. Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania. Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
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58
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Abstract
UNLABELLED The DNA-dependent protein kinase (DNA-PK) is a pivotal component of the DNA repair machinery that governs the response to DNA damage, serving to maintain genome integrity. However, the DNA-PK kinase component was initially isolated with transcriptional complexes, and recent findings have illuminated the impact of DNA-PK-mediated transcriptional regulation on tumor progression and therapeutic response. DNA-PK expression has also been correlated with poor outcome in selected tumor types, further underscoring the importance of understanding its role in disease. Herein, the molecular and cellular consequences of DNA-PK are considered, with an eye toward discerning the rationale for therapeutic targeting of DNA-PK. SIGNIFICANCE Although DNA-PK is classically considered a component of damage response, recent findings illuminate damage-independent functions of DNA-PK that affect multiple tumor-associated pathways and provide a rationale for the development of novel therapeutic strategies.
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Affiliation(s)
- Jonathan F Goodwin
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Karen E Knudsen
- Department of Cancer Biology, Thomas Jefferson University, Philadelphia, Pennsylvania. Department of Urology, Thomas Jefferson University, Philadelphia, Pennsylvania. Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania. Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania.
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DNA repair pathways in trypanosomatids: from DNA repair to drug resistance. Microbiol Mol Biol Rev 2014; 78:40-73. [PMID: 24600040 DOI: 10.1128/mmbr.00045-13] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
All living organisms are continuously faced with endogenous or exogenous stress conditions affecting genome stability. DNA repair pathways act as a defense mechanism, which is essential to maintain DNA integrity. There is much to learn about the regulation and functions of these mechanisms, not only in human cells but also equally in divergent organisms. In trypanosomatids, DNA repair pathways protect the genome against mutations but also act as an adaptive mechanism to promote drug resistance. In this review, we scrutinize the molecular mechanisms and DNA repair pathways which are conserved in trypanosomatids. The recent advances made by the genome consortiums reveal the complete genomic sequences of several pathogens. Therefore, using bioinformatics and genomic sequences, we analyze the conservation of DNA repair proteins and their key protein motifs in trypanosomatids. We thus present a comprehensive view of DNA repair processes in trypanosomatids at the crossroads of DNA repair and drug resistance.
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60
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Adverse prognostic and predictive significance of low DNA-dependent protein kinase catalytic subunit (DNA-PKcs) expression in early-stage breast cancers. Breast Cancer Res Treat 2014; 146:309-20. [PMID: 24972688 DOI: 10.1007/s10549-014-3035-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 06/10/2014] [Indexed: 10/25/2022]
Abstract
DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a serine threonine kinase belonging to the PIKK family (phosphoinositide 3-kinase-like-family of protein kinase), is a critical component of the non-homologous end-joining pathway required for the repair of DNA double-strand breaks. DNA-PKcs may be involved in breast cancer pathogenesis. We evaluated clinicopathological significance of DNA-PKcs protein expression in 1,161 tumours and DNA-PKcs mRNA expression in 1,950 tumours. We correlated DNA-PKcs to markers of aggressive phenotypes, DNA repair, apoptosis, cell cycle regulation and survival. Low DNA-PKcs protein expression was associated with higher tumour grade, higher mitotic index, tumour de-differentiation and tumour type (ps < 0.05). The absence of BRCA1, low XRCC1, low SMUG1, low APE1 and low Polβ was also more likely in low DNA-PKcs expressing tumours (ps < 0.05). Low DNA-PKcs protein expression was significantly associated with worse breast cancer-specific survival (BCSS) in univariate and multivariate analysis (ps < 0.01). At the mRNA level, similarly, low DNA-PKcs was associated with poor BCSS. In patients with ER-positive tumours who received endocrine therapy, low DNA-PKcs (protein and mRNA) was associated with poor survival. In ER-negative patients, low DNA-PKcs mRNA remains significantly associated with adverse outcome. Our study suggests that low DNA-PKcs expression may have prognostic and predictive significance in breast cancers.
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61
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Douglas P, Ye R, Trinkle-Mulcahy L, Neal J, De Wever V, Morrice N, Meek K, Lees-Miller S. Polo-like kinase 1 (PLK1) and protein phosphatase 6 (PP6) regulate DNA-dependent protein kinase catalytic subunit (DNA-PKcs) phosphorylation in mitosis. Biosci Rep 2014; 34:e00113. [PMID: 24844881 PMCID: PMC4069685 DOI: 10.1042/bsr20140051] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 04/25/2014] [Accepted: 05/20/2014] [Indexed: 01/28/2023] Open
Abstract
The protein kinase activity of the DNA-PKcs (DNA-dependent protein kinase catalytic subunit) and its autophosphorylation are critical for DBS (DNA double-strand break) repair via NHEJ (non-homologous end-joining). Recent studies have shown that depletion or inactivation of DNA-PKcs kinase activity also results in mitotic defects. DNA-PKcs is autophosphorylated on Ser2056, Thr2647 and Thr2609 in mitosis and phosphorylated DNA-PKcs localize to centrosomes, mitotic spindles and the midbody. DNA-PKcs also interacts with PP6 (protein phosphatase 6), and PP6 has been shown to dephosphorylate Aurora A kinase in mitosis. Here we report that DNA-PKcs is phosphorylated on Ser3205 and Thr3950 in mitosis. Phosphorylation of Thr3950 is DNA-PK-dependent, whereas phosphorylation of Ser3205 requires PLK1 (polo-like kinase 1). Moreover, PLK1 phosphorylates DNA-PKcs on Ser3205 in vitro and interacts with DNA-PKcs in mitosis. In addition, PP6 dephosphorylates DNA-PKcs at Ser3205 in mitosis and after IR (ionizing radiation). DNA-PKcs also phosphorylates Chk2 on Thr68 in mitosis and both phosphorylation of Chk2 and autophosphorylation of DNA-PKcs in mitosis occur in the apparent absence of Ku and DNA damage. Our findings provide mechanistic insight into the roles of DNA-PKcs and PP6 in mitosis and suggest that DNA-PKcs' role in mitosis may be mechanistically distinct from its well-established role in NHEJ.
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Key Words
- dna-dependent protein kinase
- midbody
- mitosis
- polo-like protein kinase 1
- protein phosphatase 6
- atm, ataxia telangiectasia mutated
- chk2, checkpoint kinase 2
- dmem, dulbecco’s modified eagle’s medium
- dna-pkcs, dna-dependent protein kinase catalytic subunit
- dapi, 4′,6-diamidino-2-phenylindole
- dsb, dna double-strand break
- fha, forkhead associated
- gfp, green fluorescent protein
- ir, ionizing radiation
- mem, minimum essential medium alpha
- nhej, non-homologous end-joining
- pipes, 1,4-piperazinediethanesulfonic acid
- plk1, polo-like kinase-1
- pp6, protein phosphatase 6
- sirna, small interfering rna
- tpx2, targeting protein for xklp2
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Affiliation(s)
- Pauline Douglas
- *Departments of Biochemistry & Molecular Biology and Oncology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada, T2N 4N1
| | - Ruiqiong Ye
- *Departments of Biochemistry & Molecular Biology and Oncology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada, T2N 4N1
| | - Laura Trinkle-Mulcahy
- †Department of Cellular & Molecular Medicine and Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada, K1H 8M5
| | - Jessica A. Neal
- ‡Departments of Pathobiology & Diagnostic Investigation, and Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, U.S.A
| | - Veerle De Wever
- §Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, AB, Canada T2N 4N1
| | - Nick A. Morrice
- ∥Beatson Institute for Cancer Research, Glasgow G61 1BD Scotland, U.K
| | - Katheryn Meek
- ‡Departments of Pathobiology & Diagnostic Investigation, and Microbiology & Molecular Genetics, Michigan State University, East Lansing, Michigan, U.S.A
| | - Susan P. Lees-Miller
- *Departments of Biochemistry & Molecular Biology and Oncology, Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive NW, Calgary, AB, Canada, T2N 4N1
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Kakarougkas A, Jeggo PA. DNA DSB repair pathway choice: an orchestrated handover mechanism. Br J Radiol 2014; 87:20130685. [PMID: 24363387 DOI: 10.1259/bjr.20130685] [Citation(s) in RCA: 205] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
DNA double strand breaks (DSBs) are potential lethal lesions but can also lead to chromosome rearrangements, a step promoting carcinogenesis. DNA non-homologous end-joining (NHEJ) is the major DSB rejoining process and occurs in all cell cycle stages. Homologous recombination (HR) can additionally function to repair irradiation-induced two-ended DSBs in G2 phase. In mammalian cells, HR predominantly uses a sister chromatid as a template for DSB repair; thus HR functions only in late S/G2 phase. Here, we review current insight into the interplay between HR and NHEJ in G2 phase. We argue that NHEJ represents the first choice pathway, repairing approximately 80% of X-ray-induced DSBs with rapid kinetics. However, a subset of DSBs undergoes end resection and repair by HR. 53BP1 restricts resection, thereby promoting NHEJ. During the switch from NHEJ to HR, 53BP1 is repositioned to the periphery of enlarged irradiation-induced foci (IRIF) via a BRCA1-dependent process. K63-linked ubiquitin chains, which also form at IRIF, are also repositioned as well as receptor-associated protein 80 (RAP80), a ubiquitin binding protein. RAP80 repositioning requires POH1, a proteasome component. Thus, the interfacing barriers to HR, 53BP1 and RAP80 are relieved by POH1 and BRCA1, respectively. Removal of RAP80 from the IRIF core is required for loss of the ubiquitin chains and 53BP1, and for efficient replication protein A foci formation. We propose that NHEJ is used preferentially to HR because it is a compact process that does not necessitate extensive chromatin changes in the DSB vicinity.
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Affiliation(s)
- A Kakarougkas
- Genome Damage and Stability Centre, University of Sussex, Brighton, UK
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63
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Abstract
Chromosome translocations are catastrophic genomic events and often play key roles in tumorigenesis. Yet the biogenesis of chromosome translocations is remarkably poorly understood. Recent work has delineated several distinct mechanistic steps in the formation of translocations, and it has become apparent that non-random spatial genome organization, DNA repair pathways and chromatin features, including histone marks and the dynamic motion of broken chromatin, are critical for determining translocation frequency and partner selection.
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Affiliation(s)
| | - Tom Misteli
- National Cancer Institute, Bethesda, Maryland 20892, USA
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64
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Flassig RJ, Maubach G, Täger C, Sundmacher K, Naumann M. Experimental design, validation and computational modeling uncover DNA damage sensing by DNA-PK and ATM. MOLECULAR BIOSYSTEMS 2014; 10:1978-86. [PMID: 24833308 DOI: 10.1039/c4mb00093e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Reliable and efficient detection of DNA damage constitutes a vital capability of human cells to maintain genome stability. Following DNA damage, the histone variant H2AX becomes rapidly phosphorylated by the DNA damage response kinases DNA-PKcs and ATM. H2AX phosphorylation plays a central role in signal amplification leading to chromatin remodeling and DNA repair initiation. The contribution of DNA-PKcs and ATM to H2AX phosphorylation is however puzzling. Although ATM is required, DNA-PKcs can substitute for it. Here we analyze the interplay between DNA-PKcs and ATM with a computational model derived by an iterative workflow: switching between experimental design, experiment and model analysis, we generated an extensive set of time-resolved data and identified a conclusive dynamic signaling model out of several alternatives. Our work shows that DNA-PKcs and ATM enforce a biphasic H2AX phosphorylation. DNA-PKcs can be associated to the initial, and ATM to the succeeding phosphorylation phase of H2AX resulting into a signal persistence detection function for reliable damage sensing. Further, our model predictions emphasize that DNA-PKcs inhibition significantly delays H2AX phosphorylation and associated DNA repair initiation.
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Affiliation(s)
- R J Flassig
- Process Systems Engineering Group, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany.
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65
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Liu Q, Turner KM, Alfred Yung WK, Chen K, Zhang W. Role of AKT signaling in DNA repair and clinical response to cancer therapy. Neuro Oncol 2014; 16:1313-23. [PMID: 24811392 DOI: 10.1093/neuonc/nou058] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Effective cancer treatment has been limited by the emergence of resistant cancer cells. The results of many studies indicate that AKT activation plays an important role in the acquisition of resistance to anticancer therapy. AKT is a critical effector serine/threonine kinase in the receptor tyrosine kinase/phosphatase and tensin homolog/phospho-inositide 3-kinase pathway and controls a myriad of cellular functions. Activation of AKT not only supports tumor growth and progression but also contributes to tumor-cell evasion of the cytotoxic effects of cancer therapy through many avenues including the promotion of anti-apoptosis, proliferation, and migration and regulation of the cell cycle. Accumulating evidence has implicated AKT as a direct participant in the DNA damage response and repair induced by commonly used genotoxic agents. In this review, we discuss the molecular mechanisms by which genotoxic agents activate AKT and therefore contribute to resistance to cancer therapeutics, with particular emphasis on DNA repair.
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Affiliation(s)
- Qun Liu
- Department of Neuro-Oncology, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (Q.L.); Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas (K.M.T., W.Z.); Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (W.K.A.Y.); Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (K.C.)
| | - Kristen M Turner
- Department of Neuro-Oncology, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (Q.L.); Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas (K.M.T., W.Z.); Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (W.K.A.Y.); Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (K.C.)
| | - W K Alfred Yung
- Department of Neuro-Oncology, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (Q.L.); Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas (K.M.T., W.Z.); Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (W.K.A.Y.); Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (K.C.)
| | - Kexin Chen
- Department of Neuro-Oncology, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (Q.L.); Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas (K.M.T., W.Z.); Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (W.K.A.Y.); Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (K.C.)
| | - Wei Zhang
- Department of Neuro-Oncology, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (Q.L.); Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas (K.M.T., W.Z.); Department of Neuro-Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (W.K.A.Y.); Department of Epidemiology and Biostatistics, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin, China (K.C.)
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Eid MMA, Maeda K, Almofty SA, Singh SK, Shimoda M, Sakaguchi N. GANP regulates the choice of DNA repair pathway by DNA-PKcs interaction in AID-dependent IgV region diversification. THE JOURNAL OF IMMUNOLOGY 2014; 192:5529-39. [PMID: 24808370 DOI: 10.4049/jimmunol.1400021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
RNA export factor germinal center-associated nuclear protein (GANP) interacts with activation-induced cytidine deaminase (AID) and shepherds it from the cytoplasm to the nucleus and toward the IgV region loci in B cells. In this study, we demonstrate a role for GANP in the repair of AID-initiated DNA damage in chicken DT40 B cells to generate IgV region diversity by gene conversion and somatic hypermutation. GANP plays a positive role in IgV region diversification of DT40 B cells in a nonhomologous end joining-proficient state. DNA-PKcs physically interacts with GANP, and this interaction is dissociated by dsDNA breaks induced by a topoisomerase II inhibitor, etoposide, or AID overexpression. GANP affects the choice of DNA repair mechanism in B cells toward homologous recombination rather than nonhomologous end joining repair. Thus, GANP presumably plays a critical role in protection of the rearranged IgV loci by favoring homologous recombination of the DNA breaks under accelerated AID recruitment.
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Affiliation(s)
- Mohammed Mansour Abbas Eid
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Kazuhiko Maeda
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Sarah Ameen Almofty
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Shailendra Kumar Singh
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Mayuko Shimoda
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
| | - Nobuo Sakaguchi
- Department of Immunology, Graduate School of Life Sciences, Kumamoto University, Kumamoto 860-8556, Japan
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67
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The repair of environmentally relevant DNA double strand breaks caused by high linear energy transfer irradiation – No simple task. DNA Repair (Amst) 2014; 17:64-73. [DOI: 10.1016/j.dnarep.2014.01.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 01/10/2014] [Accepted: 01/24/2014] [Indexed: 01/03/2023]
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68
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Radhakrishnan SK, Jette N, Lees-Miller SP. Non-homologous end joining: emerging themes and unanswered questions. DNA Repair (Amst) 2014; 17:2-8. [PMID: 24582502 PMCID: PMC4084493 DOI: 10.1016/j.dnarep.2014.01.009] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Revised: 01/03/2014] [Accepted: 01/24/2014] [Indexed: 11/25/2022]
Abstract
Non-homologous end joining (NHEJ) is the major pathway for the repair of ionizing radiation induced DNA double strand breaks in human cells. Here, we discuss current insights into the mechanism of NHEJ and the interplay between NHEJ and other pathways for repair of IR-induced DNA damage.
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Affiliation(s)
- Sarvan Kumar Radhakrishnan
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada T2N 4N1
| | - Nicholas Jette
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada T2N 4N1
| | - Susan P Lees-Miller
- Department of Biochemistry & Molecular Biology and Southern Alberta Cancer Research Institute, University of Calgary, 3330 Hospital Drive, NW, Calgary, Alberta, Canada T2N 4N1.
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69
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Williams GJ, Hammel M, Radhakrishnan SK, Ramsden D, Lees-Miller SP, Tainer JA. Structural insights into NHEJ: building up an integrated picture of the dynamic DSB repair super complex, one component and interaction at a time. DNA Repair (Amst) 2014; 17:110-20. [PMID: 24656613 PMCID: PMC4102006 DOI: 10.1016/j.dnarep.2014.02.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/27/2014] [Accepted: 02/10/2014] [Indexed: 10/25/2022]
Abstract
Non-homologous end joining (NHEJ) is the major pathway for repair of DNA double-strand breaks (DSBs) in human cells. NHEJ is also needed for V(D)J recombination and the development of T and B cells in vertebrate immune systems, and acts in both the generation and prevention of non-homologous chromosomal translocations, a hallmark of genomic instability and many human cancers. X-ray crystal structures, cryo-electron microscopy envelopes, and small angle X-ray scattering (SAXS) solution conformations and assemblies are defining most of the core protein components for NHEJ: Ku70/Ku80 heterodimer; the DNA dependent protein kinase catalytic subunit (DNA-PKcs); the structure-specific endonuclease Artemis along with polynucleotide kinase/phosphatase (PNKP), aprataxin and PNKP related protein (APLF); the scaffolding proteins XRCC4 and XLF (XRCC4-like factor); DNA polymerases, and DNA ligase IV (Lig IV). The dynamic assembly of multi-protein NHEJ complexes at DSBs is regulated in part by protein phosphorylation. The basic steps of NHEJ have been biochemically defined to require: (1) DSB detection by the Ku heterodimer with subsequent DNA-PKcs tethering to form the DNA-PKcs-Ku-DNA complex (termed DNA-PK), (2) lesion processing, and (3) DNA end ligation by Lig IV, which functions in complex with XRCC4 and XLF. The current integration of structures by combined methods is resolving puzzles regarding the mechanisms, coordination and regulation of these three basic steps. Overall, structural results suggest the NHEJ system forms a flexing scaffold with the DNA-PKcs HEAT repeats acting as compressible macromolecular springs suitable to store and release conformational energy to apply forces to regulate NHEJ complexes and the DNA substrate for DNA end protection, processing, and ligation.
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Affiliation(s)
- Gareth J Williams
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Michal Hammel
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Sarvan Kumar Radhakrishnan
- Department of Biochemistry & Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, T2 N 4N1 Canada
| | - Dale Ramsden
- Lineberger Comprehensive Cancer Center, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 2759, United States
| | - Susan P Lees-Miller
- Department of Biochemistry & Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, T2 N 4N1 Canada; Department of Oncology, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, T2 N 4N1 Canada.
| | - John A Tainer
- Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States; Department of Molecular Biology, Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, United States.
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70
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Pears CJ, Lakin ND. Emerging models for DNA repair: Dictyostelium discoideum as a model for nonhomologous end-joining. DNA Repair (Amst) 2014; 17:121-31. [DOI: 10.1016/j.dnarep.2014.01.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Revised: 01/09/2014] [Accepted: 01/24/2014] [Indexed: 02/03/2023]
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71
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Farber-Katz SE, Dippold HC, Buschman MD, Peterman MC, Xing M, Noakes CJ, Tat J, Ng MM, Rahajeng J, Cowan DM, Fuchs GJ, Zhou H, Field SJ. DNA damage triggers Golgi dispersal via DNA-PK and GOLPH3. Cell 2014; 156:413-27. [PMID: 24485452 DOI: 10.1016/j.cell.2013.12.023] [Citation(s) in RCA: 168] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Revised: 09/04/2013] [Accepted: 11/14/2013] [Indexed: 01/29/2023]
Abstract
The response to DNA damage, which regulates nuclear processes such as DNA repair, transcription, and cell cycle, has been studied thoroughly. However, the cytoplasmic response to DNA damage is poorly understood. Here, we demonstrate that DNA damage triggers dramatic reorganization of the Golgi, resulting in its dispersal throughout the cytoplasm. We further show that DNA-damage-induced Golgi dispersal requires GOLPH3/MYO18A/F-actin and the DNA damage protein kinase, DNA-PK. In response to DNA damage, DNA-PK phosphorylates GOLPH3, resulting in increased interaction with MYO18A, which applies a tensile force to the Golgi. Interference with the Golgi DNA damage response by depletion of DNA-PK, GOLPH3, or MYO18A reduces survival after DNA damage, whereas overexpression of GOLPH3, as is observed frequently in human cancers, confers resistance to killing by DNA-damaging agents. Identification of the DNA-damage-induced Golgi response reveals an unexpected pathway through DNA-PK, GOLPH3, and MYO18A that regulates cell survival following DNA damage.
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Affiliation(s)
- Suzette E Farber-Katz
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - Holly C Dippold
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - Matthew D Buschman
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - Marshall C Peterman
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - Mengke Xing
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - Christopher J Noakes
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - John Tat
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - Michelle M Ng
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - Juliati Rahajeng
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - David M Cowan
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA
| | - Greg J Fuchs
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093-0653, USA
| | - Huilin Zhou
- Ludwig Institute for Cancer Research, University of California, San Diego, La Jolla, CA 92093-0653, USA
| | - Seth J Field
- Division of Endocrinology and Metabolism, Department of Medicine, University of California, San Diego, La Jolla, CA 92093-0707, USA.
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72
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Unraveling the complexities of DNA-dependent protein kinase autophosphorylation. Mol Cell Biol 2014; 34:2162-75. [PMID: 24687855 DOI: 10.1128/mcb.01554-13] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
DNA-dependent protein kinase (DNA-PK) orchestrates DNA repair by regulating access to breaks through autophosphorylations within two clusters of sites (ABCDE and PQR). Blocking ABCDE phosphorylation (by alanine mutation) imparts a dominant negative effect, rendering cells hypersensitive to agents that cause DNA double-strand breaks. Here, a mutational approach is used to address the mechanistic basis of this dominant negative effect. Blocking ABCDE phosphorylation hypersensitizes cells to most types of DNA damage (base damage, cross-links, breaks, and damage induced by replication stress), suggesting that DNA-PK binds DNA ends that result from many DNA lesions and that blocking ABCDE phosphorylation sequesters these DNA ends from other repair pathways. This dominant negative effect requires DNA-PK's catalytic activity, as well as phosphorylation of multiple (non-ABCDE) DNA-PK catalytic subunit (DNA-PKcs) sites. PSIPRED analysis indicates that the ABCDE sites are located in the only contiguous extended region of this huge protein that is predicted to be disordered, suggesting a regulatory role(s) and perhaps explaining the large impact ABCDE phosphorylation has on the enzyme's function. Moreover, additional sites in this disordered region contribute to the ABCDE cluster. These data, coupled with recent structural data, suggest a model whereby early phosphorylations promote initiation of nonhomologous end joining (NHEJ), whereas ABCDE phosphorylations, potentially located in a "hinge" region between the two domains, lead to regulated conformational changes that initially promote NHEJ and eventually disengage NHEJ.
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73
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Shibata A, Jeggo PA. DNA double-strand break repair in a cellular context. Clin Oncol (R Coll Radiol) 2014; 26:243-9. [PMID: 24630811 DOI: 10.1016/j.clon.2014.02.004] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Revised: 02/05/2014] [Accepted: 02/10/2014] [Indexed: 12/20/2022]
Abstract
Substantial insight into the mechanisms responding to DNA double-strand breaks has been gained from molecular, biochemical and structural approaches. Attention is now focusing on understanding the interplay between the pathways, how they interface through the cell cycle and the communication with other DNA transactions, such as replication and transcription. Understanding these aspects will facilitate an assessment of how cancer cells have modified these processes to achieve unlimited proliferative capacity and adaptability, and pave the way to identify targets suitable for therapy. Here, we briefly overview the processes responding to double-strand breaks and discuss our current understanding of their interplay in a cellular context.
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Affiliation(s)
- A Shibata
- Advanced Scientific Research Leaders Development Unit, Gunma University, Maebashi, Gunma, Japan
| | - P A Jeggo
- Genome Damage and Stability Centre, Life Sciences at University of Sussex, Brighton, UK.
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74
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De Azevêdo Silva J, Pancotto JAT, Donadi EA, Crovella S, Sandrin-Garcia P. LIG4 and RAD52 DNA repair genes polymorphisms and systemic lupus erythematosus. Mol Biol Rep 2014; 41:2249-56. [PMID: 24415301 DOI: 10.1007/s11033-014-3076-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 01/04/2014] [Indexed: 12/12/2022]
Abstract
Systemic lupus erythematosus (SLE) is a complex autoimmune disorder with a strong genetic background. Nevertheless, SLE might also be triggered due to environmental factors, such as UV light exposure. DNA double strand breaks (DSBs) may be induced secondarily by UV radiation, increasing DNA immunogenicity and in SLE patients DNA repair is diminished, allowing the accumulation of DSBs and genomic instability. LIG4 and RAD52 genes play important roles in DNA repair mechanisms and a recent microarray analysis showed their differential expression in active SLE patients. In this study we investigated a potential association between LIG4 and RAD52 single nucleotide polymorphisms (SNPs) and SLE predisposition in a Southeast Brazilian population. We assessed four Tag SNPs in LIG4 and three in RAD52 gene region, encompassing most of the gene sequence, in 158 SLE patients and 212 healthy controls. We also performed SNPs analysis considering clinical manifestation, gender and ethnicity in SLE patients. Our data did not show association between LIG4 and RAD52 SNPs and SLE, its clinical manifestations or ethnicity in the tested population. The analysis regarding ethnicity and SLE clinical manifestations indicated Caucasian-derived patients as more susceptible to cutaneous and hematological alterations than the African-derived. To our knowledge, this is the first association study involving LIG4 and RAD52 genes and SLE predisposition.
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Affiliation(s)
- Jaqueline De Azevêdo Silva
- Department of Genetics, Federal University of Pernambuco, Av. Moraes Rego, 1235, Recife, Pernambuco, CEP 50740-600, Brazil
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75
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Interplay between the cell cycle and double-strand break response in mammalian cells. Methods Mol Biol 2014; 1170:41-59. [PMID: 24906308 DOI: 10.1007/978-1-4939-0888-2_3] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The cell cycle is intimately associated with the ability of cells to sense and respond to and repair DNA damage. Understanding how cell cycle progression, particularly DNA replication and cell division, are regulated and how DNA damage can affect these processes has been the subject of intense research. Recent evidence suggests that the repair of DNA damage is regulated by the cell cycle, and that cell cycle factors are closely associated with repair factors and participate in cellular decisions regarding how to respond to and repair damage. Precise regulation of cell cycle progression in the presence of DNA damage is essential to maintain genomic stability and avoid the accumulation of chromosomal aberrations that can promote tumor formation. In this review, we discuss the current understanding of how mammalian cells induce cell cycle checkpoints in response to DNA double-strand breaks. In addition, we discuss how cell cycle factors modulate DNA repair pathways to facilitate proper repair of DNA lesions.
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76
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Lin SF, Lin JD, Chou TC, Huang YY, Wong RJ. Utility of a histone deacetylase inhibitor (PXD101) for thyroid cancer treatment. PLoS One 2013; 8:e77684. [PMID: 24155971 PMCID: PMC3796495 DOI: 10.1371/journal.pone.0077684] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2013] [Accepted: 09/03/2013] [Indexed: 01/08/2023] Open
Abstract
Background We evaluated the therapeutic effects of the histone deacetylase inhibitor PXD101 alone and in combination with conventional chemotherapy in treating thyroid cancer. Methodology/Principal Findings We studied eight cell lines from four types of thyroid cancer (papillary, follicular, anaplastic and medullary). The cytotoxicity of PXD101 alone and in combination with three conventional chemotherapeutic agents (doxorubicin, paclitaxel and docetaxel) was measured using LDH assay. Western blot assessed expression of acetylation of histone H3, histone H4 and tubulin, proteins associated with apoptosis, RAS/RAF/ERK and PI3K/AKT/mTOR signaling pathways, DNA damage and repair. Apoptosis and intracellular reactive oxygen species (ROS) were measured by flow cytometry. Mice bearing flank anaplastic thyroid cancers (ATC) were daily treated with intraperitoneal injection of PXD101 for 5 days per week. PXD101 effectively inhibited thyroid cancer cell proliferation in a dose-dependent manner. PXD101 induced ROS accumulation and inhibited RAS/RAF/ERK and PI3K/mTOR pathways in sensitive cells. Double-stranded DNA damage and apoptosis were induced by PXD101 in both sensitive and resistant cell lines. PXD101 retarded growth of 8505C ATC xenograft tumors with promising safety. Combination therapy of PXD101with doxorubicin and paclitaxel demonstrated synergistic effects against four ATC lines invitro. Conclusions PXD101 represses thyroid cancer proliferation and has synergistic effects in combination with doxorubicin and paclitaxel in treating ATC. These findings support clinical trials using PXD101 for patients with this dismal disease.
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Affiliation(s)
- Shu-Fu Lin
- Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Jen-Der Lin
- Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan, ROC
| | - Ting-Chao Chou
- Laboratory of Preclinical Pharmacology Core, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Yu-Yao Huang
- Department of Internal Medicine, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan, ROC
- * E-mail: (YH); (RJW)
| | - Richard J. Wong
- Department of Surgery, Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
- * E-mail: (YH); (RJW)
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77
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Studying the cerebellar DNA damage response in the tissue culture dish. Mech Ageing Dev 2013; 134:496-505. [DOI: 10.1016/j.mad.2013.04.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2013] [Revised: 03/29/2013] [Accepted: 04/01/2013] [Indexed: 11/30/2022]
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78
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Deriano L, Roth DB. Modernizing the nonhomologous end-joining repertoire: alternative and classical NHEJ share the stage. Annu Rev Genet 2013; 47:433-55. [PMID: 24050180 DOI: 10.1146/annurev-genet-110711-155540] [Citation(s) in RCA: 314] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
DNA double-strand breaks (DSBs) are common lesions that continually threaten genomic integrity. Failure to repair a DSB has deleterious consequences, including cell death. Misrepair is also fraught with danger, especially inappropriate end-joining events, which commonly underlie oncogenic transformation and can scramble the genome. Canonically, cells employ two basic mechanisms to repair DSBs: homologous recombination (HR) and the classical nonhomologous end-joining pathway (cNHEJ). More recent experiments identified a highly error-prone NHEJ pathway, termed alternative NHEJ (aNHEJ), which operates in both cNHEJ-proficient and cNHEJ-deficient cells. aNHEJ is now recognized to catalyze many genome rearrangements, some leading to oncogenic transformation. Here, we review the mechanisms of cNHEJ and aNHEJ, their interconnections with the DNA damage response (DDR), and the mechanisms used to determine which of the three DSB repair pathways is used to heal a particular DSB. We briefly review recent clinical applications involving NHEJ and NHEJ inhibitors.
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Affiliation(s)
- Ludovic Deriano
- Departments of Immunology and Genomes & Genetics, Institut Pasteur, CNRS-URA 1961, 75015 Paris, France;
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79
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Muralidharan S, Mandrekar P. Cellular stress response and innate immune signaling: integrating pathways in host defense and inflammation. J Leukoc Biol 2013; 94:1167-84. [PMID: 23990626 DOI: 10.1189/jlb.0313153] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Extensive research in the past decade has identified innate immune recognition receptors and intracellular signaling pathways that culminate in inflammatory responses. Besides its role in cytoprotection, the importance of cell stress in inflammation and host defense against pathogens is emerging. Recent studies have shown that proteins in cellular stress responses, including the heat shock response, ER stress response, and DNA damage response, interact with and regulate signaling intermediates involved in the activation of innate and adaptive immune responses. The effect of such regulation by cell stress proteins may dictate the inflammatory profile of the immune response during infection and disease. In this review, we describe the regulation of innate immune cell activation by cell stress pathways, present detailed descriptions of the types of stress response proteins and their crosstalk with immune signaling intermediates that are essential in host defense, and illustrate the relevance of these interactions in diseases characteristic of aberrant immune responses, such as chronic inflammatory diseases, autoimmune disorders, and cancer. Understanding the crosstalk between cellular stress proteins and immune signaling may have translational implications for designing more effective regimens to treat immune disorders.
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Affiliation(s)
- Sujatha Muralidharan
- 1.LRB 221, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605.
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80
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Goodarzi AA, Jeggo PA. The repair and signaling responses to DNA double-strand breaks. ADVANCES IN GENETICS 2013; 82:1-45. [PMID: 23721719 DOI: 10.1016/b978-0-12-407676-1.00001-9] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
A DNA double-strand break (DSB) has long been recognized as a severe cellular lesion, potentially representing an initiating event for carcinogenesis or cell death. The evolution of DSB repair pathways as well as additional processes, such as cell cycle checkpoint arrest, to minimize the cellular impact of DSB formation was, therefore, not surprising. However, the depth and complexity of the DNA damage responses being revealed by current studies were unexpected. Perhaps the most surprising finding to emerge is the dramatic changes to chromatin architecture that arise in the DSB vicinity. In this review, we overview the cellular response to DSBs focusing on DNA repair pathways and the interface between them. We consider additional events which impact upon these DSB repair pathways, including regulated arrest of cell cycle progression and chromatin architecture alterations. Finally, we discuss the impact of defects in these processes to human disease.
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Affiliation(s)
- Aaron A Goodarzi
- Department of Biochemistry & Molecular Biology, Southern Alberta Cancer Research Institute, University of Calgary, Calgary, Alberta, Canada
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81
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Roukos V, Voss TC, Schmidt CK, Lee S, Wangsa D, Misteli T. Spatial dynamics of chromosome translocations in living cells. Science 2013; 341:660-4. [PMID: 23929981 DOI: 10.1126/science.1237150] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Chromosome translocations are a hallmark of cancer cells. We have developed an experimental system to visualize the formation of translocations in living cells and apply it to characterize the spatial and dynamic properties of translocation formation. We demonstrate that translocations form within hours of the occurrence of double-strand breaks (DSBs) and that their formation is cell cycle-independent. Translocations form preferentially between prepositioned genome elements, and perturbation of key factors of the DNA repair machinery uncouples DSB pairing from translocation formation. These observations generate a spatiotemporal framework for the formation of translocations in living cells.
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82
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Taleei R, Nikjoo H. Biochemical DSB-repair model for mammalian cells in G1 and early S phases of the cell cycle. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 756:206-12. [DOI: 10.1016/j.mrgentox.2013.06.004] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Accepted: 06/06/2013] [Indexed: 11/24/2022]
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83
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Woodbine L, Neal JA, Sasi NK, Shimada M, Deem K, Coleman H, Dobyns WB, Ogi T, Meek K, Davies EG, Jeggo PA. PRKDC mutations in a SCID patient with profound neurological abnormalities. J Clin Invest 2013; 123:2969-80. [PMID: 23722905 DOI: 10.1172/jci67349] [Citation(s) in RCA: 109] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2012] [Accepted: 03/28/2013] [Indexed: 12/30/2022] Open
Abstract
The DNA-dependent protein kinase catalytic subunit (DNA-PKcs; encoded by PRKDC) functions in DNA non-homologous end-joining (NHEJ), the major DNA double strand break (DSB) rejoining pathway. NHEJ also functions during lymphocyte development, joining V(D)J recombination intermediates during antigen receptor gene assembly. Here, we describe a patient with compound heterozygous mutations in PRKDC, low DNA-PKcs expression, barely detectable DNA-PK kinase activity, and impaired DSB repair. In a heterologous expression system, we found that one of the PRKDC mutations inactivated DNA-PKcs, while the other resulted in dramatically diminished but detectable residual function. The patient suffered SCID with reduced or absent T and B cells, as predicted from PRKDC-deficient animal models. Unexpectedly, the patient was also dysmorphic; showed severe growth failure, microcephaly, and seizures; and had profound, globally impaired neurological function. MRI scans revealed microcephaly-associated cortical and hippocampal dysplasia and progressive atrophy over 2 years of life. These neurological features were markedly more severe than those observed in patients with deficiencies in other NHEJ proteins. Although loss of DNA-PKcs in mice, dogs, and horses was previously shown not to impair neuronal development, our findings demonstrate a stringent requirement for DNA-PKcs during human neuronal development and suggest that high DNA-PK protein expression is required to sustain efficient pre- and postnatal neurogenesis.
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Affiliation(s)
- Lisa Woodbine
- Genome Damage and Stability Centre, University of Sussex, Brighton, United Kingdom
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84
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Chiruvella KK, Liang Z, Wilson TE. Repair of double-strand breaks by end joining. Cold Spring Harb Perspect Biol 2013; 5:a012757. [PMID: 23637284 DOI: 10.1101/cshperspect.a012757] [Citation(s) in RCA: 279] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Nonhomologous end joining (NHEJ) refers to a set of genome maintenance pathways in which two DNA double-strand break (DSB) ends are (re)joined by apposition, processing, and ligation without the use of extended homology to guide repair. Canonical NHEJ (c-NHEJ) is a well-defined pathway with clear roles in protecting the integrity of chromosomes when DSBs arise. Recent advances have revealed much about the identity, structure, and function of c-NHEJ proteins, but many questions exist regarding their concerted action in the context of chromatin. Alternative NHEJ (alt-NHEJ) refers to more recently described mechanism(s) that repair DSBs in less-efficient backup reactions. There is great interest in defining alt-NHEJ more precisely, including its regulation relative to c-NHEJ, in light of evidence that alt-NHEJ can execute chromosome rearrangements. Progress toward these goals is reviewed.
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85
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Ma L, Kazama Y, Inoue H, Abe T, Hatakeyama S, Tanaka S. The type of mutations induced by carbon-ion-beam irradiation of the filamentous fungus Neurospora crassa. Fungal Biol 2013; 117:227-38. [DOI: 10.1016/j.funbio.2013.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Revised: 12/24/2012] [Accepted: 01/04/2013] [Indexed: 10/27/2022]
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86
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Currall BB, Chiang C, Talkowski ME, Morton CC. Mechanisms for Structural Variation in the Human Genome. CURRENT GENETIC MEDICINE REPORTS 2013; 1:81-90. [PMID: 23730541 DOI: 10.1007/s40142-013-0012-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
It has been known for several decades that genetic variation involving changes to chromosomal structure (i.e., structural variants) can contribute to disease; however this relationship has been brought into acute focus in recent years largely based on innovative new genomics approaches and technology. Structural variants (SVs) arise from improperly repaired DNA double-strand breaks (DSB). DSBs are a frequent occurrence in all cells and two major pathways are involved in their repair: homologous recombination and non-homologous end joining. Errors during these repair mechanisms can result in SVs that involve losses, gains and rearrangements ranging from a few nucleotides to entire chromosomal arms. Factors such as rearrangements, hotspots and induced DSBs are implicated in the formation of SVs. While de novo SVs are often associated with disease, some SVs are conserved within human subpopulations and may have had a meaningful influence on primate evolution. As the ability to sequence the whole human genome rapidly evolves, the diversity of SVs is illuminated, including very complex rearrangements involving multiple DSBs in a process recently designated as "chromothripsis". Elucidating mechanisms involved in the etiology of SVs informs disease pathogenesis as well as the dynamic function associated with the biology and evolution of human genomes.
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Affiliation(s)
- Benjamin B Currall
- Departments of Obstetrics, Gynecology and Reproductive Biology, Brigham and Women's Hospital and Harvard Medical School, New Research Building, Room 160D, 77 Avenue Louis Pasteur, Boston, MA 02115, USA. Harvard Medical School, Boston, MA, USA
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87
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Shiloh Y, Ziv Y. The ATM protein kinase: regulating the cellular response to genotoxic stress, and more. Nat Rev Mol Cell Biol 2013; 14:197-210. [DOI: 10.1038/nrm3546] [Citation(s) in RCA: 1170] [Impact Index Per Article: 106.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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88
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Novotná E, Tichý A, Pejchal J, Lukášová E, Salovská B, Vávrová J. DNA-dependent protein kinase and its inhibition in support of radiotherapy. Int J Radiat Biol 2013; 89:416-23. [PMID: 23362996 DOI: 10.3109/09553002.2013.767993] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
PURPOSE Radiotherapy has been used as a treatment of almost 50% of all malignant tumors. The aim of this review is to provide a comprehensive overview of the recent knowledge in the field of molecular mechanisms of radiation-induced double-stranded breaks (DSB) repair. This paper gives particular emphasis to a key DNA repair enzyme, DNA-dependent protein kinase (DNA-PK), which plays a pivotal role in non-homologous end-joining. Furthermore, we discuss possibilities of DNA-PK inhibition and other molecular approaches employed in order to facilitate radiotherapy. CONCLUSIONS We have reviewed the recent studies using novel potent and selective small-molecular DNA-PK inhibitors and we conclude that targeted inhibition of DNA repair proteins like DNA-PK in cancer cells, in combination with ionizing radiation, improves the efficacy of cancer therapy while minimizing side-effects of ionizing radiation. Moreover, the recent discovery of short interfering RNA (siRNA) and signal interfering DNA (siDNA)-based therapeutics, or small peptides and RNA, shows a new opportunity of selective and safe application of biological treatment. All of these approaches are believed to contribute to more personalized anti-cancer therapy.
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Affiliation(s)
- Eva Novotná
- Department of Radiation Biology, Faculty of Military Health Sciences, University of Defence, Hradec Králové, Czech Republic
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89
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Detection and repair of ionizing radiation-induced DNA double strand breaks: new developments in nonhomologous end joining. Int J Radiat Oncol Biol Phys 2013; 86:440-9. [PMID: 23433795 DOI: 10.1016/j.ijrobp.2013.01.011] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 01/07/2013] [Indexed: 01/13/2023]
Abstract
DNA damage can occur as a result of endogenous metabolic reactions and replication stress or from exogenous sources such as radiation therapy and chemotherapy. DNA double strand breaks are the most cytotoxic form of DNA damage, and defects in their repair can result in genome instability, a hallmark of cancer. The major pathway for the repair of ionizing radiation-induced DSBs in human cells is nonhomologous end joining. Here we review recent advances on the mechanism of nonhomologous end joining, as well as new findings on its component proteins and regulation.
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90
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Mahaney BL, Hammel M, Meek K, Tainer JA, Lees-Miller SP. XRCC4 and XLF form long helical protein filaments suitable for DNA end protection and alignment to facilitate DNA double strand break repair. Biochem Cell Biol 2013; 91:31-41. [PMID: 23442139 DOI: 10.1139/bcb-2012-0058] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
DNA double strand breaks (DSBs), induced by ionizing radiation (IR) and endogenous stress including replication failure, are the most cytotoxic form of DNA damage. In human cells, most IR-induced DSBs are repaired by the nonhomologous end joining (NHEJ) pathway. One of the most critical steps in NHEJ is ligation of DNA ends by DNA ligase IV (LIG4), which interacts with, and is stabilized by, the scaffolding protein X-ray cross-complementing gene 4 (XRCC4). XRCC4 also interacts with XRCC4-like factor (XLF, also called Cernunnos); yet, XLF has been one of the least mechanistically understood proteins and precisely how XLF functions in NHEJ has been enigmatic. Here, we examine current combined structural and mutational findings that uncover integrated functions of XRCC4 and XLF and reveal their interactions to form long, helical protein filaments suitable to protect and align DSB ends. XLF-XRCC4 provides a global structural scaffold for ligating DSBs without requiring long DNA ends, thus ensuring accurate and efficient ligation and repair. The assembly of these XRCC4-XLF filaments, providing both DNA end protection and alignment, may commit cells to NHEJ with general biological implications for NHEJ and DSB repair processes and their links to cancer predispositions and interventions.
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Affiliation(s)
- Brandi L Mahaney
- Department of Biochemistry, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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91
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Davidson D, Amrein L, Panasci L, Aloyz R. Small Molecules, Inhibitors of DNA-PK, Targeting DNA Repair, and Beyond. Front Pharmacol 2013; 4:5. [PMID: 23386830 PMCID: PMC3560216 DOI: 10.3389/fphar.2013.00005] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/08/2013] [Indexed: 12/13/2022] Open
Abstract
Many current chemotherapies function by damaging genomic DNA in rapidly dividing cells ultimately leading to cell death. This therapeutic approach differentially targets cancer cells that generally display rapid cell division compared to normal tissue cells. However, although these treatments are initially effective in arresting tumor growth and reducing tumor burden, resistance and disease progression eventually occur. A major mechanism underlying this resistance is increased levels of cellular DNA repair. Most cells have complex mechanisms in place to repair DNA damage that occurs due to environmental exposures or normal metabolic processes. These systems, initially overwhelmed when faced with chemotherapy induced DNA damage, become more efficient under constant selective pressure and as a result chemotherapies become less effective. Thus, inhibiting DNA repair pathways using target specific small molecule inhibitors may overcome cellular resistance to DNA damaging chemotherapies. Non-homologous end joining a major mechanism for the repair of double-strand breaks (DSB) in DNA is regulated in part by the serine/threonine kinase, DNA dependent protein kinase (DNA-PK). The DNA-PK holoenzyme acts as a scaffold protein tethering broken DNA ends and recruiting other repair molecules. It also has enzymatic activity that may be involved in DNA damage signaling. Because of its’ central role in repair of DSBs, DNA-PK has been the focus of a number of small molecule studies. In these studies specific DNA-PK inhibitors have shown efficacy in synergizing chemotherapies in vitro. However, compounds currently known to specifically inhibit DNA-PK are limited by poor pharmacokinetics: these compounds have poor solubility and have high metabolic lability in vivo leading to short serum half-lives. Future improvement in DNA-PK inhibition will likely be achieved by designing new molecules based on the recently reported crystallographic structure of DNA-PK. Computer based drug design will not only assist in identifying novel functional moieties to replace the metabolically labile morpholino group but will also facilitate the design of molecules to target the DNA-PKcs/Ku80 interface or one of the autophosphorylation sites.
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Affiliation(s)
- David Davidson
- Department of Oncology, Segal Cancer Centre, Lady Davis Institute for Medical Research, Jewish General Hospital, McGill University Montreal, QC, Canada
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92
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Rass E, Chandramouly G, Zha S, Alt FW, Xie A. Ataxia telangiectasia mutated (ATM) is dispensable for endonuclease I-SceI-induced homologous recombination in mouse embryonic stem cells. J Biol Chem 2013; 288:7086-95. [PMID: 23355489 DOI: 10.1074/jbc.m112.445825] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ataxia telangiectasia mutated (ATM) is activated upon DNA double strand breaks (DSBs) and phosphorylates numerous DSB response proteins, including histone H2AX on serine 139 (Ser-139) to form γ-H2AX. Through interaction with MDC1, γ-H2AX promotes DSB repair by homologous recombination (HR). H2AX Ser-139 can also be phosphorylated by DNA-dependent protein kinase catalytic subunit and ataxia telangiectasia- and Rad3-related kinase. Thus, we tested whether ATM functions in HR, particularly that controlled by γ-H2AX, by comparing HR occurring at the euchromatic ROSA26 locus between mouse embryonic stem cells lacking either ATM, H2AX, or both. We show here that loss of ATM does not impair HR, including H2AX-dependent HR, but confers sensitivity to inhibition of poly(ADP-ribose) polymerases. Loss of ATM or H2AX has independent contributions to cellular sensitivity to ionizing radiation. The ATM-independent HR function of H2AX requires both Ser-139 phosphorylation and γ-H2AX/MDC1 interaction. Our data suggest that ATM is dispensable for HR, including that controlled by H2AX, in the context of euchromatin, excluding the implication of such an HR function in genomic instability, hypersensitivity to DNA damage, and poly(ADP-ribose) polymerase inhibition associated with ATM deficiency.
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Affiliation(s)
- Emilie Rass
- Department of Medicine, Harvard Medical School and Beth Israel Deaconess Medical Center, Boston, Massachusetts 02215, USA
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93
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Boboila C, Alt FW, Schwer B. Classical and alternative end-joining pathways for repair of lymphocyte-specific and general DNA double-strand breaks. Adv Immunol 2013; 116:1-49. [PMID: 23063072 DOI: 10.1016/b978-0-12-394300-2.00001-6] [Citation(s) in RCA: 203] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Classical nonhomologous end joining (C-NHEJ) is one of the two major known pathways for the repair of DNA double-strand breaks (DSBs) in mammalian cells. Our understanding of C-NHEJ has been derived, in significant part, through studies of programmed physiologic DNA DSBs formed during V(D)J recombination in the developing immune system. Studies of immunoglobulin heavy-chain (IgH) class-switch recombination (CSR) also have revealed that there is an "alternative" end-joining process (A-EJ) that can function, relatively robustly, in the repair of DSBs in activated mature B lymphocytes. This A-EJ process has also been implicated in the formation of oncogenic translocations found in lymphoid tumors. In this review, we discuss our current understanding of C-NHEJ and A-EJ in the context of V(D)J recombination, CSR, and the formation of chromosomal translocations.
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Affiliation(s)
- Cristian Boboila
- Howard Hughes Medical Institute, Immune Disease Institute, Program in Cellular and Molecular Medicine, Children's Hospital Boston, Boston, Massachusetts, USA
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94
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Urushihara Y, Kobayashi J, Matsumoto Y, Komatsu K, Oda S, Mitani H. DNA-PK inhibition causes a low level of H2AX phosphorylation and homologous recombination repair in Medaka (Oryzias latipes) cells. Biochem Biophys Res Commun 2012; 429:131-6. [PMID: 23142596 DOI: 10.1016/j.bbrc.2012.10.128] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 10/27/2012] [Indexed: 01/03/2023]
Abstract
Nonhomologous end joining (NHEJ) and homologous recombination (HR) are known as DNA double-strand break (DSB) repair pathways. It has been reported that DNA-PK, a member of PI3 kinase family, promotes NHEJ and aberrant DNA-PK causes NHEJ deficiency. However, in this study, we demonstrate that a wild-type cell line treated with DNA-PK inhibitor and a mutant cell line with dysfunctional DNA-PK showed decreased HR efficiency in fish cells (Medaka, Oryzias latipes). Previously, we reported that the radiation-sensitive mutant RIC1 strain has a defect in the Histone H2AX phosphorylation after γ-irradiation. Here, we showed that a DNA-PK inhibitor, NU7026, treatment resulted in significant reduction in the number of γH2AX foci after γ-irradiation in wild-type cells, but had no significant effect in RIC1 cells. In addition, RIC1 cells showed significantly lower levels of DNA-PK kinase activity compared with wild-type cells. We investigated NHEJ and HR efficiency after induction of DSBs. Wild-type cells treated with NU7026 and RIC1 cells showed decreased HR efficiency. These results indicated that aberrant DNA-PK causes the reduction in the number of γH2AX foci and HR efficiency in RIC1 cells. We performed phosphorylated DNA-PKcs (Thr2609) and 53BP1 focus assay after γ-irradiation. RIC1 cells showed significant reduction in the number of phosphorylated DNA-PKcs foci and no deference in the number of 53BP1 foci compared with wild-type cells. These results suggest that low level of DNA-PK activity causes aberrant DNA-PKcs autophosphorylation in RIC1 cells. It is known that 53BP1 is involved in both DNA-PK dependent and independent NHEJ. Therefore we suggest that DNA-PK independent NHEJ repair DSBs under the condition of decreased DNA-PK activity, which causes reduction of HR efficiency.
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Affiliation(s)
- Yusuke Urushihara
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba 277-8562, Japan
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95
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González-Marín C, Gosálvez J, Roy R. Types, causes, detection and repair of DNA fragmentation in animal and human sperm cells. Int J Mol Sci 2012; 13:14026-52. [PMID: 23203048 PMCID: PMC3509564 DOI: 10.3390/ijms131114026] [Citation(s) in RCA: 198] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/16/2012] [Accepted: 10/18/2012] [Indexed: 01/09/2023] Open
Abstract
Concentration, motility and morphology are parameters commonly used to determine the fertilization potential of an ejaculate. These parameters give a general view on the quality of sperm but do not provide information about one of the most important components of the reproductive outcome: DNA. Either single or double DNA strand breaks can set the difference between fertile and infertile males. Sperm DNA fragmentation can be caused by intrinsic factors like abortive apoptosis, deficiencies in recombination, protamine imbalances or oxidative stress. Damage can also occur due to extrinsic factors such as storage temperatures, extenders, handling conditions, time after ejaculation, infections and reaction to medicines or post-testicular oxidative stress, among others. Two singular characteristics differentiate sperm from somatic cells: Protamination and absence of DNA repair. DNA repair in sperm is terminated as transcription and translation stops post-spermiogenesis, so these cells have no mechanism to repair the damage occurred during their transit through the epididymis and post-ejaculation. Oocytes and early embryos have been shown to repair sperm DNA damage, so the effect of sperm DNA fragmentation depends on the combined effects of sperm chromatin damage and the capacity of the oocyte to repair it. In this contribution we review some of these issues.
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Affiliation(s)
- Clara González-Marín
- Sexing Technologies, 22575 State Highway 6 South, Navasota, TX 77868, USA; E-Mail:
| | - Jaime Gosálvez
- Biology Department, Universidad Autonoma of Madrid, C/ Darwin nº 2. 28049 Madrid, Spain; E-Mail:
| | - Rosa Roy
- Biology Department, Universidad Autonoma of Madrid, C/ Darwin nº 2. 28049 Madrid, Spain; E-Mail:
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96
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Nagaria P, Robert C, Rassool FV. DNA double-strand break response in stem cells: mechanisms to maintain genomic integrity. Biochim Biophys Acta Gen Subj 2012; 1830:2345-53. [PMID: 22995214 DOI: 10.1016/j.bbagen.2012.09.001] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 08/09/2012] [Accepted: 09/05/2012] [Indexed: 12/19/2022]
Abstract
BACKGROUND Embryonic stem cells (ESCs) represent the point of origin of all cells in a given organism and must protect their genomes from both endogenous and exogenous genotoxic stress. DNA double-strand breaks (DSBs) are one of the most lethal forms of damage, and failure to adequately repair DSBs would not only compromise the ability of SCs to self-renew and differentiate, but will also lead to genomic instability and disease. SCOPE OF REVIEW Herein, we describe the mechanisms by which ESCs respond to DSB-inducing agents such as reactive oxygen species (ROS) and ionizing radiation, compared to somatic cells. We will also discuss whether the DSB response is fully reprogrammed in induced pluripotent stem cells (iPSCs) and the role of the DNA damage response (DDR) in the reprogramming of these cells. MAJOR CONCLUSIONS ESCs have distinct mechanisms to protect themselves against DSBs and oxidative stress compared to somatic cells. The response to damage and stress is crucial for the maintenance of self-renewal and differentiation capacity in SCs. iPSCs appear to reprogram some of the responses to genotoxic stress. However, it remains to be determined if iPSCs also retain some DDR characteristics of the somatic cells of origin. GENERAL SIGNIFICANCE The mechanisms regulating the genomic integrity in ESCs and iPSCs are critical for its safe use in regenerative medicine and may shed light on the pathways and factors that maintain genomic stability, preventing diseases such as cancer. This article is part of a Special Issue entitled Biochemistry of Stem Cells.
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Affiliation(s)
- Pratik Nagaria
- Department of Radiation Oncology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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97
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Huda N, Abe S, Gu L, Mendonca MS, Mohanty S, Gilley D. Recruitment of TRF2 to laser-induced DNA damage sites. Free Radic Biol Med 2012; 53:1192-7. [PMID: 22841872 DOI: 10.1016/j.freeradbiomed.2012.07.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Revised: 07/10/2012] [Accepted: 07/17/2012] [Indexed: 12/18/2022]
Abstract
Several lines of evidence suggest that the telomere-associated protein TRF2 plays critical roles in the DNA damage response. TRF2 is rapidly and transiently phosphorylated by an ATM-dependent pathway in response to DNA damage and this DNA damage-induced phosphoryation is essential for the DNA-PK-dependent pathway of DNA double-strand break repair (DSB). However, the type of DNA damage that induces TRF2 localization to the damage sites, the requirement for DNA damage-induced phosphorylation of TRF2 for its recruitment, as well as the detailed kinetics of TRF2 accumulation at DNA damage sites have not been fully investigated. In order to address these questions, we used an ultrafast femtosecond multiphoton laser and a continuous wave 405-nm single photon laser to induce DNA damage at defined nuclear locations. Our results showed that DNA damage produced by a femtosecond multiphoton laser was sufficient for localization of TRF2 to these DNA damage sites. We also demonstrate that ectopically expressed TRF2 was recruited to DNA lesions created by a 405-nm laser. Our data suggest that ATM and DNA-PKcs kinases are not required for TRF2 localization to DNA damage sites. Furthermore, we found that phosphorylation of TRF2 at residue T188 was not essential for its recruitment to laser-induced DNA damage sites. Thus, we provide further evidence that a protein known to function in telomere maintenance, TRF2, is recruited to sites of DNA damage and plays critical roles in the DNA damage response.
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Affiliation(s)
- Nazmul Huda
- Indiana University School of Medicine, Department of Medical and Molecular Genetics, Indianapolis, IN 46202, USA
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98
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Sears CR, Turchi JJ. Complex cisplatin-double strand break (DSB) lesions directly impair cellular non-homologous end-joining (NHEJ) independent of downstream damage response (DDR) pathways. J Biol Chem 2012; 287:24263-72. [PMID: 22621925 PMCID: PMC3397852 DOI: 10.1074/jbc.m112.344911] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 05/18/2012] [Indexed: 11/06/2022] Open
Abstract
The treatment for advanced stage non-small cell lung cancer (NSCLC) often includes platinum-based chemotherapy and IR. Cisplatin and IR combination therapy display schedule and dose-dependent synergy, the mechanism of which is not completely understood. In a series of in vitro and cell culture assays in a NSCLC model, we investigated both the downstream and direct treatment and damage effects of cisplatin on NHEJ catalyzed repair of a DNA DSB. The results demonstrate that extracts prepared from cisplatin-treated cells are fully capable of NHEJ catalyzed repair of a DSB using a non-cisplatin-damaged DNA substrate in vitro. Similarly, using two different host cell reactivation assays, treatment of cells prior to transfection of a linear, undamaged reporter plasmid revealed no reduction in NHEJ compared with untreated cells. In contrast, transfection of a linear GFP-reporter plasmid containing site-specific, cisplatin lesions 6-bp from the termini revealed a significant impairment in DSB repair of the cisplatin-damaged DNA substrates in the absence of cellular treatment with cisplatin. Together, these data demonstrate that impaired NHEJ in combined cisplatin-IR treated cells is likely the result of a direct effect of cisplatin-DNA lesions near a DSB and that the indirect cellular effects of cisplatin treatment are not significant contributors to the synergistic cytotoxicity observed with combination cisplatin-IR treatment.
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Affiliation(s)
| | - John J. Turchi
- From the Departments of Medicine and
- Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, Indiana 46202
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99
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Martín M, Terradas M, Tusell L, Genescà A. ATM and DNA-PKcs make a complementary couple in DNA double strand break repair. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2012; 751:29-35. [DOI: 10.1016/j.mrrev.2011.12.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 01/21/2023]
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100
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Abe S, Kurata M, Suzuki S, Yamamoto K, Aisaki KI, Kanno J, Kitagawa M. Minichromosome maintenance 2 bound with retroviral Gp70 is localized to cytoplasm and enhances DNA-damage-induced apoptosis. PLoS One 2012; 7:e40129. [PMID: 22768239 PMCID: PMC3387003 DOI: 10.1371/journal.pone.0040129] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2012] [Accepted: 06/01/2012] [Indexed: 11/19/2022] Open
Abstract
The interaction of viral proteins with host-cellular proteins elicits the activation of cellular signal transduction pathways and possibly leads to viral pathogenesis as well as cellular biological events. Apoptotic signals induced by DNA-damage are remarkably up-regulated by Friend leukemia virus (FLV) exclusively in C3H hosts; however, the mechanisms underlying the apoptosis enhancement and host-specificity are unknown. Here, we show that C3H mouse-derived hematopoietic cells originally express higher levels of the minichromosome maintenance (MCM) 2 protein than BALB/c- or C57BL/6-deriverd cells, and undergo more frequent apoptosis following doxorubicin-induced DNA-damage in the presence of the FLV envelope protein gp70. Dual transfection with gp70/Mcm2 reproduced doxorubicin-induced apoptosis even in BALB/c-derived 3T3 cells. Immunoprecipitation assays using various deletion mutants of MCM2 revealed that gp70 bound to the nuclear localization signal (NLS) 1 (amino acids 18–24) of MCM2, interfered with the function of NLS2 (amino acids 132–152), and suppressed the normal nuclear-import of MCM2. Cytoplasmic MCM2 reduced the activity of protein phosphatase 2A (PP2A) leading to the subsequent hyperphosphorylation of DNA-dependent protein kinase (DNA-PK). Phosphorylated DNA-PK exhibited elevated kinase activity to phosphorylate P53, thereby up-regulating p53-dependent apoptosis. An apoptosis-enhancing domain was identified in the C-terminal portion (amino acids 703–904) of MCM2. Furthermore, simultaneous treatment with FLV and doxorubicin extended the survival of SCID mice bearing 8047 leukemia cells expressing high levels of MCM2. Thus, depending on its subcellular localization, MCM2 plays different roles. It participates in DNA replication in the nucleus as shown previously, and enhances apoptosis in the cytoplasm.
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Affiliation(s)
- Shinya Abe
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Morito Kurata
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Shiho Suzuki
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kouhei Yamamoto
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Ken-ichi Aisaki
- Division of Cellular and Molecular Toxicology, National Institute of Health Sciences, Tokyo, Japan
| | - Jun Kanno
- Division of Cellular and Molecular Toxicology, National Institute of Health Sciences, Tokyo, Japan
| | - Masanobu Kitagawa
- Department of Comprehensive Pathology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
- * E-mail:
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