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Mikhova M, Goff NJ, Janovič T, Heyza JR, Meek K, Schmidt JC. Single-molecule imaging reveals the kinetics of non-homologous end-joining in living cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.06.22.546088. [PMID: 38826211 PMCID: PMC11142080 DOI: 10.1101/2023.06.22.546088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Non-homologous end joining (NHEJ) is the predominant pathway that repairs DNA double-stranded breaks (DSBs) in vertebrates. However, due to challenges in detecting DSBs in living cells, the repair capacity of the NHEJ pathway is unknown. The DNA termini of many DSBs must be processed to allow ligation while minimizing genetic changes that result from break repair. Emerging models propose that DNA termini are first synapsed ~115Å apart in one of several long-range synaptic complexes before transitioning into a short-range synaptic complex that juxtaposes DNA ends to facilitate ligation. The transition from long-range to short-range synaptic complexes involves both conformational and compositional changes of the NHEJ factors bound to the DNA break. Importantly, it is unclear how NHEJ proceeds in vivo because of the challenges involved in analyzing recruitment of NHEJ factors to DSBs over time in living cells. Here, we develop a new approach to study the temporal and compositional dynamics of NHEJ complexes using live cell single-molecule imaging. Our results provide direct evidence for stepwise maturation of the NHEJ complex, pinpoint key regulatory steps in NHEJ progression, and define the overall repair capacity NHEJ in living cells.
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Affiliation(s)
- Mariia Mikhova
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
| | - Noah J. Goff
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing
- Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing
| | - Tomáš Janovič
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
| | - Joshua R. Heyza
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
| | - Katheryn Meek
- Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing
- Department of Pathobiology & Diagnostic Investigation, Michigan State University, East Lansing
| | - Jens C. Schmidt
- Institute for Quantitative Health Science and Engineering, Michigan State University, East Lansing
- Department of Obstetrics, Gynecology and Reproductive Biology, Michigan State University, East Lansing
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2
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Maltseva EA, Vasil’eva IA, Moor NA, Kim DV, Dyrkheeva NS, Kutuzov MM, Vokhtantsev IP, Kulishova LM, Zharkov DO, Lavrik OI. Cas9 is mostly orthogonal to human systems of DNA break sensing and repair. PLoS One 2023; 18:e0294683. [PMID: 38019812 PMCID: PMC10686484 DOI: 10.1371/journal.pone.0294683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/06/2023] [Indexed: 12/01/2023] Open
Abstract
CRISPR/Cas9 system is а powerful gene editing tool based on the RNA-guided cleavage of target DNA. The Cas9 activity can be modulated by proteins involved in DNA damage signalling and repair due to their interaction with double- and single-strand breaks (DSB and SSB, respectively) generated by wild-type Cas9 or Cas9 nickases. Here we address the interplay between Streptococcus pyogenes Cas9 and key DNA repair factors, including poly(ADP-ribose) polymerase 1 (SSB/DSB sensor), its closest homolog poly(ADP-ribose) polymerase 2, Ku antigen (DSB sensor), DNA ligase I (SSB sensor), replication protein A (DNA duplex destabilizer), and Y-box binding protein 1 (RNA/DNA binding protein). None of those significantly affected Cas9 activity, while Cas9 efficiently shielded DSBs and SSBs from their sensors. Poly(ADP-ribosyl)ation of Cas9 detected for poly(ADP-ribose) polymerase 2 had no apparent effect on the activity. In cellulo, Cas9-dependent gene editing was independent of poly(ADP-ribose) polymerase 1. Thus, Cas9 can be regarded as an enzyme mostly orthogonal to the natural regulation of human systems of DNA break sensing and repair.
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Affiliation(s)
| | - Inna A. Vasil’eva
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Nina A. Moor
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Daria V. Kim
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | | | - Mikhail M. Kutuzov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Ivan P. Vokhtantsev
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Lilya M. Kulishova
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
| | - Dmitry O. Zharkov
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
| | - Olga I. Lavrik
- SB RAS Institute of Chemical Biology and Fundamental Medicine, Novosibirsk, Russia
- Novosibirsk State University, Novosibirsk, Russia
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3
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Mechetin GV, Zharkov DO. DNA Damage Response and Repair in Boron Neutron Capture Therapy. Genes (Basel) 2023; 14:127. [PMID: 36672868 PMCID: PMC9859301 DOI: 10.3390/genes14010127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 12/28/2022] [Accepted: 12/29/2022] [Indexed: 01/03/2023] Open
Abstract
Boron neutron capture therapy (BNCT) is an approach to the radiotherapy of solid tumors that was first outlined in the 1930s but has attracted considerable attention recently with the advent of a new generation of neutron sources. In BNCT, tumor cells accumulate 10B atoms that react with epithermal neutrons, producing energetic α particles and 7Li atoms that damage the cell's genome. The damage inflicted by BNCT appears not to be easily repairable and is thus lethal for the cell; however, the molecular events underlying the action of BNCT remain largely unaddressed. In this review, the chemistry of DNA damage during BNCT is outlined, the major mechanisms of DNA break sensing and repair are summarized, and the specifics of the repair of BNCT-induced DNA lesions are discussed.
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Affiliation(s)
- Grigory V. Mechetin
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
| | - Dmitry O. Zharkov
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., 630090 Novosibirsk, Russia
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., 630090 Novosibirsk, Russia
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4
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Gao Z, Williams P, Li L, Wang Y. A Quantitative Proteomic Approach for the Identification of DNA Guanine Quadruplex-Binding Proteins. J Proteome Res 2021; 20:4919-4924. [PMID: 34570971 DOI: 10.1021/acs.jproteome.1c00603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA sequences of high guanine (G) content have the potential to form G quadruplex (G4) structures. A more complete understanding about the biological functions of G4 DNA requires the investigation about how these structures are recognized by proteins. Here, we conducted exhaustive quantitative proteomic experiments to profile the interaction proteomes of G4 structures by employing different sequences of G4 DNA derived from the human telomere and the promoters of c-MYC and c-KIT genes. Our results led to the identification of a number of candidate G4-interacting proteins, many of which were discovered here for the first time. These included three proteins that can bind to all three DNA G4 structures and 78 other proteins that can bind selectively to one or two of the three DNA G4 structure(s). We also validated that GRSF1 can bind directly and selectively toward G4 structure derived from the c-MYC promoter. Our quantitative proteomic screening also led to the identification of a number of candidate "antireader" proteins of G4 DNA. Together, we uncovered a number of cellular proteins that exhibit general and selective recognitions of G4 folding patterns, which underscore the complexity of G4 DNA in biology and the importance of understanding fully the G4-interaction proteome.
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Affiliation(s)
- Zi Gao
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Preston Williams
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Lin Li
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
| | - Yinsheng Wang
- Department of Chemistry, University of California Riverside, Riverside, California 92521-0403, United States
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5
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Holland CL, Sanderson BA, Titus JK, Weis MF, Riojas AM, Malczewskyj E, Wasko BM, Lewis LK. Suppression of telomere capping defects of Saccharomyces cerevisiae yku70 and yku80 mutants by telomerase. G3-GENES GENOMES GENETICS 2021; 11:6395363. [PMID: 34718547 PMCID: PMC8664480 DOI: 10.1093/g3journal/jkab359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/27/2021] [Indexed: 11/18/2022]
Abstract
The Ku complex performs multiple functions inside eukaryotic cells, including protection of chromosomal DNA ends from degradation and fusion events, recruitment of telomerase, and repair of double-strand breaks (DSBs). Inactivation of Ku complex genes YKU70 or YKU80 in cells of the yeast Saccharomyces cerevisiae gives rise to mutants that exhibit shortened telomeres and temperature-sensitive growth. In this study, we have investigated the mechanism by which overexpression of telomerase suppresses the temperature sensitivity of yku mutants. Viability of yku cells was restored by overexpression of the Est2 reverse transcriptase and TLC1 RNA template subunits of telomerase, but not the Est1 or Est3 proteins. Overexpression of other telomerase- and telomere-associated proteins (Cdc13, Stn1, Ten1, Rif1, Rif2, Sir3, and Sir4) did not suppress the growth defects of yku70 cells. Mechanistic features of suppression were assessed using several TLC1 RNA deletion derivatives and Est2 enzyme mutants. Supraphysiological levels of three catalytically inactive reverse transcriptase mutants (Est2-D530A, Est2-D670A, and Est2-D671A) suppressed the loss of viability as efficiently as the wild-type Est2 protein, without inducing cell senescence. Roles of proteins regulating telomere length were also determined. The results support a model in which chromosomes in yku mutants are stabilized via a replication-independent mechanism involving structural reinforcement of protective telomere cap structures.
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Affiliation(s)
- Cory L Holland
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Brian A Sanderson
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - James K Titus
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Monica F Weis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Angelica M Riojas
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Eric Malczewskyj
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
| | - Brian M Wasko
- Department of Biology and Biotechnology, University of Houston-Clear Lake, Houston, TX, 77058, USA
| | - L Kevin Lewis
- Department of Chemistry and Biochemistry, Texas State University, San Marcos, TX 78666, USA
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6
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Chuang CK, Lin WM. Points of View on the Tools for Genome/Gene Editing. Int J Mol Sci 2021; 22:9872. [PMID: 34576035 PMCID: PMC8470269 DOI: 10.3390/ijms22189872] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 08/26/2021] [Accepted: 09/09/2021] [Indexed: 12/25/2022] Open
Abstract
Theoretically, a DNA sequence-specific recognition protein that can distinguish a DNA sequence equal to or more than 16 bp could be unique to mammalian genomes. Long-sequence-specific nucleases, such as naturally occurring Homing Endonucleases and artificially engineered ZFN, TALEN, and Cas9-sgRNA, have been developed and widely applied in genome editing. In contrast to other counterparts, which recognize DNA target sites by the protein moieties themselves, Cas9 uses a single-guide RNA (sgRNA) as a template for DNA target recognition. Due to the simplicity in designing and synthesizing a sgRNA for a target site, Cas9-sgRNA has become the most current tool for genome editing. Moreover, the RNA-guided DNA recognition activity of Cas9-sgRNA is independent of both of the nuclease activities of it on the complementary strand by the HNH domain and the non-complementary strand by the RuvC domain, and HNH nuclease activity null mutant (H840A) and RuvC nuclease activity null mutant (D10A) were identified. In accompaniment with the sgRNA, Cas9, Cas9(D10A), Cas9(H840A), and Cas9(D10A, H840A) can be used to achieve double strand breakage, complementary strand breakage, non-complementary strand breakage, and no breakage on-target site, respectively. Based on such unique characteristics, many engineered enzyme activities, such as DNA methylation, histone methylation, histone acetylation, cytidine deamination, adenine deamination, and primer-directed mutation, could be introduced within or around the target site. In order to prevent off-targeting by the lasting expression of Cas9 derivatives, a lot of transient expression methods, including the direct delivery of Cas9-sgRNA riboprotein, were developed. The issue of biosafety is indispensable in in vivo applications; Cas9-sgRNA packaged into virus-like particles or extracellular vesicles have been designed and some in vivo therapeutic trials have been reported.
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Affiliation(s)
- Chin-Kai Chuang
- Animal Technology Research Center, Division of Animal Technology, Agricultural Technology Research Institute, No. 52, Kedong 2nd Rd., Zhunan Township, Miaoli County 35053, Taiwan;
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Xu W, Li Y, Li Y, Liu C, Wang Y, Xia G, Wang M. Asymmetric Somatic Hybridization Affects Synonymous Codon Usage Bias in Wheat. Front Genet 2021; 12:682324. [PMID: 34178040 PMCID: PMC8226224 DOI: 10.3389/fgene.2021.682324] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/07/2021] [Indexed: 11/24/2022] Open
Abstract
Asymmetric somatic hybridization is an efficient strategy for crop breeding by introducing exogenous chromatin fragments, which leads to whole genomic shock and local chromosomal shock that induces genome-wide genetic variation including indel (insertion and deletion) and nucleotide substitution. Nucleotide substitution causes synonymous codon usage bias (SCUB), an indicator of genomic mutation and natural selection. However, how asymmetric somatic hybridization affects SCUB has not been addressed. Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Asymmetric somatic hybridization affected SCUB and promoted the bias to A- and T-ending synonymous codon (SCs). SCUB frequencies in chromosomes introgressed with exogenous fragments were comparable to those in chromosomes without exogenous fragments, showing that exogenous fragments had no local chromosomal effect. Asymmetric somatic hybridization affected SCUB frequencies in indel-flanking sequences more strongly than in non-flanking sequences, and this stronger effect was present in both chromosomes with and without exogenous fragments. DNA methylation-driven SCUB shift was more pronounced than other SC pairs. SCUB shift was similar among seven groups of allelic chromosomes as well as three sub-genomes. Our work demonstrates that the SCUB shift induced by asymmetric somatic hybridization is attributed to the whole genomic shock, and DNA methylation is a putative force of SCUB shift during asymmetric somatic hybridization. Asymmetric somatic hybridization provides an available method for deepening the nature of SCUB shift and genetic variation induced by genomic shock.
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Affiliation(s)
- Wenjing Xu
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Yingchun Li
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Yajing Li
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Chun Liu
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, China
| | - Guangmin Xia
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
| | - Mengcheng Wang
- The Key Laboratory of Plant Development and Environmental Adaption, Ministry of Education, School of Life Science, Shandong University, Jinan, China
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Boivin M, Deng J, Pfister V, Grandgirard E, Oulad-Abdelghani M, Morlet B, Ruffenach F, Negroni L, Koebel P, Jacob H, Riet F, Dijkstra AA, McFadden K, Clayton WA, Hong D, Miyahara H, Iwasaki Y, Sone J, Wang Z, Charlet-Berguerand N. Translation of GGC repeat expansions into a toxic polyglycine protein in NIID defines a novel class of human genetic disorders: The polyG diseases. Neuron 2021; 109:1825-1835.e5. [PMID: 33887199 PMCID: PMC8186563 DOI: 10.1016/j.neuron.2021.03.038] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 01/08/2021] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Neuronal intranuclear inclusion disease (NIID) is a neurodegenerative disease characterized by the presence of intranuclear inclusions of unknown origin. NIID is caused by an expansion of GGC repeats in the 5′ UTR of the NOTCH2NLC (N2C) gene. We found that these repeats are embedded in a small upstream open reading frame (uORF) (uN2C), resulting in their translation into a polyglycine-containing protein, uN2CpolyG. This protein accumulates in intranuclear inclusions in cell and mouse models and in tissue samples of individuals with NIID. Furthermore, expression of uN2CpolyG in mice leads to locomotor alterations, neuronal cell loss, and premature death of the animals. These results suggest that translation of expanded GGC repeats into a novel and pathogenic polyglycine-containing protein underlies the presence of intranuclear inclusions and neurodegeneration in NIID. NIID is a neurodegenerative disease caused by expansion of GGC repeats in NOTCH2NLC These GGC repeats are translated into a polyglycine (polyG) protein The polyG protein is toxic and forms intranuclear inclusions in cells and animals Similarities between FXTAS and NIID define a new set of disorders: polyG diseases
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Affiliation(s)
- Manon Boivin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Jianwen Deng
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Véronique Pfister
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Erwan Grandgirard
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Mustapha Oulad-Abdelghani
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Frank Ruffenach
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Luc Negroni
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Pascale Koebel
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Hugues Jacob
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Fabrice Riet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France
| | - Anke A Dijkstra
- Department of Pathology, Amsterdam University Medical Centre, Amsterdam Neuroscience, VUmc, Amsterdam, the Netherlands
| | - Kathryn McFadden
- Department of Pathology, IWK Health Centre, Halifax, NS B3K 6R8, Canada
| | - Wiley A Clayton
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Daojun Hong
- Department of Neurology, First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hiroaki Miyahara
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Yasushi Iwasaki
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan
| | - Jun Sone
- Department of Neuropathology, Institute for Medical Science of Aging, Aichi Medical University, Nagakute, Japan; Department of Neurology, Suzuka National Hospital, Suzuka 513-8501, Japan
| | - Zhaoxia Wang
- Department of Neurology, Peking University First Hospital, Beijing 100034, China
| | - Nicolas Charlet-Berguerand
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U 1258, CNRS UMR 7104, University of Strasbourg, 67404 Illkirch, France.
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Zahid S, Seif El Dahan M, Iehl F, Fernandez-Varela P, Le Du MH, Ropars V, Charbonnier JB. The Multifaceted Roles of Ku70/80. Int J Mol Sci 2021; 22:ijms22084134. [PMID: 33923616 PMCID: PMC8073936 DOI: 10.3390/ijms22084134] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/11/2022] Open
Abstract
DNA double-strand breaks (DSBs) are accidental lesions generated by various endogenous or exogenous stresses. DSBs are also genetically programmed events during the V(D)J recombination process, meiosis, or other genome rearrangements, and they are intentionally generated to kill cancer during chemo- and radiotherapy. Most DSBs are processed in mammalian cells by the classical nonhomologous end-joining (c-NHEJ) pathway. Understanding the molecular basis of c-NHEJ has major outcomes in several fields, including radiobiology, cancer therapy, immune disease, and genome editing. The heterodimer Ku70/80 (Ku) is a central actor of the c-NHEJ as it rapidly recognizes broken DNA ends in the cell and protects them from nuclease activity. It subsequently recruits many c-NHEJ effectors, including nucleases, polymerases, and the DNA ligase 4 complex. Beyond its DNA repair function, Ku is also involved in several other DNA metabolism processes. Here, we review the structural and functional data on the DNA and RNA recognition properties of Ku implicated in DNA repair and in telomeres maintenance.
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Improved Autophagic Flux in Escapers from Doxorubicin-Induced Senescence/Polyploidy of Breast Cancer Cells. Int J Mol Sci 2020; 21:ijms21176084. [PMID: 32846959 PMCID: PMC7504443 DOI: 10.3390/ijms21176084] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/22/2022] Open
Abstract
The induction of senescence/polyploidization and their role in cancer recurrence is still a poorly explored issue. We showed that MDA-MB-231 and MCF-7 breast cancer cells underwent reversible senescence/polyploidization upon pulse treatment with doxorubicin (dox). Subsequently, senescent/polyploid cells produced progeny (escapers) that possessed the same amount of DNA as parental cells. In a dox-induced senescence/polyploidization state, the accumulation of autophagy protein markers, such as LC3B II and p62/SQSTM1, was observed. However, the senescent cells were characterized by a very low rate of new autophagosome formation and degradation, estimated by autophagic index. In contrast to senescent cells, escapers had a substantially increased autophagic index and transcription factor EB activation, but a decreased level of an autophagy inhibitor, Rubicon, and autophagic vesicles with non-degraded cargo. These results strongly suggested that autophagy in escapers was improved, especially in MDA-MB-231 cells. The escapers of both cell lines were also susceptible to dox-induced senescence. However, MDA-MB-231 cells which escaped from senescence were characterized by a lower number of γH2AX foci and a different pattern of interleukin synthesis than senescent cells. Thus, our studies showed that breast cancer cells can undergo senescence uncoupled from autophagy status, but autophagic flux resumption may be indispensable in cancer cell escape from senescence/polyploidy.
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DNA-PK in human malignant disorders: Mechanisms and implications for pharmacological interventions. Pharmacol Ther 2020; 215:107617. [PMID: 32610116 DOI: 10.1016/j.pharmthera.2020.107617] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/15/2020] [Indexed: 12/12/2022]
Abstract
The DNA-PK holoenzyme is a fundamental element of the DNA damage response machinery (DDR), which is responsible for cellular genomic stability. Consequently, and predictably, over the last decades since its identification and characterization, numerous pre-clinical and clinical studies reported observations correlating aberrant DNA-PK status and activity with cancer onset, progression and responses to therapeutic modalities. Notably, various studies have established in recent years the role of DNA-PK outside the DDR network, corroborating its role as a pleiotropic complex involved in transcriptional programs that operate biologic processes as epithelial to mesenchymal transition (EMT), hypoxia, metabolism, nuclear receptors signaling and inflammatory responses. In particular tumor entities as prostate cancer, immense research efforts assisted mapping and describing the overall signaling networks regulated by DNA-PK that control metastasis and tumor progression. Correspondingly, DNA-PK emerges as an obvious therapeutic target in cancer and data pertaining to various pharmacological approaches have been published, largely in context of combination with DNA-damaging agents (DDAs) that act by inflicting DNA double strand breaks (DSBs). Currently, new generation inhibitors are tested in clinical trials. Several excellent reviews have been published in recent years covering the biology of DNA-PK and its role in cancer. In the current article we are aiming to systematically describe the main findings on DNA-PK signaling in major cancer types, focusing on both preclinical and clinical reports and present a detailed current status of the DNA-PK inhibitors repertoire.
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12
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Functional diversification of Paramecium Ku80 paralogs safeguards genome integrity during precise programmed DNA elimination. PLoS Genet 2020; 16:e1008723. [PMID: 32298257 PMCID: PMC7161955 DOI: 10.1371/journal.pgen.1008723] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/18/2020] [Indexed: 11/19/2022] Open
Abstract
Gene duplication and diversification drive the emergence of novel functions during evolution. Because of whole genome duplications, ciliates from the Paramecium aurelia group constitute a remarkable system to study the evolutionary fate of duplicated genes. Paramecium species harbor two types of nuclei: a germline micronucleus (MIC) and a somatic macronucleus (MAC) that forms from the MIC at each sexual cycle. During MAC development, ~45,000 germline Internal Eliminated Sequences (IES) are excised precisely from the genome through a 'cut-and-close' mechanism. Here, we have studied the P. tetraurelia paralogs of KU80, which encode a key DNA double-strand break repair factor involved in non-homologous end joining. The three KU80 genes have different transcription patterns, KU80a and KU80b being constitutively expressed, while KU80c is specifically induced during MAC development. Immunofluorescence microscopy and high-throughput DNA sequencing revealed that Ku80c stably anchors the PiggyMac (Pgm) endonuclease in the developing MAC and is essential for IES excision genome-wide, providing a molecular explanation for the previously reported Ku-dependent licensing of DNA cleavage at IES ends. Expressing Ku80a under KU80c transcription signals failed to complement a depletion of endogenous Ku80c, indicating that the two paralogous proteins have distinct properties. Domain-swap experiments identified the α/β domain of Ku80c as the major determinant for its specialized function, while its C-terminal part is required for excision of only a small subset of IESs located in IES-dense regions. We conclude that Ku80c has acquired the ability to license Pgm-dependent DNA cleavage, securing precise DNA elimination during programmed rearrangements. The present study thus provides novel evidence for functional diversification of genes issued from a whole-genome duplication.
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MiRNAs Targeting Double Strand DNA Repair Pathways Lurk in Genomically Unstable Rare Fragile Sites and Determine Cancer Outcomes. Cancers (Basel) 2020; 12:cancers12040876. [PMID: 32260317 PMCID: PMC7226545 DOI: 10.3390/cancers12040876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/12/2022] Open
Abstract
Double strand break (DSB) repair mechanisms guard genome integrity and their deterioration causes genomic instability. Common and rare fragile sites (CFS and RFS, respectively) are particularly vulnerable to instability, and there is an inverse correlation between fragile site (FS) expression and DSB repair protein levels. Upon DSB repair dysfunction, genes residing at these sites are at greater risk of deregulation compared to genes located at non-FS. In this regard, it remains enigmatic why the incidence of miRNA genes at FS is higher compared to non-FS. Herein, using bioinformatics, we examined whether miRNA genes localized at FS inhibit components of DSB repair pathways and assessed their effects on cancer. We show that such miRNAs over-accumulate in RFS, and that FRAXA, which is expressed in Fragile X syndrome, is a conserved hotspot for miRNAs inhibiting DSB repair. Axes of FRAXA-residing miRNAs/DSB repair targets affect survival in a cancer type-specific manner. Moreover, copy number variations in the region encompassing these miRNA genes discriminate survival between male and female patients. Given that, thus far, only CFS have been considered relevant for carcinogenesis, our data are the first to associate RFS with cancer, through the impairment of DSB repair by the FRAXA-residing miRNAs.
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Wang Y, Lai L, Guo W, Peng S, Liu R, Hong P, Wei G, Li F, Jiang S, Wang P, Li J, Lei H, Zhao W, Xu S. Inhibition of Ku70 in a high-glucose environment aggravates bupivacaine-induced dorsal root ganglion neurotoxicity. Toxicol Lett 2020; 318:104-113. [DOI: 10.1016/j.toxlet.2019.10.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 12/11/2022]
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Kim K, Min J, Kirby TW, Gabel SA, Pedersen LC, London RE. Ligand binding characteristics of the Ku80 von Willebrand domain. DNA Repair (Amst) 2020; 85:102739. [PMID: 31733588 PMCID: PMC7495496 DOI: 10.1016/j.dnarep.2019.102739] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Revised: 09/18/2019] [Accepted: 10/21/2019] [Indexed: 10/25/2022]
Abstract
The N-terminal von Willebrand domain of Ku80 supports interactions with a Ku binding motif (KBM) that has been identified in at least three other DNA repair proteins: the non-homologous end joining (NHEJ) scaffold APLF, the modulator of retrovirus infection, MRI, and the Werner syndrome protein (WRN). A second, more recently identified Ku binding motif present in XLF and several other proteins (KBMX) has also been reported to interact with this domain. The isolated Ku80 von Willebrand antigen domain (vWA) from Xenopus laevis has a sequence that is 60% identical with the human domain, is readily expressed and has been used to investigate these interactions. Structural characterization of the complexes formed with the KBM motifs in human APLF, MRI, and WRN identify a conserved binding site that is consistent with previously-reported mutational studies. In contrast with the KBM binding site, structural studies indicate that the KBMX site is occluded by a distorted helix. Fluorescence polarization and 19F NMR studies of a fluorinated XLF C-terminal peptide failed to indicate any interaction with the frog vWA. It was hypothesized that availability of this binding site is conditional, i.e., dependent on specific experimental conditions or other repair factors to make the site available for binding. Modulating the fraction of KBMX-accessible binding site mutationally demonstrated that the more open site is capable of binding the KBMXXLF motif peptide. It is suggested that the conditional nature of KBMX binding limits formation of non-productive complexes so that activation-dependent site availability can more optimally support advancing the synapsis process.
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Affiliation(s)
- Kyungmin Kim
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Jungki Min
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Thomas W Kirby
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Scott A Gabel
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Lars C Pedersen
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA
| | - Robert E London
- Genome Integrity and Structural Biology Laboratory, National Institute of Environment and Health Sciences, National Institutes of Health, Research Triangle Park, NC, 27709, USA.
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16
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Toma M, Skorski T, Sliwinski T. DNA Double Strand Break Repair - Related Synthetic Lethality. Curr Med Chem 2019; 26:1446-1482. [PMID: 29421999 DOI: 10.2174/0929867325666180201114306] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Revised: 11/10/2017] [Accepted: 11/16/2017] [Indexed: 12/25/2022]
Abstract
Cancer is a heterogeneous disease with a high degree of diversity between and within tumors. Our limited knowledge of their biology results in ineffective treatment. However, personalized approach may represent a milestone in the field of anticancer therapy. It can increase specificity of treatment against tumor initiating cancer stem cells (CSCs) and cancer progenitor cells (CPCs) with minimal effect on normal cells and tissues. Cancerous cells carry multiple genetic and epigenetic aberrations which may disrupt pathways essential for cell survival. Discovery of synthetic lethality has led a new hope of creating effective and personalized antitumor treatment. Synthetic lethality occurs when simultaneous inactivation of two genes or their products causes cell death whereas individual inactivation of either gene is not lethal. The effectiveness of numerous anti-tumor therapies depends on induction of DNA damage therefore tumor cells expressing abnormalities in genes whose products are crucial for DNA repair pathways are promising targets for synthetic lethality. Here, we discuss mechanistic aspects of synthetic lethality in the context of deficiencies in DNA double strand break repair pathways. In addition, we review clinical trials utilizing synthetic lethality interactions and discuss the mechanisms of resistance.
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Affiliation(s)
- Monika Toma
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
| | - Tomasz Skorski
- Department of Microbiology and Immunology, 3400 North Broad Street, Temple University Lewis Katz School of Medicine, Philadelphia, PA 19140, United States
| | - Tomasz Sliwinski
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Pomorska 141/143, 90-236 Lodz, Poland
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Plugged into the Ku-DNA hub: The NHEJ network. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:62-76. [PMID: 30851288 DOI: 10.1016/j.pbiomolbio.2019.03.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 02/26/2019] [Accepted: 03/01/2019] [Indexed: 12/16/2022]
Abstract
In vertebrates, double-strand breaks in DNA are primarily repaired by Non-Homologous End-Joining (NHEJ). The ring-shaped Ku heterodimer rapidly senses and threads onto broken DNA ends forming a recruiting hub. Through protein-protein contacts eventually reinforced by protein-DNA interactions, the Ku-DNA hub attracts a series of specialized proteins with scaffolding and/or enzymatic properties. To shed light on these dynamic interplays, we review here current knowledge on proteins directly interacting with Ku and on the contact points involved, with a particular accent on the different classes of Ku-binding motifs identified in several Ku partners. An integrated structural model of the core NHEJ network at the synapsis step is proposed.
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18
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Targeting the DNA-PK complex: Its rationale use in cancer and HIV-1 infection. Biochem Pharmacol 2018; 160:80-91. [PMID: 30529192 DOI: 10.1016/j.bcp.2018.12.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 12/04/2018] [Indexed: 02/07/2023]
Abstract
The DNA-PK complex is the major component of the predominant mechanism of DSB repair in humans. In addition, this complex is involved in many other processes such as DNA recombination, genome maintenance, apoptosis and transcription regulation. Several studies have linked the decrease of the DNA-PK activity with cancer initiation, due to defects in the repair. On another hand, higher DNA-PK expression and activity have been observed in various other tumor cells and have been linked with a decrease of the efficiency of anti-tumor drugs. It has also been shown that DNA-PK is critical for the integration of the HIV-1 DNA into the cell host genome and promotes replication and transcription of the virus. Targeting this complex makes therefore sense to treat these two pathologies. However, according to the status of HIV-1 replication (active versus latent replication) or to the tumor grade cells (initiation versus metastasis), the way to target this DNA-PK complex might be rather different. In this review, we discuss the importance of DNA-PK complex in two major pathologies i.e. HIV-1 infection and cancer, and the rationale use of therapies aiming to target this complex.
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Wang M, Ji Y, Feng S, Liu C, Xiao Z, Wang X, Wang Y, Xia G. The non-random patterns of genetic variation induced by asymmetric somatic hybridization in wheat. BMC PLANT BIOLOGY 2018; 18:244. [PMID: 30332989 PMCID: PMC6192298 DOI: 10.1186/s12870-018-1474-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 10/05/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND Asymmetric somatic hybridization is an efficient crop breeding approach by introducing several exogenous chromatin fragments, which leads to genomic shock and therefore induces genome-wide genetic variation. However, the fundamental question concerning the genetic variation such as whether it occurs randomly and suffers from selection pressure remains unknown. RESULTS Here, we explored this issue by comparing expressed sequence tags of a common wheat cultivar and its asymmetric somatic hybrid line. Both nucleotide substitutions and indels (insertions and deletions) had lower frequencies in coding sequences than in un-translated regions. The frequencies of nucleotide substitutions and indels were both comparable between chromosomes with and without introgressed fragments. Nucleotide substitutions distributed unevenly and were preferential to indel-flanking sequences, and the frequency of nucleotide substitutions at 5'-flanking sequences of indels was obviously higher in chromosomes with introgressed fragments than in those without exogenous fragment. Nucleotide substitutions and indels both had various frequencies among seven groups of allelic chromosomes, and the frequencies of nucleotide substitutions were strongly negatively correlative to those of indels. Among three sets of genomes, the frequencies of nucleotide substitutions and indels were both heterogeneous, and the frequencies of nucleotide substitutions exhibited drastically positive correlation to those of indels. CONCLUSIONS Our work demonstrates that the genetic variation induced by asymmetric somatic hybridization is attributed to both whole genomic shock and local chromosomal shock, which is a predetermined and non-random genetic event being closely associated with selection pressure. Asymmetric somatic hybrids provide a worthwhile model to further investigate the nature of genomic shock induced genetic variation.
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Affiliation(s)
- Mengcheng Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Yujie Ji
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, 210095 China
| | - Shiting Feng
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Chun Liu
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Zhen Xiao
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Xiaoping Wang
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
| | - Yanxia Wang
- Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050041 China
| | - Guangmin Xia
- The Key Laboratory of Plant Cell Engineering and Germplasm Innovation, Ministry of Education, School of Life Science, Shandong University, 27 Shandanan Road, Jinan, Shandong 250100 People’s Republic of China
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20
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Nemoz C, Ropars V, Frit P, Gontier A, Drevet P, Yu J, Guerois R, Pitois A, Comte A, Delteil C, Barboule N, Legrand P, Baconnais S, Yin Y, Tadi S, Barbet-Massin E, Berger I, Le Cam E, Modesti M, Rothenberg E, Calsou P, Charbonnier JB. XLF and APLF bind Ku80 at two remote sites to ensure DNA repair by non-homologous end joining. Nat Struct Mol Biol 2018; 25:971-980. [PMID: 30291363 PMCID: PMC6234012 DOI: 10.1038/s41594-018-0133-6] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 08/21/2018] [Indexed: 12/20/2022]
Abstract
The Ku70-Ku80 (Ku) heterodimer binds rapidly and tightly to the ends of DNA double-strand breaks and recruits factors of the non-homologous end-joining (NHEJ) repair pathway through molecular interactions that remain unclear. We have determined crystal structures of the Ku-binding motifs (KBM) of the NHEJ proteins APLF (A-KBM) and XLF (X-KBM) bound to a Ku-DNA complex. The two KBM motifs bind remote sites of the Ku80 α/β domain. The X-KBM occupies an internal pocket formed by an unprecedented large outward rotation of the Ku80 α/β domain. We observe independent recruitment of the APLF-interacting protein XRCC4 and of XLF to laser-irradiated sites via binding of A- and X-KBMs, respectively, to Ku80. Finally, we show that mutation of the X-KBM and A-KBM binding sites in Ku80 compromises both the efficiency and accuracy of end joining and cellular radiosensitivity. A- and X-KBMs may represent two initial anchor points to build the intricate interaction network required for NHEJ.
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Affiliation(s)
- Clement Nemoz
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Virginie Ropars
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Philippe Frit
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Amandine Gontier
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Pascal Drevet
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Jinchao Yu
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Raphaël Guerois
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurelien Pitois
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Audrey Comte
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Christine Delteil
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Nadia Barboule
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France
| | - Pierre Legrand
- Synchrotron Soleil, L'Orme des Merisiers, Saint-Aubin, Gif-sur-Yvette, France
| | - Sonia Baconnais
- Signalisations, Noyaux et Innovations en Cancérologie, UMR 8126, CNRS, Université Paris-Sud, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Yandong Yin
- New York University School of Medicine, Perlmutter Cancer Center, New York, USA
| | - Satish Tadi
- Cancer Research Center of Marseille, CNRS UMR 7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | | | - Imre Berger
- BrisSynBio Centre, School of Biochemistry, Faculty of Biomedical Sciences, University of Bristol, Bristol, UK
| | - Eric Le Cam
- Signalisations, Noyaux et Innovations en Cancérologie, UMR 8126, CNRS, Université Paris-Sud, Gustave Roussy, Université Paris-Saclay, Villejuif, France
| | - Mauro Modesti
- Cancer Research Center of Marseille, CNRS UMR 7258, Inserm U1068, Institut Paoli-Calmettes, Aix-Marseille Université UM105, Marseille, France
| | - Eli Rothenberg
- New York University School of Medicine, Perlmutter Cancer Center, New York, USA
| | - Patrick Calsou
- Institut de Pharmacologie et Biologie Structurale, IPBS, Université de Toulouse, CNRS, UPS, Toulouse, France.
- Equipe Labellisée Ligue Contre le Cancer 2018, Toulouse, France.
| | - Jean Baptiste Charbonnier
- Institute for Integrative Biology of the Cell, Institute Joliot, CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette, France.
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George VC, Ansari SA, Chelakkot VS, Chelakkot AL, Chelakkot C, Menon V, Ramadan W, Ethiraj KR, El-Awady R, Mantso T, Mitsiogianni M, Panagiotidis MI, Dellaire G, Vasantha Rupasinghe HP. DNA-dependent protein kinase: Epigenetic alterations and the role in genomic stability of cancer. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 780:92-105. [PMID: 31395353 DOI: 10.1016/j.mrrev.2018.06.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/13/2018] [Indexed: 12/28/2022]
Abstract
DNA-dependent protein kinase (DNA-PK), a member of phosphatidylinositol-kinase family, is a key protein in mammalian DNA double-strand break (DSB) repair that helps to maintain genomic integrity. DNA-PK also plays a central role in immune cell development and protects telomerase during cellular aging. Epigenetic deregulation due to endogenous and exogenous factors may affect the normal function of DNA-PK, which in turn could impair DNA repair and contribute to genomic instability. Recent studies implicate a role for epigenetics in the regulation of DNA-PK expression in normal and cancer cells, which may impact cancer progression and metastasis as well as provide opportunities for treatment and use of DNA-PK as a novel cancer biomarker. In addition, several small molecules and biological agents have been recently identified that can inhibit DNA-PK function or expression, and thus hold promise for cancer treatments. This review discusses the impact of epigenetic alterations and the expression of DNA-PK in relation to the DNA repair mechanisms with a focus on its differential levels in normal and cancer cells.
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Affiliation(s)
- Vazhappilly Cijo George
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada; Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Shabbir Ahmed Ansari
- Department of Cellular and Molecular Biology, The University of Texas Health Science Center at Tyler, Tyler, TX, United States
| | - Vipin Shankar Chelakkot
- Division of BioMedical Sciences, Faculty of Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada
| | | | - Chaithanya Chelakkot
- Division of Integrative Biosciences and Biotechnology, Pohang University of Science and Technology, Pohang, Republic of Korea
| | - Varsha Menon
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates
| | - Wafaa Ramadan
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Medicine, University of Sharjah, Sharjah, United Arab Emirates
| | | | - Raafat El-Awady
- Sharjah Institute for Medical Research, University of Sharjah, Sharjah, United Arab Emirates; College of Pharmacy, University of Sharjah, Sharjah, United Arab Emirates; Cancer Biology Department, National Cancer Institute and College of Medicine, Cairo University, Cairo, Egypt
| | - Theodora Mantso
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada; Department of Applied Sciences, Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Melina Mitsiogianni
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada; Department of Applied Sciences, Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Mihalis I Panagiotidis
- Department of Applied Sciences, Faculty of Health & Life Sciences, Northumbria University, Newcastle upon Tyne, United Kingdom
| | - Graham Dellaire
- Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada
| | - H P Vasantha Rupasinghe
- Department of Plant, Food, and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, NS, Canada; Department of Pathology, Faculty of Medicine, Dalhousie University, Halifax, NS, Canada.
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22
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Torrecilla I, Oehler J, Ramadan K. The role of ubiquitin-dependent segregase p97 (VCP or Cdc48) in chromatin dynamics after DNA double strand breaks. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0282. [PMID: 28847819 PMCID: PMC5577460 DOI: 10.1098/rstb.2016.0282] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 12/27/2022] Open
Abstract
DNA double strand breaks (DSBs) are the most cytotoxic DNA lesions and, if not repaired, lead to chromosomal rearrangement, genomic instability and cell death. Cells have evolved a complex network of DNA repair and signalling molecules which promptly detect and repair DSBs, commonly known as the DNA damage response (DDR). The DDR is orchestrated by various post-translational modifications such as phosphorylation, methylation, ubiquitination or SUMOylation. As DSBs are located in complex chromatin structures, the repair of DSBs is engineered at two levels: (i) at sites of broken DNA and (ii) at chromatin structures that surround DNA lesions. Thus, DNA repair and chromatin remodelling machineries must work together to efficiently repair DSBs. Here, we summarize the current knowledge of the ubiquitin-dependent molecular unfoldase/segregase p97 (VCP in vertebrates and Cdc48 in worms and lower eukaryotes) in DSB repair. We identify p97 as an essential factor that regulates DSB repair. p97-dependent extraction of ubiquitinated substrates mediates spatio-temporal protein turnover at and around the sites of DSBs, thus orchestrating chromatin remodelling and DSB repair. As p97 is a druggable target, p97 inhibition in the context of DDR has great potential for cancer therapy, as shown for other DDR components such as PARP, ATR and CHK1.This article is part of the themed issue 'Chromatin modifiers and remodellers in DNA repair and signalling'.
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Affiliation(s)
- Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Judith Oehler
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, UK
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23
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Khodaverdian VY, Hanscom T, Yu AM, Yu TL, Mak V, Brown AJ, Roberts SA, McVey M. Secondary structure forming sequences drive SD-MMEJ repair of DNA double-strand breaks. Nucleic Acids Res 2018; 45:12848-12861. [PMID: 29121353 PMCID: PMC5728401 DOI: 10.1093/nar/gkx1056] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 10/18/2017] [Indexed: 12/29/2022] Open
Abstract
Alternative end-joining (alt-EJ) repair of DNA double-strand breaks is associated with deletions, chromosome translocations, and genome instability. Alt-EJ frequently uses annealing of microhomologous sequences to tether broken ends. When accessible pre-existing microhomologies do not exist, we have postulated that new microhomologies can be created via limited DNA synthesis at secondary-structure forming sequences. This model, called synthesis-dependent microhomology-mediated end joining (SD-MMEJ), predicts that differences between DNA sequences near double-strand breaks should alter repair outcomes in predictable ways. To test this hypothesis, we injected plasmids with sequence variations flanking an I-SceI endonuclease recognition site into I-SceI expressing Drosophila embryos and used Illumina amplicon sequencing to compare repair junctions. As predicted by the model, we found that small changes in sequences near the I-SceI site had major impacts on the spectrum of repair junctions. Bioinformatic analyses suggest that these repair differences arise from transiently forming loops and hairpins within 30 nucleotides of the break. We also obtained evidence for ‘trans SD-MMEJ,’ involving at least two consecutive rounds of microhomology annealing and synthesis across the break site. These results highlight the importance of sequence context for alt-EJ repair and have important implications for genome editing and genome evolution.
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Affiliation(s)
- Varandt Y Khodaverdian
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Terrence Hanscom
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Amy Marie Yu
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Taylor L Yu
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Victoria Mak
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
| | - Alexander J Brown
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Steven A Roberts
- School of Molecular Biosciences, Washington State University, P100 Dairy Road, Pullman, WA 99164, USA
| | - Mitch McVey
- Department of Biology, Tufts University, 200 Boston Avenue, Suite 4700, Medford, MA 02155, USA
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24
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Sidorova J. A game of substrates: replication fork remodeling and its roles in genome stability and chemo-resistance. Cell Stress 2017; 1:115-133. [PMID: 29355244 PMCID: PMC5771654 DOI: 10.15698/cst2017.12.114] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 11/27/2017] [Accepted: 11/29/2017] [Indexed: 01/06/2023] Open
Abstract
During the hours that human cells spend in the DNA synthesis (S) phase of the cell cycle, they may encounter adversities such as DNA damage or shortage of nucleotides. Under these stresses, replication forks in DNA may experience slowing, stalling, and breakage. Fork remodeling mechanisms, which stabilize slow or stalled replication forks and ensure their ability to continue or resume replication, protect cells from genomic instability and carcinogenesis. Fork remodeling includes DNA strand exchanges that result in annealing of newly synthesized strands (fork reversal), controlled DNA resection, and cleavage of DNA strands. Defects in major tumor suppressor genes BRCA1 and BRCA2, and a subset of the Fanconi Anemia genes have been shown to result in deregulation in fork remodeling, and most prominently, loss of kilobases of nascent DNA from stalled replication forks. This phenomenon has recently gained spotlight as a potential marker and mediator of chemo-sensitivity in cancer cells and, conversely, its suppression - as a hallmark of acquired chemo-resistance. Moreover, nascent strand degradation at forks is now known to also trigger innate immune response to self-DNA. An increasingly sophisticated molecular description of these events now points at a combination of unbalanced fork reversal and end-resection as a root cause, yet also reveals the multi-layered complexity and heterogeneity of the underlying processes in normal and cancer cells.
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Affiliation(s)
- Julia Sidorova
- Department of Pathology, University of Washington, Seattle, Washington, USA
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25
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Myler LR, Gallardo IF, Soniat MM, Deshpande RA, Gonzalez XB, Kim Y, Paull TT, Finkelstein IJ. Single-Molecule Imaging Reveals How Mre11-Rad50-Nbs1 Initiates DNA Break Repair. Mol Cell 2017; 67:891-898.e4. [PMID: 28867292 PMCID: PMC5609712 DOI: 10.1016/j.molcel.2017.08.002] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 06/07/2017] [Accepted: 08/04/2017] [Indexed: 11/21/2022]
Abstract
DNA double-strand break (DSB) repair is essential for maintaining our genomes. Mre11-Rad50-Nbs1 (MRN) and Ku70-Ku80 (Ku) direct distinct DSB repair pathways, but the interplay between these complexes at a DSB remains unclear. Here, we use high-throughput single-molecule microscopy to show that MRN searches for free DNA ends by one-dimensional facilitated diffusion, even on nucleosome-coated DNA. Rad50 binds homoduplex DNA and promotes facilitated diffusion, whereas Mre11 is required for DNA end recognition and nuclease activities. MRN gains access to occluded DNA ends by removing Ku or other DNA adducts via an Mre11-dependent nucleolytic reaction. Next, MRN loads exonuclease 1 (Exo1) onto the free DNA ends to initiate DNA resection. In the presence of replication protein A (RPA), MRN acts as a processivity factor for Exo1, retaining the exonuclease on DNA for long-range resection. Our results provide a mechanism for how MRN promotes homologous recombination on nucleosome-coated DNA.
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Affiliation(s)
- Logan R Myler
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ignacio F Gallardo
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Michael M Soniat
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Rajashree A Deshpande
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xenia B Gonzalez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Yoori Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Tanya T Paull
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Howard Hughes Medical Institute, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ilya J Finkelstein
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712, USA; Center for Systems and Synthetic Biology, The University of Texas at Austin, Austin, TX 78712, USA.
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26
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Chandra A, Wang L, Young T, Zhong L, Tseng WJ, Levine MA, Cengel K, Liu XS, Zhang Y, Pignolo RJ, Qin L. Proteasome inhibitor bortezomib is a novel therapeutic agent for focal radiation-induced osteoporosis. FASEB J 2017; 32:52-62. [PMID: 28860152 DOI: 10.1096/fj.201700375r] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 08/14/2017] [Indexed: 12/23/2022]
Abstract
Bone atrophy and its related fragility fractures are frequent, late side effects of radiotherapy in cancer survivors and have a detrimental impact on their quality of life. In another study, we showed that parathyroid hormone 1-34 and anti-sclerostin antibody attenuates radiation-induced bone damage by accelerating DNA repair in osteoblasts. DNA damage responses are partially regulated by the ubiquitin proteasome pathway. In the current study, we examined whether proteasome inhibitors have similar bone-protective effects against radiation damage. MG132 treatment greatly reduced radiation-induced apoptosis in cultured osteoblastic cells. This survival effect was owing to accelerated DNA repair as revealed by γH2AX foci and comet assays and to the up-regulation of Ku70 and DNA-dependent protein kinase, catalytic subunit, essential DNA repair proteins in the nonhomologous end-joining pathway. Administration of bortezomib (Bzb) reversed the loss of trabecular bone structure and strength in mice at 4 wk after focal radiation. Histomorphometry revealed that Bzb significantly increased the number of osteoblasts and activity in the irradiated area and suppressed the number and activity of osteoclasts, regardless of irradiation. Two weeks of Bzb treatment accelerated DNA repair in bone-lining osteoblasts and thus promoted their survival. Meanwhile, it also inhibited bone marrow adiposity. Taken together, we demonstrate a novel role of proteasome inhibitors in treating radiation-induced osteoporosis.-Chandra, A., Wang, L., Young, T., Zhong, L., Tseng, W.-J., Levine, M. A., Cengel, K., Liu, X. S., Zhang, Y., Pignolo, R. J., Qin, L. Proteasome inhibitor bortezomib is a novel therapeutic agent for focal radiation-induced osteoporosis.
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Affiliation(s)
- Abhishek Chandra
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA.,Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Luqiang Wang
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Tiffany Young
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Leilei Zhong
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Wei-Ju Tseng
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Michael A Levine
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Endocrinology and Diabetes Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Center for Bone Health, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Keith Cengel
- Department of Radiation Oncology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - X Sherry Liu
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Yejia Zhang
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Department of Physical Medicine and Rehabilitation, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Translational Musculoskeletal Research Center (TMRC), Corporal Michael J. Crescenz Veterans Affairs Medical Center, Philadelphia, Pennsylvania, USA
| | | | - Ling Qin
- Department of Orthopaedic Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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27
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Xing M, Bjørås M, Daniel JA, Alt FW, Oksenych V. Synthetic lethality between murine DNA repair factors XLF and DNA-PKcs is rescued by inactivation of Ku70. DNA Repair (Amst) 2017; 57:133-138. [PMID: 28759779 PMCID: PMC5584571 DOI: 10.1016/j.dnarep.2017.07.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 06/25/2017] [Accepted: 07/24/2017] [Indexed: 11/18/2022]
Abstract
DNA double-strand breaks (DSBs) are recognized and repaired by the Classical Non-Homologous End-Joining (C-NHEJ) and Homologous Recombination pathways. C-NHEJ includes the core Ku70 and Ku80 (or Ku86) heterodimer that binds DSBs and thus promotes recruitment of accessory downstream NHEJ factors XLF, PAXX, DNA-PKcs, Artemis and other core subunits, XRCC4 and DNA Ligase 4 (Lig4). In the absence of core C-NHEJ factors, DNA repair can be performed by Alternative End-Joining, which likely depends on DNA Ligase 1 and DNA Ligase 3. Genetic inactivation of C-NHEJ factors, such as Ku70, Ku80, XLF, PAXX and DNA-PKcs results in viable mice showing increased levels of genomic instability and sensitivity to DSBs. Knockouts of XRCC4 or Lig4, on the other hand, as well as combined inactivation of XLF and DNA-PKcs, or XLF and PAXX, result in late embryonic lethality in mice, which in most cases correlate with severe apoptosis in the central nervous system. Here, we demonstrate that inactivation of the Ku70 gene rescues the synthetic lethality between XLF and DNA-PKcs, resulting in triple knockout mice that are indistinguishable from Ku70-deficient littermates by size or levels of genomic instability. Moreover, we find that combined inactivation of Ku70 and XLF results in viable mice. Together, these findings suggest that Ku70 is epistatic with XLF and DNA-PKcs and support a model in which inactivation of Ku70 allows DNA lesions to become accessible to alternative DNA repair pathways.
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Affiliation(s)
- Mengtan Xing
- Institute for Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons Gate 1, 7491 Trondheim, Norway
| | - Magnar Bjørås
- Institute for Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons Gate 1, 7491 Trondheim, Norway
| | - Jeremy A Daniel
- The NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States.
| | - Valentyn Oksenych
- Institute for Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Laboratory Center, Erling Skjalgssons Gate 1, 7491 Trondheim, Norway; The NNF Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, 2200 Copenhagen, Denmark; Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine, Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02115, United States; St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway.
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28
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Qiu Z, Zhang Z, Roschke A, Varga T, Aplan PD. Generation of Gross Chromosomal Rearrangements by a Single Engineered DNA Double Strand Break. Sci Rep 2017; 7:43156. [PMID: 28225067 PMCID: PMC5320478 DOI: 10.1038/srep43156] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/19/2017] [Indexed: 01/08/2023] Open
Abstract
Gross chromosomal rearrangements (GCRs), including translocations, inversions amplifications, and deletions, can be causal events leading to malignant transformation. GCRs are thought to be triggered by DNA double strand breaks (DSBs), which in turn can be spontaneous or induced by external agents (eg. cytotoxic chemotherapy, ionizing radiation). It has been shown that induction of DNA DSBs at two defined loci can produce stable balanced chromosomal translocations, however, a single engineered DNA DSB could not. Herein, we report that although a single engineered DNA DSB in H2AX “knockdown” cells did not generate GCRs, repair of a single engineered DNA DSB in fibroblasts that had ablated H2ax did produce clonal, stable GCRs, including balanced translocations and megabase-pair inversions. Upon correction of the H2ax deficiency, cells no longer generated GCRs following a single engineered DNA DSB. These findings demonstrate that clonal, stable GCRs can be produced by a single engineered DNA DSB in H2ax knockout cells, and that the production of these GCRs is ameliorated by H2ax expression.
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Affiliation(s)
- Zhijun Qiu
- Genetics Branch National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zhenhua Zhang
- Genetics Branch National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anna Roschke
- Genetics Branch National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tamas Varga
- Genetics Branch National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter D Aplan
- Genetics Branch National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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29
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Brown JS, O'Carrigan B, Jackson SP, Yap TA. Targeting DNA Repair in Cancer: Beyond PARP Inhibitors. Cancer Discov 2017; 7:20-37. [PMID: 28003236 PMCID: PMC5300099 DOI: 10.1158/2159-8290.cd-16-0860] [Citation(s) in RCA: 431] [Impact Index Per Article: 61.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/03/2016] [Accepted: 11/07/2016] [Indexed: 01/14/2023]
Abstract
Germline aberrations in critical DNA-repair and DNA damage-response (DDR) genes cause cancer predisposition, whereas various tumors harbor somatic mutations causing defective DDR/DNA repair. The concept of synthetic lethality can be exploited in such malignancies, as exemplified by approval of poly(ADP-ribose) polymerase inhibitors for treating BRCA1/2-mutated ovarian cancers. Herein, we detail how cellular DDR processes engage various proteins that sense DNA damage, initiate signaling pathways to promote cell-cycle checkpoint activation, trigger apoptosis, and coordinate DNA repair. We focus on novel therapeutic strategies targeting promising DDR targets and discuss challenges of patient selection and the development of rational drug combinations. SIGNIFICANCE Various inhibitors of DDR components are in preclinical and clinical development. A thorough understanding of DDR pathway complexities must now be combined with strategies and lessons learned from the successful registration of PARP inhibitors in order to fully exploit the potential of DDR inhibitors and to ensure their long-term clinical success. Cancer Discov; 7(1); 20-37. ©2016 AACR.
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Affiliation(s)
| | | | - Stephen P Jackson
- The Wellcome Trust/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom
| | - Timothy A Yap
- Royal Marsden NHS Foundation Trust, London, United Kingdom.
- The Institute of Cancer Research, London, United Kingdom
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30
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Abstract
DNA transposons are defined segments of DNA that are able to move from one genomic location to another. Movement is facilitated by one or more proteins, called the transposase, typically encoded by the mobile element itself. Here, we first provide an overview of the classification of such mobile elements in a variety of organisms. From a mechanistic perspective, we have focused on one particular group of DNA transposons that encode a transposase with a DD(E/D) catalytic domain that is topologically similar to RNase H. For these, a number of three-dimensional structures of transpososomes (transposase-nucleic acid complexes) are available, and we use these to describe the basics of their mechanisms. The DD(E/D) group, in addition to being the largest and most common among all DNA transposases, is the one whose members have been used for a wide variety of genomic applications. Therefore, a second focus of the article is to provide a nonexhaustive overview of transposon applications. Although several non-transposon-based approaches to site-directed genome modifications have emerged in the past decade, transposon-based applications are highly relevant when integration specificity is not sought. In fact, for many applications, the almost-perfect randomness and high frequency of integration make transposon-based approaches indispensable.
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Affiliation(s)
- Alison B. Hickman
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - Fred Dyda
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, United States
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31
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Balmus G, Barros AC, Wijnhoven PWG, Lescale C, Hasse HL, Boroviak K, le Sage C, Doe B, Speak AO, Galli A, Jacobsen M, Deriano L, Adams DJ, Blackford AN, Jackson SP. Synthetic lethality between PAXX and XLF in mammalian development. Genes Dev 2016; 30:2152-2157. [PMID: 27798842 PMCID: PMC5088564 DOI: 10.1101/gad.290510.116] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 09/21/2016] [Indexed: 12/14/2022]
Abstract
PAXX was identified recently as a novel nonhomologous end-joining DNA repair factor in human cells. To characterize its physiological roles, we generated Paxx-deficient mice. Like Xlf-/- mice, Paxx-/- mice are viable, grow normally, and are fertile but show mild radiosensitivity. Strikingly, while Paxx loss is epistatic with Ku80, Lig4, and Atm deficiency, Paxx/Xlf double-knockout mice display embryonic lethality associated with genomic instability, cell death in the central nervous system, and an almost complete block in lymphogenesis, phenotypes that closely resemble those of Xrcc4-/- and Lig4-/- mice. Thus, combined loss of Paxx and Xlf is synthetic-lethal in mammals.
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Affiliation(s)
- Gabriel Balmus
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | - Ana C Barros
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | - Paul W G Wijnhoven
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Chloé Lescale
- Department of Immunology, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Hélène Lenden Hasse
- Department of Immunology, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | | | - Carlos le Sage
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
| | - Brendan Doe
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | | | - Antonella Galli
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | | | - Ludovic Deriano
- Department of Immunology, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
| | - Andrew N Blackford
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
- Cancer Research UK/Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge CB2 1QN, United Kingdom
- Wellcome Trust Sanger Institute, Cambridge CB10 1HH, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
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32
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Knyazhanskaya ES, Shadrina OA, Anisenko AN, Gottikh MB. Role of DNA-dependent protein kinase in the HIV-1 replication cycle. Mol Biol 2016. [DOI: 10.1134/s0026893316040075] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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33
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McGovern S, Baconnais S, Roblin P, Nicolas P, Drevet P, Simonson H, Piétrement O, Charbonnier JB, Le Cam E, Noirot P, Lecointe F. C-terminal region of bacterial Ku controls DNA bridging, DNA threading and recruitment of DNA ligase D for double strand breaks repair. Nucleic Acids Res 2016; 44:4785-4806. [PMID: 26961308 PMCID: PMC4889933 DOI: 10.1093/nar/gkw149] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2015] [Revised: 02/26/2016] [Accepted: 02/29/2016] [Indexed: 01/15/2023] Open
Abstract
Non-homologous end joining is a ligation process repairing DNA double strand breaks in eukaryotes and many prokaryotes. The ring structured eukaryotic Ku binds DNA ends and recruits other factors which can access DNA ends through the threading of Ku inward the DNA, making this protein a key ingredient for the scaffolding of the NHEJ machinery. However, this threading ability seems unevenly conserved among bacterial Ku. As bacterial Ku differ mainly by their C-terminus, we evaluate the role of this region in the loading and the threading abilities of Bacillus subtilis Ku and the stimulation of the DNA ligase LigD. We identify two distinct sub-regions: a ubiquitous minimal C-terminal region and a frequent basic C-terminal extension. We show that truncation of one or both of these sub-regions in Bacillus subtilis Ku impairs the stimulation of the LigD end joining activity in vitro. We further demonstrate that the minimal C-terminus is required for the Ku-LigD interaction, whereas the basic extension controls the threading and DNA bridging abilities of Ku. We propose that the Ku basic C-terminal extension increases the concentration of Ku near DNA ends, favoring the recruitment of LigD at the break, thanks to the minimal C-terminal sub-region.
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Affiliation(s)
- Stephen McGovern
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Sonia Baconnais
- UMR 8126, CNRS, Gustave Roussy Université Paris Sud, Université Paris-Saclay, F-94805 Villejuif, France
| | - Pierre Roblin
- SOLEIL Synchrotron, F- 91192 Gif-sur-Yvette, INRA-URBIA, F-44316 Nantes, France
| | - Pierre Nicolas
- MaIAGE, INRA, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Pascal Drevet
- I2BC, iBiTec-S, CEA Saclay, UMR 9198, F-91191 Gif-sur-Yvette, France
| | - Héloïse Simonson
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Olivier Piétrement
- UMR 8126, CNRS, Gustave Roussy Université Paris Sud, Université Paris-Saclay, F-94805 Villejuif, France
| | | | - Eric Le Cam
- UMR 8126, CNRS, Gustave Roussy Université Paris Sud, Université Paris-Saclay, F-94805 Villejuif, France
| | - Philippe Noirot
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - François Lecointe
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
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34
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Grundy GJ, Rulten SL, Arribas-Bosacoma R, Davidson K, Kozik Z, Oliver AW, Pearl LH, Caldecott KW. The Ku-binding motif is a conserved module for recruitment and stimulation of non-homologous end-joining proteins. Nat Commun 2016; 7:11242. [PMID: 27063109 PMCID: PMC4831024 DOI: 10.1038/ncomms11242] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 03/04/2016] [Indexed: 02/04/2023] Open
Abstract
The Ku-binding motif (KBM) is a short peptide module first identified in APLF that we now show is also present in Werner syndrome protein (WRN) and in Modulator of retrovirus infection homologue (MRI). We also identify a related but functionally distinct motif in XLF, WRN, MRI and PAXX, which we denote the XLF-like motif. We show that WRN possesses two KBMs; one at the N terminus next to the exonuclease domain and one at the C terminus next to an XLF-like motif. We reveal that the WRN C-terminal KBM and XLF-like motif function cooperatively to bind Ku complexes and that the N-terminal KBM mediates Ku-dependent stimulation of WRN exonuclease activity. We also show that WRN accelerates DSB repair by a mechanism requiring both KBMs, demonstrating the importance of WRN interaction with Ku. These data define a conserved family of KBMs that function as molecular tethers to recruit and/or stimulate enzymes during NHEJ.
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Affiliation(s)
- Gabrielle J. Grundy
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Stuart L. Rulten
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Raquel Arribas-Bosacoma
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Kathryn Davidson
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Zuzanna Kozik
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Antony W. Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Laurence H. Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
| | - Keith W. Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton BN1 9RQ, UK
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35
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Dai L, Cao Y, Chen Y, Kaleeba JAR, Zabaleta J, Qin Z. Genomic analysis of xCT-mediated regulatory network: Identification of novel targets against AIDS-associated lymphoma. Oncotarget 2016; 6:12710-22. [PMID: 25860939 PMCID: PMC4494968 DOI: 10.18632/oncotarget.3710] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 03/10/2015] [Indexed: 02/06/2023] Open
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the etiological agent of primary effusion lymphoma (PEL), a rapidly progressing malignancy mostly arising in HIV-infected patients. Even under conventional chemotherapy, PEL continues to portend nearly 100% mortality within several months, which urgently requires novel therapeutic strategies. We have previously demonstrated that targeting xCT, an amino acid transporter for cystine/glutamate exchange, induces significant PEL cell apoptosis through regulation of multiple host and viral factors. More importantly, one of xCT selective inhibitors, Sulfasalazine (SASP), effectively prevents PEL tumor progression in an immune-deficient xenograft model. In the current study, we use Illumina microarray to explore the profile of genes altered by SASP treatment within 3 KSHV+ PEL cell-lines, and discover that many genes involved in oxidative stress/antioxidant defense system, apoptosis/anti-apoptosis/cell death, and cellular response to unfolded proteins/topologically incorrect proteins are potentially regulated by xCT. We further validate 2 downstream candidates, OSGIN1 (oxidative stress-induced growth inhibitor 1) and XRCC5 (X-ray repair cross-complementing protein 5), and evaluate their functional relationship with PEL cell survival/proliferation and chemoresistance, respectively. Together, our data indicate that targeting these novel xCT-regulated downstream genes may represent a promising new therapeutic strategy against PEL and/or other AIDS-related lymphoma.
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Affiliation(s)
- Lu Dai
- Research Center for Translational Medicine and Key Laboratory of Arrhythmias of The Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Medicine, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
| | - Yueyu Cao
- Research Center for Translational Medicine and Key Laboratory of Arrhythmias of The Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yihan Chen
- Research Center for Translational Medicine and Key Laboratory of Arrhythmias of The Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Johnan A R Kaleeba
- Department of Microbiology and Immunology, Uniformed Services University of The Health Sciences, Bethesda, MD, USA
| | - Jovanny Zabaleta
- Department of Pediatrics, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
| | - Zhiqiang Qin
- Research Center for Translational Medicine and Key Laboratory of Arrhythmias of The Ministry of Education of China, East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Microbiology/Immunology/Parasitology, Louisiana State University Health Sciences Center, Louisiana Cancer Research Center, New Orleans, LA, USA
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36
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Berthelot V, Mouta-Cardoso G, Hégarat N, Guillonneau F, François JC, Giovannangeli C, Praseuth D, Rusconi F. The human DNA ends proteome uncovers an unexpected entanglement of functional pathways. Nucleic Acids Res 2016; 44:4721-33. [PMID: 26921407 PMCID: PMC4889927 DOI: 10.1093/nar/gkw121] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/17/2016] [Indexed: 01/06/2023] Open
Abstract
DNA ends get exposed in cells upon either normal or dysfunctional cellular processes or molecular events. Telomeres need to be protected by the shelterin complex to avoid junctions occurring between chromosomes while failing topoisomerases or clustered DNA damage processing may produce double-strand breaks, thus requiring swift repair to avoid cell death. The rigorous study of the great many proteins involved in the maintenance of DNA integrity is a challenging task because of the innumerous unspecific electrostatic and/or hydrophobic DNA—protein interactions that arise due to the chemical nature of DNA. We devised a technique that discriminates the proteins recruited specifically at DNA ends from those that bind to DNA because of a generic affinity for the double helix. Our study shows that the DNA ends proteome comprises proteins of an unexpectedly wide functional spectrum, ranging from DNA repair to ribosome biogenesis and cytoskeleton, including novel proteins of undocumented function. A global mapping of the identified proteome on published DNA repair protein networks demonstrated the excellent specificity and functional coverage of our purification technique. Finally, the native nucleoproteic complexes that assembled specifically onto DNA ends were shown to be endowed with a highly efficient DNA repair activity.
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Affiliation(s)
- Vivien Berthelot
- Laboratoire de chimie physique, UMR CNRS 8000, University of Paris-Sud, F-91400 Orsay, France
| | - Gildas Mouta-Cardoso
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - Nadia Hégarat
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - François Guillonneau
- Plateforme de spectrométrie de masse 3P5, Institut Cochin, F-75014 Paris, France
| | - Jean-Christophe François
- Inserm and Sorbonne Universities, UPMC, UMR_S 938, Research Center Saint-Antoine, F-75012 Paris, France
| | - Carine Giovannangeli
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - Danièle Praseuth
- Structure et Instabilité des Génomes, INSERM U1154, UMR CNRS/MNHN 7196, F-75005 Paris, France
| | - Filippo Rusconi
- Laboratoire de chimie physique, UMR CNRS 8000, University of Paris-Sud, F-91400 Orsay, France
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37
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Chang CH, Zhang M, Rajapakshe K, Coarfa C, Edwards D, Huang S, Rosen JM. Mammary Stem Cells and Tumor-Initiating Cells Are More Resistant to Apoptosis and Exhibit Increased DNA Repair Activity in Response to DNA Damage. Stem Cell Reports 2015; 5:378-91. [PMID: 26300228 PMCID: PMC4618454 DOI: 10.1016/j.stemcr.2015.07.009] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Revised: 07/22/2015] [Accepted: 07/23/2015] [Indexed: 01/05/2023] Open
Abstract
Adult stem cells and tumor-initiating cells (TICs) often employ different mechanisms of DNA damage response (DDR) as compared to other tissue cell types. However, little is known about how mammary stem cells (MaSCs) and mammary TICs respond to DNA damage. Using the mouse mammary gland and syngeneic p53-null tumors as models, we investigated the molecular and physiological consequences of DNA damage in wild-type MaSCs, p53-null MaSCs, and p53-null TICs. We showed that wild-type MaSCs and basal cells are more resistant to apoptosis and exhibit increased non-homologous end joining (NHEJ) activity. Loss of p53 in mammary epithelium affected both cell-cycle regulation and DNA repair efficiency. In p53-null tumors, we showed that TICs are more resistant to ionizing radiation (IR) due to decreased apoptosis, elevated NHEJ activity, and more-rapid DNA repair. These results have important implications for understanding DDR mechanisms involved in both tumorigenesis and therapy resistance. MaSCs are more resistant to apoptosis and exhibit increased NHEJ activity Loss of p53 in MECs impairs cell-cycle regulation and DNA repair efficiency TICs exhibit decreased apoptosis, increased DNA repair efficiency, and NHEJ activity TICs are highly proliferative and exhibit improper cell-cycle regulation after IR
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Affiliation(s)
- Chi-Hsuan Chang
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mei Zhang
- Department of Developmental Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Kimal Rajapakshe
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Dean Edwards
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shixia Huang
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jeffrey M Rosen
- Integrative Molecular and Biomedical Sciences Graduate Program, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
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38
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Mikhed Y, Görlach A, Knaus UG, Daiber A. Redox regulation of genome stability by effects on gene expression, epigenetic pathways and DNA damage/repair. Redox Biol 2015; 5:275-289. [PMID: 26079210 PMCID: PMC4475862 DOI: 10.1016/j.redox.2015.05.008] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 05/28/2015] [Accepted: 05/29/2015] [Indexed: 02/07/2023] Open
Abstract
Reactive oxygen and nitrogen species (e.g. H2O2, nitric oxide) confer redox regulation of essential cellular signaling pathways such as cell differentiation, proliferation, migration and apoptosis. In addition, classical regulation of gene expression or activity, including gene transcription to RNA followed by translation to the protein level, by transcription factors (e.g. NF-κB, HIF-1α) and mRNA binding proteins (e.g. GAPDH, HuR) is subject to redox regulation. This review will give an update of recent discoveries in this field, and specifically highlight the impact of reactive oxygen and nitrogen species on DNA repair systems that contribute to genomic stability. Emphasis will be placed on the emerging role of redox mechanisms regulating epigenetic pathways (e.g. miRNA, DNA methylation and histone modifications). By providing clinical correlations we discuss how oxidative stress can impact on gene regulation/activity and vise versa, how epigenetic processes, other gene regulatory mechanisms and DNA repair can influence the cellular redox state and contribute or prevent development or progression of disease.
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Affiliation(s)
- Yuliya Mikhed
- 2nd Medical Clinic, Department of Cardiology, Medical Center of the Johannes Gutenberg University, Mainz, Germany
| | - Agnes Görlach
- German Heart Center Munich at the Technical University Munich, DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - Ulla G Knaus
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - Andreas Daiber
- 2nd Medical Clinic, Department of Cardiology, Medical Center of the Johannes Gutenberg University, Mainz, Germany.
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39
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Richter KS, Jeske H. KU80, a key factor for non-homologous end-joining, retards geminivirus multiplication. J Gen Virol 2015; 96:2913-2918. [PMID: 26297035 DOI: 10.1099/jgv.0.000224] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
KU80 is well-known as a key component of the non-homologous end-joining pathway used to repair DNA double-strand breaks. In addition, the KU80-containing DNA-dependent protein kinase complex in mammals can act as a cytoplasmic sensor for viral DNA to activate innate immune response. We have now, to our knowledge for the first time, demonstrated that the speed of a systemic infection with a plant DNA geminivirus in Arabidopsis thaliana is KU80-dependent. The early emergence of Euphorbia yellow mosaic virus DNA was significantly increased in ku80 knockout mutants compared with wild-type sibling controls. The possible impact of KU80 on geminivirus multiplication by generating non-productive viral DNAs or its role as a pattern-recognition receptor against DNA virus infection is discussed.
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Affiliation(s)
- Kathrin S Richter
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
| | - Holger Jeske
- Institute of Biomaterials and Biomolecular Systems, Department of Molecular Biology and Plant Virology, University of Stuttgart, Pfaffenwaldring 57, D-70550 Stuttgart, Germany
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40
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XRCC4/XLF Interaction Is Variably Required for DNA Repair and Is Not Required for Ligase IV Stimulation. Mol Cell Biol 2015; 35:3017-28. [PMID: 26100018 DOI: 10.1128/mcb.01503-14] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 06/15/2015] [Indexed: 01/21/2023] Open
Abstract
The classic nonhomologous end-joining (c-NHEJ) pathway is largely responsible for repairing double-strand breaks (DSBs) in mammalian cells. XLF stimulates the XRCC4/DNA ligase IV complex by an unknown mechanism. XLF interacts with XRCC4 to form filaments of alternating XRCC4 and XLF dimers that bridge DNA ends in vitro, providing a mechanism by which XLF might stimulate ligation. Here, we characterize two XLF mutants that do not interact with XRCC4 and cannot form filaments or bridge DNA in vitro. One mutant is fully sufficient in stimulating ligation by XRCC4/Lig4 in vitro; the other is not. This separation-of-function mutant (which must function as an XLF homodimer) fully complements the c-NHEJ deficits of some XLF-deficient cell strains but not others, suggesting a variable requirement for XRCC4/XLF interaction in living cells. To determine whether the lack of XRCC4/XLF interaction (and potential bridging) can be compensated for by other factors, candidate repair factors were disrupted in XLF- or XRCC4-deficient cells. The loss of either ATM or the newly described XRCC4/XLF-like factor, PAXX, accentuates the requirement for XLF. However, in the case of ATM/XLF loss (but not PAXX/XLF loss), this reflects a greater requirement for XRCC4/XLF interaction.
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41
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Mistrik M, Bartek J. What a 'Ku'incidence!: parallel discoveries of a new DNA repair factor. Cell Death Differ 2015; 22:888-9. [PMID: 25941165 PMCID: PMC4423193 DOI: 10.1038/cdd.2015.32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- M Mistrik
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
| | - J Bartek
- Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacky University, Olomouc, Czech Republic
- Danish Cancer Society Research Center, Copenhagen, Denmark
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42
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Brown JS, Lukashchuk N, Sczaniecka-Clift M, Britton S, le Sage C, Calsou P, Beli P, Galanty Y, Jackson SP. Neddylation promotes ubiquitylation and release of Ku from DNA-damage sites. Cell Rep 2015; 11:704-14. [PMID: 25921528 PMCID: PMC4431666 DOI: 10.1016/j.celrep.2015.03.058] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 11/12/2014] [Accepted: 03/25/2015] [Indexed: 11/24/2022] Open
Abstract
The activities of many DNA-repair proteins are controlled through reversible covalent modification by ubiquitin and ubiquitin-like molecules. Nonhomologous end-joining (NHEJ) is the predominant DNA double-strand break (DSB) repair pathway in mammalian cells and is initiated by DSB ends being recognized by the Ku70/Ku80 (Ku) heterodimer. By using MLN4924, an anti-cancer drug in clinical trials that specifically inhibits conjugation of the ubiquitin-like protein, NEDD8, to target proteins, we demonstrate that NEDD8 accumulation at DNA-damage sites is a highly dynamic process. In addition, we show that depleting cells of the NEDD8 E2-conjugating enzyme, UBE2M, yields ionizing radiation hypersensitivity and reduced cell survival following NHEJ. Finally, we demonstrate that neddylation promotes Ku ubiquitylation after DNA damage and release of Ku and Ku-associated proteins from damage sites following repair. These studies provide insights into how the NHEJ core complex dissociates from repair sites and highlight its importance for cell survival following DSB induction.
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Affiliation(s)
- Jessica S Brown
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Natalia Lukashchuk
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Matylda Sczaniecka-Clift
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Sébastien Britton
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK; Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse-Université Paul Sabatier, Equipe Labellisée Ligue contre le Cancer, 31077 Toulouse, France
| | - Carlos le Sage
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK
| | - Patrick Calsou
- Institut de Pharmacologie et de Biologie Structurale, CNRS, Université de Toulouse-Université Paul Sabatier, Equipe Labellisée Ligue contre le Cancer, 31077 Toulouse, France
| | - Petra Beli
- Institute of Molecular Biology (IMB), 55128 Mainz, Germany.
| | - Yaron Galanty
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK.
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge 2 1QN, UK.
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43
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Koike M, Yutoku Y, Koike A. Nuclear localization of mouse Ku70 in interphase cells and focus formation of mouse Ku70 at DNA damage sites immediately after irradiation. J Vet Med Sci 2015; 77:1137-42. [PMID: 25947323 PMCID: PMC4591156 DOI: 10.1292/jvms.14-0651] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
To elucidate the mechanisms of DNA repair pathway is critical for developing next-generation radiotherapies and chemotherapeutic drugs for cancer. Ionizing radiation and many chemotherapeutic drugs kill tumor cells mainly by inducing DNA double-strand breaks (DSBs). The classical nonhomologous DNA-end joining (NHEJ) (C-NHEJ) pathway repairs a predominant fraction of DSBs in mammalian cells. The C-NHEJ pathway appears to start with the binding of Ku (heterodimer of Ku70 and Ku80) to DNA break ends. Therefore, recruitment of Ku to DSB sites might play a critical role in regulating NHEJ activity. Indeed, human Ku70 and Ku80 localize in the nuclei and accumulate at microirradiated DSB sites. However, the localization and regulation mechanisms of Ku70 and Ku80 homologues in animal models, such as mice and other species, have not been elucidated in detail, particularly in cells immediately after microirradiation. Here, we show that EYFP-tagged mouse Ku70 localizes in the interphase nuclei of mouse fibroblasts and epithelial cells. Furthermore, our findings indicate that EYFP-mouse Ku70 accumulates with its heterodimeric partner Ku80 immediately at laser-microirradiated DSB sites. We also confirmed that the structure of Ku70 nuclear localization signal (NLS) is highly conserved among various rodent species, such as the mouse, rat, degu and ground squirrel, supporting the idea that NLS is important for the regulation of rodent Ku70 function. Collectively, these results suggest that the mechanisms of regulating the localization and accumulation of Ku70 at DSBs might be well conserved between the mouse and human species.
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Affiliation(s)
- Manabu Koike
- Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555, Japan
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44
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Craxton A, Somers J, Munnur D, Jukes-Jones R, Cain K, Malewicz M. XLS (c9orf142) is a new component of mammalian DNA double-stranded break repair. Cell Death Differ 2015; 22:890-7. [PMID: 25941166 PMCID: PMC4423191 DOI: 10.1038/cdd.2015.22] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Accepted: 02/09/2015] [Indexed: 12/18/2022] Open
Abstract
Repair of double-stranded DNA breaks (DSBs) in mammalian cells primarily occurs by the non-homologous end-joining (NHEJ) pathway, which requires seven core proteins (Ku70/Ku86, DNA-PKcs (DNA-dependent protein kinase catalytic subunit), Artemis, XRCC4-like factor (XLF), XRCC4 and DNA ligase IV). Here we show using combined affinity purification and mass spectrometry that DNA-PKcs co-purifies with all known core NHEJ factors. Furthermore, we have identified a novel evolutionary conserved protein associated with DNA-PKcs—c9orf142. Computer-based modelling of c9orf142 predicted a structure very similar to XRCC4, hence we have named c9orf142—XLS (XRCC4-like small protein). Depletion of c9orf142/XLS in cells impaired DSB repair consistent with a defect in NHEJ. Furthermore, c9orf142/XLS interacted with other core NHEJ factors. These results demonstrate the existence of a new component of the NHEJ DNA repair pathway in mammalian cells.
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Affiliation(s)
- A Craxton
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - J Somers
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - D Munnur
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - R Jukes-Jones
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - K Cain
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
| | - M Malewicz
- MRC Toxicology Unit, Hodgkin Building, Lancaster Road, Leicester LE1 9HN, UK
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45
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Involvement of the insulin-like growth factor binding proteins in the cancer cell response to DNA damage. J Cell Commun Signal 2015; 9:167-76. [PMID: 25617051 DOI: 10.1007/s12079-015-0262-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 01/12/2015] [Indexed: 10/24/2022] Open
Abstract
The complex mechanisms that cells have evolved to meet the challenge of constant exposure to DNA-damaging stimuli, also serve to protect cancer cells from the cytotoxic effects of chemo- and radiotherapy. IGFBPs appear to be involved, directly or indirectly, in some of these protective mechanisms. Activation of p53 is an early response to genotoxic stress, and all six human IGFBP genes have predicted p53 response elements in their promoter and/or intronic regions, at least some of which are functional. IGFBP3 has been extensively characterized as a p53-inducible gene, but in some cases it is suppressed by mutant p53 forms. DNA double-strand breaks (DSBs), induced by radiotherapy and some chemotherapies, potentially lead to apoptotic cell death, senescence, or repair and recovery. DSB damage can be repaired by homologous recombination or non-homologous end-joining (NHEJ), depending on the cell cycle stage, availability of key repair proteins, and other factors. The epidermal growth factor receptor (EGFR) has been implicated in the NHEJ pathway, and EGFR inhibition may inhibit repair, promoting apoptosis and thus improving sensitivity to chemotherapy or radiotherapy. Both IGFBP-3 and IGFBP-6 interact with components of the NHEJ pathway, and IGFBP-3 can facilitate this process through direct interaction with both EGFR and the catalytic subunit of DNA-PK. Cell fate after DNA damage may in part be regulated by the balance between the sphingolipids ceramide and sphingosine-1-phosphate, and IGFBPs can influence the production of both lipids. A better understanding of the involvement of IGFBPs in the DNA damage response in cancer cells may lead to improved methods of sensitizing cancers to DNA-damaging therapies.
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46
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Sun L, Hartson SD, Matts RL. Identification of proteins associated with Aha1 in HeLa cells by quantitative proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:365-80. [PMID: 25614414 DOI: 10.1016/j.bbapap.2015.01.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/20/2014] [Accepted: 01/09/2015] [Indexed: 01/17/2023]
Abstract
The identification of the activator of heat shock protein 90 (Hsp90) ATPase's (Aha1) protein-protein interaction (PPI) network will provide critical insights into the relationship of Aha1 with multi-molecular complexes and shed light onto Aha1's interconnections with Hsp90-regulated biological functions. Flag-tagged Aha1 was over-expressed in HeLa cells and isolated by anti-Flag affinity pull downs, followed by trypsin digestion and identification co-adsorbing proteins by liquid chromatography-tandem mass spectroscopy (LC-MS/MS). A probability-based identification of Aha1 PPIs was generated from the LC-MS/MS analysis by using a relative quantification strategy, spectral counting (SC). By comparing the SC-based protein levels between Aha1 pull-down samples and negative controls, 164 Aha1-interacting proteins were identified that were quantitatively enriched in the pull-down samples over the controls. The identified Aha1-interacting proteins are involved in a wide number of intracellular bioprocesses, including DNA maintenance, chromatin structure, RNA processing, translation, nucleocytoplasmic and vesicle transport, among others. The interactions of 33 of the identified proteins with Aha1 were further confirmed by Western blotting, demonstrating the reliability of our affinity-purification-coupled quantitative SC-MS strategy. Our proteomic data suggests that Aha1 may participate in diverse biological pathways to facilitate Hsp90 chaperone functions in response to stress.
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Affiliation(s)
- Liang Sun
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Steven D Hartson
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Robert L Matts
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA.
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47
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Dorsett Y, Zhou Y, Tubbs AT, Chen BR, Purman C, Lee BS, George R, Bredemeyer AL, Zhao JY, Sodergen E, Weinstock GM, Han ND, Reyes A, Oltz EM, Dorsett D, Misulovin Z, Payton JE, Sleckman BP. HCoDES reveals chromosomal DNA end structures with single-nucleotide resolution. Mol Cell 2014; 56:808-18. [PMID: 25435138 DOI: 10.1016/j.molcel.2014.10.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2014] [Revised: 10/21/2014] [Accepted: 10/23/2014] [Indexed: 01/27/2023]
Abstract
The structure of broken DNA ends is a critical determinant of the pathway used for DNA double-strand break (DSB) repair. Here, we develop an approach involving the hairpin capture of DNA end structures (HCoDES), which elucidates chromosomal DNA end structures at single-nucleotide resolution. HCoDES defines structures of physiologic DSBs generated by the RAG endonuclease, as well as those generated by nucleases widely used for genome editing. Analysis of G1 phase cells deficient in H2AX or 53BP1 reveals DNA ends that are frequently resected to form long single-stranded overhangs that can be repaired by mutagenic pathways. In addition to 3' overhangs, many of these DNA ends unexpectedly form long 5' single-stranded overhangs. The divergence in DNA end structures resolved by HCoDES suggests that H2AX and 53BP1 may have distinct activities in end protection. Thus, the high-resolution end structures obtained by HCoDES identify features of DNA end processing during DSB repair.
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Affiliation(s)
- Yair Dorsett
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Yanjiao Zhou
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO 63110, USA; Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Anthony T Tubbs
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Bo-Ruei Chen
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Caitlin Purman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Baeck-Seung Lee
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Rosmy George
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Andrea L Bredemeyer
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Jiang-Yang Zhao
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Erica Sodergen
- Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - George M Weinstock
- Genome Institute, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nathan D Han
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Alejandro Reyes
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA; Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Eugene M Oltz
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Dale Dorsett
- Biochemistry Department, St. Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Ziva Misulovin
- Biochemistry Department, St. Louis University School of Medicine, St. Louis, MO 63104, USA
| | - Jacqueline E Payton
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
| | - Barry P Sleckman
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO 63110, USA.
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48
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Ho TT, Zhou N, Huang J, Koirala P, Xu M, Fung R, Wu F, Mo YY. Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines. Nucleic Acids Res 2014; 43:e17. [PMID: 25414344 PMCID: PMC4330338 DOI: 10.1093/nar/gku1198] [Citation(s) in RCA: 190] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
The CRISPR/Cas has been recently shown to be a powerful genome-editing tool in a variety of organisms. However, these studies are mainly focused on protein-coding genes. The present study aims to determine whether this technology can be applied to non-coding genes. One of the challenges for knockout of non-coding genes is that a small deletion or insertion generated by the standard CRISPR/Cas system may not necessarily lead to functional loss of a given non-coding gene because of lacking an open reading frame, especially in polyploidy human cell lines. To overcome this challenge, we adopt a selection system that allows for marker genes to integrate into the genome through homologous recombination (HR). Moreover, we construct a dual guide RNA vector that can make two cuts simultaneously at designated sites such that a large fragment can be deleted. With these approaches, we are able to successfully generate knockouts for miR-21, miR-29a, lncRNA-21A, UCA1 and AK023948 in various human cell lines. Finally, we show that the HR-mediated targeting efficiency can be further improved by suppression of the non-homologous end joining pathway. Together, these results demonstrate the feasibility of knockout for non-coding genes by the CRISPR/Cas system in human cell lines.
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Affiliation(s)
- Tsui-Ting Ho
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Nanjiang Zhou
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Jianguo Huang
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Pratirodh Koirala
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Min Xu
- Department of Gastroenterology, Affiliated Hospital of Jiangsu University, Zhenjiang, Jiangsu 212001, China
| | - Roland Fung
- System Biosciences, Mountain View, CA 94043, USA
| | - Fangting Wu
- System Biosciences, Mountain View, CA 94043, USA
| | - Yin-Yuan Mo
- Department of Pharmacology/Toxicology and Cancer Institute, University of Mississippi Medical Center, Jackson, MS 39216, USA
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49
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Marcand S. How do telomeres and NHEJ coexist? Mol Cell Oncol 2014; 1:e963438. [PMID: 27308342 PMCID: PMC4904885 DOI: 10.4161/23723548.2014.963438] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2014] [Revised: 08/01/2014] [Accepted: 08/07/2014] [Indexed: 12/21/2022]
Abstract
The telomeres of eukaryotes are stable open double-strand ends that coexist with nonhomologous end joining (NHEJ), the repair pathway that directly ligates DNA ends generated by double-strand breaks. Since a single end-joining event between 2 telomeres generates a circular chromosome or an unstable dicentric chromosome, NHEJ must be prevented from acting on telomeres. Multiple mechanisms mediated by telomere factors act in synergy to achieve this inhibition.
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Affiliation(s)
- Stéphane Marcand
- CEA; DSV/IRCM/SIGRR/LTR; Fontenay-aux-roses; France; INSERM UMR 967; Fontenay-aux-roses; France
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50
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The Ku heterodimer: function in DNA repair and beyond. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2014; 763:15-29. [PMID: 25795113 DOI: 10.1016/j.mrrev.2014.06.002] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/07/2014] [Accepted: 06/25/2014] [Indexed: 01/11/2023]
Abstract
Ku is an abundant, highly conserved DNA binding protein found in both prokaryotes and eukaryotes that plays essential roles in the maintenance of genome integrity. In eukaryotes, Ku is a heterodimer comprised of two subunits, Ku70 and Ku80, that is best characterized for its central role as the initial DNA end binding factor in the "classical" non-homologous end joining (C-NHEJ) pathway, the main DNA double-strand break (DSB) repair pathway in mammals. Ku binds double-stranded DNA ends with high affinity in a sequence-independent manner through a central ring formed by the intertwined strands of the Ku70 and Ku80 subunits. At the break, Ku directly and indirectly interacts with several C-NHEJ factors and processing enzymes, serving as the scaffold for the entire DNA repair complex. There is also evidence that Ku is involved in signaling to the DNA damage response (DDR) machinery to modulate the activation of cell cycle checkpoints and the activation of apoptosis. Interestingly, Ku is also associated with telomeres, where, paradoxically to its DNA end-joining functions, it protects the telomere ends from being recognized as DSBs, thereby preventing their recombination and degradation. Ku, together with the silent information regulator (Sir) complex is also required for transcriptional silencing through telomere position effect (TPE). How Ku associates with telomeres, whether it is through direct DNA binding, or through protein-protein interactions with other telomere bound factors remains to be determined. Ku is central to the protection of organisms through its participation in C-NHEJ to repair DSBs generated during V(D)J recombination, a process that is indispensable for the establishment of the immune response. Ku also functions to prevent tumorigenesis and senescence since Ku-deficient mice show increased cancer incidence and early onset of aging. Overall, Ku function is critical to the maintenance of genomic integrity and to proper cellular and organismal development.
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