1
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Moor NA, Vasil'eva IA, Lavrik OI. Human DNA ligases I and IIIα as determinants of accuracy and efficiency of base excision DNA repair. Biochimie 2024; 219:84-95. [PMID: 37573020 DOI: 10.1016/j.biochi.2023.08.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/17/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
Mammalian Base Excision Repair (BER) DNA ligases I and IIIα (LigI, LigIIIα) are major determinants of DNA repair fidelity, alongside with DNA polymerases. Here we compared activities of human LigI and LigIIIα on specific and nonspecific substrates representing intermediates of distinct BER sub-pathways. The enzymes differently discriminate mismatches in the nicked DNA, depending on their identity and position, but are both more selective against the 3'-end non-complementarity. LigIIIα is less active than LigI in premature ligation of one-nucleotide gapped DNA and more efficiently discriminates misinsertion products of DNA polymerase β-catalyzed gap filling, that reinforces a leading role of LigIIIα in the accuracy of short-patch BER. LigI and LigIIIα reseal the intermediate of long-patch BER containing an incised synthetic AP site (F) with different efficiencies, depending on the DNA sequence context, 3'-end mismatch presence and coupling of the ligation reaction with DNA repair synthesis. Processing of this intermediate in the absence of flap endonuclease 1 generates non-canonical DNAs with bulged F site, which are very inefficiently repaired by AP endonuclease 1 and represent potential mutagenic repair products. The extent of conversion of the 5'-adenylated intermediates of specific and nonspecific substrates is revealed to depend on the DNA sequence context; a higher sensitivity of LigI to the sequence is in line with the enzyme structural feature of DNA binding. LigIIIα exceeds LigI in generation of potential abortive ligation products, justifying importance of XRCC1-mediated coordination of LigIIIα and aprataxin activities for the efficient DNA repair.
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Affiliation(s)
- Nina A Moor
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Inna A Vasil'eva
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia
| | - Olga I Lavrik
- Institute of Chemical Biology and Fundamental Medicine, SB RAS, Novosibirsk, Russia.
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2
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Jiang B, Murray C, Cole BL, Glover JNM, Chan GK, Deschenes J, Mani RS, Subedi S, Nerva JD, Wang AC, Lockwood CM, Mefford HC, Leary SES, Ojemann JG, Weinfeld M, Ene CI. Mutations of the DNA repair gene PNKP in a patient with microcephaly, seizures, and developmental delay (MCSZ) presenting with a high-grade brain tumor. Sci Rep 2022; 12:5386. [PMID: 35354845 PMCID: PMC8967877 DOI: 10.1038/s41598-022-09097-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/04/2022] [Indexed: 11/08/2022] Open
Abstract
Polynucleotide Kinase-Phosphatase (PNKP) is a bifunctional enzyme that possesses both DNA 3'-phosphatase and DNA 5'-kinase activities, which are required for processing termini of single- and double-strand breaks generated by reactive oxygen species (ROS), ionizing radiation and topoisomerase I poisons. Even though PNKP is central to DNA repair, there have been no reports linking PNKP mutations in a Microcephaly, Seizures, and Developmental Delay (MSCZ) patient to cancer. Here, we characterized the biochemical significance of 2 germ-line point mutations in the PNKP gene of a 3-year old male with MSCZ who presented with a high-grade brain tumor (glioblastoma multiforme) within the cerebellum. Functional and biochemical studies demonstrated these PNKP mutations significantly diminished DNA kinase/phosphatase activities, altered its cellular distribution, caused defective repair of DNA single/double stranded breaks, and were associated with a higher propensity for oncogenic transformation. Our findings indicate that specific PNKP mutations may contribute to tumor initiation within susceptible cells in the CNS by limiting DNA damage repair and increasing rates of spontaneous mutations resulting in pediatric glioma associated driver mutations such as ATRX and TP53.
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Affiliation(s)
- Bingcheng Jiang
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Cameron Murray
- Department of Biochemistry, University of Alberta, Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada
| | - Bonnie L Cole
- Department of Pathology, University of Washington, Seattle, WA, USA
| | - J N Mark Glover
- Department of Biochemistry, University of Alberta, Medical Sciences Building, Edmonton, AB, T6G 2H7, Canada
| | - Gordon K Chan
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Jean Deschenes
- Department of Laboratory Medicine and Pathology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Rajam S Mani
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - Sudip Subedi
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada
| | - John D Nerva
- Department of Neurological Surgery, Tulane University, New Orleans, LA, USA
| | - Anthony C Wang
- Department of Neurological Surgery, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Heather C Mefford
- Division of Genetics Medicine, University of Washington, Seattle, WA, USA
| | - Sarah E S Leary
- Division of Pediatric Hematology/Oncology, Seattle Children's Hospital, Seattle, WA, USA
| | - Jeffery G Ojemann
- Department of Neurological Surgery, University of Washington, Seattle, WA, USA
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, 11560 University Ave., Edmonton, AB, T6G 1Z2, Canada.
| | - Chibawanye I Ene
- Department of Neurological Surgery, MD Anderson Cancer Center, Houston, TX, USA.
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3
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Martinez-Pastor B, Silveira GG, Clarke TL, Chung D, Gu Y, Cosentino C, Davidow LS, Mata G, Hassanieh S, Salsman J, Ciccia A, Bae N, Bedford MT, Megias D, Rubin LL, Efeyan A, Dellaire G, Mostoslavsky R. Assessing kinetics and recruitment of DNA repair factors using high content screens. Cell Rep 2021; 37:110176. [PMID: 34965416 PMCID: PMC8763642 DOI: 10.1016/j.celrep.2021.110176] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 10/08/2021] [Accepted: 12/04/2021] [Indexed: 11/30/2022] Open
Abstract
Repair of genetic damage is coordinated in the context of chromatin, so cells dynamically modulate accessibility at DNA breaks for the recruitment of DNA damage response (DDR) factors. The identification of chromatin factors with roles in DDR has mostly relied on loss-of-function screens while lacking robust high-throughput systems to study DNA repair. In this study, we have developed two high-throughput systems that allow the study of DNA repair kinetics and the recruitment of factors to double-strand breaks in a 384-well plate format. Using a customized gain-of-function open-reading frame library ("ChromORFeome" library), we identify chromatin factors with putative roles in the DDR. Among these, we find the PHF20 factor is excluded from DNA breaks, affecting DNA repair by competing with 53BP1 recruitment. Adaptable for genetic perturbations, small-molecule screens, and large-scale analysis of DNA repair, these resources can aid our understanding and manipulation of DNA repair.
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Affiliation(s)
- Barbara Martinez-Pastor
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; Molecular Oncology Program, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain.
| | - Giorgia G Silveira
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Thomas L Clarke
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Yuchao Gu
- School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Claudia Cosentino
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Lance S Davidow
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Gadea Mata
- Confocal Microscopy Unit, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Sylvana Hassanieh
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
| | - Jayme Salsman
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Alberto Ciccia
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA; Herbert Irving Comprehensive Cancer Center, Columbia University Medical Center, New York, NY 10032, USA
| | - Narkhyun Bae
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032, USA
| | - Mark T Bedford
- Department of Epigenetics & Molecular Carcinogenesis, M.D.Anderson Cancer Center, University of Texas, Smithville, TX 78957, USA
| | - Diego Megias
- Confocal Microscopy Unit, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology and Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA
| | - Alejo Efeyan
- Molecular Oncology Program, Spanish National Cancer Research Center (CNIO), Madrid 28029, Spain
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada.
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA; The Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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4
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Kumamoto S, Nishiyama A, Chiba Y, Miyashita R, Konishi C, Azuma Y, Nakanishi M. HPF1-dependent PARP activation promotes LIG3-XRCC1-mediated backup pathway of Okazaki fragment ligation. Nucleic Acids Res 2021; 49:5003-5016. [PMID: 33872376 PMCID: PMC8136790 DOI: 10.1093/nar/gkab269] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 03/29/2021] [Accepted: 04/01/2021] [Indexed: 12/20/2022] Open
Abstract
DNA ligase 1 (LIG1) is known as the major DNA ligase responsible for Okazaki fragment joining. Recent studies have implicated LIG3 complexed with XRCC1 as an alternative player in Okazaki fragment joining in cases where LIG1 is not functional, although the underlying mechanisms are largely unknown. Here, using a cell-free system derived from Xenopus egg extracts, we demonstrated the essential role of PARP1-HPF1 in LIG3-dependent Okazaki fragment joining. We found that Okazaki fragments were eventually ligated even in the absence of LIG1, employing in its place LIG3-XRCC1, which was recruited onto chromatin. Concomitantly, LIG1 deficiency induces ADP-ribosylation of histone H3 in a PARP1-HPF1-dependent manner. The depletion of PARP1 or HPF1 resulted in a failure to recruit LIG3 onto chromatin and a subsequent failure in Okazaki fragment joining in LIG1-depleted extracts. Importantly, Okazaki fragments were not ligated at all when LIG1 and XRCC1 were co-depleted. Our results suggest that a unique form of ADP-ribosylation signaling promotes the recruitment of LIG3 on chromatin and its mediation of Okazaki fragment joining as a backup system for LIG1 perturbation.
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Affiliation(s)
- Soichiro Kumamoto
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Atsuya Nishiyama
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshie Chiba
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Ryota Miyashita
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Chieko Konishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yoshiaki Azuma
- Department of Molecular Biosciences, University of Kansas, Lawrence, KS 66045, USA
| | - Makoto Nakanishi
- Division of Cancer Cell Biology, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
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5
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Zilio N, Ulrich HD. Exploring the SSBreakome: genome-wide mapping of DNA single-strand breaks by next-generation sequencing. FEBS J 2020; 288:3948-3961. [PMID: 32965079 DOI: 10.1111/febs.15568] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 11/29/2022]
Abstract
Mapping the genome-wide distribution of DNA lesions is key to understanding damage signalling and DNA repair in the context of genome and chromatin structure. Analytical tools based on high-throughput next-generation sequencing have revolutionized our progress with such investigations, and numerous methods are now available for various base lesions and modifications as well as for DNA double-strand breaks. Considering that single-strand breaks are by far the most common type of lesion and arise not only from exposure to exogenous DNA-damaging agents, but also as obligatory intermediates of DNA replication, recombination and repair, it is surprising that our insight into their genome-wide patterns, that is the 'SSBreakome', has remained rather obscure until recently, due to a lack of suitable mapping technology. Here we briefly review classical methods for analysing single-strand breaks and discuss and compare in detail a series of recently developed high-resolution approaches for the genome-wide mapping of these lesions, their advantages and limitations and how they have already provided valuable insight into the impact of this type of damage on the genome.
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Affiliation(s)
- Nicola Zilio
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
| | - Helle D Ulrich
- Institute of Molecular Biology (IMB) gGmbH, Mainz, Germany
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6
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Mei C, Lei L, Tan LM, Xu XJ, He BM, Luo C, Yin JY, Li X, Zhang W, Zhou HH, Liu ZQ. The role of single strand break repair pathways in cellular responses to camptothecin induced DNA damage. Biomed Pharmacother 2020; 125:109875. [DOI: 10.1016/j.biopha.2020.109875] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 12/24/2019] [Accepted: 01/06/2020] [Indexed: 12/12/2022] Open
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7
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Abstract
Genomic DNA is susceptible to endogenous and environmental stresses that modify DNA structure and its coding potential. Correspondingly, cells have evolved intricate DNA repair systems to deter changes to their genetic material. Base excision DNA repair involves a number of enzymes and protein cofactors that hasten repair of damaged DNA bases. Recent advances have identified macromolecular complexes that assemble at the DNA lesion and mediate repair. The repair of base lesions generally requires five enzymatic activities: glycosylase, endonuclease, lyase, polymerase, and ligase. The protein cofactors and mechanisms for coordinating the sequential enzymatic steps of repair are being revealed through a range of experimental approaches. We discuss the enzymes and protein cofactors involved in eukaryotic base excision repair, emphasizing the challenge of integrating findings from multiple methodologies. The results provide an opportunity to assimilate biochemical findings with cell-based assays to uncover new insights into this deceptively complex repair pathway.
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Affiliation(s)
- William A Beard
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
| | - Julie K Horton
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
| | - Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Science, National Institutes of Health, Research Triangle Park, North Carolina 27709-2233, USA;
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8
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Kohutova A, Raška J, Kruta M, Seneklova M, Barta T, Fojtik P, Jurakova T, Walter CA, Hampl A, Dvorak P, Rotrekl V. Ligase 3–mediated end‐joining maintains genome stability of human embryonic stem cells. FASEB J 2019; 33:6778-6788. [DOI: 10.1096/fj.201801877rr] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Aneta Kohutova
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Jan Raška
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | - Miriama Kruta
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | | | - Tomas Barta
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | - Petr Fojtik
- Department of BiologyMasaryk UniversityBrnoCzech Republic
| | | | - Christi A. Walter
- Department of Cell Systems and AnatomyThe University of Texas Health Science Center at San AntonioSan AntonioTexasUSA
| | - Ales Hampl
- Department of Histology and EmbryologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Petr Dvorak
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
| | - Vladimir Rotrekl
- Department of BiologyMasaryk UniversityBrnoCzech Republic
- International Clinical Research Center (ICRC)St. Anne's University HospitalBrnoCzech Republic
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9
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Augustine T, Maitra R, Zhang J, Nayak J, Goel S. Sensitization of colorectal cancer to irinotecan therapy by PARP inhibitor rucaparib. Invest New Drugs 2019; 37:948-960. [PMID: 30612311 DOI: 10.1007/s10637-018-00717-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 12/19/2018] [Indexed: 12/11/2022]
Abstract
Intended to explore synthetic lethality and develop better combinatorial regimens, we screened colorectal cancer (CRC) cells using poly ADP-ribose (PAR) polymerase (PARP) inhibitors and cytotoxic agents. We studied four PARP inhibitors and three DNA-damaging agents, and their combinations using sulforhodamine B assay. Rucaparib demonstrated the greatest synergy with irinotecan, followed by olaparib and PJ34. Rucaparib and irinotecan was further subjected to detailed examination to determine combination index (CI) and underlying mechanism of action. Effectiveness and sequence dependence of this combination were assessed in microsatellite stable (MSS) and unstable (MSI) CRC and HCT116 isogenic cell lines. The degree of cell cycle arrest and apoptosis was determined by FACS. In vivo studies were performed to confirm efficacy of this combination. PAR levels in MSI and PARP expression in MSI and MSS cell lines were diminished upon combinatorial treatment. HCT116 isogenic cells revealed the importance of p21, p53 and PTEN in exerting synergy. In MSI cells, administration of rucaparib prior to irinotecan enhanced cytotoxicity compared to other strategies explored. FACS revealed S-phase arrest and increased late-stage apoptosis in MSS, and G2-M arrest and total and early-stage apoptosis in MSI cells. In in vivo murine xenograft models, a significant reduction in tumor volume and expression of Ki67, pancytokeratin and RPS6KB1, and increase in expression of caspase 3 were observed with the combination. In conclusion, among the various combinations studied, rucaparib plus irinotecan was the most synergistic one. Alterations in cell cycle arrest and apoptosis were dependent on MSI status in CRC cells.
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Affiliation(s)
- Titto Augustine
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Radhashree Maitra
- Department of Medical Oncology, Montefiore Medical Center, Bronx, NY, 10461, USA
| | - Jinghang Zhang
- Department of Microbiology & Immunology and Flow Cytometry Core Facility, Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Jay Nayak
- Department of Medical Oncology, Montefiore Medical Center, Bronx, NY, 10461, USA
| | - Sanjay Goel
- Department of Medicine, Albert Einstein College of Medicine, Bronx, NY, 10461, USA. .,Department of Medical Oncology, Montefiore Medical Center, Bronx, NY, 10461, USA.
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10
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Moor NA, Lavrik OI. Protein–Protein Interactions in DNA Base Excision Repair. BIOCHEMISTRY (MOSCOW) 2018; 83:411-422. [DOI: 10.1134/s0006297918040120] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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11
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Canovas Nunes S, Manzoni M, Pizzi M, Mandato E, Carrino M, Quotti Tubi L, Zambello R, Adami F, Visentin A, Barilà G, Trentin L, Manni S, Neri A, Semenzato G, Piazza F. The small GTPase RhoU lays downstream of JAK/STAT signaling and mediates cell migration in multiple myeloma. Blood Cancer J 2018; 8:20. [PMID: 29440639 PMCID: PMC5811530 DOI: 10.1038/s41408-018-0053-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Revised: 12/19/2017] [Accepted: 01/08/2018] [Indexed: 12/22/2022] Open
Abstract
Multiple myeloma is a post-germinal center B-cell neoplasm, characterized by the proliferation of malignant bone marrow plasma cells, whose survival and proliferation is sustained by growth factors and cytokines present in the bone marrow microenvironment. Among them, IL-6 triggers the signal downstream of its receptor, leading to the activation of the JAK/STAT pathway. The atypical GTPase RhoU lays downstream of STAT3 transcription factor and could be responsible for mediating its effects on cytoskeleton dynamics. Here we demonstrate that RHOU is heterogeneously expressed in primary multiple myeloma cells and significantly modulated with disease progression. At the mRNA level, RHOU expression in myeloma patients correlated with the expression of STAT3 and its targets MIR21 and SOCS3. Also, IL-6 stimulation of human myeloma cell lines up-regulated RHOU through STAT3 activation. On the other hand, RhoU silencing led to a decrease in cell migration with the accumulation of actin stress fibers, together with a decrease in cyclin D2 expression and in cell cycle progression. Furthermore, we found that even though lenalidomide positively regulated RhoU expression leading to higher cell migration rates, it actually led to cell cycle arrest probably through a p21 dependent mechanism. Lenalidomide treatment in combination with RhoU silencing determined a loss of cytoskeletal organization inhibiting cell migration, and a further increase in the percentage of cells in a resting phase. These results unravel a role for RhoU not only in regulating the migratory features of malignant plasma cells, but also in controlling cell cycle progression.
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Affiliation(s)
- Sara Canovas Nunes
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy.,Laboratory of Normal and Malignant Hematopoiesis, Venetian Institute of Molecular Medicine, Padova, Italy
| | - Martina Manzoni
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy
| | - Marco Pizzi
- Surgical Pathology and Cytopathology Unit, Department of Medicine - DIMED, University of Padova, Padova, Italy
| | - Elisa Mandato
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy.,Laboratory of Normal and Malignant Hematopoiesis, Venetian Institute of Molecular Medicine, Padova, Italy.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Marilena Carrino
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy.,Laboratory of Normal and Malignant Hematopoiesis, Venetian Institute of Molecular Medicine, Padova, Italy
| | - Laura Quotti Tubi
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy.,Laboratory of Normal and Malignant Hematopoiesis, Venetian Institute of Molecular Medicine, Padova, Italy
| | - Renato Zambello
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy.,Laboratory of Normal and Malignant Hematopoiesis, Venetian Institute of Molecular Medicine, Padova, Italy
| | - Fausto Adami
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy
| | - Andrea Visentin
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy
| | - Gregorio Barilà
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy
| | - Livio Trentin
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy.,Laboratory of Normal and Malignant Hematopoiesis, Venetian Institute of Molecular Medicine, Padova, Italy
| | - Sabrina Manni
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy.,Laboratory of Normal and Malignant Hematopoiesis, Venetian Institute of Molecular Medicine, Padova, Italy
| | - Antonino Neri
- Hematology Unit, Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico, Milan, Italy.,Department of Oncology and Hemato-Oncology, University of Milano, Milano, Italy
| | - Gianpietro Semenzato
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy.,Laboratory of Normal and Malignant Hematopoiesis, Venetian Institute of Molecular Medicine, Padova, Italy
| | - Francesco Piazza
- Department of Medicine, Division of Hematology, University of Padova, Padova, Italy. .,Laboratory of Normal and Malignant Hematopoiesis, Venetian Institute of Molecular Medicine, Padova, Italy.
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12
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Kochan JA, Desclos EC, Bosch R, Meister L, Vriend LE, van Attikum H, Krawczyk PM. Meta-analysis of DNA double-strand break response kinetics. Nucleic Acids Res 2017; 45:12625-12637. [PMID: 29182755 PMCID: PMC5728399 DOI: 10.1093/nar/gkx1128] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 10/24/2017] [Accepted: 11/13/2017] [Indexed: 12/12/2022] Open
Abstract
Most proteins involved in the DNA double-strand break response (DSBR) accumulate at the damage sites, where they perform functions related to damage signaling, chromatin remodeling and repair. Over the last two decades, studying the accumulation of many DSBR proteins provided information about their functionality and underlying mechanisms of action. However, comparison and systemic interpretation of these data is challenging due to their scattered nature and differing experimental approaches. Here, we extracted, analyzed and compared the available results describing accumulation of 79 DSBR proteins at sites of DNA damage, which can be further explored using Cumulus (http://www.dna-repair.live/cumulus/)-the accompanying interactive online application. Despite large inter-study variability, our analysis revealed that the accumulation of most proteins starts immediately after damage induction, occurs in parallel and peaks within 15-20 min. Various DSBR pathways are characterized by distinct accumulation kinetics with major non-homologous end joining proteins being generally faster than those involved in homologous recombination, and signaling and chromatin remodeling factors accumulating with varying speeds. Our meta-analysis provides, for the first time, comprehensive overview of the temporal organization of the DSBR in mammalian cells and could serve as a reference for future mechanistic studies of this complex process.
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Affiliation(s)
- Jakub A. Kochan
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Emilie C.B. Desclos
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Ruben Bosch
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Luna Meister
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Lianne E.M. Vriend
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, The Netherlands
| | - Przemek M. Krawczyk
- Department of Medical Biology and Laboratory of Experimental Oncology and Radiobiology (LEXOR), Cancer Center Amsterdam, Academic Medical Center, Meibergdreef 15, 1105 AZ Amsterdam, The Netherlands
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13
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Horton JK, Stefanick DF, Zhao ML, Janoshazi AK, Gassman NR, Seddon HJ, Wilson SH. XRCC1-mediated repair of strand breaks independent of PNKP binding. DNA Repair (Amst) 2017; 60:52-63. [PMID: 29100039 PMCID: PMC5696015 DOI: 10.1016/j.dnarep.2017.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/03/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
Abstract
Repair of DNA-protein crosslinks and oxidatively damaged DNA base lesions generates intermediates with nicks or gaps with abnormal and blocked 3'-phosphate and 5'-OH ends that prevent the activity of DNA polymerases and ligases. End cleaning in mammalian cells by Tdp1 and PNKP produces the conventional 3'-OH and 5'-phosphate DNA ends suitable for completion of repair. This repair function of PNKP is facilitated by its binding to the scaffold protein XRCC1, and phosphorylation of XRCC1 by CK2 at several consensus sites enables PNKP binding and recruitment to DNA damage. To evaluate this documented repair process, a phosphorylation mutant of XRCC1, designed to eliminate PNKP binding, was stably expressed in Xrcc1-/- mouse fibroblast cells. Analysis of PNKP-GFP accumulation at micro-irradiation induced damage confirmed that the XRCC1 phosphorylation mutant failed to support efficient PNKP recruitment, whereas there was rapid recruitment in cells expressing wild-type XRCC1. Recruitment of additional fluorescently-tagged repair factors PARP-1-YFP, GFF-XRCC1, PNKP-GFP and Tdp1-GFP to micro-irradiation induced damage was assessed in wild-type XRCC1-expressing cells. PARP-1-YFP recruitment was best fit to two exponentials, whereas kinetics for the other proteins were fit to a single exponential. The similar half-times of recruitment suggest that XRCC1 may be recruited with other proteins possibly as a pre-formed complex. Xrcc1-/- cells are hypersensitive to the DNA-protein cross-link inducing agent camptothecin (CPT) and the DNA oxidative agent H2O2 due in part to compromised PNKP-mediated repair. However, cells expressing the PNKP interaction mutant of XRCC1 demonstrated marked reversal of CPT hypersensitivity. This reversal represents XRCC1-dependent repair in the absence of the phosphorylation-dependent PNKP recruitment and suggests either an XRCC1-independent mechanism of PNKP recruitment or a functional back-up pathway for cleaning of blocked DNA ends.
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Affiliation(s)
- Julie K Horton
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Donna F Stefanick
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Ming-Lang Zhao
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Agnes K Janoshazi
- Signal Transduction Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA
| | - Natalie R Gassman
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Hannah J Seddon
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genomic Integrity and Structural Biology Laboratory, NIEHS, National Institutes of Health, Research Triangle Park, NC 27709, USA.
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14
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Yang L, Sun L, Teng Y, Chen H, Gao Y, Levine AS, Nakajima S, Lan L. Tankyrase1-mediated poly(ADP-ribosyl)ation of TRF1 maintains cell survival after telomeric DNA damage. Nucleic Acids Res 2017; 45:3906-3921. [PMID: 28160604 PMCID: PMC5397190 DOI: 10.1093/nar/gkx083] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Accepted: 01/27/2017] [Indexed: 12/17/2022] Open
Abstract
Oxidative DNA damage triggers telomere erosion and cellular senescence. However, how repair is initiated at telomeres is largely unknown. Here, we found unlike PARP1-mediated Poly-ADP-Ribosylation (PARylation) at genomic damage sites, PARylation at telomeres is mainly dependent on tankyrase1 (TNKS1). TNKS1 is recruited to damaged telomeres via its interaction with TRF1, which subsequently facilitates the PARylation of TRF1 after damage. TNKS inhibition abolishes the recruitment of the repair proteins XRCC1 and polymerase β at damaged telomeres, while the PARP1/2 inhibitor only has such an effect at non-telomeric damage sites. The ANK domain of TNKS1 is essential for the telomeric damage response and TRF1 interaction. Mutation of the tankyrase-binding motif (TBM) on TRF1 (13R/18G to AA) disrupts its interaction with TNKS1 concomitant recruitment of TNKS1 and repair proteins after damage. Either TNKS1 inhibition or TBM mutated TRF1 expression markedly sensitizes cells to telomere oxidative damage as well as XRCC1 inhibition. Together, our data reveal a novel role of TNKS1 in facilitating SSBR at damaged telomeres through PARylation of TRF1, thereby protecting genome stability and cell viability.
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Affiliation(s)
- Lu Yang
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Luxi Sun
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Yaqun Teng
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Hao Chen
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Ying Gao
- School of Medicine, Tsinghua University, No.1 Tsinghua Yuan, Haidian District, Beijing 100084, China.,University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Arthur S Levine
- University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Satoshi Nakajima
- University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
| | - Li Lan
- University of Pittsburgh Cancer Institute; University of Pittsburgh School of Medicine; 5117 Centre Avenue, Pittsburgh, PA 15213, USA.,Department of Microbiology and Molecular Genetics; University of Pittsburgh School of Medicine; 450 Technology Drive, 523 Bridgeside Point II, Pittsburgh, PA 15219, USA
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15
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Ramdzan ZM, Ginjala V, Pinder JB, Chung D, Donovan CM, Kaur S, Leduy L, Dellaire G, Ganesan S, Nepveu A. The DNA repair function of CUX1 contributes to radioresistance. Oncotarget 2017; 8:19021-19038. [PMID: 28147323 PMCID: PMC5386666 DOI: 10.18632/oncotarget.14875] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 01/19/2017] [Indexed: 01/19/2023] Open
Abstract
Ionizing radiation generates a broad spectrum of oxidative DNA lesions, including oxidized base products, abasic sites, single-strand breaks and double-strand breaks. The CUX1 protein was recently shown to function as an auxiliary factor that stimulates enzymatic activities of OGG1 through its CUT domains. In the present study, we investigated the requirement for CUX1 and OGG1 in the resistance to radiation. Cancer cell survival following ionizing radiation is reduced by CUX1 knockdown and increased by higher CUX1 expression. However, CUX1 knockdown is sufficient by itself to reduce viability in many cancer cell lines that exhibit high levels of reactive oxygen species (ROS). Consequently, clonogenic results expressed relative to that of non-irradiated cells indicate that CUX1 knockdown confers no or modest radiosensitivity to cancer cells with high ROS. A recombinant protein containing only two CUT domains is sufficient for rapid recruitment to DNA damage, acceleration of DNA repair and increased survival following radiation. In agreement with these findings, OGG1 knockdown and treatment of cells with OGG1 inhibitors sensitize cancer cells to radiation. Together, these results validate CUX1 and more specifically the CUT domains as therapeutic targets.
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Affiliation(s)
- Zubaidah M Ramdzan
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Vasudeva Ginjala
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - Jordan B Pinder
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Dudley Chung
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Caroline M Donovan
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Simran Kaur
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Lam Leduy
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada
| | - Graham Dellaire
- Department of Pathology, Dalhousie University, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Shridar Ganesan
- Department of Medicine, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, New Jersey 08903, USA
| | - Alain Nepveu
- Goodman Cancer Research Centre, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Medicine, McGill University, Montreal, Quebec, H3A 1A3, Canada.,Department of Oncology, McGill University, Montreal, Quebec, H3A 1A3, Canada
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16
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Hanzlikova H, Gittens W, Krejcikova K, Zeng Z, Caldecott KW. Overlapping roles for PARP1 and PARP2 in the recruitment of endogenous XRCC1 and PNKP into oxidized chromatin. Nucleic Acids Res 2017; 45:2546-2557. [PMID: 27965414 PMCID: PMC5389470 DOI: 10.1093/nar/gkw1246] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 12/11/2016] [Indexed: 01/01/2023] Open
Abstract
A critical step of DNA single-strand break repair is the rapid recruitment of the scaffold protein XRCC1 that interacts with, stabilizes and stimulates multiple enzymatic components of the repair process. XRCC1 recruitment is promoted by PARP1, an enzyme that is activated following DNA damage and synthesizes ADP-ribose polymers that XRCC1 binds directly. However, cells possess two other DNA strand break-induced PARP enzymes, PARP2 and PARP3, for which the roles are unclear. To address their involvement in the recruitment of endogenous XRCC1 into oxidized chromatin we have established ‘isogenic’ human diploid cells in which PARP1 and/or PARP2, or PARP3 are deleted. Surprisingly, we show that either PARP1 or PARP2 are sufficient for near-normal XRCC1 recruitment at oxidative single-strand breaks (SSBs) as indicated by the requirement for loss of both proteins to greatly reduce or ablate XRCC1 chromatin binding following H2O2 treatment. Similar results were observed for PNKP; an XRCC1 protein partner important for repair of oxidative SSBs. Notably, concentrations of PARP inhibitor >1000-fold higher than the IC50 were required to ablate both ADP-ribosylation and XRCC1 chromatin binding following H2O2 treatment. These results demonstrate that very low levels of ADP-ribosylation, synthesized by either PARP1 or PARP2, are sufficient for XRCC1 recruitment following oxidative stress.
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Affiliation(s)
- Hana Hanzlikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - William Gittens
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Katerina Krejcikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | | | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
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17
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Dutta A, Eckelmann B, Adhikari S, Ahmed KM, Sengupta S, Pandey A, Hegde PM, Tsai MS, Tainer JA, Weinfeld M, Hegde ML, Mitra S. Microhomology-mediated end joining is activated in irradiated human cells due to phosphorylation-dependent formation of the XRCC1 repair complex. Nucleic Acids Res 2017; 45:2585-2599. [PMID: 27994036 PMCID: PMC5389627 DOI: 10.1093/nar/gkw1262] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 12/15/2016] [Indexed: 02/06/2023] Open
Abstract
Microhomology-mediated end joining (MMEJ), an error-prone pathway for DNA double-strand break (DSB) repair, is implicated in genomic rearrangement and oncogenic transformation; however, its contribution to repair of radiation-induced DSBs has not been characterized. We used recircularization of a linearized plasmid with 3΄-P-blocked termini, mimicking those at X-ray-induced strand breaks, to recapitulate DSB repair via MMEJ or nonhomologous end-joining (NHEJ). Sequence analysis of the circularized plasmids allowed measurement of relative activity of MMEJ versus NHEJ. While we predictably observed NHEJ to be the predominant pathway for DSB repair in our assay, MMEJ was significantly enhanced in preirradiated cells, independent of their radiation-induced arrest in the G2/M phase. MMEJ activation was dependent on XRCC1 phosphorylation by casein kinase 2 (CK2), enhancing XRCC1's interaction with the end resection enzymes MRE11 and CtIP. Both endonuclease and exonuclease activities of MRE11 were required for MMEJ, as has been observed for homology-directed DSB repair (HDR). Furthermore, the XRCC1 co-immunoprecipitate complex (IP) displayed MMEJ activity in vitro, which was significantly elevated after irradiation. Our studies thus suggest that radiation-mediated enhancement of MMEJ in cells surviving radiation therapy may contribute to their radioresistance and could be therapeutically targeted.
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Affiliation(s)
- Arijit Dutta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA
| | - Bradley Eckelmann
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Texas A&M Health Science Center, College of Medicine, Bryan, TX 77807, USA
| | | | - Kazi Mokim Ahmed
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Shiladitya Sengupta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, New York, NY 10065, USA
| | - Arvind Pandey
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Pavana M Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Miaw-Sheue Tsai
- Department of Cell and Molecular Biology, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA
| | - John A Tainer
- Department of Cell and Molecular Biology, Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA 94720, USA.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michael Weinfeld
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta T6G 1Z2, Canada
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, New York, NY 10065, USA.,Houston Methodist Neurological Institute, Houston, TX 77030, USA
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Department of Biochemistry and Molecular Biology, University of Texas Medical Branch (UTMB), Galveston, TX 77555, USA.,Texas A&M Health Science Center, College of Medicine, Bryan, TX 77807, USA.,Weill Cornell Medical College, New York, NY 10065, USA
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18
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Zhang L, Reyes A, Wang X. The Role of DNA Repair in Maintaining Mitochondrial DNA Stability. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1038:85-105. [PMID: 29178071 DOI: 10.1007/978-981-10-6674-0_7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mitochondria are vital double-membrane organelles that act as a "powerhouse" inside the cell and have essential roles to maintain cellular functions, e.g., ATP production, iron-sulfur synthesis metabolism, and steroid synthesis. An important difference with other organelles is that they contain their own mitochondrial DNA (mtDNA). Such powerful organelles are also sensitive to both endogenous and exogenous factors that can cause lesions to their structural components and their mtDNA, resulting in gene mutations and eventually leading to diseases. In this review, we will mainly focus on mammalian mitochondrial DNA repair pathways that safeguard mitochondrial DNA integrity and several important factors involved in the repair process, especially on an essential pathway, base excision repair. We eagerly anticipate to explore more methods to treat related diseases by constantly groping for these complexes and precise repair mechanisms.
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Affiliation(s)
- Linlin Zhang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China.
| | - Aurelio Reyes
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
| | - Xiangdong Wang
- Zhongshan Hospital Institute of Clinical Science, Fudan University, Shanghai Medical College, Shanghai, China.
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19
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Zhdanov VP. Kinetic aspects of enzyme-mediated repair of DNA single-strand breaks. Biosystems 2016; 150:194-199. [PMID: 27771386 DOI: 10.1016/j.biosystems.2016.09.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 09/22/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
Abstract
In cells and bacteria, DNA can be damaged in different ways. The efficient damage repair, mediated by various enzymes, is crucial for their survival. Most frequently, the damage is reduced to single-strand breaks. In human cells, according to the experiments, the repair of such breaks can mechanistically be divided into four steps including (i) the break detection, (ii) processing of damaged ends, (iii) gap filling, and (iv) ligation of unbound ends of the broken strand. The first and second steps run in parallel while the third and fourth steps are sequential. The author proposes a kinetic model describing these steps. It allows one to understand the likely dependence of the number of breaks in different states on enzyme concentrations. The dependence of these concentrations on the rate of the formation of breaks can be understood as well. In addition, the likely role of unzipping and zipping of the fragments of broken ends of the strand in the ligation step has been scrutinized taking the specifics of binding of DNA stands into account.
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Affiliation(s)
- Vladimir P Zhdanov
- Division of Biological Physics, Department of Physics, Chalmers University of Technology, S-41296 Göteborg, Sweden; Boreskov Institute of Catalysis, Russian Academy of Sciences, Novosibirsk 630090, Russia.
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20
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Yuan Y, Britton S, Delteil C, Coates J, Jackson SP, Barboule N, Frit P, Calsou P. Single-stranded DNA oligomers stimulate error-prone alternative repair of DNA double-strand breaks through hijacking Ku protein. Nucleic Acids Res 2015; 43:10264-76. [PMID: 26350212 PMCID: PMC4666393 DOI: 10.1093/nar/gkv894] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Revised: 08/26/2015] [Accepted: 08/26/2015] [Indexed: 11/17/2022] Open
Abstract
In humans, DNA double-strand breaks (DSBs) are repaired by two mutually-exclusive mechanisms, homologous recombination or end-joining. Among end-joining mechanisms, the main process is classical non-homologous end-joining (C-NHEJ) which relies on Ku binding to DNA ends and DNA Ligase IV (Lig4)-mediated ligation. Mostly under Ku- or Lig4-defective conditions, an alternative end-joining process (A-EJ) can operate and exhibits a trend toward microhomology usage at the break junction. Homologous recombination relies on an initial MRN-dependent nucleolytic degradation of one strand at DNA ends. This process, named DNA resection generates 3' single-stranded tails necessary for homologous pairing with the sister chromatid. While it is believed from the current literature that the balance between joining and recombination processes at DSBs ends is mainly dependent on the initiation of resection, it has also been shown that MRN activity can generate short single-stranded DNA oligonucleotides (ssO) that may also be implicated in repair regulation. Here, we evaluate the effect of ssO on end-joining at DSB sites both in vitro and in cells. We report that under both conditions, ssO inhibit C-NHEJ through binding to Ku and favor repair by the Lig4-independent microhomology-mediated A-EJ process.
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Affiliation(s)
- Ying Yuan
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Sébastien Britton
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Christine Delteil
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Julia Coates
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN England, UK
| | - Stephen P Jackson
- The Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, CB2 1QN England, UK
| | - Nadia Barboule
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Philippe Frit
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
| | - Patrick Calsou
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), BP 64182, 205 route de Narbonne, F-31077 Toulouse, Cedex4, France Université de Toulouse, UPS, IPBS, F-31077 Toulouse, France Equipe labellisée Ligue Nationale Contre le Cancer, France
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21
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Nuclear Localization of the DNA Repair Scaffold XRCC1: Uncovering the Functional Role of a Bipartite NLS. Sci Rep 2015; 5:13405. [PMID: 26304019 PMCID: PMC4548243 DOI: 10.1038/srep13405] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 07/17/2015] [Indexed: 12/23/2022] Open
Abstract
We have characterized the nuclear localization signal (NLS) of XRCC1 structurally using X-ray crystallography and functionally using fluorescence imaging. Crystallography and binding studies confirm the bipartite nature of the XRCC1 NLS interaction with Importin α (Impα) in which the major and minor binding motifs are separated by >20 residues, and resolve previous inconsistent determinations. Binding studies of peptides corresponding to the bipartite NLS, as well as its major and minor binding motifs, to both wild-type and mutated forms of Impα reveal pronounced cooperative binding behavior that is generated by the proximity effect of the tethered major and minor motifs of the NLS. The cooperativity stems from the increased local concentration of the second motif near its cognate binding site that is a consequence of the stepwise binding behavior of the bipartite NLS. We predict that the stepwise dissociation of the NLS from Impα facilitates unloading by providing a partially complexed intermediate that is available for competitive binding by Nup50 or the Importin β binding domain. This behavior provides a basis for meeting the intrinsically conflicting high affinity and high flux requirements of an efficient nuclear transport system.
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22
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Breslin C, Hornyak P, Ridley A, Rulten SL, Hanzlikova H, Oliver AW, Caldecott KW. The XRCC1 phosphate-binding pocket binds poly (ADP-ribose) and is required for XRCC1 function. Nucleic Acids Res 2015; 43:6934-44. [PMID: 26130715 PMCID: PMC4538820 DOI: 10.1093/nar/gkv623] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/01/2015] [Accepted: 06/04/2015] [Indexed: 12/29/2022] Open
Abstract
Poly (ADP-ribose) is synthesized at DNA single-strand breaks and can promote the recruitment of the scaffold protein, XRCC1. However, the mechanism and importance of this process has been challenged. To address this issue, we have characterized the mechanism of poly (ADP-ribose) binding by XRCC1 and examined its importance for XRCC1 function. We show that the phosphate-binding pocket in the central BRCT1 domain of XRCC1 is required for selective binding to poly (ADP-ribose) at low levels of ADP-ribosylation, and promotes interaction with cellular PARP1. We also show that the phosphate-binding pocket is required for EGFP-XRCC1 accumulation at DNA damage induced by UVA laser, H2O2, and at sites of sub-nuclear PCNA foci, suggesting that poly (ADP-ribose) promotes XRCC1 recruitment both at single-strand breaks globally across the genome and at sites of DNA replication stress. Finally, we show that the phosphate-binding pocket is required following DNA damage for XRCC1-dependent acceleration of DNA single-strand break repair, DNA base excision repair, and cell survival. These data support the hypothesis that poly (ADP-ribose) synthesis promotes XRCC1 recruitment at DNA damage sites and is important for XRCC1 function.
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Affiliation(s)
- Claire Breslin
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Peter Hornyak
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Andrew Ridley
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Stuart L Rulten
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Hana Hanzlikova
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Antony W Oliver
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Keith W Caldecott
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
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Kukshal V, Kim IK, Hura GL, Tomkinson AE, Tainer JA, Ellenberger T. Human DNA ligase III bridges two DNA ends to promote specific intermolecular DNA end joining. Nucleic Acids Res 2015; 43:7021-31. [PMID: 26130724 PMCID: PMC4538836 DOI: 10.1093/nar/gkv652] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 06/15/2015] [Indexed: 12/14/2022] Open
Abstract
Mammalian DNA ligase III (LigIII) functions in both nuclear and mitochondrial DNA metabolism. In the nucleus, LigIII has functional redundancy with DNA ligase I whereas LigIII is the only mitochondrial DNA ligase and is essential for the survival of cells dependent upon oxidative respiration. The unique LigIII zinc finger (ZnF) domain is not required for catalytic activity but senses DNA strand breaks and stimulates intermolecular ligation of two DNAs by an unknown mechanism. Consistent with this activity, LigIII acts in an alternative pathway of DNA double strand break repair that buttresses canonical non-homologous end joining (NHEJ) and is manifest in NHEJ-defective cancer cells, but how LigIII acts in joining intermolecular DNA ends versus nick ligation is unclear. To investigate how LigIII efficiently joins two DNAs, we developed a real-time, fluorescence-based assay of DNA bridging suitable for high-throughput screening. On a nicked duplex DNA substrate, the results reveal binding competition between the ZnF and the oligonucleotide/oligosaccharide-binding domain, one of three domains constituting the LigIII catalytic core. In contrast, these domains collaborate and are essential for formation of a DNA-bridging intermediate by adenylated LigIII that positions a pair of blunt-ended duplex DNAs for efficient and specific intermolecular ligation.
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Affiliation(s)
- Vandna Kukshal
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - In-Kwon Kim
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Gregory L Hura
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Alan E Tomkinson
- Department of Internal Medicine and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA
| | - John A Tainer
- Life Science Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Tom Ellenberger
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, Saint Louis, MO 63110, USA
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Arakawa H, Iliakis G. Alternative Okazaki Fragment Ligation Pathway by DNA Ligase III. Genes (Basel) 2015; 6:385-98. [PMID: 26110316 PMCID: PMC4488670 DOI: 10.3390/genes6020385] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 06/10/2015] [Accepted: 06/18/2015] [Indexed: 01/18/2023] Open
Abstract
Higher eukaryotes have three types of DNA ligases: DNA ligase 1 (Lig1), DNA ligase 3 (Lig3) and DNA ligase 4 (Lig4). While Lig1 and Lig4 are present in all eukaryotes from yeast to human, Lig3 appears sporadically in evolution and is uniformly present only in vertebrates. In the classical, textbook view, Lig1 catalyzes Okazaki-fragment ligation at the DNA replication fork and the ligation steps of long-patch base-excision repair (BER), homologous recombination repair (HRR) and nucleotide excision repair (NER). Lig4 is responsible for DNA ligation at DNA double strand breaks (DSBs) by the classical, DNA-PKcs-dependent pathway of non-homologous end joining (C-NHEJ). Lig3 is implicated in a short-patch base excision repair (BER) pathway, in single strand break repair in the nucleus, and in all ligation requirements of the DNA metabolism in mitochondria. In this scenario, Lig1 and Lig4 feature as the major DNA ligases serving the most essential ligation needs of the cell, while Lig3 serves in the cell nucleus only minor repair roles. Notably, recent systematic studies in the chicken B cell line, DT40, involving constitutive and conditional knockouts of all three DNA ligases individually, as well as of combinations thereof, demonstrate that the current view must be revised. Results demonstrate that Lig1 deficient cells proliferate efficiently. Even Lig1/Lig4 double knockout cells show long-term viability and proliferate actively, demonstrating that, at least in DT40, Lig3 can perform all ligation reactions of the cellular DNA metabolism as sole DNA ligase. Indeed, in the absence of Lig1, Lig3 can efficiently support semi-conservative DNA replication via an alternative Okazaki-fragment ligation pathway. In addition, Lig3 can back up NHEJ in the absence of Lig4, and can support NER and HRR in the absence of Lig1. Supporting observations are available in less elaborate genetic models in mouse cells. Collectively, these observations raise Lig3 from a niche-ligase to a universal DNA ligase, which can potentially substitute or backup the repair and replication functions of all other DNA ligases in the cell nucleus. Thus, the old model of functionally dedicated DNA ligases is now replaced by one in which only Lig4 remains dedicated to C-NHEJ, with Lig1 and Lig3 showing an astounding functional flexibility and interchangeability for practically all nuclear ligation functions. The underlying mechanisms of Lig3 versus Lig1 utilization in DNA repair and replication are expected to be partly different and remain to be elucidated.
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Affiliation(s)
- Hiroshi Arakawa
- IFOM-FIRC Institute of Molecular Oncology Foundation, IFOM-IEO Campus, Via Adamello 16, Milano 20139, Italy.
| | - George Iliakis
- Institute of Medical Radiation Biology, University of Duisburg-Essen Medical School, Essen 45122, Germany.
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Micro-irradiation tools to visualize base excision repair and single-strand break repair. DNA Repair (Amst) 2015; 31:52-63. [PMID: 25996408 DOI: 10.1016/j.dnarep.2015.05.001] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/30/2015] [Accepted: 05/02/2015] [Indexed: 12/30/2022]
Abstract
Microscopy and micro-irradiation imaging techniques have significantly advanced our knowledge of DNA damage tolerance and the assembly of DNA repair proteins at the sites of damage. While these tools have been extensively applied to the study of nucleotide excision repair and double-strand break repair, their application to the repair of oxidatively-induced base lesions and single-strand breaks is just beginning to yield new insights. This review will focus on examining micro-irradiation techniques reported to create base lesions and single-strand breaks; these lesions are considered to be primarily addressed by proteins involved in the base excision repair (BER) pathway. By examining conditions for generating these DNA lesions and reviewing information on the assembly and dissociation of repair complexes at the induced lesion sites, we hope to promote further investigations into BER and to stimulate further development and enhancement of these techniques for the study of BER.
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