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Sriramareddy SN, Jamakhani M, Vilanova L, Brossel H, Staumont B, Hamaidia M. Selective inhibition of DNA ligase IV provides additional efficacy to the treatment of anaplastic thyroid cancer. Front Oncol 2024; 14:1323313. [PMID: 38380364 PMCID: PMC10876873 DOI: 10.3389/fonc.2024.1323313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/19/2024] [Indexed: 02/22/2024] Open
Abstract
Background Although the incidence of anaplastic thyroid carcinoma (ATC) is low (2.5% of thyroid cancer cases), this cancer has a very poor prognosis (survival rates < 5 months) and accounts for 14-39% of deaths. Conventional therapies based on surgery in combination with radiotherapy or chemotherapy showed limited effectiveness primarily due to the robust and protective DNA damage response in thyroid cancer cells. Methods We used single-cell transcriptomic data from patients with different subtypes of thyroid cancer to study expression of genes involved in homologous recombination (HR) and non-homologous end joining (NHEJ) pathways. Then, we investigated the mechanisms of DNA damage and repair in anaplastic (C643 and Hth74) and papillary (TPC-1) thyroid cancer cell lines. The effect of caffeine (inhibitor of ATM and ATR) and UCN-01 (CHK1 inhibitor) was evaluated in cell cycle progression of thyroid cancer cells after γ-radiation or doxorubicin treatment. The DNA damage response was monitored after staining of phosphorylated γ-H2AX and 53BP1. Reporter plasmids were used to determine the efficacy of double-strand DNA breaks (DSBs) repair by HR and NHEJ in thyroid cancer cells. We evaluated the combination of selective inhibition of the DNA ligase IV by SCR7 and doxorubicin on cellular apoptosis and tumor growth in xenograft murine models of anaplastic thyroid cancer. Results Single-cell RNA-Seq showed that NHEJ- and HR-related genes are expressed in ATC and PTC patients. We showed that ATC cells undergo mitosis in the presence of unrepaired DNA damage caused by γ-radiation and doxorubicin treatment. To proliferate and survive, these cells efficiently repair DNA lesions using homologous recombination (HR) and non-homologous end joining (NHEJ). The combination of SCR7 with doxorubicin, significantly increased apoptosis and impaired ATC tumor growth in a xenograft mouse model compared to doxorubicin monotherapy. Conclusion This study shows the therapeutic value of the combination of a DNA ligase IV inhibitor and DNA-damaging agents (doxorubicin and/or γ-radiation) for the treatment of anaplastic thyroid cancer.
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Affiliation(s)
- Sathya Neelature Sriramareddy
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), University of Liège, Liège, Belgium
- Molecular Biology (TERRA), University of Liege, Gembloux, Belgium
| | - Majeed Jamakhani
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), University of Liège, Liège, Belgium
- Molecular Biology (TERRA), University of Liege, Gembloux, Belgium
| | - Léa Vilanova
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), University of Liège, Liège, Belgium
- Molecular Biology (TERRA), University of Liege, Gembloux, Belgium
| | - Hélène Brossel
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), University of Liège, Liège, Belgium
- Molecular Biology (TERRA), University of Liege, Gembloux, Belgium
| | - Bernard Staumont
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), University of Liège, Liège, Belgium
- Molecular Biology (TERRA), University of Liege, Gembloux, Belgium
| | - Malik Hamaidia
- Molecular and Cellular Epigenetics, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), University of Liège, Liège, Belgium
- Molecular Biology (TERRA), University of Liege, Gembloux, Belgium
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2
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De Bragança S, Aicart-Ramos C, Arribas-Bosacoma R, Rivera-Calzada A, Unfried JP, Prats-Mari L, Marin-Baquero M, Fortes P, Llorca O, Moreno-Herrero F. APLF and long non-coding RNA NIHCOLE promote stable DNA synapsis in non-homologous end joining. Cell Rep 2023; 42:111917. [PMID: 36640344 DOI: 10.1016/j.celrep.2022.111917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 10/26/2022] [Accepted: 12/13/2022] [Indexed: 01/01/2023] Open
Abstract
The synapsis of DNA ends is a critical step for the repair of double-strand breaks by non-homologous end joining (NHEJ). This is performed by a multicomponent protein complex assembled around Ku70-Ku80 heterodimers and regulated by accessory factors, including long non-coding RNAs, through poorly understood mechanisms. Here, we use magnetic tweezers to investigate the contributions of core NHEJ proteins and APLF and lncRNA NIHCOLE to DNA synapsis. APLF stabilizes DNA end bridging and, together with Ku70-Ku80, establishes a minimal complex that supports DNA synapsis for several minutes under piconewton forces. We find the C-terminal acidic region of APLF to be critical for bridging. NIHCOLE increases the dwell time of the synapses by Ku70-Ku80 and APLF. This effect is further enhanced by a small and structured RNA domain within NIHCOLE. We propose a model where Ku70-Ku80 can simultaneously bind DNA, APLF, and structured RNAs to promote the stable joining of DNA ends.
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Affiliation(s)
- Sara De Bragança
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Clara Aicart-Ramos
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Raquel Arribas-Bosacoma
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| | - Angel Rivera-Calzada
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Juan Pablo Unfried
- Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel; Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Laura Prats-Mari
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain
| | - Mikel Marin-Baquero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain
| | - Puri Fortes
- Department of Gene Therapy and Regulation of Gene Expression, Center for Applied Medical Research (CIMA), University of Navarra (UNAV), Pamplona, Spain; Navarra Institute for Health Research (IdiSNA), Pamplona, Spain; Liver and Digestive Diseases Networking Biomedical Research Centre (CIBERehd), Spanish Network for Advanced Therapies (TERAV ISCIII), Madrid, Spain
| | - Oscar Llorca
- Structural Biology Programme, Spanish National Cancer Research Center (CNIO), Madrid, Spain.
| | - Fernando Moreno-Herrero
- Department of Macromolecular Structures, Centro Nacional de Biotecnología (CNB), CSIC, Madrid, Spain.
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Wang C, Sun Z, Wang M, Jiang Z, Zhang M, Cao H, Luo L, Qiao C, Xiao H, Chen G, Li X, Liu J, Wei Z, Shen B, Wang J, Feng J. Novel CRISPR/Cas9-mediated knockout of LIG4 increases efficiency of site-specific integration in Chinese hamster ovary cell line. Biotechnol Lett 2022. [PMID: 35918621 DOI: 10.1007/s10529-022-03282-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 07/11/2022] [Indexed: 11/02/2022]
Abstract
AIM To investigate the impact of deficiency of LIG4 gene on site-specific integration in CHO cells. RESULTS CHO cells are considered the most valuable mammalian cells in the manufacture of biological medicines, and genetic engineering of CHO cells can improve product yield and stability. The traditional method of inserting foreign genes by random integration (RI) requires multiple rounds of screening and selection, which may lead to location effects and gene silencing, making it difficult to obtain stable, high-yielding cell lines. Although site-specific integration (SSI) techniques may overcome the challenges with RI, its feasibility is limited by the very low efficiency of the technique. Recently, SSI efficiency has been enhanced in other mammalian cell types by inhibiting DNA ligase IV (Lig4) activity, which is indispensable in DNA double-strand break repair by NHEJ. However, this approach has not been evaluated in CHO cells. In this study, the LIG4 gene was knocked out of CHO cells using CRISPR/Cas9-mediated genome editing. Efficiency of gene targeting in LIG4-/--CHO cell lines was estimated by a green fluorescence protein promoterless reporter system. Notably, the RI efficiency, most likely mediated by NHEJ in CHO, was inhibited by LIG4 knockout, whereas SSI efficiency strongly increased 9.2-fold under the precise control of the promoter in the ROSA26 site in LIG4-/--CHO cells. Moreover, deletion of LIG4 had no obvious side effects on CHO cell proliferation. CONCLUSIONS Deficiency of LIG4 represents a feasible strategy to improve SSI efficiency and suggests it can be applied to develop and engineer CHO cell lines in the future.
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4
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Joshi R, Banerjee SJ, Curtiss J, Ashley AK. DNA ligase IV mutations confer shorter lifespan and increased sensitivity to nutrient stress in Drosophila melanogaster. J Appl Genet 2021. [PMID: 34817771 DOI: 10.1007/s13353-021-00637-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 03/09/2021] [Accepted: 05/04/2021] [Indexed: 12/04/2022]
Abstract
The nonhomologous end-joining pathway is a primary DNA double-strand break repair pathway in eukaryotes. DNA ligase IV (Lig4) catalyzes the final step of DNA end ligation in this pathway. Partial loss of Lig4 in mammals causes Lig4 syndrome, while complete loss is embryonically lethal. DNA ligase 4 (DNAlig4) null Drosophila melanogaster is viable, but sensitive to ionizing radiation during early development. We proposed to explore if DNAlig4 loss induced other long-term sensitivities and defects in D. melanogaster. We demonstrated that DNAlig4 mutant strains had decreased lifespan and lower resistance to nutrient deprivation, indicating Lig4 is required for maintaining health and longevity in D. melanogaster.
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5
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Joshi JS, Vora HH, Ghosh NR, Tankshali RN, Jetly DH, Trivedi TI. Nonhomologous end joining repair pathway molecules as predictive biomarkers for patients with oral squamous cell carcinoma. J Cancer Res Ther 2021; 17:1031-1038. [PMID: 34528560 DOI: 10.4103/jcrt.jcrt_582_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Purpose Nonhomologous end-joining (NHEJ) is critical for the repair of either pathologic double-strand breaks (DSBs) and/or for the repair of physiologic DSBs created during radiotherapy to kill the tumor cell. Therefore, patients with higher expression of NHEJ repair proteins might develop resistance to ionizing radiation, allowing the disease to recur. As cancer of the oral cavity is a serious health problem globally, the present study aimed to examine the expression of Ku70/80, X-ray repair cross-complementing protein 4 (XRCC4) and DNA ligase IV-core molecules of the NHEJ pathway in patients with oral cancer. Materials and Methods Protein expression of Ku70/80, XRCC4, and DNA ligase IV were studied by Immunohistochemistry and mRNA expression of Ku70 and Ku80 were studied using reverse transcription polymerase chain reaction. Data were analyzed statistically using SPSS. Results A univariate survival analysis revealed an association of Ku70 mRNA with shorter overall survival (OS). While protein expression of XRCC4 showed an association with reduced relapse-free survival and shorter OS. Multivariate survival analysis demonstrated that XRCC4 and DNA ligase IV are independent prognosticators for predicting adverse disease outcomes. Conclusion Strong expression of repair proteins - XRCC4 and DNA ligase IV is associated with unfavorable disease outcome in patients with oral squamous cell carcinoma.
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Affiliation(s)
- Jigna S Joshi
- Stem Cell Biology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Hemangini H Vora
- Immunohematology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Nandita R Ghosh
- Tumor Biology Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Rajen N Tankshali
- Department of Surgical Oncology, Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Dhaval H Jetly
- Department of Onco-Pathology, Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
| | - Trupti I Trivedi
- Clinical Carcinogenesis Lab, Department of Cancer Biology, The Gujarat Cancer & Research Institute, Ahmedabad, Gujarat, India
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6
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Gopalakrishnan V, Sharma S, Ray U, Manjunath M, Lakshmanan D, Vartak SV, Gopinatha VK, Srivastava M, Kempegowda M, Choudhary B, Raghavan SC. SCR7, an inhibitor of NHEJ can sensitize tumor cells to ionization radiation. Mol Carcinog 2021; 60:627-643. [PMID: 34192388 DOI: 10.1002/mc.23329] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 06/01/2021] [Accepted: 06/07/2021] [Indexed: 12/30/2022]
Abstract
Nonhomologous end joining (NHEJ), one of the major DNA double-strand break repair pathways, plays a significant role in cancer cell proliferation and resistance to radio and chemotherapeutic agents. Previously, we had described a small molecule inhibitor, SCR7, which inhibited NHEJ in a DNA Ligase IV dependent manner. Here, we report that SCR7 potentiates the effect of γ-radiation (IR) that induces DNA breaks as intermediates to eradicate cancer cells. Dose fractionation studies revealed that coadministration of SCR7 and IR (0.5 Gy) in mice Dalton's lymphoma (DLA) model led to a significant reduction in mice tumor cell proliferation, which was equivalent to that observed for 2 Gy dose when both solid and liquid tumor models were used. Besides, co-treatment with SCR7 and 1 Gy of IR further improved the efficacy. Notably, there was no significant change in blood parameters, kidney and liver functions upon combinatorial treatment of SCR7 and IR. Further, the co-treatment of SCR7 and IR resulted in a significant increase in unrepaired DSBs within cancer cells compared to either of the agent alone. Anatomy, histology, and other studies in tumor models confirmed the cumulative effects of both agents in activating apoptotic pathways to induce cytotoxicity by modulating DNA damage response and repair pathways. Thus, we report that SCR7 has the potential to reduce the side effects of radiotherapy by lowering its effective dose ex vivo and in mice tumor models, with implications in cancer therapy.
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Affiliation(s)
- Vidya Gopalakrishnan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India.,Department of Zoology, St. Joseph's College (Autonomous), Irinjalakuda, Kerala, India
| | - Shivangi Sharma
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.,Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India
| | - Ujjayinee Ray
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Meghana Manjunath
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India.,Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Divya Lakshmanan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Supriya V Vartak
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Vindya K Gopinatha
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
| | - Mrinal Srivastava
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India.,Tata Institute of Fundamental Research, Hyderabad, Telangana, India
| | | | - Bibha Choudhary
- Institute of Bioinformatics and Applied Biotechnology, Electronics City, Bangalore, Karnataka, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore, Karnataka, India
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7
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Maddi ER, Raghavan SC, Natesh R. Hypomorphic mutations in human DNA ligase IV lead to compromised DNA binding efficiency, hydrophobicity and thermal stability. Protein Eng Des Sel 2021; 34:6135054. [PMID: 33586762 DOI: 10.1093/protein/gzab001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 12/12/2020] [Accepted: 12/30/2020] [Indexed: 11/13/2022] Open
Abstract
Studies have shown that Lig4 syndrome mutations in DNA ligase IV (LigIV) are compromised in its function with residual level of double strand break ligation activity in vivo. It was speculated that Lig4 syndrome mutations adversely affect protein folding and stability. Though there are crystal structures of LigIV, there are no reports of crystal structures of Lig4 syndrome mutants and their biophysical characterization to date. Here, we have examined the conformational states, thermal stability, hydrophobicity and DNA binding efficiency of human DNA LigIV wild type and its hypomorphic mutants by far-UV circular dichroism, tyrosine and tryptophan fluorescence, and 1-anilino-8-naphthalene-sulfonate binding, dynamic light scattering, size exclusion chromatography, multi-angle light scattering and electrophoretic mobility shift assay. We show here that LigIV hypomorphic mutants have reduced DNA-binding efficiency, a shift in secondary structure content from the helical to random coil, marginal reduction in their thermal stability and increased hydrophobicity as compared to the wild-type LigIV.
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Affiliation(s)
- Eswar Reddy Maddi
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala 695551, India
| | - Sathees C Raghavan
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
| | - Ramanathan Natesh
- School of Biology, Indian Institute of Science Education and Research Thiruvananthapuram, Thiruvananthapuram, Kerala 695551, India
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8
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Cao X, Kouyama-Suzuki E, Pang B, Kurihara T, Mori T, Yanagawa T, Shirai Y, Tabuchi K. Inhibition of DNA ligase IV enhances the CRISPR/Cas9-mediated knock-in efficiency in mouse brain neurons. Biochem Biophys Res Commun 2020; 533:449-57. [PMID: 32972746 DOI: 10.1016/j.bbrc.2020.09.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 09/13/2020] [Indexed: 11/21/2022]
Abstract
CRISPR/Cas9-mediated gene knock-in in in vivo neurons using in utero electroporation is a powerful technique, but the knock-in efficiency is generally low. We previously demonstrated that co-transfection with RAD51, a key molecule of the initial step of homology-directed repair (HDR), expression vector increased EGFP knock-in efficiency in the β-actin site up to 2.5-fold in the pyramidal neurons in layer 2/3 of the somatosensory cortex of mouse brain. To further improve the efficiency, we examined the effect of inhibition of DNA ligase IV (LIG4) that is an essential molecule for non-homologous end joining (NHEJ). Co-transfection with small hairpin RNA for LIG4 (shlig4) expression vector increased the EGFP knock-in efficiency in the β-actin site up to 3.6-fold compared to the condition without shlig4. RAD51 and shlig4 expression vector co-transfection further increased the knock-in efficiency up to 4.7-fold of the control condition. These results suggest that the inhibition of LIG4 is more effective than RAD51 overexpression, and it enhances the effect of RAD51 overexpression on HDR-mediated gene knock-in in vivo neurons.
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9
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Chappidi N, Nascakova Z, Boleslavska B, Zellweger R, Isik E, Andrs M, Menon S, Dobrovolna J, Balbo Pogliano C, Matos J, Porro A, Lopes M, Janscak P. Fork Cleavage-Religation Cycle and Active Transcription Mediate Replication Restart after Fork Stalling at Co-transcriptional R-Loops. Mol Cell 2019; 77:528-541.e8. [PMID: 31759821 DOI: 10.1016/j.molcel.2019.10.026] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 07/03/2019] [Accepted: 10/16/2019] [Indexed: 01/08/2023]
Abstract
Formation of co-transcriptional R-loops underlies replication fork stalling upon head-on transcription-replication encounters. Here, we demonstrate that RAD51-dependent replication fork reversal induced by R-loops is followed by the restart of semiconservative DNA replication mediated by RECQ1 and RECQ5 helicases, MUS81/EME1 endonuclease, RAD52 strand-annealing factor, the DNA ligase IV (LIG4)/XRCC4 complex, and the non-catalytic subunit of DNA polymerase δ, POLD3. RECQ5 disrupts RAD51 filaments assembled on stalled forks after RECQ1-mediated reverse branch migration, preventing a new round of fork reversal and facilitating fork cleavage by MUS81/EME1. MUS81-dependent DNA breaks accumulate in cells lacking RAD52 or LIG4 upon induction of R-loop formation, suggesting that RAD52 acts in concert with LIG4/XRCC4 to catalyze fork religation, thereby mediating replication restart. The resumption of DNA synthesis after R-loop-associated fork stalling also requires active transcription, the restoration of which depends on MUS81, RAD52, LIG4, and the transcription elongation factor ELL. These findings provide mechanistic insights into transcription-replication conflict resolution.
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Affiliation(s)
- Nagaraja Chappidi
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Zuzana Nascakova
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Barbora Boleslavska
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Ralph Zellweger
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Esin Isik
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Martin Andrs
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | - Shruti Menon
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Jana Dobrovolna
- Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic
| | | | - Joao Matos
- Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Pavel Janscak
- Institute of Molecular Cancer Research, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland; Institute of Molecular Genetics of the Czech Academy of Sciences, Videnska 1083, 142 20 Prague, Czech Republic.
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10
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Angstenberger M, Krischer J, Aktaş O, Büchel C. Knock-Down of a ligIV Homologue Enables DNA Integration via Homologous Recombination in the Marine Diatom Phaeodactylum tricornutum. ACS Synth Biol 2019; 8:57-69. [PMID: 30525458 DOI: 10.1021/acssynbio.8b00234] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Genetic engineering of Phaeodactylum tricornutum as a model organism for diatoms is the basis of molecular and biochemical research, and can also be used in biotechnological approaches. So far, integration of foreign DNA into the genome happens randomly by nonhomologous end joining (NHEJ), if the classical method of particle bombardment is used, with the danger of negative physiological side effects. Here we show that a putative gene for a DNA ligase IV homologue ( ligIV) in P. tricornutum codes for a functional LigIV. The knock-down of ligIV in P. tricornutum via antisense RNA drastically enhances homologous recombination (HR) by interfering with the NHEJ pathway at its central DNA ligation step done by LigIV. This enables a specific integration of DNA at desired locations, greatly enhanced transformation rates and provides a new way of specifically altering the genome of P. tricornutum.
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Affiliation(s)
- Max Angstenberger
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, Biozentrum, 60438 Frankfurt am Main, Germany
| | - Julia Krischer
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, Biozentrum, 60438 Frankfurt am Main, Germany
| | - Ozan Aktaş
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, Biozentrum, 60438 Frankfurt am Main, Germany
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue-Straße 9, Biozentrum, 60438 Frankfurt am Main, Germany
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11
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Taskiran EZ, Sonmez HE, Kosukcu C, Tavukcuoglu E, Yazici G, Esendagli G, Batu ED, Kiper POS, Bilginer Y, Alikasifoglu M, Ozen S. A Novel Missense LIG4 Mutation in a Patient With a Phenotype Mimicking Behçet's Disease. J Clin Immunol 2019; 39:99-105. [PMID: 30617623 DOI: 10.1007/s10875-018-0587-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2018] [Accepted: 12/27/2018] [Indexed: 01/15/2023]
Abstract
DNA ligase IV (LIG4) syndrome is a rare autosomal recessive disorder, manifesting with variable immune deficiency, growth failure, predisposition to malignancy, and cellular sensitivity to ionizing radiation. The facial features are subtle and variable, as well. Herein, we described an 18-year-old boy, the first child of consanguineous parents who presented with Behçet's disease (BD)-like phenotype, developmental delay, and dysembryoplastic neuroepithelial tumor (DNET). Whole-exome sequencing revealed a homozygous p.Arg871His (c.2612G > A) mutation in LIG4. To date, 35 cases have been reported with LIG4 syndrome. Peripheral blood mononuclear cells of the patient displayed notable sensitivity to ionizing radiation. Flow cytometric annexin V-propidium iodide (PI) and eFluor670 proliferation assays showed accelerated radiation-induced apoptosis and diminished proliferation, respectively. To our knowledge, this is the first case presenting with a BD-like phenotype. This case provides further evidence that rare monogenic defects could be the underlying cause of atypical presentations of some well-described disorders. Moreover, this clinical report further expands the phenotypical spectrum of LIG4 deficiency.
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Affiliation(s)
- Ekim Z Taskiran
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Hafize E Sonmez
- Department of Pediatrics, Division of Rheumatology, Hacettepe University Faculty of Medicine, 06100, Ankara, Turkey
| | - Can Kosukcu
- Department of Bioinformatics, Institute of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Ece Tavukcuoglu
- Department of Basic Oncology, Hacettepe University Cancer Institute, Ankara, Turkey
| | - Gozde Yazici
- Faculty of Medicine, Department of Radiation Oncology, Hacettepe University, Ankara, Turkey
| | - Gunes Esendagli
- Department of Basic Oncology, Hacettepe University Cancer Institute, Ankara, Turkey
| | - Ezgi D Batu
- Department of Pediatrics, Division of Rheumatology, Hacettepe University Faculty of Medicine, 06100, Ankara, Turkey
| | - Pelin O S Kiper
- Department of Pediatrics, Division of Pediatric Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Yelda Bilginer
- Department of Pediatrics, Division of Rheumatology, Hacettepe University Faculty of Medicine, 06100, Ankara, Turkey
| | - Mehmet Alikasifoglu
- Department of Medical Genetics, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Seza Ozen
- Department of Pediatrics, Division of Rheumatology, Hacettepe University Faculty of Medicine, 06100, Ankara, Turkey.
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12
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Conlin MP, Reid DA, Small GW, Chang HH, Watanabe G, Lieber MR, Ramsden DA, Rothenberg E. DNA Ligase IV Guides End-Processing Choice during Nonhomologous End Joining. Cell Rep 2018; 20:2810-2819. [PMID: 28930678 DOI: 10.1016/j.celrep.2017.08.091] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 08/22/2017] [Accepted: 08/25/2017] [Indexed: 12/15/2022] Open
Abstract
Nonhomologous end joining (NHEJ) must adapt to diverse end structures during repair of chromosome breaks. Here, we investigate the mechanistic basis for this flexibility. DNA ends are aligned in a paired-end complex (PEC) by Ku, XLF, XRCC4, and DNA ligase IV (LIG4); we show by single-molecule analysis how terminal mispairs lead to mobilization of ends within PECs and consequent sampling of more end-alignment configurations. This remodeling is essential for direct ligation of damaged and mispaired ends during cellular NHEJ, since remodeling and ligation of such ends both require a LIG4-specific structural motif, insert1. Insert1 is also required for PEC remodeling that enables nucleolytic processing when end structures block direct ligation. Accordingly, cells expressing LIG4 lacking insert1 are sensitive to ionizing radiation. Cellular NHEJ of diverse ends thus identifies the steps necessary for repair through LIG4-mediated sensing of differences in end structure and consequent dynamic remodeling of aligned ends.
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Affiliation(s)
- Michael P Conlin
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Dylan A Reid
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA
| | - George W Small
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Howard H Chang
- University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Go Watanabe
- University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Michael R Lieber
- University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA
| | - Dale A Ramsden
- Lineberger Comprehensive Cancer Center, Curriculum in Genetics and Molecular Biology, and Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC 27599, USA.
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA.
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13
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Luteijn RD, Drexler I, Smith GL, Lebbink RJ, Wiertz EJHJ. Mutagenic repair of double-stranded DNA breaks in vaccinia virus genomes requires cellular DNA ligase IV activity in the cytosol. J Gen Virol 2018; 99:790-804. [PMID: 29676720 PMCID: PMC7614823 DOI: 10.1099/jgv.0.001034] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Poxviruses comprise a group of large dsDNA viruses that include members relevant to human and animal health, such as variola virus, monkeypox virus, cowpox virus and vaccinia virus (VACV). Poxviruses are remarkable for their unique replication cycle, which is restricted to the cytoplasm of infected cells. The independence from the host nucleus requires poxviruses to encode most of the enzymes involved in DNA replication, transcription and processing. Here, we use the CRISPR/Cas9 genome engineering system to induce DNA damage to VACV (strain Western Reserve) genomes. We show that targeting CRISPR/Cas9 to essential viral genes limits virus replication efficiently. Although VACV is a strictly cytoplasmic pathogen, we observed extensive viral genome editing at the target site; this is reminiscent of a non-homologous end-joining DNA repair mechanism. This pathway was not dependent on the viral DNA ligase, but critically involved the cellular DNA ligase IV. Our data show that DNA ligase IV can act outside of the nucleus to allow repair of dsDNA breaks in poxvirus genomes. This pathway might contribute to the introduction of mutations within the genome of poxviruses and may thereby promote the evolution of these viruses.
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Affiliation(s)
- Rutger David Luteijn
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands.,Present address: Department of Molecular and Cell Biology, University of California, Berkeley, USA
| | - Ingo Drexler
- Institute for Virology, University Hospital Düsseldorf, Düsseldorf, Germany
| | | | - Robert Jan Lebbink
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Emmanuel J H J Wiertz
- Department of Medical Microbiology, University Medical Center Utrecht, Utrecht, The Netherlands
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14
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Qin X, Li R, Luo X, Lin Y, Feng JX. Deletion of ligD significantly improves gene targeting frequency in the lignocellulolytic filamentous fungus Penicillium oxalicum. Fungal Biol 2017; 121:615-623. [PMID: 28606356 DOI: 10.1016/j.funbio.2017.04.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/29/2017] [Accepted: 04/17/2017] [Indexed: 01/05/2023]
Abstract
To improve the gene targeting frequency (GTF) in the lignocellulolytic filamentous fungus Penicillium oxalicum HP7-1, the non-homologous end-joining (NHEJ) gene ligD was deleted. The obtained PoligD deletion mutant ΔPoligD showed no apparent defect in cellulase production, growth rate, and sensitivity towards osmotic stress and mutagen ethyl methanesulphonate (EMS), while increased sensitivity to high concentrations of methyl methanesulfonate (MMS). Deletion of PoligD gene resulted in significantly increased GTFs at three different loci in P. oxalicum, which are even higher than those in Poku70 deletion mutant. The GTF in ΔPoligD at PoargB (reached 97 %) and PoagaA (reached 90 %) loci increased 5.1- and 1.2-fold compared with that in wild-type strain (WT), while at the Podpp4 locus GTF was up to 27 % in ΔPoligD but close to 0 % in WT, with 0.5 kb homologous flanking regions. Furthermore, the argB and agaA nutritional selection in P. oxalicum was demonstrated and the PoargB and PoagaA genes could be used as selective markers in this fungus. Thus, the PoligD deletion mutant can be an important tool for the functional analysis of genes in P. oxalicum.
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Affiliation(s)
- Xiulin Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
| | - Ruijie Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
| | - Xiang Luo
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
| | - Yanmei Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
| | - Jia-Xun Feng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning, Guangxi, 530004, PR China.
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15
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Hammel M, Yu Y, Radhakrishnan SK, Chokshi C, Tsai MS, Matsumoto Y, Kuzdovich M, Remesh SG, Fang S, Tomkinson AE, Lees-Miller SP, Tainer JA. An Intrinsically Disordered APLF Links Ku, DNA-PKcs, and XRCC4- DNA Ligase IV in an Extended Flexible Non-homologous End Joining Complex. J Biol Chem 2016; 291:26987-27006. [PMID: 27875301 PMCID: PMC5207133 DOI: 10.1074/jbc.m116.751867] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Revised: 11/03/2016] [Indexed: 11/29/2022] Open
Abstract
DNA double-strand break (DSB) repair by non-homologous end joining (NHEJ) in human cells is initiated by Ku heterodimer binding to a DSB, followed by recruitment of core NHEJ factors including DNA-dependent protein kinase catalytic subunit (DNA-PKcs), XRCC4-like factor (XLF), and XRCC4 (X4)-DNA ligase IV (L4). Ku also interacts with accessory factors such as aprataxin and polynucleotide kinase/phosphatase-like factor (APLF). Yet, how these factors interact to tether, process, and ligate DSB ends while allowing regulation and chromatin interactions remains enigmatic. Here, small angle X-ray scattering (SAXS) and mutational analyses show APLF is largely an intrinsically disordered protein that binds Ku, Ku/DNA-PKcs (DNA-PK), and X4L4 within an extended flexible NHEJ core complex. X4L4 assembles with Ku heterodimers linked to DNA-PKcs via flexible Ku80 C-terminal regions (Ku80CTR) in a complex stabilized through APLF interactions with Ku, DNA-PK, and X4L4. Collective results unveil the solution architecture of the six-protein complex and suggest cooperative assembly of an extended flexible NHEJ core complex that supports APLF accessibility while possibly providing flexible attachment of the core complex to chromatin. The resulting dynamic tethering furthermore, provides geometric access of L4 catalytic domains to the DNA ends during ligation and of DNA-PKcs for targeted phosphorylation of other NHEJ proteins as well as trans-phosphorylation of DNA-PKcs on the opposing DSB without disrupting the core ligation complex. Overall the results shed light on evolutionary conservation of Ku, X4, and L4 activities, while explaining the observation that Ku80CTR and DNA-PKcs only occur in a subset of higher eukaryotes.
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Affiliation(s)
- Michal Hammel
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720,
| | - Yaping Yu
- the Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Sarvan K Radhakrishnan
- the Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Chirayu Chokshi
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Miaw-Sheue Tsai
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Yoshihiro Matsumoto
- the University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico 87131, and
| | - Monica Kuzdovich
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Soumya G Remesh
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Shujuan Fang
- the Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Alan E Tomkinson
- the University of New Mexico Health Sciences Center, University of New Mexico, Albuquerque, New Mexico 87131, and
| | - Susan P Lees-Miller
- the Department of Biochemistry and Molecular Biology, Arnie Charbonneau Cancer Institute, University of Calgary, Calgary, Alberta T2N 4N1, Canada,
| | - John A Tainer
- From the Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, California 94720, .,the Department of Molecular and Cellular Oncology, University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
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16
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Abstract
DNA double strand breaks (DSBs) are dangerous sources of genome instability and must be repaired by the cell. Nonhomologous end-joining (NHEJ) is an evolutionarily conserved pathway to repair DSBs by direct ligation of the ends, with no requirement for a homologous template. While NHEJ is the primary DSB repair pathway in mammalian cells, conservation of the core NHEJ factors throughout eukaryotes makes the pathway attractive for study in model organisms. The budding yeast, Saccharomyces cerevisiae, has been used extensively to develop a functional picture of NHEJ. In this review, we will discuss the current understanding of NHEJ in S. cerevisiae. Topics include canonical end-joining, alternative end-joining, and pathway regulation. Particular attention will be paid to the NHEJ mechanism involving core factors, including Yku70/80, Dnl4, Lif1, and Nej1, as well as the various factors implicated in the processing of the broken ends. The relevance of chromatin dynamics to NHEJ will also be discussed. This review illustrates the use of S. cerevisiae as a powerful system to understand the principles of NHEJ, as well as in pioneering the direction of the field.
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Affiliation(s)
- Charlene H Emerson
- a Graduate Program in Genetics, Baylor College of Medicine, Houston, TX 77030, USA.,b Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alison A Bertuch
- b Departments of Pediatrics and Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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17
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Kondo N, Sakurai Y, Hirota Y, Tanaka H, Watanabe T, Nakagawa Y, Narabayashi M, Kinashi Y, Miyatake SI, Hasegawa M, Suzuki M, Masunaga SI, Ohnishi T, Ono K. DNA damage induced by boron neutron capture therapy is partially repaired by DNA ligase IV. Radiat Environ Biophys 2016; 55:89-94. [PMID: 26573366 DOI: 10.1007/s00411-015-0625-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Accepted: 11/03/2015] [Indexed: 06/05/2023]
Abstract
Boron neutron capture therapy (BNCT) is a particle radiation therapy that involves the use of a thermal or epithermal neutron beam in combination with a boron ((10)B)-containing compound that specifically accumulates in tumor. (10)B captures neutrons and the resultant fission reaction produces an alpha ((4)He) particle and a recoiled lithium nucleus ((7)Li). These particles have the characteristics of high linear energy transfer (LET) radiation and therefore have marked biological effects. High-LET radiation is a potent inducer of DNA damage, specifically of DNA double-strand breaks (DSBs). The aim of the present study was to clarify the role of DNA ligase IV, a key player in the non-homologous end-joining repair pathway, in the repair of BNCT-induced DSBs. We analyzed the cellular sensitivity of the mouse embryonic fibroblast cell lines Lig4-/- p53-/- and Lig4+/+ p53-/- to irradiation using a thermal neutron beam in the presence or absence of (10)B-para-boronophenylalanine (BPA). The Lig4-/- p53-/- cell line had a higher sensitivity than the Lig4+/+ p53-/-cell line to irradiation with the beam alone or the beam in combination with BPA. In BNCT (with BPA), both cell lines exhibited a reduction of the 50 % survival dose (D 50) by a factor of 1.4 compared with gamma-ray and neutron mixed beam (without BPA). Although it was found that (10)B uptake was higher in the Lig4+/+ p53-/- than in the Lig4-/- p53-/- cell line, the latter showed higher sensitivity than the former, even when compared at an equivalent (10)B concentration. These results indicate that BNCT-induced DNA damage is partially repaired using DNA ligase IV.
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Affiliation(s)
- Natsuko Kondo
- Particle Radiation Oncology Research Center, Research Reactor Institute, Kyoto University, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, Japan.
| | - Yoshinori Sakurai
- Division of Medical Physics, Research Reactor Institute, Kyoto University, Sennan-gun, Osaka, 590-0494, Japan
| | - Yuki Hirota
- Department of Neurosurgery, Osaka Medical College, Takatsuki, Osaka, 569-8686, Japan
| | - Hiroki Tanaka
- Division of Medical Physics, Research Reactor Institute, Kyoto University, Sennan-gun, Osaka, 590-0494, Japan
| | - Tsubasa Watanabe
- Particle Radiation Oncology Research Center, Research Reactor Institute, Kyoto University, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, Japan
| | - Yosuke Nakagawa
- Particle Radiation Oncology Research Center, Research Reactor Institute, Kyoto University, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, Japan
| | - Masaru Narabayashi
- Particle Radiation Oncology Research Center, Research Reactor Institute, Kyoto University, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, Japan
| | - Yuko Kinashi
- Particle Radiation Oncology Research Center, Research Reactor Institute, Kyoto University, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, Japan
| | - Shin-ichi Miyatake
- Department of Neurosurgery, Osaka Medical College, Takatsuki, Osaka, 569-8686, Japan
| | - Masatoshi Hasegawa
- Department of Radiation Oncology, School of Medicine, Nara Medical University, Kashihara, Nara, 634-8522, Japan
| | - Minoru Suzuki
- Particle Radiation Oncology Research Center, Research Reactor Institute, Kyoto University, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, Japan
| | - Shin-ichiro Masunaga
- Particle Radiation Oncology Research Center, Research Reactor Institute, Kyoto University, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, Japan
| | - Takeo Ohnishi
- Department of Radiation Oncology, School of Medicine, Nara Medical University, Kashihara, Nara, 634-8522, Japan
| | - Koji Ono
- Particle Radiation Oncology Research Center, Research Reactor Institute, Kyoto University, Asashiro-Nishi, Kumatori-cho, Sennan-gun, Osaka, 590-0494, Japan
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18
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Tamura S, Higuchi K, Tamaki M, Inoue C, Awazawa R, Mitsuki N, Nakazawa Y, Mishima H, Takahashi K, Kondo O, Imai K, Morio T, Ohara O, Ogi T, Furukawa F, Inoue M, Yoshiura KI, Kanazawa N. Novel compound heterozygous DNA ligase IV mutations in an adolescent with a slowly-progressing radiosensitive-severe combined immunodeficiency. Clin Immunol 2015; 160:255-60. [PMID: 26172957 DOI: 10.1016/j.clim.2015.07.004] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Revised: 07/05/2015] [Accepted: 07/06/2015] [Indexed: 11/18/2022]
Abstract
We herein describe a case of a 17-year-old boy with intractable common warts, short stature, microcephaly and slowly-progressing pancytopenia. Simultaneous quantification of T-cell receptor recombination excision circles (TREC) and immunoglobulin κ-deleting recombination excision circles (KREC) suggested very poor generation of both T-cells and B-cells. By whole exome sequencing, novel compound heterozygous mutations were identified in the patient's DNA ligase IV (LIG4) gene. The diagnosis of LIG4 syndrome was confirmed by delayed DNA double-strand break repair kinetics in γ-irradiated fibroblasts from the patient and their restoration by an introduction of wild-type LIG4. Although the patient received allogeneic hematopoietic stem cell transplantation from his haploidentical mother, he unfortunately expired due to an insufficiently reconstructed immune system. An earlier definitive diagnosis using TREC/KREC quantification and whole exome sequencing would thereby allow earlier intervention, which would be essential for improving long-term survival in similar cases with slowly-progressing LIG4 syndrome masked in adolescents.
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Affiliation(s)
- Shinobu Tamura
- Department of Hematology and Oncology, Kinan Hospital, Wakayama, Japan
| | - Kohei Higuchi
- Department of Hematology and Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Masaharu Tamaki
- Department of Hematology and Oncology, Kinan Hospital, Wakayama, Japan
| | | | - Ryoko Awazawa
- Department of Dermatology, University of the Ryukyus, Okinawa, Japan
| | - Noriko Mitsuki
- Department of Pediatrics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yuka Nakazawa
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis, Nagasaki University, Nagasaki, Japan; Department of Genome Repair, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Hiroyuki Mishima
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Kenzo Takahashi
- Department of Dermatology, University of the Ryukyus, Okinawa, Japan
| | - Osamu Kondo
- Department of Hematology and Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Kohsuke Imai
- Department of Pediatrics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomohiro Morio
- Department of Pediatrics, Tokyo Medical and Dental University, Tokyo, Japan
| | - Osamu Ohara
- Department of Technology Development, Kazusa DNA Research Institute, Kisarazu, Japan
| | - Tomoo Ogi
- Nagasaki University Research Centre for Genomic Instability and Carcinogenesis, Nagasaki University, Nagasaki, Japan; Department of Genome Repair, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan; Department of Genetics, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Fukumi Furukawa
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan
| | - Masami Inoue
- Department of Hematology and Oncology, Osaka Medical Center and Research Institute for Maternal and Child Health, Osaka, Japan
| | - Koh-ichiro Yoshiura
- Department of Human Genetics, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Nobuo Kanazawa
- Department of Dermatology, Wakayama Medical University, Wakayama, Japan.
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19
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Fukuchi M, Wanotayan R, Liu S, Imamichi S, Sharma MK, Matsumoto Y. Lysine 271 but not lysine 210 of XRCC4 is required for the nuclear localization of XRCC4 and DNA ligase IV. Biochem Biophys Res Commun 2015; 461:687-94. [PMID: 25934149 DOI: 10.1016/j.bbrc.2015.04.093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Accepted: 04/18/2015] [Indexed: 11/16/2022]
Abstract
XRCC4 and DNA Ligase IV (LIG4) cooperate to join two DNA ends at the final step of DNA double-strand break (DSB) repair through non-homologous end-joining (NHEJ). However, it is not fully understood how these proteins are localized to the nucleus. Here we created XRCC4(K271R) mutant, as Lys271 lies within the putative nuclear localization signal (NLS), and XRCC4(K210R) mutant, as Lys210 was reported to undergo SUMOylation, implicated in the nuclear localization of XRCC4. Wild-type and mutated XRCC4 with EGFP tag were introduced into HeLa cell, in which endogenous XRCC4 had been knocked down using siRNA directed to 3'-untranslated region, and tested for the nuclear localization function by fluorescence microscopy. XRCC4(K271R) was defective in the nuclear localization of itself and LIG4, whereas XRCC4(K210R) was competent for the nuclear localization with LIG4. To examine DSB repair function, wild-type and mutated XRCC4 were introduced into XRCC4-deficient M10. M10-XRCC4(K271R), but not M10-XRCC4(K210R), showed significantly reduced surviving fraction after 2 Gy γ-ray irradiation as compared to M10-XRCC4(WT). The number of γ-H2AX foci remaining 2 h after 2 Gy γ-ray irradiation was significantly greater in M10-XRCC4(K271R) than in M10-XRCC4(WT), whereas it was only marginally increased in M10-XRCC4(K210R) as compared to M10-XRCC4(WT). The present results collectively indicated that Lys271, but not Lys210, of XRCC4 is required for the nuclear localization of XRCC4 and LIG4 and that the nuclear localizing ability is essential for DSB repair function of XRCC4.
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Affiliation(s)
- Mikoto Fukuchi
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Rujira Wanotayan
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Sicheng Liu
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Shoji Imamichi
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Mukesh Kumar Sharma
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan
| | - Yoshihisa Matsumoto
- Research Laboratory for Nuclear Reactors, Tokyo Institute of Technology, Tokyo 152-8550, Japan.
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20
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He Y, Shao Y, Chen F. Efficient gene targeting in ligase IV-deficient Monascus ruber M7 by perturbing the non-homologous end joining pathway. Fungal Biol 2014; 118:846-54. [PMID: 25209642 DOI: 10.1016/j.funbio.2014.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2014] [Revised: 07/06/2014] [Accepted: 07/07/2014] [Indexed: 11/21/2022]
Abstract
Inactivating the non-homologous end joining (NHEJ) pathway is a well established method to increase gene replacement frequency (GRF) in filamentous fungi because NHEJ is predominant for the repair of DNA double strand breaks (DSBs), while gene targeting is based on homologous recombination (HR). DNA ligase IV, a component of the NHEJ system, is strictly required for the NHEJ in Saccharomyces cerevisiae and Neurospora crassa. To enhance the GRF in Monascus ruber M7, we deleted the Mrlig4 gene encoding a homolog of N. crassa DNA ligase IV. The obtained mutant (MrΔlig4) showed no apparent defects in vegetative growth, colony phenotype, microscopic morphology, spore yield, and production of Monascus pigments and citrinin compared with the wild-type strain (M. ruber M7). Gene targeting of ku70 and triA genes revealed that GRF in the MrΔlig4 strain increased four-fold compared with that in the wild-type strain, reached 68 % and 85 %, respectively. Thus, the MrΔlig4 strain is a promising host for efficient genetic manipulation. In addition, the MrΔlig4 strain is more sensitive than M. ruber M7 to a DNA-damaging agent, methyl methanesulfonate.
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21
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Davis AJ, Chen BP, Chen DJ. DNA-PK: a dynamic enzyme in a versatile DSB repair pathway. DNA Repair (Amst) 2014; 17:21-9. [PMID: 24680878 DOI: 10.1016/j.dnarep.2014.02.020] [Citation(s) in RCA: 250] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2013] [Revised: 02/17/2014] [Accepted: 02/24/2014] [Indexed: 11/23/2022]
Abstract
DNA double stranded breaks (DSBs) are the most cytoxic DNA lesion as the inability to properly repair them can lead to genomic instability and tumorigenesis. The prominent DSB repair pathway in humans is non-homologous end-joining (NHEJ). In the simplest sense, NHEJ mediates the direct re-ligation of the broken DNA molecule. However, NHEJ is a complex and versatile process that can repair DSBs with a variety of damages and ends via the utilization of a significant number of proteins. In this review we will describe the important factors and mechanisms modulating NHEJ with emphasis given to the versatility of this repair process and the DNA-PK complex.
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Nishida Y, Mizutani N, Inoue M, Omori Y, Tamiya-Koizumi K, Takagi A, Kojima T, Suzuki M, Nozawa Y, Minami Y, Ohnishi K, Naoe T, Murate T. Phosphorylated Sp1 is the regulator of DNA-PKcs and DNA ligase IV transcription of daunorubicin-resistant leukemia cell lines. Biochim Biophys Acta 2014; 1839:265-74. [PMID: 24530422 DOI: 10.1016/j.bbagrm.2014.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2013] [Revised: 02/01/2014] [Accepted: 02/06/2014] [Indexed: 01/29/2023]
Abstract
Multidrug resistance (MDR) is a serious problem faced in the treatment of malignant tumors. In this study, we characterized the expression of non-homologous DNA end joining (NHEJ) components, a major DNA double strand break (DSB) repair mechanism in mammals, in K562 cell and its daunorubicin (DNR)-resistant subclone (K562/DNR). K562/DNR overexpressed major enzymes of NHEJ, DNA-PKcs and DNA ligase IV, and K562/DNR repaired DSB more rapidly than K562 after DNA damage by neocarzinostatin (MDR1-independent radiation-mimetic). Overexpressed DNA-PKcs and DNA ligase IV were also observed in DNR-resistant HL60 (HL60/DNR) cells as compared with parental HL60 cells. Expression level of DNA-PKcs mRNA paralleled its protein level, and the promoter activity of DNA-PKcs of K562/DNR was higher than that of K562, and the 5'-region between -49bp and the first exon was important for its activity. Because this region is GC-rich, we tried to suppress Sp1 family transcription factor using mithramycin A (MMA), a specific Sp1 family inhibitor, and siRNAs for Sp1 and Sp3. Both MMA and siRNAs suppressed DNA-PKcs expression. Higher serine-phosphorylated Sp1 but not total Sp1 of both K562/DNR and HL60/DNR was observed compared with their parental K562 and HL60 cells. DNA ligase IV expression of K562/DNR was also suppressed significantly with Sp1 family protein inhibition. EMSA and ChIP assay confirmed higher binding of Sp1 and Sp3 with DNA-PKcs 5'-promoter region of DNA-PKcs of K562/DNR than that of K562. Thus, the Sp1 family transcription factor affects important NHEJ component expressions in anti-cancer drug-resistant malignant cells, leading to the more aggressive MDR phenotype.
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Affiliation(s)
- Yayoi Nishida
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Naoki Mizutani
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Minami Inoue
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yukari Omori
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keiko Tamiya-Koizumi
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Akira Takagi
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tetsuhito Kojima
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Motoshi Suzuki
- Division of Molecular Carcinogenesis, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Yosuke Minami
- Division of Blood Transfusion/Division of Oncology and Hematology, Kobe University Hospital, Kobe, Japan
| | - Kazunori Ohnishi
- Oncology Center, Hamamatsu University Graduate School of Medicine, Hamamatsu, Japan
| | - Tomoki Naoe
- National Hospital Organization, Nagoya Medical Center, Nagoya, Japan
| | - Takashi Murate
- Department of Pathophysiological Laboratory Science, Nagoya University Graduate School of Medicine, Nagoya, Japan.
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Assis J, Pereira D, Medeiros R. Ovarian cancer and DNA repair: DNA ligase IV as a potential key. World J Clin Oncol 2013; 4:14-24. [PMID: 23538968 PMCID: PMC3609013 DOI: 10.5306/wjco.v4.i1.14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Revised: 11/21/2012] [Accepted: 01/21/2013] [Indexed: 02/06/2023] Open
Abstract
Ovarian cancer (OC) is the sixth most common cancer and the seventh cause of death from cancer in women. The etiology and the ovarian carcinogenesis still need clarification although ovulation may be determinant due to its carcinogenic role in ovarian surface epithelium. The link between ovarian carcinogenesis and DNA repair is well established and it became clear that alterations in DNA damage response may affect the risk to develop OC. Polymorphisms are variations in the DNA sequence that exist in normal individuals of a population and are capable to change, among other mechanisms, the balance between DNA damage and cellular response. Consequently, genetic variability of the host has a great role in the development, progression and consequent prognosis of the oncologic patient as well as in treatment response. Standard treatment for OC patients is based on cytoreductive surgery, followed by chemotherapy with a platinum agent and a taxane. Although 80% of the patients respond to the first-line therapy, the development of resistance is common although the mechanisms underlying therapy failure remain mostly unknown. Because of their role in oncology, enzymes involved in the DNA repair pathways, like DNA Ligase IV (LIG4), became attractive study targets. It has been reported that variations in LIG4 activity can lead to a hyper-sensitivity to DNA damage, deregulation of repair and apoptosis mechanisms, affecting the susceptibility to cancer development and therapy response. To overcome resistance mechanisms, several investigations have been made and the strategy to target crucial molecular pathways, such as DNA repair, became one of the important areas in clinical oncology. This review aims to elucidate the link between DNA repair and OC, namely which concerns the role of LIG4 enzyme, and how genetic polymorphisms in LIG4 gene can modulate the activity of the enzyme and affect the ovarian carcinogenesis and treatment response. Moreover, we try to understand how LIG4 inhibition can be a potential contributor for the development of new cancer treatment strategies.
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