1
|
Alajlan H, Raducanu VS, Lopez de Los Santos Y, Tehseen M, Alruwaili H, Al-Mazrou A, Mohammad R, Al-Alwan M, De Biasio A, Merzaban JS, Al-Mousa H, Hamdan SM, Alazami AM. Severe Combined Immunodeficiency from a Homozygous DNA Ligase 1 Mutant with Reduced Catalytic Activity but Increased Ligation Fidelity. J Clin Immunol 2024; 44:151. [PMID: 38896336 PMCID: PMC11186889 DOI: 10.1007/s10875-024-01754-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024]
Abstract
A cell's ability to survive and to evade cancer is contingent on its ability to retain genomic integrity, which can be seriously compromised when nucleic acid phosphodiester bonds are disrupted. DNA Ligase 1 (LIG1) plays a key role in genome maintenance by sealing single-stranded nicks that are produced during DNA replication and repair. Autosomal recessive mutations in a limited number of individuals have been previously described for this gene. Here we report a homozygous LIG1 mutation (p.A624T), affecting a universally conserved residue, in a patient presenting with leukopenia, neutropenia, lymphopenia, pan-hypogammaglobulinemia, and diminished in vitro response to mitogen stimulation. Patient fibroblasts expressed normal levels of LIG1 protein but exhibited impaired growth, poor viability, high baseline levels of gamma-H2AX foci, and an enhanced susceptibility to DNA-damaging agents. The mutation reduced LIG1 activity by lowering its affinity for magnesium 2.5-fold. Remarkably, it also increased LIG1 fidelity > 50-fold against 3' end 8-Oxoguanine mismatches, exhibiting a marked reduction in its ability to process such nicks. This is expected to yield increased ss- and dsDNA breaks. Molecular dynamic simulations, and Residue Interaction Network studies, predicted an allosteric effect for this mutation on the protein loops associated with the LIG1 high-fidelity magnesium, as well as on DNA binding within the adenylation domain. These dual alterations of suppressed activity and enhanced fidelity, arising from a single mutation, underscore the mechanistic picture of how a LIG1 defect can lead to severe immunological disease.
Collapse
Affiliation(s)
- Huda Alajlan
- Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Vlad-Stefan Raducanu
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
| | - Yossef Lopez de Los Santos
- Cell Migration and Signaling Laboratory, Bioscience Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Muhammad Tehseen
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
| | - Hibah Alruwaili
- Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Amer Al-Mazrou
- Cell Therapy and Immunobiology Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
| | - Reem Mohammad
- Pediatric Allergy & Immunology, Department of Pediatrics, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia
| | - Monther Al-Alwan
- Cell Therapy and Immunobiology Department, King Faisal Specialist Hospital & Research Centre, Riyadh, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia
| | - Alfredo De Biasio
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia
| | - Jasmeen S Merzaban
- Cell Migration and Signaling Laboratory, Bioscience Program, Division of Biological & Environmental Science & Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Hamoud Al-Mousa
- Pediatric Allergy & Immunology, Department of Pediatrics, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia.
- College of Medicine, Alfaisal University, Riyadh, Saudi Arabia.
| | - Samir M Hamdan
- Bioscience Program, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955, Thuwal, Saudi Arabia.
| | - Anas M Alazami
- Translational Genomics, Centre for Genomic Medicine, King Faisal Specialist Hospital & Research Centre, MBC 3, P.O. Box 3354, 11211, Riyadh, Saudi Arabia.
| |
Collapse
|
2
|
Balu KE, Almohdar D, Ratcliffe J, Tang Q, Parwal T, Çağlayan M. Structural and biochemical characterization of LIG1 during mutagenic nick sealing of oxidatively damaged ends at the final step of DNA repair. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.06.592774. [PMID: 38766188 PMCID: PMC11100680 DOI: 10.1101/2024.05.06.592774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
DNA ligase 1 (LIG1) joins broken strand-breaks in the phosphodiester backbone to finalize DNA repair pathways. We previously reported that LIG1 fails on nick repair intermediate with 3'-oxidative damage incorporated by DNA polymerase (pol) β at the downstream steps of base excision repair (BER) pathway. Here, we determined X-ray structures of LIG1/nick DNA complexes containing 3'-8oxodG and 3'-8oxorG opposite either a templating Cytosine or Adenine and demonstrated that the ligase active site engages with mutagenic repair intermediates during steps 2 and 3 of the ligation reaction referring to the formation of DNA-AMP intermediate and a final phosphodiester bond, respectively. Furthermore, we showed the mutagenic nick sealing of DNA substrates with 3'-8oxodG:A and 3'-8oxorG:A by LIG1 wild-type, immunodeficiency disease-associated variants, and DNA ligase 3α (LIG3α) in vitro . Finally, we observed that LIG1 and LIG3α seal resulting nick after an incorporation of 8oxorGTP:A by polβ and AP-Endonuclease 1 (APE1) can clean oxidatively damaged ends at the final steps. Overall, our findings uncover a mechanistic insight into how LIG1 discriminates DNA or DNA/RNA junctions including oxidative damage and a functional coordination between the downstream enzymes, polβ, APE1, and BER ligases, to process mutagenic repair intermediates to maintain repair efficiency.
Collapse
|
3
|
Sallmyr A, Bhandari SK, Naila T, Tomkinson AE. Mammalian DNA ligases; roles in maintaining genome integrity. J Mol Biol 2024; 436:168276. [PMID: 37714297 PMCID: PMC10843057 DOI: 10.1016/j.jmb.2023.168276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 09/07/2023] [Accepted: 09/08/2023] [Indexed: 09/17/2023]
Abstract
The joining of breaks in the DNA phosphodiester backbone is essential for genome integrity. Breaks are generated during normal processes such as DNA replication, cytosine demethylation during differentiation, gene rearrangement in the immune system and germ cell development. In addition, they are generated either directly by a DNA damaging agent or indirectly due to damage excision during repair. Breaks are joined by a DNA ligase that catalyzes phosphodiester bond formation at DNA nicks with 3' hydroxyl and 5' phosphate termini. Three human genes encode ATP-dependent DNA ligases. These enzymes have a conserved catalytic core consisting of three subdomains that encircle nicked duplex DNA during ligation. The DNA ligases are targeted to different nuclear DNA transactions by specific protein-protein interactions. Both DNA ligase IIIα and DNA ligase IV form stable complexes with DNA repair proteins, XRCC1 and XRCC4, respectively. There is functional redundancy between DNA ligase I and DNA ligase IIIα in DNA replication, excision repair and single-strand break repair. Although DNA ligase IV is a core component of the major double-strand break repair pathway, non-homologous end joining, the other enzymes participate in minor, alternative double-strand break repair pathways. In contrast to the nucleus, only DNA ligase IIIα is present in mitochondria and is essential for maintaining the mitochondrial genome. Human immunodeficiency syndromes caused by mutations in either LIG1 or LIG4 have been described. Preclinical studies with DNA ligase inhibitors have identified potentially targetable abnormalities in cancer cells and evidence that DNA ligases are potential targets for cancer therapy.
Collapse
Affiliation(s)
- Annahita Sallmyr
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Seema Khattri Bhandari
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Tasmin Naila
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States
| | - Alan E Tomkinson
- University of New Mexico Comprehensive Cancer Center and the Departments of Internal Medicine, and Molecular Genetics & Microbiology, University of New Mexico Health Sciences Center, United States.
| |
Collapse
|
4
|
Gulkis M, Tang Q, Petrides M, Çağlayan M. Structures of LIG1 active site mutants reveal the importance of DNA end rigidity for mismatch discrimination. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533718. [PMID: 36993234 PMCID: PMC10055324 DOI: 10.1101/2023.03.21.533718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
ATP-dependent DNA ligases catalyze phosphodiester bond formation in the conserved three-step chemical reaction of nick sealing. Human DNA ligase I (LIG1) finalizes almost all DNA repair pathways following DNA polymerase-mediated nucleotide insertion. We previously reported that LIG1 discriminates mismatches depending on the architecture of the 3'-terminus at a nick, however the contribution of conserved active site residues to faithful ligation remains unknown. Here, we comprehensively dissect the nick DNA substrate specificity of LIG1 active site mutants carrying Ala(A) and Leu(L) substitutions at Phe(F)635 and Phe(F)F872 residues and show completely abolished ligation of nick DNA substrates with all 12 non-canonical mismatches. LIG1 EE/AA structures of F635A and F872A mutants in complex with nick DNA containing A:C and G:T mismatches demonstrate the importance of DNA end rigidity, as well as uncover a shift in a flexible loop near 5'-end of the nick, which causes an increased barrier to adenylate transfer from LIG1 to the 5'-end of the nick. Furthermore, LIG1 EE/AA /8oxoG:A structures of both mutants demonstrated that F635 and F872 play critical roles during steps 1 or 2 of the ligation reaction depending on the position of the active site residue near the DNA ends. Overall, our study contributes towards a better understanding of the substrate discrimination mechanism of LIG1 against mutagenic repair intermediates with mismatched or damaged ends and reveals the importance of conserved ligase active site residues to maintain ligation fidelity.
Collapse
|
5
|
Bhandari SK, Wiest N, Sallmyr A, Du R, Ferry L, Defossez PA, Tomkinson AE. Unchanged PCNA and DNMT1 dynamics during replication in DNA ligase I-deficient cells but abnormal chromatin levels of non-replicative histone H1. Sci Rep 2023; 13:4363. [PMID: 36928068 PMCID: PMC10020546 DOI: 10.1038/s41598-023-31367-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/10/2023] [Indexed: 03/18/2023] Open
Abstract
DNA ligase I (LigI), the predominant enzyme that joins Okazaki fragments, interacts with PCNA and Pol δ. LigI also interacts with UHRF1, linking Okazaki fragment joining with DNA maintenance methylation. Okazaki fragments can also be joined by a relatively poorly characterized DNA ligase IIIα (LigIIIα)-dependent backup pathway. Here we examined the effect of LigI-deficiency on proteins at the replication fork. Notably, LigI-deficiency did not alter the kinetics of association of the PCNA clamp, the leading strand polymerase Pol ε, DNA maintenance methylation proteins and core histones with newly synthesized DNA. While the absence of major changes in replication and methylation proteins is consistent with the similar proliferation rate and DNA methylation levels of the LIG1 null cells compared with the parental cells, the increased levels of LigIIIα/XRCC1 and Pol δ at the replication fork and in bulk chromatin indicate that there are subtle replication defects in the absence of LigI. Interestingly, the non-replicative histone H1 variant, H1.0, is enriched in the chromatin of LigI-deficient mouse CH12F3 and human 46BR.1G1 cells. This alteration was not corrected by expression of wild type LigI, suggesting that it is a relatively stable epigenetic change that may contribute to the immunodeficiencies linked with inherited LigI-deficiency syndrome.
Collapse
Affiliation(s)
- Seema Khattri Bhandari
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Nathaniel Wiest
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
- Division of Hematology and Medical Oncology, Department of Internal Medicine, Mayo Clinic, Jacksonville, FL, 32224, USA
| | - Annahita Sallmyr
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
| | - Ruofei Du
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA
- Department of Biostatistics, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Laure Ferry
- Epigenetics and Cell Fate, CNRS, Université Paris Cité, 750013, Paris, France
| | | | - Alan E Tomkinson
- Cancer Research Facility, Departments of Internal Medicine and Molecular Genetics & Microbiology, University of New Mexico Comprehensive Cancer Center, University of New Mexico Health Sciences Center, 915 Camino de Salud, 1 University of New Mexico, Albuquerque, NM, 87131, USA.
| |
Collapse
|
6
|
Yilmaz Demirdag Y, Gupta S. Infections in DNA Repair Defects. Pathogens 2023; 12:pathogens12030440. [PMID: 36986362 PMCID: PMC10054915 DOI: 10.3390/pathogens12030440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
DNA repair defects are heterogenous conditions characterized by a wide spectrum of clinical phenotypes. The common presentations of DNA repair defects include increased risk of cancer, accelerated aging, and defects in the development of various organs and systems. The immune system can be affected in a subset of these disorders leading to susceptibility to infections and autoimmunity. Infections in DNA repair defects may occur due to primary defects in T, B, or NK cells and other factors such as anatomic defects, neurologic disorders, or during chemotherapy. Consequently, the characteristics of the infections may vary from mild upper respiratory tract infections to severe, opportunistic, and even fatal infections with bacteria, viruses, or fungi. Here, infections in 15 rare and sporadic DNA repair defects that are associated with immunodeficiencies are discussed. Because of the rarity of some of these conditions, limited information is available regarding infectious complications.
Collapse
|
7
|
Anurag M, Jaehnig EJ, Krug K, Lei JT, Bergstrom EJ, Kim BJ, Vashist TD, Huynh AMT, Dou Y, Gou X, Huang C, Shi Z, Wen B, Korchina V, Gibbs RA, Muzny DM, Doddapaneni H, Dobrolecki LE, Rodriguez H, Robles AI, Hiltke T, Lewis MT, Nangia JR, Nemati Shafaee M, Li S, Hagemann IS, Hoog J, Lim B, Osborne CK, Mani D, Gillette MA, Zhang B, Echeverria GV, Miles G, Rimawi MF, Carr SA, Ademuyiwa FO, Satpathy S, Ellis MJ. Proteogenomic Markers of Chemotherapy Resistance and Response in Triple-Negative Breast Cancer. Cancer Discov 2022; 12:2586-2605. [PMID: 36001024 PMCID: PMC9627136 DOI: 10.1158/2159-8290.cd-22-0200] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 06/08/2022] [Accepted: 08/18/2022] [Indexed: 01/12/2023]
Abstract
Microscaled proteogenomics was deployed to probe the molecular basis for differential response to neoadjuvant carboplatin and docetaxel combination chemotherapy for triple-negative breast cancer (TNBC). Proteomic analyses of pretreatment patient biopsies uniquely revealed metabolic pathways, including oxidative phosphorylation, adipogenesis, and fatty acid metabolism, that were associated with resistance. Both proteomics and transcriptomics revealed that sensitivity was marked by elevation of DNA repair, E2F targets, G2-M checkpoint, interferon-gamma signaling, and immune-checkpoint components. Proteogenomic analyses of somatic copy-number aberrations identified a resistance-associated 19q13.31-33 deletion where LIG1, POLD1, and XRCC1 are located. In orthogonal datasets, LIG1 (DNA ligase I) gene deletion and/or low mRNA expression levels were associated with lack of pathologic complete response, higher chromosomal instability index (CIN), and poor prognosis in TNBC, as well as carboplatin-selective resistance in TNBC preclinical models. Hemizygous loss of LIG1 was also associated with higher CIN and poor prognosis in other cancer types, demonstrating broader clinical implications. SIGNIFICANCE Proteogenomic analysis of triple-negative breast tumors revealed a complex landscape of chemotherapy response associations, including a 19q13.31-33 somatic deletion encoding genes serving lagging-strand DNA synthesis (LIG1, POLD1, and XRCC1), that correlate with lack of pathologic response, carboplatin-selective resistance, and, in pan-cancer studies, poor prognosis and CIN. This article is highlighted in the In This Issue feature, p. 2483.
Collapse
Affiliation(s)
- Meenakshi Anurag
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Eric J. Jaehnig
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Karsten Krug
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Jonathan T. Lei
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Erik J. Bergstrom
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Beom-Jun Kim
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Tanmayi D. Vashist
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Anh Minh Tran Huynh
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Yongchao Dou
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Xuxu Gou
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Chen Huang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Zhiao Shi
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Bo Wen
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Viktoriya Korchina
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Richard A. Gibbs
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Donna M. Muzny
- The Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | | | - Lacey E. Dobrolecki
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, Maryland
| | - Ana I. Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, Maryland
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, Maryland
| | - Michael T. Lewis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Julie R. Nangia
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Maryam Nemati Shafaee
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Shunqiang Li
- Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, Missouri
| | - Ian S. Hagemann
- Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, Missouri
| | - Jeremy Hoog
- Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, Missouri
| | - Bora Lim
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - C. Kent Osborne
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - D.R. Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Michael A. Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
| | - Bing Zhang
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Gloria V. Echeverria
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - George Miles
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Mothaffar F. Rimawi
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Steven A. Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Foluso O. Ademuyiwa
- Siteman Comprehensive Cancer Center and Washington University School of Medicine, St. Louis, Missouri
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts
| | - Matthew J. Ellis
- Lester and Sue Smith Breast Center and Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| |
Collapse
|
8
|
Ekuban A, Shichino S, Zong C, Ekuban FA, Kinoshita K, Ichihara S, Matsushima K, Ichihara G. Transcriptome analysis of human cholangiocytes exposed to carcinogenic 1,2-dichloropropane in the presence of macrophages in vitro. Sci Rep 2022; 12:11222. [PMID: 35780190 PMCID: PMC9250500 DOI: 10.1038/s41598-022-15295-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 06/22/2022] [Indexed: 11/09/2022] Open
Abstract
1,2-Dichloropropane (1,2-DCP), a synthetic organic solvent, has been implicated in causality of cholangiocarcinoma (bile duct cancer). 1,2-DCP-induced occupational cholangiocarcinoma show a different carcinogenic process compared to common cholangiocarcinoma, but its mechanism remains elusive. We reported previously that exposure of MMNK-1 cholangiocytes co-cultured with THP-1 macrophages, but not monocultured MMNK-1 cholangiocytes, to 1,2-DCP induced activation-induced cytidine deaminase (AID) expression, DNA damage and ROS production. The aim of this study was to identify relevant biological processes or target genes expressed in response to 1,2-DCP, using an in vitro system where cholangiocytes are co-cultured with macrophages. The co-cultured cells were exposed to 1,2-DCP at 0, 0.1 or 0.4 mM for 24 h, and then the cell lysates were assessed by transcriptome analysis. 1,2-DCP upregulated the expression of base excision repair genes in MMNK-1 cholangiocytes in the co-cultures, whereas it upregulated the expression of cell cycle-related genes in THP-1 macrophages. Activation of the base excision repair pathway might result from the previously observed DNA damage in MMNK-1 cholangiocytes co-cultured with THP-1 macrophages, although involvement of other mechanisms such as DNA replication, cell death or other types of DNA repair was not disproved. Cross talk interactions between cholangiocytes and macrophages leading to DNA damage in the cholangiocytes should be explored.
Collapse
Affiliation(s)
- Abigail Ekuban
- Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Building No. 15, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Shigeyuki Shichino
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, 278-0022, Japan
| | - Cai Zong
- Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Building No. 15, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Frederick Adams Ekuban
- Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Building No. 15, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan
| | - Kazuo Kinoshita
- Evolutionary Medicine, Shizuoka Graduate University of Public Health, Shizuoka, 420-0881, Japan
| | - Sahoko Ichihara
- Department of Environmental and Preventive Medicine, Jichi Medical University School of Medicine, Shimotsuke, 329-0498, Japan
| | - Kouji Matsushima
- Division of Molecular Regulation of Inflammatory and Immune Diseases, Research Institute of Biomedical Sciences, Tokyo University of Science, Noda, 278-0022, Japan
| | - Gaku Ichihara
- Department of Occupational and Environmental Health, Faculty of Pharmaceutical Sciences, Building No. 15, Tokyo University of Science, 2641 Yamazaki, Noda, Chiba, 278-8510, Japan.
| |
Collapse
|
9
|
Fueling genome maintenance: On the versatile roles of NAD + in preserving DNA integrity. J Biol Chem 2022; 298:102037. [PMID: 35595095 PMCID: PMC9194868 DOI: 10.1016/j.jbc.2022.102037] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 05/05/2022] [Accepted: 05/09/2022] [Indexed: 12/13/2022] Open
Abstract
NAD+ is a versatile biomolecule acting as a master regulator and substrate in various cellular processes, including redox regulation, metabolism, and various signaling pathways. In this article, we concisely and critically review the role of NAD+ in mechanisms promoting genome maintenance. Numerous NAD+-dependent reactions are involved in the preservation of genome stability, the cellular DNA damage response, and other pathways regulating nucleic acid metabolism, such as gene expression and cell proliferation pathways. Of note, NAD+ serves as a substrate to ADP-ribosyltransferases, sirtuins, and potentially also eukaryotic DNA ligases, all of which regulate various aspects of DNA integrity, damage repair, and gene expression. Finally, we critically analyze recent developments in the field as well as discuss challenges associated with therapeutic actions intended to raise NAD+ levels.
Collapse
|
10
|
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.
Collapse
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
| |
Collapse
|
11
|
Jurkiw TJ, Tumbale PP, Schellenberg MJ, Cunningham-Rundles C, Williams RS, O’Brien PJ. LIG1 syndrome mutations remodel a cooperative network of ligand binding interactions to compromise ligation efficiency. Nucleic Acids Res 2021; 49:1619-1630. [PMID: 33444456 PMCID: PMC7897520 DOI: 10.1093/nar/gkaa1297] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/28/2020] [Accepted: 01/06/2021] [Indexed: 11/14/2022] Open
Abstract
Human DNA ligase I (LIG1) is the main replicative ligase and it also seals DNA breaks to complete DNA repair and recombination pathways. Immune compromised patients harbor hypomorphic LIG1 alleles encoding substitutions of conserved arginine residues, R771W and R641L, that compromise LIG1 activity through poorly defined mechanisms. To understand the molecular basis of LIG1 syndrome mutations, we determined high resolution X-ray structures and performed systematic biochemical characterization of LIG1 mutants using steady-state and pre-steady state kinetic approaches. Our results unveil a cooperative network of plastic DNA-LIG1 interactions that connect DNA substrate engagement with productive binding of Mg2+ cofactors for catalysis. LIG1 syndrome mutations destabilize this network, compromising Mg2+ binding affinity, decreasing ligation efficiency, and leading to elevated abortive ligation that may underlie the disease pathology. These findings provide novel insights into the fundamental mechanism by which DNA ligases engage with a nicked DNA substrate, and they suggest that disease pathology of LIG1 syndrome could be modulated by Mg2+ levels.
Collapse
Affiliation(s)
- Thomas J Jurkiw
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| | - Percy P Tumbale
- Structural Cell Biology group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Matthew J Schellenberg
- Structural Cell Biology group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Charlotte Cunningham-Rundles
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and Graduate School of Biomedical Sciences, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - R Scott Williams
- Structural Cell Biology group, Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Patrick J O’Brien
- Department of Biological Chemistry, University of Michigan School of Medicine, Ann Arbor, MI, 48109, USA
| |
Collapse
|
12
|
DNA ligase I fidelity mediates the mutagenic ligation of pol β oxidized and mismatch nucleotide insertion products in base excision repair. J Biol Chem 2021; 296:100427. [PMID: 33600799 PMCID: PMC8024709 DOI: 10.1016/j.jbc.2021.100427] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 02/08/2021] [Accepted: 02/12/2021] [Indexed: 11/22/2022] Open
Abstract
DNA ligase I (LIG1) completes the base excision repair (BER) pathway at the last nick-sealing step after DNA polymerase (pol) β gap-filling DNA synthesis. However, the mechanism by which LIG1 fidelity mediates the faithful substrate-product channeling and ligation of repair intermediates at the final steps of the BER pathway remains unclear. We previously reported that pol β 8-oxo-2'-deoxyribonucleoside 5'-triphosphate insertion confounds LIG1, leading to the formation of ligation failure products with a 5'-adenylate block. Here, using reconstituted BER assays in vitro, we report the mutagenic ligation of pol β 8-oxo-2'-deoxyribonucleoside 5'-triphosphate insertion products and an inefficient ligation of pol β Watson-Crick-like dG:T mismatch insertion by the LIG1 mutant with a perturbed fidelity (E346A/E592A). Moreover, our results reveal that the substrate discrimination of LIG1 for the nicked repair intermediates with preinserted 3'-8-oxodG or mismatches is governed by mutations at both E346 and E592 residues. Finally, we found that aprataxin and flap endonuclease 1, as compensatory DNA-end processing enzymes, can remove the 5'-adenylate block from the abortive ligation products harboring 3'-8-oxodG or the 12 possible noncanonical base pairs. These findings contribute to the understanding of the role of LIG1 as an important determinant in faithful BER and how a multiprotein complex (LIG1, pol β, aprataxin, and flap endonuclease 1) can coordinate to prevent the formation of mutagenic repair intermediates with damaged or mismatched ends at the downstream steps of the BER pathway.
Collapse
|
13
|
Tomkinson AE, Naila T, Khattri Bhandari S. Altered DNA ligase activity in human disease. Mutagenesis 2021; 35:51-60. [PMID: 31630206 DOI: 10.1093/mutage/gez026] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 09/09/2019] [Indexed: 12/18/2022] Open
Abstract
The joining of interruptions in the phosphodiester backbone of DNA is critical to maintain genome stability. These breaks, which are generated as part of normal DNA transactions, such as DNA replication, V(D)J recombination and meiotic recombination as well as directly by DNA damage or due to DNA damage removal, are ultimately sealed by one of three human DNA ligases. DNA ligases I, III and IV each function in the nucleus whereas DNA ligase III is the sole enzyme in mitochondria. While the identification of specific protein partners and the phenotypes caused either by genetic or chemical inactivation have provided insights into the cellular functions of the DNA ligases and evidence for significant functional overlap in nuclear DNA replication and repair, different results have been obtained with mouse and human cells, indicating species-specific differences in the relative contributions of the DNA ligases. Inherited mutations in the human LIG1 and LIG4 genes that result in the generation of polypeptides with partial activity have been identified as the causative factors in rare DNA ligase deficiency syndromes that share a common clinical symptom, immunodeficiency. In the case of DNA ligase IV, the immunodeficiency is due to a defect in V(D)J recombination whereas the cause of the immunodeficiency due to DNA ligase I deficiency is not known. Overexpression of each of the DNA ligases has been observed in cancers. For DNA ligase I, this reflects increased proliferation. Elevated levels of DNA ligase III indicate an increased dependence on an alternative non-homologous end-joining pathway for the repair of DNA double-strand breaks whereas elevated level of DNA ligase IV confer radioresistance due to increased repair of DNA double-strand breaks by the major non-homologous end-joining pathway. Efforts to determine the potential of DNA ligase inhibitors as cancer therapeutics are on-going in preclinical cancer models.
Collapse
Affiliation(s)
- Alan E Tomkinson
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Tasmin Naila
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| | - Seema Khattri Bhandari
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, USA
| |
Collapse
|
14
|
Kontizas E, Tastsoglou S, Karamitros T, Karayiannis Y, Kollia P, Hatzigeorgiou AG, Sgouras DN. Impact of Helicobacter pylori Infection and Its Major Virulence Factor CagA on DNA Damage Repair. Microorganisms 2020; 8:microorganisms8122007. [PMID: 33339161 PMCID: PMC7765595 DOI: 10.3390/microorganisms8122007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/10/2023] Open
Abstract
Helicobacter pylori infection induces a plethora of DNA damages. Gastric epithelial cells, in order to maintain genomic integrity, require an integrous DNA damage repair (DDR) machinery, which, however, is reported to be modulated by the infection. CagA is a major H. pylori virulence factor, associated with increased risk for gastric carcinogenesis. Its pathogenic activity is partly regulated by phosphorylation on EPIYA motifs. Our aim was to identify effects of H. pylori infection and CagA on DDR, investigating the transcriptome of AGS cells, infected with wild-type, ΔCagA and EPIYA-phosphorylation-defective strains. Upon RNA-Seq-based transcriptomic analysis, we observed that a notable number of DDR genes were found deregulated during the infection, potentially resulting to base excision repair and mismatch repair compromise and an intricate deregulation of nucleotide excision repair, homologous recombination and non-homologous end-joining. Transcriptome observations were further investigated on the protein expression level, utilizing infections of AGS and GES-1 cells. We observed that CagA contributed to the downregulation of Nth Like DNA Glycosylase 1 (NTHL1), MutY DNA Glycosylase (MUTYH), Flap Structure-Specific Endonuclease 1 (FEN1), RAD51 Recombinase, DNA Polymerase Delta Catalytic Subunit (POLD1), and DNA Ligase 1 (LIG1) and, contrary to transcriptome results, Apurinic/Apyrimidinic Endodeoxyribonuclease 1 (APE1) upregulation. Our study accentuates the role of CagA as a significant contributor of H. pylori infection-mediated DDR modulation, potentially disrupting the balance between DNA damage and repair, thus favoring genomic instability and carcinogenesis.
Collapse
Affiliation(s)
- Eleftherios Kontizas
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
- Correspondence: (E.K.); (D.N.S.); Tel.: +30-210-647-8812 (E.K.); +30-210-647-8824 (D.N.S.)
| | - Spyros Tastsoglou
- Department of Electrical and Computer Engineering, University of Thessaly, 38221 Volos, Greece;
- DIANA-Lab, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - Timokratis Karamitros
- Bioinformatics and Applied Genomics Unit, Hellenic Pasteur Institute, 11521 Athens, Greece;
| | - Yiannis Karayiannis
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Panagoula Kollia
- Department of Genetics and Biotechnology, Faculty of Biology, National and Kapodistrian University of Athens, 15772 Athens, Greece;
| | - Artemis G. Hatzigeorgiou
- DIANA-Lab, Hellenic Pasteur Institute, 11521 Athens, Greece;
- DIANA-Lab, Department of Computer Science and Biomedical Informatics, University of Thessaly, 35131 Lamia, Greece
| | - Dionyssios N. Sgouras
- Laboratory of Medical Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece;
- Correspondence: (E.K.); (D.N.S.); Tel.: +30-210-647-8812 (E.K.); +30-210-647-8824 (D.N.S.)
| |
Collapse
|
15
|
Tang Q, Kamble P, Çağlayan M. DNA ligase I variants fail in the ligation of mutagenic repair intermediates with mismatches and oxidative DNA damage. Mutagenesis 2020; 35:391-404. [PMID: 32914844 PMCID: PMC7846189 DOI: 10.1093/mutage/geaa023] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 08/10/2020] [Indexed: 01/26/2023] Open
Abstract
DNA ligase I (LIG1) joins DNA strand breaks during DNA replication and repair transactions and contributes to genome integrity. The mutations (P529L, E566K, R641L and R771W) in LIG1 gene are described in patients with LIG1-deficiency syndrome that exhibit immunodeficiency. LIG1 senses 3'-DNA ends with a mismatch or oxidative DNA base inserted by a repair DNA polymerase. However, the ligation efficiency of the LIG1 variants for DNA polymerase-promoted mutagenesis products with 3'-DNA mismatches or 8-oxo-2'-deoxyguanosine (8-oxodG) remains undefined. Here, we report that R641L and R771W fail in the ligation of nicked DNA with 3'-8-oxodG, leading to an accumulation of 5'-AMP-DNA intermediates in vitro. Moreover, we found that the presence of all possible 12 non-canonical base pairs variously impacts the ligation efficiency by P529L and R771W depending on the architecture at the DNA end, whereas E566K exhibits no activity against all substrates tested. Our results contribute to the understanding of the substrate specificity and mismatch discrimination of LIG1 for mutagenic repair intermediates and the effect of non-synonymous mutations on ligase fidelity.
Collapse
Affiliation(s)
- Qun Tang
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Pradnya Kamble
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| | - Melike Çağlayan
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, FL, USA
| |
Collapse
|
16
|
Wright GEB, Black HF, Collins JA, Gall-Duncan T, Caron NS, Pearson CE, Hayden MR. Interrupting sequence variants and age of onset in Huntington's disease: clinical implications and emerging therapies. Lancet Neurol 2020; 19:930-939. [PMID: 33098802 DOI: 10.1016/s1474-4422(20)30343-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 08/23/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
Abstract
BACKGROUND Huntington's disease is a fatal neurodegenerative disorder that is caused by CAG-CAA repeat expansion, encoding polyglutamine, in the huntingtin (HTT) gene. Current age-of-clinical-onset prediction models for Huntington's disease are based on polyglutamine length and explain only a proportion of the variability in age of onset observed between patients. These length-based assays do not interrogate the underlying genetic variation, because known genetic variants in this region do not alter the protein coding sequence. Given that individuals with identical repeat lengths can present with Huntington's disease decades apart, the search for genetic modifiers of clinical age of onset has become an active area of research. RECENT DEVELOPMENTS Results from three independent genetic studies of Huntington's disease have shown that glutamine-encoding CAA variants that interrupt DNA CAG repeat tracts, but do not alter polyglutamine length or polyglutamine homogeneity, are associated with substantial differences in age of onset of Huntington's disease in carriers. A variant that results in the loss of CAA interruption is associated with early onset and is particularly relevant to individuals that carry alleles in the reduced penetrance range (ie, CAG 36-39). Approximately a third of clinically manifesting carriers of reduced penetrance alleles, defined by current diagnostics, carry this variant. Somatic repeat instability, modified by interrupted CAG tracts, is the most probable cause mediating this effect. This relationship is supported by genome-wide screens for disease modifiers, which have revealed the importance of DNA-repair genes in Huntington's disease (ie, FAN1, LIG1, MLH1, MSH3, PMS1, and PMS2). WHERE NEXT?: Focus needs to be placed on refining our understanding of the effect of the loss-of-interruption and duplication-of-interruption variants and other interrupting sequence variants on age of onset, and assessing their effect in disease-relevant brain tissues, as well as in diverse population groups, such as individuals from Africa and Asia. Diagnostic tests should be augmented or updated, since current tests do not assess the underlying DNA sequence variation, especially when assessing individuals that carry alleles in the reduced penetrance range. Future studies should explore somatic repeat instability and DNA repair as new therapeutic targets to modify age of onset in Huntington's disease and in other repeat-mediated disorders. Disease-modifying therapies could potentially be developed by therapeutically targeting these processes. Promising approaches include therapeutically targeting the expanded repeat or directly perturbing key DNA-repair genes (eg, with antisense oligonucleotides or small molecules). Targeting the CAG repeat directly with naphthyridine-azaquinolone, a compound that induces contractions, and altering the expression of MSH3, represent two viable therapeutic strategies. However, as a first step, the capability of such novel therapeutic approaches to delay clinical onset in animal models should be assessed.
Collapse
Affiliation(s)
- Galen E B Wright
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada; Neuroscience Research Program, Kleysen Institute for Advanced Medicine, Department of Pharmacology and Therapeutics, University of Manitoba, Winnipeg, MB, Canada
| | - Hailey Findlay Black
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Jennifer A Collins
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Terence Gall-Duncan
- Program of Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Nicholas S Caron
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada
| | - Christopher E Pearson
- Program of Genetics and Genome Biology, Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, ON, Canada; Program of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Michael R Hayden
- Centre for Molecular Medicine and Therapeutics, Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada; BC Children's Hospital Research Institute, Vancouver, BC, Canada.
| |
Collapse
|
17
|
Amir M, Mohammad T, Dohare R, Islam A, Ahmad F, Imtaiyaz Hassan M. Structure, function and therapeutic implications of OB-fold proteins: A lesson from past to present. Brief Funct Genomics 2020; 19:377-389. [PMID: 32393969 DOI: 10.1093/bfgp/elaa008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Oligonucleotide/oligosaccharide-binding (OB)-fold proteins play essential roles in the regulation of genome and its correct transformation to the subsequent generation. To maintain the genomic stability, OB-fold proteins are implicated in various cellular processes including DNA replication, DNA repair, cell cycle regulation and maintenance of telomere. The diverse functional spectrums of OB-fold proteins are mainly due to their involvement in protein-DNA and protein-protein complexes. Mutations and consequential structural alteration in the OB-fold proteins often lead to severe diseases. Here, we have investigated the structure, function and mode of action of OB-fold proteins (RPA, BRCA2, DNA ligases and SSBs1/2) in cellular pathways and their relationship with diseases and their possible use in therapeutic intervention. Due to the crucial role of OB-fold proteins in regulating the key physiological process, a detailed structural understanding in the context of underlying mechanism of action and cellular complexity offers a new avenue to target OB-proteins for therapeutic intervention.
Collapse
|
18
|
Kim DV, Makarova AV, Miftakhova RR, Zharkov DO. Base Excision DNA Repair Deficient Cells: From Disease Models to Genotoxicity Sensors. Curr Pharm Des 2020; 25:298-312. [PMID: 31198112 DOI: 10.2174/1381612825666190319112930] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 03/13/2019] [Indexed: 12/29/2022]
Abstract
Base excision DNA repair (BER) is a vitally important pathway that protects the cell genome from many kinds of DNA damage, including oxidation, deamination, and hydrolysis. It involves several tightly coordinated steps, starting from damaged base excision and followed by nicking one DNA strand, incorporating an undamaged nucleotide, and DNA ligation. Deficiencies in BER are often embryonic lethal or cause morbid diseases such as cancer, neurodegeneration, or severe immune pathologies. Starting from the early 1980s, when the first mammalian cell lines lacking BER were produced by spontaneous mutagenesis, such lines have become a treasure trove of valuable information about the mechanisms of BER, often revealing unexpected connections with other cellular processes, such as antibody maturation or epigenetic demethylation. In addition, these cell lines have found an increasing use in genotoxicity testing, where they provide increased sensitivity and representativity to cell-based assay panels. In this review, we outline current knowledge about BER-deficient cell lines and their use.
Collapse
Affiliation(s)
- Daria V Kim
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation
| | - Alena V Makarova
- RAS Institute of Molecular Genetics, 2 Kurchatova Sq., Moscow 123182, Russian Federation
| | - Regina R Miftakhova
- Kazan Federal University, 18 Kremlevsakaya St., Kazan 420008, Russian Federation
| | - Dmitry O Zharkov
- Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russian Federation.,SB RAS Institute of Chemical Biology and Fu ndamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russian Federation
| |
Collapse
|
19
|
Tumbale PP, Jurkiw TJ, Schellenberg MJ, Riccio AA, O'Brien PJ, Williams RS. Two-tiered enforcement of high-fidelity DNA ligation. Nat Commun 2019; 10:5431. [PMID: 31780661 PMCID: PMC6882888 DOI: 10.1038/s41467-019-13478-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 11/05/2019] [Indexed: 01/07/2023] Open
Abstract
DNA ligases catalyze the joining of DNA strands to complete DNA replication, recombination and repair transactions. To protect the integrity of the genome, DNA ligase 1 (LIG1) discriminates against DNA junctions harboring mutagenic 3'-DNA mismatches or oxidative DNA damage, but how such high-fidelity ligation is enforced is unknown. Here, X-ray structures and kinetic analyses of LIG1 complexes with undamaged and oxidatively damaged DNA unveil that LIG1 employs Mg2+-reinforced DNA binding to validate DNA base pairing during the adenylyl transfer and nick-sealing ligation reaction steps. Our results support a model whereby LIG1 fidelity is governed by a high-fidelity (HiFi) interface between LIG1, Mg2+, and the DNA substrate that tunes the enzyme to release pro-mutagenic DNA nicks. In a second tier of protection, LIG1 activity is surveilled by Aprataxin (APTX), which suppresses mutagenic and abortive ligation at sites of oxidative DNA damage.
Collapse
Affiliation(s)
- Percy P Tumbale
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Thomas J Jurkiw
- Biological Chemistry, University of Michigan, 1150 W Medical Center Drive Ann Arbor, Ann Arbor, MI, 48109, USA
| | - Matthew J Schellenberg
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Amanda A Riccio
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA
| | - Patrick J O'Brien
- Biological Chemistry, University of Michigan, 1150 W Medical Center Drive Ann Arbor, Ann Arbor, MI, 48109, USA.
| | - R Scott Williams
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, 111 TW Alexander Drive, Research Triangle Park, NC, 27709, USA.
| |
Collapse
|
20
|
Saquib M, Ansari MI, Johnson CR, Khatoon S, Kamil Hussain M, Coop A. Recent advances in the targeting of human DNA ligase I as a potential new strategy for cancer treatment. Eur J Med Chem 2019; 182:111657. [PMID: 31499361 DOI: 10.1016/j.ejmech.2019.111657] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 08/24/2019] [Accepted: 08/28/2019] [Indexed: 11/29/2022]
Abstract
The emergence of drug resistance, coupled with the issue of low tumor selectivity and toxicity is a major pitfall in cancer chemotherapy. It has necessitated the urgent need for the discovery of less toxic and more potent new anti-cancer pharmaceuticals, which target the interactive mechanisms involved in division and metastasis of cancer cells. Human DNA ligase I (hligI) plays an important role in DNA replication by linking Okazaki fragments on the lagging strand of DNA, and also participates in DNA damage repair processes. Dysregulation of the functioning of such ligases can severely impact DNA replication and repair pathways events that are generally targeted in cancer treatment. Although, several human DNA ligase inhibitors have been reported in the literature but unfortunately not a single inhibitor is currently being used in cancer chemotherapy. Results of pre-clinical studies also support the fact that human DNA ligases are an attractive target for the development of new anticancer agents which work by the selective inhibition of rapidly proliferating cancer cells. In this manuscript, we discuss, in brief, the structure, synthesis, structure-activity-relationship (SAR) and anticancer activity of recently reported hLigI inhibitors.
Collapse
Affiliation(s)
- Mohammad Saquib
- Department of Chemistry, University of Allahabad, Allahabad, 211002, India
| | - Mohd Imran Ansari
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD, 21201, USA
| | - Chad R Johnson
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD, 21201, USA
| | | | - Mohd Kamil Hussain
- Department of Chemistry, Govt. Raza Post Graduate College, Rampur, 244901, India.
| | - Andrew Coop
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD, 21201, USA.
| |
Collapse
|
21
|
Liddiard K, Ruis B, Kan Y, Cleal K, Ashelford KE, Hendrickson EA, Baird DM. DNA Ligase 1 is an essential mediator of sister chromatid telomere fusions in G2 cell cycle phase. Nucleic Acids Res 2019; 47:2402-2424. [PMID: 30590694 PMCID: PMC6411840 DOI: 10.1093/nar/gky1279] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 12/11/2018] [Accepted: 12/14/2018] [Indexed: 12/27/2022] Open
Abstract
Fusion of critically short or damaged telomeres is associated with the genomic rearrangements that support malignant transformation. We have demonstrated the fundamental contribution of DNA ligase 4-dependent classical non-homologous end-joining to long-range inter-chromosomal telomere fusions. In contrast, localized genomic recombinations initiated by sister chromatid fusion are predominantly mediated by alternative non-homologous end-joining activity that may employ either DNA ligase 3 or DNA ligase 1. In this study, we sought to discriminate the relative involvement of these ligases in sister chromatid telomere fusion through a precise genetic dissociation of functional activity. We have resolved an essential and non-redundant role for DNA ligase 1 in the fusion of sister chromatids bearing targeted double strand DNA breaks that is entirely uncoupled from its requisite engagement in DNA replication. Importantly, this fusogenic repair occurs in cells fully proficient for non-homologous end-joining and is not compensated by DNA ligases 3 or 4. The dual functions of DNA ligase 1 in replication and non-homologous end-joining uniquely position and capacitate this ligase for DNA repair at stalled replication forks, facilitating mitotic progression.
Collapse
Affiliation(s)
- Kate Liddiard
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Brian Ruis
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Yinan Kan
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kez Cleal
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Kevin E Ashelford
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Eric A Hendrickson
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Duncan M Baird
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| |
Collapse
|
22
|
Maffucci P, Chavez J, Jurkiw TJ, O’Brien PJ, Abbott JK, Reynolds PR, Worth A, Notarangelo LD, Felgentreff K, Cortes P, Boisson B, Radigan L, Cobat A, Dinakar C, Ehlayel M, Ben-Omran T, Gelfand EW, Casanova JL, Cunningham-Rundles C. Biallelic mutations in DNA ligase 1 underlie a spectrum of immune deficiencies. J Clin Invest 2018; 128:5489-5504. [PMID: 30395541 PMCID: PMC6264644 DOI: 10.1172/jci99629] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 09/04/2018] [Indexed: 12/30/2022] Open
Abstract
We report the molecular, cellular, and clinical features of 5 patients from 3 kindreds with biallelic mutations in the autosomal LIG1 gene encoding DNA ligase 1. The patients exhibited hypogammaglobulinemia, lymphopenia, increased proportions of circulating γδT cells, and erythrocyte macrocytosis. Clinical severity ranged from a mild antibody deficiency to a combined immunodeficiency requiring hematopoietic stem cell transplantation. Using engineered LIG1-deficient cell lines, we demonstrated chemical and radiation defects associated with the mutant alleles, which variably impaired the DNA repair pathway. We further showed that these LIG1 mutant alleles are amorphic or hypomorphic, and exhibited variably decreased enzymatic activities, which lead to premature release of unligated adenylated DNA. The variability of the LIG1 genotypes in the patients was consistent with that of their immunological and clinical phenotypes. These data suggest that different forms of autosomal recessive, partial DNA ligase 1 deficiency underlie an immunodeficiency of variable severity.
Collapse
Affiliation(s)
- Patrick Maffucci
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and
- Graduate School of Biomedical Sciences, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Jose Chavez
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and
| | - Thomas J. Jurkiw
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Patrick J. O’Brien
- Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
| | - Jordan K. Abbott
- Immunodeficiency Diagnosis and Treatment Program, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Paul R. Reynolds
- Immunodeficiency Diagnosis and Treatment Program, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Austen Worth
- Department of Pediatric Medicine, Great Ormond Street Hospital for Children, London, United Kingdom
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kerstin Felgentreff
- Department of Pediatrics and Adolescent Medicine, University Medical Center Ulm, Ulm, Germany
| | - Patricia Cortes
- Department of Molecular, Cellular and Biomedical Science, CUNY School of Medicine, City College of New York, New York, New York, USA
| | - Bertrand Boisson
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Paris Descartes University, Imagine Institute, Paris, France
| | - Lin Radigan
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and
| | - Aurélie Cobat
- Paris Descartes University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
| | - Chitra Dinakar
- Allergy, Asthma & Immunodeficiency, Division of Pulmonary and Critical Care Medicine, Department of Medicine, Stanford University, Stanford, California, USA
| | - Mohammad Ehlayel
- Section of Pediatric Allergy-Immunology, Department of Pediatrics, Weill Cornell Medical College, Hamad Medical Corporation, Doha, Qatar
| | - Tawfeg Ben-Omran
- Department of Clinical and Metabolic Genetics, Department of Pediatrics, Weill Cornell Medical College, Hamad Medical Corporation, Doha, Qatar
| | - Erwin W. Gelfand
- Immunodeficiency Diagnosis and Treatment Program, Department of Pediatrics, National Jewish Health, Denver, Colorado, USA
| | - Jean-Laurent Casanova
- St. Giles Laboratory of Human Genetics of Infectious Diseases, Rockefeller Branch, The Rockefeller University, New York, New York, USA
- Paris Descartes University, Imagine Institute, Paris, France
- Laboratory of Human Genetics of Infectious Diseases, Necker Branch, INSERM U1163, Necker Hospital for Sick Children, Paris, France
- Howard Hughes Medical Institute, New York, New York, USA
- Pediatric Hematology-Immunology Unit, Necker Hospital for Sick Children, Paris, France
| | - Charlotte Cunningham-Rundles
- Division of Clinical Immunology, Departments of Medicine and Pediatrics, and
- Graduate School of Biomedical Sciences, Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| |
Collapse
|
23
|
Hanzlikova H, Kalasova I, Demin AA, Pennicott LE, Cihlarova Z, Caldecott KW. The Importance of Poly(ADP-Ribose) Polymerase as a Sensor of Unligated Okazaki Fragments during DNA Replication. Mol Cell 2018; 71:319-331.e3. [PMID: 29983321 PMCID: PMC6060609 DOI: 10.1016/j.molcel.2018.06.004] [Citation(s) in RCA: 239] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 05/11/2018] [Accepted: 06/01/2018] [Indexed: 01/08/2023]
Abstract
Poly(ADP-ribose) is synthesized by PARP enzymes during the repair of stochastic DNA breaks. Surprisingly, however, we show that most if not all endogenous poly(ADP-ribose) is detected in normal S phase cells at sites of DNA replication. This S phase poly(ADP-ribose) does not result from damaged or misincorporated nucleotides or from DNA replication stress. Rather, perturbation of the DNA replication proteins LIG1 or FEN1 increases S phase poly(ADP-ribose) more than 10-fold, implicating unligated Okazaki fragments as the source of S phase PARP activity. Indeed, S phase PARP activity is ablated by suppressing Okazaki fragment formation with emetine, a DNA replication inhibitor that selectively inhibits lagging strand synthesis. Importantly, PARP activation during DNA replication recruits the single-strand break repair protein XRCC1, and human cells lacking PARP activity and/or XRCC1 are hypersensitive to FEN1 perturbation. Collectively, our data indicate that PARP1 is a sensor of unligated Okazaki fragments during DNA replication and facilitates their repair.
Collapse
Affiliation(s)
- Hana Hanzlikova
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic.
| | - Ilona Kalasova
- Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic
| | - Annie A Demin
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Lewis E Pennicott
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Zuzana Cihlarova
- Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic
| | - Keith W Caldecott
- Genome Damage and Stability Centre & Sussex Drug Discovery Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK; Department of Genome Dynamics, Institute of Molecular Genetics of the ASCR, v.v.i., 142 20 Prague 4, Czech Republic.
| |
Collapse
|
24
|
Structures of DNA-bound human ligase IV catalytic core reveal insights into substrate binding and catalysis. Nat Commun 2018; 9:2642. [PMID: 29980672 PMCID: PMC6035275 DOI: 10.1038/s41467-018-05024-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 05/16/2018] [Indexed: 11/26/2022] Open
Abstract
DNA ligase IV (LigIV) performs the final DNA nick-sealing step of classical nonhomologous end-joining, which is critical for immunoglobulin gene maturation and efficient repair of genotoxic DNA double-strand breaks. Hypomorphic LigIV mutations cause extreme radiation sensitivity and immunodeficiency in humans. To better understand the unique features of LigIV function, here we report the crystal structure of the catalytic core of human LigIV in complex with a nicked nucleic acid substrate in two distinct states—an open lysyl-AMP intermediate, and a closed DNA–adenylate form. Results from structural and mutagenesis experiments unveil a dynamic LigIV DNA encirclement mechanism characterized by extensive interdomain interactions and active site phosphoanhydride coordination, all of which are required for efficient DNA nick sealing. These studies provide a scaffold for defining impacts of LigIV catalytic core mutations and deficiencies in human LIG4 syndrome. DNA Ligase IV (LigIV) catalyzes nick sealing of DNA double-strand break substrates during non-homologous end-joining. Here the authors present the crystal structures of two human LigIV DNA-bound catalytic states, which provide insights into its catalytic mechanism and the molecular basis of LIG4 syndrome causing disease mutations.
Collapse
|
25
|
Reduced expression of DNA repair genes and chemosensitivity in 1p19q codeleted lower-grade gliomas. J Neurooncol 2018; 139:563-571. [PMID: 29923053 DOI: 10.1007/s11060-018-2915-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 05/27/2018] [Indexed: 12/17/2022]
Abstract
BACKGROUND Lower-grade gliomas (LGGs, defined as WHO grades II and III) with 1p19q codeletion have increased chemosensitivity when compared to LGGs without 1p19q codeletion, but the mechanism is currently unknown. METHODS RNAseq data from 515 LGG patients in the Cancer Genome Atlas (TCGA) were analyzed to compare the effect of expression of the 9 DNA repair genes located on chromosome arms 1p and 19q on progression free survival (PFS) and overall survival (OS) between patients who received chemotherapy and those who did not. Chemosensitivity of cells with DNA repair genes knocked down was tested using MTS cell proliferation assay in HS683 cell line and U251 cell line. RESULTS The expression of 9 DNA repair genes on 1p and 19q was significantly lower in 1p19q-codeleted tumors (n = 175) than in tumors without the codeletion (n = 337) (p < 0.001). In LGG patients who received chemotherapy, lower expression of LIG1, POLD1, PNKP, RAD54L and MUTYH was associated with longer PFS and OS. This difference between chemotherapy and non-chemotherapy groups in the association of gene expression with survival was not observed in non-DNA repair genes located on chromosome arms 1p and 19q. MTS assays showed that knockdown of DNA repair genes LIG1, POLD1, PNKP, RAD54L and MUTYH significantly inhibited recovery in response to temozolomide when compared with control group (p < 0.001). CONCLUSIONS Our results suggest that reduced expression of DNA repair genes on chromosome arms 1p and 19q may account for the increased chemosensitivity of LGGs with 1p19q codeletion.
Collapse
|
26
|
Pritchard AL, Johansson PA, Nathan V, Howlie M, Symmons J, Palmer JM, Hayward NK. Germline mutations in candidate predisposition genes in individuals with cutaneous melanoma and at least two independent additional primary cancers. PLoS One 2018; 13:e0194098. [PMID: 29641532 PMCID: PMC5894988 DOI: 10.1371/journal.pone.0194098] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Accepted: 02/23/2018] [Indexed: 12/30/2022] Open
Abstract
Background While a number of autosomal dominant and autosomal recessive cancer syndromes have an associated spectrum of cancers, the prevalence and variety of cancer predisposition mutations in patients with multiple primary cancers have not been extensively investigated. An understanding of the variants predisposing to more than one cancer type could improve patient care, including screening and genetic counselling, as well as advancing the understanding of tumour development. Methods A cohort of 57 patients ascertained due to their cutaneous melanoma (CM) diagnosis and with a history of two or more additional non-cutaneous independent primary cancer types were recruited for this study. Patient blood samples were assessed by whole exome or whole genome sequencing. We focussed on variants in 525 pre-selected genes, including 65 autosomal dominant and 31 autosomal recessive cancer predisposition genes, 116 genes involved in the DNA repair pathway, and 313 commonly somatically mutated in cancer. The same genes were analysed in exome sequence data from 1358 control individuals collected as part of non-cancer studies (UK10K). The identified variants were classified for pathogenicity using online databases, literature and in silico prediction tools. Results No known pathogenic autosomal dominant or previously described compound heterozygous mutations in autosomal recessive genes were observed in the multiple cancer cohort. Variants typically found somatically in haematological malignancies (in JAK1, JAK2, SF3B1, SRSF2, TET2 and TYK2) were present in lymphocyte DNA of patients with multiple primary cancers, all of whom had a history of haematological malignancy and cutaneous melanoma, as well as colorectal cancer and/or prostate cancer. Other potentially pathogenic variants were discovered in BUB1B, POLE2, ROS1 and DNMT3A. Compared to controls, multiple cancer cases had significantly more likely damaging mutations (nonsense, frameshift ins/del) in tumour suppressor and tyrosine kinase genes and higher overall burden of mutations in all cancer genes. Conclusions We identified several pathogenic variants that likely predispose to at least one of the tumours in patients with multiple cancers. We additionally present evidence that there may be a higher burden of variants of unknown significance in ‘cancer genes’ in patients with multiple cancer types. Further screens of this nature need to be carried out to build evidence to show if the cancers observed in these patients form part of a cancer spectrum associated with single germline variants in these genes, whether multiple layers of susceptibility exist (oligogenic or polygenic), or if the occurrence of multiple different cancers is due to random chance.
Collapse
Affiliation(s)
- Antonia L. Pritchard
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
- * E-mail:
| | - Peter A. Johansson
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Vaishnavi Nathan
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Madeleine Howlie
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Judith Symmons
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Jane M. Palmer
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Nicholas K. Hayward
- Oncogenomics Group, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| |
Collapse
|
27
|
Gupta S, Maurya P, Upadhyay A, Kushwaha P, Krishna S, Siddiqi MI, Sashidhara KV, Banerjee D. Synthesis and bio-evaluation of indole-chalcone based benzopyrans as promising antiligase and antiproliferative agents. Eur J Med Chem 2018; 143:1981-1996. [DOI: 10.1016/j.ejmech.2017.11.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Revised: 10/16/2017] [Accepted: 11/04/2017] [Indexed: 02/06/2023]
|
28
|
Howes TRL, Sallmyr A, Brooks R, Greco GE, Jones DE, Matsumoto Y, Tomkinson AE. Structure-activity relationships among DNA ligase inhibitors: Characterization of a selective uncompetitive DNA ligase I inhibitor. DNA Repair (Amst) 2017; 60:29-39. [PMID: 29078112 DOI: 10.1016/j.dnarep.2017.10.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 10/09/2017] [Indexed: 11/28/2022]
Abstract
In human cells, there are three genes that encode DNA ligase polypeptides with distinct but overlapping functions. Previously small molecule inhibitors of human DNA ligases were identified using a structure-based approach. Three of these inhibitors, L82, a DNA ligase I (LigI)-selective inhibitor, and L67, an inhibitor of LigI and DNA ligases III (LigIII), and L189, an inhibitor of all three human DNA ligases, have related structures that are composed of two 6-member aromatic rings separated by different linkers. Here we have performed a structure-activity analysis to identify determinants of activity and selectivity. The majority of the LigI-selective inhibitors had a pyridazine ring whereas the LigI/III- and LigIII-selective inhibitors did not. In addition, the aromatic rings in LigI-selective inhibitors had either arylhydrazone or acylhydrazone, but not vinyl linkers. Among the LigI-selective inhibitors, L82-G17 exhibited increased activity against and selectivity for LigI compared with L82. Notably. L82-G17 is an uncompetitive inhibitor of the third step of the ligation reaction, phosphodiester bond formation. Cells expressing LigI were more sensitive to L82-G17 than isogenic LIG1 null cells. Furthermore, cells lacking nuclear LigIIIα, which can substitute for LigI in DNA replication, were also more sensitive to L82-G17 than isogenic parental cells. Together, our results demonstrate that L82-G17 is a LigI-selective inhibitor with utility as a probe of the catalytic activity and cellular functions of LigI and provide a framework for the future design of DNA ligase inhibitors.
Collapse
Affiliation(s)
- Timothy R L Howes
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - Annahita Sallmyr
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - Rhys Brooks
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - George E Greco
- Department of Chemistry, Goucher College, Baltimore, MD 21204, United States
| | - Darin E Jones
- Department of Chemistry, University of Arkansas at Little Rock, Little Rock, AR 72204, United States
| | - Yoshihiro Matsumoto
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States
| | - Alan E Tomkinson
- Departments of Internal Medicine, Molecular Genetics and Microbiology and the University of New Mexico Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM 87131, United States.
| |
Collapse
|
29
|
McNally JR, O'Brien PJ. Kinetic analyses of single-stranded break repair by human DNA ligase III isoforms reveal biochemical differences from DNA ligase I. J Biol Chem 2017; 292:15870-15879. [PMID: 28751376 DOI: 10.1074/jbc.m117.804625] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 07/21/2017] [Indexed: 01/09/2023] Open
Abstract
Humans have three genes encoding DNA ligases with conserved structural features and activities, but they also have notable differences. The LIG3 gene encodes a ubiquitous isoform in all tissues (LIG3α) and a germ line-specific splicing isoform (LIG3β) that differs in the C-terminal domain. Both isoforms are found in the nucleus and the mitochondria. Here, we determined the kinetics and thermodynamics of single-stranded break ligation by LIG3α and LIG3β and compared this framework to that of LIG1, the nuclear replicative ligase. The kinetic parameters of the LIG3 isoforms are nearly identical under all tested conditions, indicating that the BRCA1 C terminal (BRCT) domain specific to LIG3α does not alter ligation kinetics. Although LIG3 is only 22% identical to LIG1 across their conserved domains, the two enzymes had very similar maximal ligation rates. Comparison of the rate and equilibrium constants for LIG3 and LIG1 nevertheless revealed important differences. The LIG3 isoforms were seven times more efficient than LIG1 at ligating nicked DNA under optimal conditions, mainly because of their lower Km value for the DNA substrate. This could explain why LIG3 is less prone to abortive ligation than LIG1. Surprisingly, the affinity of LIG3 for Mg2+ was ten times weaker than that of LIG1, suggesting that Mg2+ availability regulates DNA ligation in vivo, because Mg2+ levels are higher in the mitochondria than in the nucleus. The biochemical differences between the LIG3 isoforms and LIG1 identified here will guide the understanding of both unique and overlapping biological roles of these critical enzymes.
Collapse
Affiliation(s)
- Justin R McNally
- From the Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109
| | - Patrick J O'Brien
- From the Department of Biological Chemistry, Michigan Medicine, University of Michigan, Ann Arbor, Michigan 48109
| |
Collapse
|
30
|
O'Driscoll M. The pathological consequences of impaired genome integrity in humans; disorders of the DNA replication machinery. J Pathol 2017; 241:192-207. [PMID: 27757957 DOI: 10.1002/path.4828] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 12/13/2022]
Abstract
Accurate and efficient replication of the human genome occurs in the context of an array of constitutional barriers, including regional topological constraints imposed by chromatin architecture and processes such as transcription, catenation of the helical polymer and spontaneously generated DNA lesions, including base modifications and strand breaks. DNA replication is fundamentally important for tissue development and homeostasis; differentiation programmes are intimately linked with stem cell division. Unsurprisingly, impairments of the DNA replication machinery can have catastrophic consequences for genome stability and cell division. Functional impacts on DNA replication and genome stability have long been known to play roles in malignant transformation through a variety of complex mechanisms, and significant further insights have been gained from studying model organisms in this context. Congenital hypomorphic defects in components of the DNA replication machinery have been and continue to be identified in humans. These disorders present with a wide range of clinical features. Indeed, in some instances, different mutations in the same gene underlie different clinical presentations. Understanding the origin and molecular basis of these features opens a window onto the range of developmental impacts of suboptimal DNA replication and genome instability in humans. Here, I will briefly overview the basic steps involved in DNA replication and the key concepts that have emerged from this area of research, before switching emphasis to the pathological consequences of defects within the DNA replication network; the human disorders. Copyright © 2016 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Collapse
Affiliation(s)
- Mark O'Driscoll
- Human DNA Damage Response Disorders Group, Genome Damage & Stability Centre, School of Life Sciences, University of Sussex, Brighton, UK
| |
Collapse
|
31
|
Sallmyr A, Matsumoto Y, Roginskaya V, Van Houten B, Tomkinson AE. Inhibiting Mitochondrial DNA Ligase IIIα Activates Caspase 1-Dependent Apoptosis in Cancer Cells. Cancer Res 2016; 76:5431-41. [PMID: 27503931 PMCID: PMC5036517 DOI: 10.1158/0008-5472.can-15-3243] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 06/30/2016] [Indexed: 01/09/2023]
Abstract
Elevated levels of DNA ligase IIIα (LigIIIα) have been identified as a biomarker of an alteration in DNA repair in cancer cells that confers hypersensitivity to a LigIIIα inhibitor, L67, in combination with a poly (ADP-ribose) polymerase inhibitor. Because LigIIIα functions in the nucleus and mitochondria, we examined the effect of L67 on these organelles. Here, we show that, although the DNA ligase inhibitor selectively targets mitochondria, cancer and nonmalignant cells respond differently to disruption of mitochondrial DNA metabolism. Inhibition of mitochondrial LigIIIα in cancer cells resulted in abnormal mitochondrial morphology, reduced levels of mitochondrial DNA, and increased levels of mitochondrially generated reactive oxygen species that caused nuclear DNA damage. In contrast, these effects did not occur in nonmalignant cells. Furthermore, inhibition of mitochondrial LigIIIα activated a caspase 1-dependent apoptotic pathway, which is known to be part of inflammatory responses induced by pathogenic microorganisms in cancer, but not nonmalignant cells. These results demonstrate that the disruption of mitochondrial DNA metabolism elicits different responses in nonmalignant and cancer cells and suggests that the abnormal response in cancer cells may be exploited in the development of novel therapeutic strategies that selectively target cancer cells. Cancer Res; 76(18); 5431-41. ©2016 AACR.
Collapse
Affiliation(s)
- Annahita Sallmyr
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico
| | - Yoshihiro Matsumoto
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico
| | - Vera Roginskaya
- Department of Pharmacology and Cell Biology, University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Bennett Van Houten
- Department of Pharmacology and Cell Biology, University of Pittsburgh School of Medicine and The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Alan E Tomkinson
- Departments of Internal Medicine and Molecular Genetics and Microbiology, and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico.
| |
Collapse
|
32
|
Peng Z, Liao Z, Matsumoto Y, Yang A, Tomkinson AE. Human DNA Ligase I Interacts with and Is Targeted for Degradation by the DCAF7 Specificity Factor of the Cul4-DDB1 Ubiquitin Ligase Complex. J Biol Chem 2016; 291:21893-21902. [PMID: 27573245 DOI: 10.1074/jbc.m116.746198] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Indexed: 11/06/2022] Open
Abstract
The synthesis, processing, and joining of Okazaki fragments during DNA replication is complex, requiring the sequential action of a large number of proteins. Proliferating cell nuclear antigen, a DNA sliding clamp, interacts with and coordinates the activity of several DNA replication proteins, including the enzymes flap endonuclease 1 (FEN-1) and DNA ligase I that complete the processing and joining of Okazaki fragments, respectively. Although it is evident that maintaining the appropriate relative stoichiometry of FEN-1 and DNA ligase I, which compete for binding to proliferating cell nuclear antigen, is critical to prevent genomic instability, little is known about how the steady state levels of DNA replication proteins are regulated, in particular the proteolytic mechanisms involved in their turnover. Because DNA ligase I has been reported to be ubiquitylated, we used a proteomic approach to map ubiquitylation sites and screen for DNA ligase I-associated E3 ubiquitin ligases. We identified three ubiquitylated lysine residues and showed that DNA ligase I interacts with and is targeted for ubiquitylation by DCAF7, a specificity factor for the Cul4-DDB1 complex. Notably, knockdown of DCAF7 reduced the degradation of DNA ligase I in response to inhibition of proliferation and replacement of ubiquitylated lysine residues reduced the in vitro ubiquitylation of DNA ligase I by Cul4-DDB1 and DCAF7. In contrast, a different E3 ubiquitin ligase regulates FEN-1 turnover. Thus, although the expression of many of the genes encoding DNA replication proteins is coordinately regulated, our studies reveal that different mechanisms are involved in the turnover of these proteins.
Collapse
Affiliation(s)
- Zhimin Peng
- From the Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico 87131 and
| | - Zhongping Liao
- the Department of Anatomy and Neurobiology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Yoshihiro Matsumoto
- From the Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico 87131 and
| | - Austin Yang
- the Department of Anatomy and Neurobiology and Marlene and Stewart Greenebaum Cancer Center, University of Maryland School of Medicine, Baltimore, Maryland 21201
| | - Alan E Tomkinson
- From the Departments of Internal Medicine and Molecular Genetics and Microbiology, and the University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico 87131 and
| |
Collapse
|
33
|
Deshmukh AL, Kumar C, Singh DK, Maurya P, Banerjee D. Dynamics of replication proteins during lagging strand synthesis: A crossroads for genomic instability and cancer. DNA Repair (Amst) 2016; 42:72-81. [DOI: 10.1016/j.dnarep.2016.04.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/22/2016] [Accepted: 04/22/2016] [Indexed: 01/18/2023]
|
34
|
Absence of MutSβ leads to the formation of slipped-DNA for CTG/CAG contractions at primate replication forks. DNA Repair (Amst) 2016; 42:107-18. [PMID: 27155933 DOI: 10.1016/j.dnarep.2016.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Revised: 03/22/2016] [Accepted: 04/05/2016] [Indexed: 11/22/2022]
Abstract
Typically disease-causing CAG/CTG repeats expand, but rare affected families can display high levels of contraction of the expanded repeat amongst offspring. Understanding instability is important since arresting expansions or enhancing contractions could be clinically beneficial. The MutSβ mismatch repair complex is required for CAG/CTG expansions in mice and patients. Oddly, by unknown mechanisms MutSβ-deficient mice incur contractions instead of expansions. Replication using CTG or CAG as the lagging strand template is known to cause contractions or expansions respectively; however, the interplay between replication and repair leading to this instability remains unclear. Towards understanding how repeat contractions may arise, we performed in vitro SV40-mediated replication of repeat-containing plasmids in the presence or absence of mismatch repair. Specifically, we separated repair from replication: Replication mediated by MutSβ- and MutSα-deficient human cells or cell extracts produced slipped-DNA heteroduplexes in the contraction- but not expansion-biased replication direction. Replication in the presence of MutSβ disfavoured the retention of replication products harbouring slipped-DNA heteroduplexes. Post-replication repair of slipped-DNAs by MutSβ-proficient extracts eliminated slipped-DNAs. Thus, a MutSβ-deficiency likely enhances repeat contractions because MutSβ protects against contractions by repairing template strand slip-outs. Replication deficient in LigaseI or PCNA-interaction mutant LigaseI revealed slipped-DNA formation at lagging strands. Our results reveal that distinct mechanisms lead to expansions or contractions and support inhibition of MutSβ as a therapeutic strategy to enhance the contraction of expanded repeats.
Collapse
|
35
|
Mandalapu D, Singh DK, Gupta S, Balaramnavar VM, Shafiq M, Banerjee D, Sharma VL. Discovery of monocarbonyl curcumin hybrids as a novel class of human DNA ligase I inhibitors: in silico design, synthesis and biology. RSC Adv 2016. [DOI: 10.1039/c5ra25853g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A pharmacophore model identified a novel class of hLigI inhibitors to treat cancer. 36 compounds were synthesized and the identified inhibitor, compound 23 shown antiligase activity at IC50 24.9 μM by abolishing the interaction between hLigI and DNA.
Collapse
Affiliation(s)
- Dhanaraju Mandalapu
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Deependra Kumar Singh
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Sonal Gupta
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Vishal M. Balaramnavar
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Mohammad Shafiq
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
| | - Dibyendu Banerjee
- Molecular & Structural Biology Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
- Academy of Scientific and Innovative Research (AcSIR)
| | - Vishnu Lal Sharma
- Medicinal & Process Chemistry Division
- CSIR-Central Drug Research Institute (CSIR-CDRI)
- Lucknow
- India
- Academy of Scientific and Innovative Research (AcSIR)
| |
Collapse
|
36
|
Sashidhara KV, Singh LR, Shameem M, Shakya S, Kumar A, Laxman TS, Krishna S, Siddiqi MI, Bhatta RS, Banerjee D. Design, synthesis and anticancer activity of dihydropyrimidinone–semicarbazone hybrids as potential human DNA ligase 1 inhibitors. MEDCHEMCOMM 2016. [DOI: 10.1039/c6md00447d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
A series of rationally designed new class of hLig1 inhibitors with potentin vitroanti-cancer properties is presented.
Collapse
Affiliation(s)
- Koneni V. Sashidhara
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
| | - L. Ravithej Singh
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
| | - Mohammad Shameem
- Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
| | - Sarika Shakya
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
| | - Anoop Kumar
- Medicinal and Process Chemistry Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
| | | | - Shagun Krishna
- Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
| | - Rabi S. Bhatta
- Pharmacokinetics and Metabolism Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
| | - Dibyendu Banerjee
- Molecular and Structural Biology Division
- CSIR-Central Drug Research Institute
- Lucknow
- India
| |
Collapse
|
37
|
Paul-Konietzko K, Thomale J, Arakawa H, Iliakis G. DNA Ligases I and III Support Nucleotide Excision Repair in DT40 Cells with Similar Efficiency. Photochem Photobiol 2015; 91:1173-80. [DOI: 10.1111/php.12487] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Accepted: 06/15/2015] [Indexed: 12/01/2022]
Affiliation(s)
- Katja Paul-Konietzko
- Institute of Medical Radiation Biology; University of Duisburg-Essen Medical School; Essen Germany
| | - Juergen Thomale
- Institute of Cell Biology; University of Duisburg-Essen Medical School; Essen Germany
| | - Hiroshi Arakawa
- Institute for Radiocytogenetics; Helmholtz Zentrum München; German Research Center for Environmental Health; Neuherberg Germany
| | - George Iliakis
- Institute of Medical Radiation Biology; University of Duisburg-Essen Medical School; Essen Germany
| |
Collapse
|
38
|
Cremaschi P, Oliverio M, Leva V, Bione S, Carriero R, Mazzucco G, Palamidessi A, Scita G, Biamonti G, Montecucco A. Chronic Replication Problems Impact Cell Morphology and Adhesion of DNA Ligase I Defective Cells. PLoS One 2015; 10:e0130561. [PMID: 26151554 PMCID: PMC4495043 DOI: 10.1371/journal.pone.0130561] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 05/22/2015] [Indexed: 12/18/2022] Open
Abstract
Moderate DNA damage resulting from metabolic activities or sub-lethal doses of exogenous insults may eventually lead to cancer onset. Human 46BR.1G1 cells bear a mutation in replicative DNA ligase I (LigI) which results in low levels of replication-dependent DNA damage. This replication stress elicits a constitutive phosphorylation of the ataxia telangiectasia mutated (ATM) checkpoint kinase that fails to arrest cell cycle progression or to activate apoptosis or cell senescence. Stable transfection of wild type LigI, as in 7A3 cells, prevents DNA damage and ATM activation. Here we show that parental 46BR.1G1 and 7A3 cells differ in important features such as cell morphology, adhesion and migration. Comparison of gene expression profiles in the two cell lines detects Bio-Functional categories consistent with the morphological and migration properties of LigI deficient cells. Interestingly, ATM inhibition makes 46BR.1G1 more similar to 7A3 cells for what concerns morphology, adhesion and expression of cell-cell adhesion receptors. These observations extend the influence of the DNA damage response checkpoint pathways and unveil a role for ATM kinase activity in modulating cell biology parameters relevant to cancer progression.
Collapse
Affiliation(s)
- Paolo Cremaschi
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
| | - Matteo Oliverio
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Valentina Leva
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Silvia Bione
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Roberta Carriero
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- Istituto Universitario di Studi Superiori (IUSS), Pavia, Italy
| | - Giulia Mazzucco
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università degli Studi di Pavia, Pavia, Italy
| | | | - Giorgio Scita
- IFOM, Fondazione Istituto FIRC di Oncologia Molecolare, Milano, Italy
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Milano, Italy
| | - Giuseppe Biamonti
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
| | - Alessandra Montecucco
- Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (CNR), Pavia, Italy
- * E-mail:
| |
Collapse
|
39
|
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.
Collapse
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.
| |
Collapse
|
40
|
Shameem M, Kumar R, Krishna S, Kumar C, Siddiqi MI, Kundu B, Banerjee D. Synthetic modified pyrrolo[1,4] benzodiazepine molecules demonstrate selective anticancer activity by targeting the human ligase 1 enzyme: An in silico and in vitro mechanistic study. Chem Biol Interact 2015; 237:115-24. [PMID: 26079053 DOI: 10.1016/j.cbi.2015.05.024] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 05/15/2015] [Accepted: 05/26/2015] [Indexed: 11/18/2022]
Abstract
Human DNA ligase1 (hLig1) is the major replicative enzyme in proliferating mammalian cells that join Okazaki fragments of the lagging strand during DNA replication. Interruptions in the process of ligation cause DNA damage to accumulate, resulting in cytotoxicity and cell death. In the present study we demonstrate that pyrrolo[1,4] benzodiazepine (PBD) derivatives exhibit anticancer properties by targeting the nick sealing activity of hLig1 as opposed to the DNA interaction activity known for such compounds. Our in silico and in vitro assays demonstrate the binding of these molecules with amino acid residues present in the DNA binding domain (DBD) of the hLig1 enzyme. Two of these hLig1 inhibitors S010-015 and S010-018 demonstrated selective cytotoxicity against DLD-1 (colon cancer) and HepG2 (hepatic cancer) cells in a dose dependant manner. The molecules also reduced cell viability and colony formation at concentrations of ⩽20μM in DLD-1 and HepG2 cells and induced apoptotic cell death. In yet another significant finding, the molecules reduced the migration of cancer cells in wound healing experiments, indicating their anti-metastatic property. In summary, we report the anticancer activity of PBD derivatives against DLD-1 and HepG2 cells and propose a new molecular target for their activity.
Collapse
Affiliation(s)
- Mohammad Shameem
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Ravi Kumar
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Shagun Krishna
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Chandan Kumar
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Mohammad Imran Siddiqi
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow 226031, India
| | - Bijoy Kundu
- Medicinal and Process Chemistry Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow 226031, India.
| | - Dibyendu Banerjee
- Molecular and Structural Biology Division, CSIR-Central Drug Research Institute, B.S. 10/1, Janakipuram Extension, Sitapur Road, Lucknow 226031, India.
| |
Collapse
|
41
|
Abstract
Chemical modification and spontaneous loss of nucleotide bases from DNA are estimated to occur at the rate of thousands per human cell per day. DNA base excision repair (BER) is a critical mechanism for repairing such lesions in nuclear and mitochondrial DNA. Defective expression or function of proteins required for BER or proteins that regulate BER have been consistently associated with neurological dysfunction and disease in humans. Recent studies suggest that DNA lesions in the nuclear and mitochondrial compartments and the cellular response to those lesions have a profound effect on cellular energy homeostasis, mitochondrial function and cellular bioenergetics, with especially strong influence on neurological function. Further studies in this area could lead to novel approaches to prevent and treat human neurodegenerative disease.
Collapse
|
42
|
Tang KW, Norberg P, Holmudden M, Elias P, Liljeqvist JÅ. Rad51 and Rad52 are involved in homologous recombination of replicating herpes simplex virus DNA. PLoS One 2014; 9:e111584. [PMID: 25365323 PMCID: PMC4218770 DOI: 10.1371/journal.pone.0111584] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 10/04/2014] [Indexed: 12/27/2022] Open
Abstract
Replication of herpes simplex virus 1 is coupled to recombination, but the molecular mechanisms underlying this process are poorly characterized. The role of Rad51 and Rad52 recombinases in viral recombination was examined in human fibroblast cells 1BR.3.N (wild type) and in GM16097 with replication defects caused by mutations in DNA ligase I. Intermolecular recombination between viruses, tsS and tsK, harboring genetic markers gave rise to ∼17% recombinants in both cell lines. Knock-down of Rad51 and Rad52 by siRNA reduced production of recombinants to 11% and 5%, respectively, in wild type cells and to 3% and 5%, respectively, in GM16097 cells. The results indicate a specific role for Rad51 and Rad52 in recombination of replicating herpes simplex virus 1 DNA. Mixed infections using clinical isolates with restriction enzyme polymorphisms in the US4 and US7 genes revealed recombination frequencies of 0.7%/kbp in wild type cells and 4%/kbp in GM16097 cells. Finally, tandem repeats in the US7 gene remained stable upon serial passage, indicating a high fidelity of recombination in infected cells.
Collapse
Affiliation(s)
- Ka-Wei Tang
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Peter Norberg
- Department of Infectious Diseases, Section of Virology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Martin Holmudden
- Department of Infectious Diseases, Section of Virology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Per Elias
- Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Jan-Åke Liljeqvist
- Department of Infectious Diseases, Section of Virology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| |
Collapse
|
43
|
Baple EL, Chambers H, Cross HE, Fawcett H, Nakazawa Y, Chioza BA, Harlalka GV, Mansour S, Sreekantan-Nair A, Patton MA, Muggenthaler M, Rich P, Wagner K, Coblentz R, Stein CK, Last JI, Taylor AMR, Jackson AP, Ogi T, Lehmann AR, Green CM, Crosby AH. Hypomorphic PCNA mutation underlies a human DNA repair disorder. J Clin Invest 2014; 124:3137-46. [PMID: 24911150 PMCID: PMC4071375 DOI: 10.1172/jci74593] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 04/17/2014] [Indexed: 11/17/2022] Open
Abstract
Numerous human disorders, including Cockayne syndrome, UV-sensitive syndrome, xeroderma pigmentosum, and trichothiodystrophy, result from the mutation of genes encoding molecules important for nucleotide excision repair. Here, we describe a syndrome in which the cardinal clinical features include short stature, hearing loss, premature aging, telangiectasia, neurodegeneration, and photosensitivity, resulting from a homozygous missense (p.Ser228Ile) sequence alteration of the proliferating cell nuclear antigen (PCNA). PCNA is a highly conserved sliding clamp protein essential for DNA replication and repair. Due to this fundamental role, mutations in PCNA that profoundly impair protein function would be incompatible with life. Interestingly, while the p.Ser228Ile alteration appeared to have no effect on protein levels or DNA replication, patient cells exhibited marked abnormalities in response to UV irradiation, displaying substantial reductions in both UV survival and RNA synthesis recovery. The p.Ser228Ile change also profoundly altered PCNA's interaction with Flap endonuclease 1 and DNA Ligase 1, DNA metabolism enzymes. Together, our findings detail a mutation of PCNA in humans associated with a neurodegenerative phenotype, displaying clinical and molecular features common to other DNA repair disorders, which we showed to be attributable to a hypomorphic amino acid alteration.
Collapse
Affiliation(s)
- Emma L. Baple
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Helen Chambers
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Harold E. Cross
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Heather Fawcett
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Yuka Nakazawa
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Barry A. Chioza
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Gaurav V. Harlalka
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Sahar Mansour
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Ajith Sreekantan-Nair
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Michael A. Patton
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Martina Muggenthaler
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Phillip Rich
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Karin Wagner
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Roselyn Coblentz
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Constance K. Stein
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - James I. Last
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - A. Malcolm R. Taylor
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrew P. Jackson
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tomoo Ogi
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Alan R. Lehmann
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Catherine M. Green
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Andrew H. Crosby
- Medical Research, RILD Wellcome Wolfson Centre, University of Exeter Medical School, Exeter, Devon, United Kingdom. Department of Zoology, University of Cambridge, Cambridge, United Kingdom. Department of Ophthalmology, University of Arizona College of Medicine, Tucson, Arizona, USA. Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, United Kingdom. Nagasaki University Research Centre for Genomic Instability and Carcinogenesis (NRGIC), Nagasaki, Japan. Department of Molecular Medicine, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan. SW Thames Regional Genetics Service, St. George’s Healthcare NHS Trust, London, United Kingdom. Department of Neuroradiology, St. George’s Hospital, London, United Kingdom. Windows of Hope Genetic Study, Walnut Creek, Ohio, USA. SUNY Upstate Medical University, Syracuse, New York, USA. School of Cancer Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom. MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom. Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
44
|
Tomkinson AE, Sallmyr A. Structure and function of the DNA ligases encoded by the mammalian LIG3 gene. Gene 2013; 531:150-7. [PMID: 24013086 DOI: 10.1016/j.gene.2013.08.061] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2012] [Revised: 08/15/2013] [Accepted: 08/20/2013] [Indexed: 11/30/2022]
Abstract
Among the mammalian genes encoding DNA ligases (LIG), the LIG3 gene is unique in that it encodes multiple DNA ligase polypeptides with different cellular functions. Notably, this nuclear gene encodes the only mitochondrial DNA ligase and so is essential for this organelle. In the nucleus, there is significant functional redundancy between DNA ligase IIIα and DNA ligase I in excision repair. In addition, DNA ligase IIIα is essential for DNA replication in the absence of the replicative DNA ligase, DNA ligase I. DNA ligase IIIα is a component of an alternative non-homologous end joining (NHEJ) pathway for DNA double-strand break (DSB) repair that is more active when the major DNA ligase IV-dependent pathway is defective. Unlike its other nuclear functions, the role of DNA ligase IIIα in alternative NHEJ is independent of its nuclear partner protein, X-ray repair cross-complementing protein 1 (XRCC1). DNA ligase IIIα is frequently overexpressed in cancer cells, acting as a biomarker for increased dependence upon alternative NHEJ for DSB repair and it is a promising novel therapeutic target.
Collapse
Affiliation(s)
- Alan E Tomkinson
- Department of Internal Medicine and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, NM 87131, USA.
| | | |
Collapse
|
45
|
Singh DK, Krishna S, Chandra S, Shameem M, Deshmukh AL, Banerjee D. Human DNA Ligases: A Comprehensive New Look for Cancer Therapy. Med Res Rev 2013; 34:567-95. [DOI: 10.1002/med.21298] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Deependra Kumar Singh
- CSIR-Central Drug Research Institute; B.S. 10/1, Janakipuram Extension, Sitapur Road Lucknow 226021 Uttar Pradesh India
| | - Shagun Krishna
- CSIR-Central Drug Research Institute; B.S. 10/1, Janakipuram Extension, Sitapur Road Lucknow 226021 Uttar Pradesh India
| | - Sharat Chandra
- CSIR-Central Drug Research Institute; B.S. 10/1, Janakipuram Extension, Sitapur Road Lucknow 226021 Uttar Pradesh India
| | - Mohammad Shameem
- CSIR-Central Drug Research Institute; B.S. 10/1, Janakipuram Extension, Sitapur Road Lucknow 226021 Uttar Pradesh India
| | - Amit Laxmikant Deshmukh
- CSIR-Central Drug Research Institute; B.S. 10/1, Janakipuram Extension, Sitapur Road Lucknow 226021 Uttar Pradesh India
| | - Dibyendu Banerjee
- CSIR-Central Drug Research Institute; B.S. 10/1, Janakipuram Extension, Sitapur Road Lucknow 226021 Uttar Pradesh India
| |
Collapse
|
46
|
Nguyen HD, Becker J, Thu YM, Costanzo M, Koch EN, Smith S, Myung K, Myers CL, Boone C, Bielinsky AK. Unligated Okazaki Fragments Induce PCNA Ubiquitination and a Requirement for Rad59-Dependent Replication Fork Progression. PLoS One 2013; 8:e66379. [PMID: 23824283 PMCID: PMC3688925 DOI: 10.1371/journal.pone.0066379] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2012] [Accepted: 05/07/2013] [Indexed: 11/28/2022] Open
Abstract
Deficiency in DNA ligase I, encoded by CDC9 in budding yeast, leads to the accumulation of unligated Okazaki fragments and triggers PCNA ubiquitination at a non-canonical lysine residue. This signal is crucial to activate the S phase checkpoint, which promotes cell cycle delay. We report here that a pol30-K107 mutation alleviated cell cycle delay in cdc9 mutants, consistent with the idea that the modification of PCNA at K107 affects the rate of DNA synthesis at replication forks. To determine whether PCNA ubiquitination occurred in response to nicks or was triggered by the lack of PCNA-DNA ligase interaction, we complemented cdc9 cells with either wild-type DNA ligase I or a mutant form, which fails to interact with PCNA. Both enzymes reversed PCNA ubiquitination, arguing that the modification is likely an integral part of a novel nick-sensory mechanism and not due to non-specific secondary mutations that could have occurred spontaneously in cdc9 mutants. To further understand how cells cope with the accumulation of nicks during DNA replication, we utilized cdc9-1 in a genome-wide synthetic lethality screen, which identified RAD59 as a strong negative interactor. In comparison to cdc9 single mutants, cdc9 rad59Δ double mutants did not alter PCNA ubiquitination but enhanced phosphorylation of the mediator of the replication checkpoint, Mrc1. Since Mrc1 resides at the replication fork and is phosphorylated in response to fork stalling, these results indicate that Rad59 alleviates nick-induced replication fork slowdown. Thus, we propose that Rad59 promotes fork progression when Okazaki fragment processing is compromised and counteracts PCNA-K107 mediated cell cycle arrest.
Collapse
Affiliation(s)
- Hai Dang Nguyen
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, Minnesota, United States of America
| | - Jordan Becker
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, Minnesota, United States of America
| | - Yee Mon Thu
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, Minnesota, United States of America
| | - Michael Costanzo
- Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
| | - Elizabeth N. Koch
- University of Minnesota, Department of Computer Science and Engineering, Minneapolis, Minnesota, United States of America
| | - Stephanie Smith
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Kyungjae Myung
- Genome Instability Section, Genetics and Molecular Biology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Chad L. Myers
- University of Minnesota, Department of Computer Science and Engineering, Minneapolis, Minnesota, United States of America
| | - Charles Boone
- Banting and Best Department of Medical Research, The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Anja-Katrin Bielinsky
- University of Minnesota, Department of Biochemistry, Molecular Biology and Biophysics, Minneapolis, Minnesota, United States of America
- * E-mail:
| |
Collapse
|
47
|
Genome-wide ENU mutagenesis in combination with high density SNP analysis and exome sequencing provides rapid identification of novel mouse models of developmental disease. PLoS One 2013; 8:e55429. [PMID: 23469164 PMCID: PMC3585849 DOI: 10.1371/journal.pone.0055429] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 12/22/2012] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND Mice harbouring gene mutations that cause phenotypic abnormalities during organogenesis are invaluable tools for linking gene function to normal development and human disorders. To generate mouse models harbouring novel alleles that are involved in organogenesis we conducted a phenotype-driven, genome-wide mutagenesis screen in mice using the mutagen N-ethyl-N-nitrosourea (ENU). METHODOLOGY/PRINCIPAL FINDINGS ENU was injected into male C57BL/6 mice and the mutations transmitted through the germ-line. ENU-induced mutations were bred to homozygosity and G3 embryos screened at embryonic day (E) 13.5 and E18.5 for abnormalities in limb and craniofacial structures, skin, blood, vasculature, lungs, gut, kidneys, ureters and gonads. From 52 pedigrees screened 15 were detected with anomalies in one or more of the structures/organs screened. Using single nucleotide polymorphism (SNP)-based linkage analysis in conjunction with candidate gene or next-generation sequencing (NGS) we identified novel recessive alleles for Fras1, Ift140 and Lig1. CONCLUSIONS/SIGNIFICANCE In this study we have generated mouse models in which the anomalies closely mimic those seen in human disorders. The association between novel mutant alleles and phenotypes will lead to a better understanding of gene function in normal development and establish how their dysfunction causes human anomalies and disease.
Collapse
|
48
|
Peng Z, Liao Z, Dziegielewska B, Matsumoto Y, Thomas S, Wan Y, Yang A, Tomkinson AE. Phosphorylation of serine 51 regulates the interaction of human DNA ligase I with replication factor C and its participation in DNA replication and repair. J Biol Chem 2012; 287:36711-9. [PMID: 22952233 DOI: 10.1074/jbc.m112.383570] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Human DNA ligase I (hLigI) joins Okazaki fragments during DNA replication and completes excision repair via interactions with proliferating cell nuclear antigen and replication factor C (RFC). Unlike proliferating cell nuclear antigen, the interaction with RFC is regulated by hLigI phosphorylation. To identity of the site(s) involved in this regulation, we analyzed phosphorylated hLigI purified from insect cells by mass spectrometry. These results suggested that serine 51 phosphorylation negatively regulates the interaction with RFC. Therefore, we constructed versions of hLigI in which serine 51 was replaced with either alanine (hLigI51A) to prevent phosphorylation or aspartic acid (hLigI51D) to mimic phosphorylation. hLigI51D but not hLigI51A was defective in binding to purified RFC and in associating with RFC in cell extracts. Although DNA synthesis and proliferation of hLigI-deficient cells expressing either hLig51A or hLig51 was reduced compared with cells expressing wild-type hLigI, cellular senescence was only observed in the cells expressing hLigI51D. Notably, these cells had increased levels of spontaneous DNA damage and phosphorylated CHK2. In addition, although expression of hLigI51A complemented the sensitivity of hLigI-deficient cells to a poly (ADP-ribose polymerase (PARP) inhibitor, expression of hLig151D did not, presumably because these cells are more dependent upon PARP-dependent repair pathways to repair the damage resulting from the abnormal DNA replication. Finally, neither expression of hLigI51D nor hLigI51A fully complemented the sensitivity of hLigI-deficient cells to DNA alkylation. Thus, phosphorylation of serine 51 on hLigI plays a critical role in regulating the interaction between hLigI and RFC, which is required for efficient DNA replication and repair.
Collapse
Affiliation(s)
- Zhimin Peng
- Department of Internal Medicine and University of New Mexico Cancer Center, University of New Mexico, Albuquerque, New Mexico 87131, USA
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Lehmann AR. DNA repair, DNA replication and human disorders: a personal journey. DNA Repair (Amst) 2012; 11:328-34. [PMID: 22570876 DOI: 10.1016/j.dnarep.2011.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Alan R Lehmann
- Genome Damage and Stability Centre, University of Sussex, Falmer, Brighton, UK.
| |
Collapse
|
50
|
Kim YJ, Wilson DM. Overview of base excision repair biochemistry. Curr Mol Pharmacol 2012; 5:3-13. [PMID: 22122461 DOI: 10.2174/1874467211205010003] [Citation(s) in RCA: 218] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 11/25/2010] [Indexed: 02/06/2023]
Abstract
Base excision repair (BER) is an evolutionarily conserved pathway, which could be considered the "workhorse" repair mechanism of the cell. In particular, BER corrects most forms of spontaneous hydrolytic decay products in DNA, as well as everyday oxidative and alkylative modifications to bases or the sugar phosphate backbone. The repair response involves five key enzymatic steps that aim to remove the initial DNA lesion and restore the genetic material back to its original state: (i) excision of a damaged or inappropriate base, (ii) incision of the phosphodiester backbone at the resulting abasic site, (iii) termini clean-up to permit unabated repair synthesis and/or nick ligation, (iv) gap-filling to replace the excised nucleotide, and (v) sealing of the final, remaining DNA nick. These repair steps are executed by a collection of enzymes that include DNA glycosylases, apurinic/apyrimidinic endonucleases, phosphatases, phosphodiesterases, kinases, polymerases and ligases. Defects in BER components lead to reduced cell survival, elevated mutation rates, and DNA-damaging agent hypersensitivities. In addition, the pathway plays a significant role in determining cellular responsiveness to relevant clinical anti-cancer agents, such as alkylators (e.g. temozolomide), nucleoside analogs (e.g. 5-fluorouracil), and ionizing radiation. The molecular details of BER and the contribution of the pathway to therapeutic agent resistance are reviewed herein.
Collapse
Affiliation(s)
- Yun-Jeong Kim
- Laboratory of Molecular Gerontology, Biomedical Research Center, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | | |
Collapse
|