1
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Li L, Wang F, Deng Z, Zhang G, Zhu L, Zhao Z, Liu R. DCLRE1B promotes tumor progression and predicts immunotherapy response through METTL3-mediated m6A modification in pancreatic cancer. BMC Cancer 2023; 23:1073. [PMID: 37936074 PMCID: PMC10629169 DOI: 10.1186/s12885-023-11524-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/13/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND DCLRE1B is a 5'-to-3' exonuclease, which is involved in repairing ICL-related DNA damage. DCLRE1B has been reported to cause poor prognosis in a variety of cancers. Nonetheless, there is no research on DCLRE1B's biological role in pan-cancer datasets. Thus, ascertaining the processes via which DCLRE1B modulates tumorigenesis was the goal of the extensive bioinformatics investigation of pan-cancer datasets in the present research. METHODS In our research, employing internet websites and databases including TIMER, GEPIA, TISIDB, Kaplan-Meier Plotter, SangerBox, cBioPortal, and LinkedOmics, DCLRE1B-related data in numerous tumors were extracted. To ascertain the association among DCLRE1B expression, prognosis, genetic changes, and tumor immunity, the pan-cancer datasets were examined. The DCLRE1B's biological roles in pancreatic cancer cells were ascertained by employing wound healing, in vitro CCK-8, and MeRIP-qPCR assays. RESULT According to the pan-cancer analysis, in numerous solid tumors, DCLRE1B upregulation was observed. Expression of DCLRE1B was found to be substantially related to the cancer patients' prognoses. Similarly, expression of DCLRE1B exhibited substantial association with immune cells in several cancer types. DCLRE1B expression correlated with immune checkpoint (ICP) gene expression and impacted immunotherapy sensitivity. According to in vitro trials, DCLRE1B promoted PC cells' proliferation and migration capacities. Also, according to GSEA enrichment analysis, DCLRE1B might participate in the JAK-STAT signaling pathway, which was confirmed by western blotting. In addition, we also found that the downregulation of DCLRE1B may be regulated by METTL3-mediated m6A modification. CONCLUSIONS In human cancer, the overexpression of DCLRE1B was generally observed, which aided cancer onset and advancement via a variety of processes comprising control of the immune cells' tumor infiltration. According to this study's findings, in a few malignant tumors, DCLRE1B is a candidate immunotherapeutic and prognostic biomarker.
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Affiliation(s)
- Lincheng Li
- Faculty of Hepato-Pancreato-Biliary Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing, China
- Department of Surgery, Second Mobile Corps Hospital of Chinese People's Armed Police Force, Wuxi, China
| | - Fei Wang
- Faculty of Hepato-Pancreato-Biliary Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhaoda Deng
- Faculty of Hepato-Pancreato-Biliary Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Gong Zhang
- Faculty of Hepato-Pancreato-Biliary Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Lin Zhu
- Faculty of Hepato-Pancreato-Biliary Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing, China
| | - Zhiming Zhao
- Faculty of Hepato-Pancreato-Biliary Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing, China.
| | - Rong Liu
- Faculty of Hepato-Pancreato-Biliary Surgery, the First Medical Center, Chinese PLA General Hospital, Beijing, China.
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2
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Somashekara SC, Dhyani KM, Thakur M, Muniyappa K. SUMOylation of yeast Pso2 enhances its translocation and accumulation in the mitochondria and suppresses methyl methanesulfonate-induced mitochondrial DNA damage. Mol Microbiol 2023; 120:587-607. [PMID: 37649278 DOI: 10.1111/mmi.15145] [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: 03/27/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 09/01/2023]
Abstract
Saccharomyces cerevisiae Pso2/SNM1 is essential for DNA interstrand crosslink (ICL) repair; however, its mechanism of action remains incompletely understood. While recent work has revealed that Pso2/Snm1 is dual-localized in the nucleus and mitochondria, it remains unclear whether cell-intrinsic and -extrinsic factors regulate its subcellular localization and function. Herein, we show that Pso2 undergoes ubiquitination and phosphorylation, but not SUMOylation, in unstressed cells. Unexpectedly, we found that methyl methanesulfonate (MMS), rather than ICL-forming agents, induced robust SUMOylation of Pso2 on two conserved residues, K97 and K575, and that SUMOylation markedly increased its abundance in the mitochondria. Reciprocally, SUMOylation had no discernible impact on Pso2 translocation to the nucleus, despite the presence of steady-state levels of SUMOylated Pso2 across the cell cycle. Furthermore, substitution of the invariant residues K97 and K575 by arginine in the Pso2 SUMO consensus motifs severely impaired SUMOylation and abolished its translocation to the mitochondria of MMS-treated wild type cells, but not in unstressed cells. We demonstrate that whilst Siz1 and Siz2 SUMO E3 ligases catalyze Pso2 SUMOylation, the former plays a dominant role. Notably, we found that the phenotypic characteristics of the SUMOylation-defective mutant Pso2K97R/K575R closely mirrored those observed in the Pso2Δ petite mutant. Additionally, leveraging next-generation sequencing analysis, we demonstrate that Pso2 mitigates MMS-induced damage to mitochondrial DNA (mtDNA). Viewed together, our work offers previously unknown insights into the link between genotoxic stress-induced SUMOylation of Pso2 and its preferential targeting to the mitochondria, as well as its role in attenuating MMS-induced mtDNA damage.
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Affiliation(s)
| | - Kshitiza M Dhyani
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
| | - Manoj Thakur
- Sri Venkateswara College, University of Delhi, New Delhi, India
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore, India
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3
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Diene SM, Pontarotti P, Azza S, Armstrong N, Pinault L, Chabrière E, Colson P, Rolain JM, Raoult D. Origin, Diversity, and Multiple Roles of Enzymes with Metallo-β-Lactamase Fold from Different Organisms. Cells 2023; 12:1752. [PMID: 37443786 PMCID: PMC10340364 DOI: 10.3390/cells12131752] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/23/2023] [Accepted: 06/28/2023] [Indexed: 07/15/2023] Open
Abstract
β-lactamase enzymes have generated significant interest due to their ability to confer resistance to the most commonly used family of antibiotics in human medicine. Among these enzymes, the class B β-lactamases are members of a superfamily of metallo-β-lactamase (MβL) fold proteins which are characterised by conserved motifs (i.e., HxHxDH) and are not only limited to bacteria. Indeed, as the result of several barriers, including low sequence similarity, default protein annotation, or untested enzymatic activity, MβL fold proteins have long been unexplored in other organisms. However, thanks to search approaches which are more sensitive compared to classical Blast analysis, such as the use of common ancestors to identify distant homologous sequences, we are now able to highlight their presence in different organisms including Bacteria, Archaea, Nanoarchaeota, Asgard, Humans, Giant viruses, and Candidate Phyla Radiation (CPR). These MβL fold proteins are multifunctional enzymes with diverse enzymatic or non-enzymatic activities of which, at least thirteen activities have been reported such as β-lactamase, ribonuclease, nuclease, glyoxalase, lactonase, phytase, ascorbic acid degradation, anti-cancer drug degradation, or membrane transport. In this review, we (i) discuss the existence of MβL fold enzymes in the different domains of life, (ii) present more suitable approaches to better investigating their homologous sequences in unsuspected sources, and (iii) report described MβL fold enzymes with demonstrated enzymatic or non-enzymatic activities.
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Affiliation(s)
- Seydina M. Diene
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Pierre Pontarotti
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- CNRS SNC5039, 13005 Marseille, France
| | - Saïd Azza
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Nicholas Armstrong
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Lucile Pinault
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
- Assistance Publique-Hôpitaux de Marseille (AP-HM), IHU-Méditerranée Infection, 13005 Marseille, France
| | - Eric Chabrière
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Philippe Colson
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Jean-Marc Rolain
- MEPHI, IRD, AP-HM, IHU-Méditerranée Infection, Aix Marseille University, 13005 Marseille, France
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
| | - Didier Raoult
- IHU-Méditerranée Infection, 13005 Marseille, France; (S.A.)
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4
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Martinez MZ, Olmo F, Taylor MC, Caudron F, Wilkinson SR. Dissecting the interstrand crosslink DNA repair system of Trypanosoma cruzi. DNA Repair (Amst) 2023; 125:103485. [PMID: 36989950 DOI: 10.1016/j.dnarep.2023.103485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023]
Abstract
DNA interstrand crosslinks (ICLs) are toxic lesions that can block essential biological processes. Here we show Trypanosoma cruzi, the causative agent of Chagas disease, is susceptible to ICL-inducing compounds including mechlorethamine and novel nitroreductase-activated prodrugs that have potential in treating this infection. To resolve such lesions, cells co-opt enzymes from "classical" DNA repair pathways that alongside dedicated factors operate in replication-dependent and -independent mechanisms. To assess ICL repair in T. cruzi, orthologues of SNM1, MRE11 and CSB were identified and their function assessed. The T. cruzi enzymes could complement the mechlorethamine susceptibility phenotype displayed by corresponding yeast and/or T. brucei null confirming their role as ICL repair factors while GFP-tagged TcSNM1, TcMRE11 and TcCSB were shown to localise to the nuclei of insect and/or intracellular form parasites. Gene disruption demonstrated that while each activity was non-essential for T. cruzi viability, nulls displayed a growth defect in at least one life cycle stage with TcMRE11-deficient trypomastigotes also compromised in mammalian cell infectivity. Phenotyping revealed all nulls were more susceptible to mechlorethamine than controls, a trait complemented by re-expression of the deleted gene. To assess interplay, the gene disruption approach was extended to generate T. cruzi deficient in TcSNM1/TcMRE11 or in TcSNM1/TcCSB. Analysis demonstrated these activities functioned across two ICL repair pathways with TcSNM1 and TcMRE11 postulated to operate in a replication-dependent system while TcCSB helps resolve transcription-blocking lesions. By unravelling how T. cruzi repairs ICL damage, specific inhibitors targeting repair components could be developed and used to increase the potency of trypanocidal ICL-inducing compounds.
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Affiliation(s)
- Monica Zavala Martinez
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Francisco Olmo
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Martin C Taylor
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Fabrice Caudron
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Shane R Wilkinson
- School of Biological & Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK.
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5
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Somashekara SC, Muniyappa K. Dual targeting of Saccharomyces cerevisiae Pso2 to mitochondria and the nucleus, and its functional relevance in the repair of DNA interstrand crosslinks. G3 (BETHESDA, MD.) 2022; 12:jkac066. [PMID: 35482533 PMCID: PMC9157068 DOI: 10.1093/g3journal/jkac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/15/2022] [Indexed: 11/12/2022]
Abstract
Repair of DNA interstrand crosslinks involves a functional interplay among different DNA surveillance and repair pathways. Previous work has shown that interstrand crosslink-inducing agents cause damage to Saccharomyces cerevisiae nuclear and mitochondrial DNA, and its pso2/snm1 mutants exhibit a petite phenotype followed by loss of mitochondrial DNA integrity and copy number. Complex as it is, the cause and underlying molecular mechanisms remains elusive. Here, by combining a wide range of approaches with in vitro and in vivo analyses, we interrogated the subcellular localization and function of Pso2. We found evidence that the nuclear-encoded Pso2 contains 1 mitochondrial targeting sequence and 2 nuclear localization signals (NLS1 and NLS2), although NLS1 resides within the mitochondrial targeting sequence. Further analysis revealed that Pso2 is a dual-localized interstrand crosslink repair protein; it can be imported into both nucleus and mitochondria and that genotoxic agents enhance its abundance in the latter. While mitochondrial targeting sequence is essential for mitochondrial Pso2 import, either NLS1 or NLS2 is sufficient for its nuclear import; this implies that the 2 nuclear localization signal motifs are functionally redundant. Ablation of mitochondrial targeting sequence abrogated mitochondrial Pso2 import, and concomitantly, raised its levels in the nucleus. Strikingly, mutational disruption of both nuclear localization signal motifs blocked the nuclear Pso2 import; at the same time, they enhanced its translocation into the mitochondria, consistent with the notion that the relationship between mitochondrial targeting sequence and nuclear localization signal motifs is competitive. However, the nuclease activity of import-deficient species of Pso2 was not impaired. The potential relevance of dual targeting of Pso2 into 2 DNA-bearing organelles is discussed.
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Affiliation(s)
| | - Kalappa Muniyappa
- Department of Biochemistry, Indian Institute of Science, Bangalore 560 012, India
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6
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Wu HY, Zheng Y, Laciak AR, Huang NN, Koszelak-Rosenblum M, Flint AJ, Carr G, Zhu G. Structure and Function of SNM1 Family Nucleases. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022; 1414:1-26. [PMID: 35708844 DOI: 10.1007/5584_2022_724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/09/2022]
Abstract
Three human nucleases, SNM1A, SNM1B/Apollo, and SNM1C/Artemis, belong to the SNM1 gene family. These nucleases are involved in various cellular functions, including homologous recombination, nonhomologous end-joining, cell cycle regulation, and telomere maintenance. These three proteins share a similar catalytic domain, which is characterized as a fused metallo-β-lactamase and a CPSF-Artemis-SNM1-PSO2 domain. SNM1A and SNM1B/Apollo are exonucleases, whereas SNM1C/Artemis is an endonuclease. This review contains a summary of recent research on SNM1's cellular and biochemical functions, as well as structural biology studies. In addition, protein structure prediction by the artificial intelligence program AlphaFold provides a different view of the proteins' non-catalytic domain features, which may be used in combination with current results from X-ray crystallography and cryo-EM to understand their mechanism more clearly.
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7
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González-Acosta D, Blanco-Romero E, Ubieto-Capella P, Mutreja K, Míguez S, Llanos S, García F, Muñoz J, Blanco L, Lopes M, Méndez J. PrimPol-mediated repriming facilitates replication traverse of DNA interstrand crosslinks. EMBO J 2021; 40:e106355. [PMID: 34128550 PMCID: PMC8280817 DOI: 10.15252/embj.2020106355] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 05/04/2021] [Accepted: 05/04/2021] [Indexed: 12/22/2022] Open
Abstract
DNA interstrand crosslinks (ICLs) induced by endogenous aldehydes or chemotherapeutic agents interfere with essential processes such as replication and transcription. ICL recognition and repair by the Fanconi Anemia pathway require the formation of an X‐shaped DNA structure that may arise from convergence of two replication forks at the crosslink or traversing of the lesion by a single replication fork. Here, we report that ICL traverse strictly requires DNA repriming events downstream of the lesion, which are carried out by PrimPol, the second primase‐polymerase identified in mammalian cells after Polα/Primase. The recruitment of PrimPol to the vicinity of ICLs depends on its interaction with RPA, but not on FANCM translocase or the BLM/TOP3A/RMI1‐2 (BTR) complex that also participate in ICL traverse. Genetic ablation of PRIMPOL makes cells more dependent on the fork convergence mechanism to initiate ICL repair, and PRIMPOL KO cells and mice display hypersensitivity to ICL‐inducing drugs. These results open the possibility of targeting PrimPol activity to enhance the efficacy of chemotherapy based on DNA crosslinking agents.
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Affiliation(s)
- Daniel González-Acosta
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Elena Blanco-Romero
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Patricia Ubieto-Capella
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Karun Mutreja
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Samuel Míguez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Susana Llanos
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Fernando García
- Proteomics Unit-ProteoRed-ISCIII, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Javier Muñoz
- Proteomics Unit-ProteoRed-ISCIII, Biotechnology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
| | - Luis Blanco
- Centro de Biología Molecular Severo Ochoa, CSIC-UAM, Madrid, Spain
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Juan Méndez
- DNA Replication Group, Molecular Oncology Programme, Spanish National Cancer Research Centre (CNIO), Madrid, Spain
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8
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Abstract
DNA interstrand cross-links (ICLs) covalently connect the two strands of the double helix and are extremely cytotoxic. Defective ICL repair causes the bone marrow failure and cancer predisposition syndrome, Fanconi anemia, and upregulation of repair causes chemotherapy resistance in cancer. The central event in ICL repair involves resolving the cross-link (unhooking). In this review, we discuss the chemical diversity of ICLs generated by exogenous and endogenous agents. We then describe how proliferating and nonproliferating vertebrate cells unhook ICLs. We emphasize fundamentally new unhooking strategies, dramatic progress in the structural analysis of the Fanconi anemia pathway, and insights into how cells govern the choice between different ICL repair pathways. Throughout, we highlight the many gaps that remain in our knowledge of these fascinating DNA repair pathways.
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Affiliation(s)
- Daniel R Semlow
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Current affiliation: Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, Massachusetts 02115, USA; .,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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9
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Buzon B, Grainger RA, Rzadki C, Huang SYM, Junop M. Identification of Bioactive SNM1A Inhibitors. ACS OMEGA 2021; 6:9352-9361. [PMID: 33869915 PMCID: PMC8047731 DOI: 10.1021/acsomega.0c03528] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 03/02/2021] [Indexed: 06/12/2023]
Abstract
SNM1A is a nuclease required to repair DNA interstrand cross-links (ICLs) caused by some anticancer compounds, including cisplatin. Unlike other nucleases involved in ICL repair, SNM1A is not needed to restore other forms of DNA damage. As such, SNM1A is an attractive target for selectively increasing the efficacy of ICL-based chemotherapy. Using a fluorescence-based exonuclease assay, we screened a bioactive library of compounds for inhibition of SNM1A. Of the 52 compounds initially identified as hits, 22 compounds showed dose-response inhibition of SNM1A. An orthogonal gel-based assay further confirmed nine small molecules as SNM1A nuclease activity inhibitors with IC50 values in the mid-nanomolar to low micromolar range. Finally, three compounds showed no toxicity at concentrations able to significantly potentiate the cytotoxicity of cisplatin. These compounds represent potential leads for further optimization to sensitize cells toward chemotherapeutic agents inducing ICL damage.
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Affiliation(s)
- Beverlee Buzon
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department
of Biochemistry, Western University, London, Ontario N6A 5C1, Canada
| | - Ryan A. Grainger
- Department
of Biochemistry, Western University, London, Ontario N6A 5C1, Canada
| | - Cameron Rzadki
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Simon York Ming Huang
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Murray Junop
- Department
of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario L8S 4L8, Canada
- Department
of Biochemistry, Western University, London, Ontario N6A 5C1, Canada
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10
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Probing the Binding Requirements of Modified Nucleosides with the DNA Nuclease SNM1A. Molecules 2021; 26:molecules26020320. [PMID: 33435514 PMCID: PMC7827217 DOI: 10.3390/molecules26020320] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 12/22/2020] [Accepted: 12/31/2020] [Indexed: 11/16/2022] Open
Abstract
SNM1A is a nuclease that is implicated in DNA interstrand crosslink repair and, as such, its inhibition is of interest for overcoming resistance to chemotherapeutic crosslinking agents. However, the number and identity of the metal ion(s) in the active site of SNM1A are still unconfirmed, and only a limited number of inhibitors have been reported to date. Herein, we report the synthesis and evaluation of a family of malonate-based modified nucleosides to investigate the optimal positioning of metal-binding groups in nucleoside-derived inhibitors for SNM1A. These compounds include ester, carboxylate and hydroxamic acid malonate derivatives which were installed in the 5'-position or 3'-position of thymidine or as a linkage between two nucleosides. Evaluation as inhibitors of recombinant SNM1A showed that nine of the twelve compounds tested had an inhibitory effect at 1 mM concentration. The most potent compound contains a hydroxamic acid malonate group at the 5'-position. Overall, our studies advance the understanding of requirements for nucleoside-derived inhibitors for SNM1A and indicate that groups containing a negatively charged group in close proximity to a metal chelator, such as hydroxamic acid malonates, are promising structures in the design of inhibitors.
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11
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Baddock HT, Yosaatmadja Y, Newman JA, Schofield CJ, Gileadi O, McHugh PJ. The SNM1A DNA repair nuclease. DNA Repair (Amst) 2020; 95:102941. [PMID: 32866775 PMCID: PMC7607226 DOI: 10.1016/j.dnarep.2020.102941] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2020] [Accepted: 07/25/2020] [Indexed: 01/17/2023]
Abstract
Unrepaired, or misrepaired, DNA damage can contribute to the pathogenesis of a number of conditions, or disease states; thus, DNA damage repair pathways, and the proteins within them, are required for the safeguarding of the genome. Human SNM1A is a 5'-to-3' exonuclease that plays a role in multiple DNA damage repair processes. To date, most data suggest a role of SNM1A in primarily ICL repair: SNM1A deficient cells exhibit hypersensitivity to ICL-inducing agents (e.g. mitomycin C and cisplatin); and both in vivo and in vitro experiments demonstrate SNM1A and XPF-ERCC1 can function together in the 'unhooking' step of ICL repair. SNM1A further interacts with a number of other proteins that contribute to genome integrity outside canonical ICL repair (e.g. PCNA and CSB), and these may play a role in regulating SNM1As function, subcellular localisation, and post-translational modification state. These data also provide further insight into other DNA repair pathways to which SNM1A may contribute. This review aims to discuss all aspects of the exonuclease, SNM1A, and its contribution to DNA damage tolerance.
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Affiliation(s)
- Hannah T Baddock
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK
| | | | - Joseph A Newman
- Chemistry Research Laboratory, University of Oxford, 12 Mansfield Road, OX1 3TA, UK
| | | | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, OX3 7DQ, UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, OX3 9DS, UK.
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12
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Zwane AA, Schnabel RD, Hoff J, Choudhury A, Makgahlela ML, Maiwashe A, Van Marle-Koster E, Taylor JF. Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa. Front Genet 2019; 10:273. [PMID: 30988672 PMCID: PMC6452414 DOI: 10.3389/fgene.2019.00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits. However, the majority of validated SNPs for which allele frequencies have been estimated are limited primarily to European breeds. The objective of this study was to perform SNP discovery in three South African indigenous breeds (Afrikaner, Drakensberger, and Nguni) using whole genome sequencing. DNA was extracted from blood and hair samples, quantified and prepared at 50 ng/μl concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2500. The fastq files were used to call the variants using the Genome Analysis Tool Kit. A total of 1,678,360 were identified as novel using Run 6 of 1000 Bull Genomes Project. Annotation of the identified variants classified them into functional categories. Within the coding regions, about 30% of the SNPs were non-synonymous substitutions that encode for alternate amino acids. The study of distribution of SNP across the genome identified regions showing notable differences in the densities of SNPs among the breeds and highlighted many regions of functional significance. Gene ontology terms identified genes such as MLANA, SYT10, and CDC42EP5 that have been associated with coat color in mouse, and ADAMS3, DNAJC3, and PAG5 genes have been associated with fertility in cattle. Further analysis of the variants detected 688 candidate selective sweeps (ZHp Z-scores ≤ -4) across all three breeds, of which 223 regions were assigned as being putative selective sweeps (ZHp scores ≤-5). We also identified 96 regions with extremely low ZHp Z-scores (≤-6) in Afrikaner and Nguni. Genes such as KIT and MITF that have been associated with skin pigmentation in cattle and CACNA1C, which has been associated with biopolar disorder in human, were identified in these regions. This study provides the first analysis of sequence data to discover SNPs in indigenous South African cattle breeds. The information will play an important role in our efforts to understand the genetic history of our cattle and in designing appropriate breed improvement programmes.
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Affiliation(s)
- Avhashoni A. Zwane
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
- Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jesse Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Ananyo Choudhury
- Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Mahlako Linah Makgahlela
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Azwihangwisi Maiwashe
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Este Van Marle-Koster
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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13
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Madi A, Fisher D, Maughan TS, Colley JP, Meade AM, Maynard J, Humphreys V, Wasan H, Adams RA, Idziaszczyk S, Harris R, Kaplan RS, Cheadle JP. Pharmacogenetic analyses of 2183 patients with advanced colorectal cancer; potential role for common dihydropyrimidine dehydrogenase variants in toxicity to chemotherapy. Eur J Cancer 2018; 102:31-39. [PMID: 30114658 DOI: 10.1016/j.ejca.2018.07.009] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 06/29/2018] [Accepted: 07/08/2018] [Indexed: 12/20/2022]
Abstract
BACKGROUND Inherited genetic variants may influence response to, and side-effects from, chemotherapy. We sought to generate a comprehensive inherited pharmacogenetic profile for oxaliplatin and 5FU/capecitabine therapy in advanced colorectal cancer (aCRC). METHODS We analysed more than 200 potentially functional, common, inherited variants in genes within the 5FU, capecitabine, oxaliplatin and DNA repair pathways, together with four rare dihydropyrimidine dehydrogenase (DPYD) variants, in 2183 aCRC patients treated with oxaliplatin-fluoropyrimidine chemotherapy with, or without, cetuximab (from MRC COIN and COIN-B trials). Primary end-points were response, any toxicity and peripheral neuropathy. We had >85% power to detect odds ratios (ORs) = 1.3 for variants with minor allele frequencies >20%. RESULTS Variants in DNA repair genes (Asn279Ser in EXO1 and Arg399Gln in XRCC1) were most associated with response (OR 1.9, 95% confidence interval [CI] 1.2-2.9, P = 0.004, and OR 0.7, 95% CI 0.5-0.9, P = 0.003, respectively). Common variants in DPYD (Cys29Arg and Val732Ile) were most associated with toxicity (OR 0.8, 95% CI 0.7-1.0, P = 0.008, and OR 1.6, 95% CI 1.1-2.1, P = 0.006, respectively). Two rare DPYD variants were associated with increased toxicity (Asp949Val with neutropenia, nausea and vomiting, diarrhoea and infection; IVS14+1G>A with lethargy, diarrhoea, stomatitis, hand-foot syndrome and infection; all ORs > 3). Asp317His in DCLRE1A was most associated with peripheral neuropathy (OR 1.3, 95% CI 1.1-1.6, P = 0.003). No common variant associations remained significant after Bonferroni correction. CONCLUSIONS DNA repair genes may play a significant role in the pharmacogenetics of aCRC. Our data suggest that both common and rare DPYD variants may be associated with toxicity to fluoropyrimidine-based chemotherapy.
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Affiliation(s)
- Ayman Madi
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - David Fisher
- MRC Clinical Trials Unit, Aviation House, 125 Kingsway, London, WC2B 6NH, UK
| | - Timothy S Maughan
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - James P Colley
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Angela M Meade
- MRC Clinical Trials Unit, Aviation House, 125 Kingsway, London, WC2B 6NH, UK
| | - Julie Maynard
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Vikki Humphreys
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Harpreet Wasan
- Imperial College Healthcare NHS Trust, Hammersmith Hospital, Du Cane Road, London, W12 0HS, UK
| | - Richard A Adams
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Shelley Idziaszczyk
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Rebecca Harris
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK
| | - Richard S Kaplan
- MRC Clinical Trials Unit, Aviation House, 125 Kingsway, London, WC2B 6NH, UK
| | - Jeremy P Cheadle
- Division of Cancer and Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff, CF14 4XN, UK.
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14
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Yates M, Maréchal A. Ubiquitylation at the Fork: Making and Breaking Chains to Complete DNA Replication. Int J Mol Sci 2018; 19:E2909. [PMID: 30257459 PMCID: PMC6213728 DOI: 10.3390/ijms19102909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 09/20/2018] [Accepted: 09/24/2018] [Indexed: 12/11/2022] Open
Abstract
The complete and accurate replication of the genome is a crucial aspect of cell proliferation that is often perturbed during oncogenesis. Replication stress arising from a variety of obstacles to replication fork progression and processivity is an important contributor to genome destabilization. Accordingly, cells mount a complex response to this stress that allows the stabilization and restart of stalled replication forks and enables the full duplication of the genetic material. This response articulates itself on three important platforms, Replication Protein A/RPA-coated single-stranded DNA, the DNA polymerase processivity clamp PCNA and the FANCD2/I Fanconi Anemia complex. On these platforms, the recruitment, activation and release of a variety of genome maintenance factors is regulated by post-translational modifications including mono- and poly-ubiquitylation. Here, we review recent insights into the control of replication fork stability and restart by the ubiquitin system during replication stress with a particular focus on human cells. We highlight the roles of E3 ubiquitin ligases, ubiquitin readers and deubiquitylases that provide the required flexibility at stalled forks to select the optimal restart pathways and rescue genome stability during stressful conditions.
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Affiliation(s)
- Maïlyn Yates
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
| | - Alexandre Maréchal
- Department of Biology, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada.
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15
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Gunn AR, Banos-Pinero B, Paschke P, Sanchez-Pulido L, Ariza A, Day J, Emrich M, Leys D, Ponting CP, Ahel I, Lakin ND. The role of ADP-ribosylation in regulating DNA interstrand crosslink repair. J Cell Sci 2016; 129:3845-3858. [PMID: 27587838 PMCID: PMC5087659 DOI: 10.1242/jcs.193375] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/22/2016] [Indexed: 12/11/2022] Open
Abstract
ADP-ribosylation by ADP-ribosyltransferases (ARTs) has a well-established role in DNA strand break repair by promoting enrichment of repair factors at damage sites through ADP-ribose interaction domains. Here, we exploit the simple eukaryote Dictyostelium to uncover a role for ADP-ribosylation in regulating DNA interstrand crosslink repair and redundancy of this pathway with non-homologous end-joining (NHEJ). In silico searches were used to identify a protein that contains a permutated macrodomain (which we call aprataxin/APLF-and-PNKP-like protein; APL). Structural analysis reveals that this permutated macrodomain retains features associated with ADP-ribose interactions and that APL is capable of binding poly(ADP-ribose) through this macrodomain. APL is enriched in chromatin in response to cisplatin treatment, an agent that induces DNA interstrand crosslinks (ICLs). This is dependent on the macrodomain of APL and the ART Adprt2, indicating a role for ADP-ribosylation in the cellular response to cisplatin. Although adprt2− cells are sensitive to cisplatin, ADP-ribosylation is evident in these cells owing to redundant signalling by the double-strand break (DSB)-responsive ART Adprt1a, promoting NHEJ-mediated repair. These data implicate ADP-ribosylation in DNA ICL repair and identify that NHEJ can function to resolve this form of DNA damage in the absence of Adprt2. Summary: Here, we identify a role for post-translational modification ADP-ribosylation in the response to DNA interstrand crosslinks in the model Dictyostelium.
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Affiliation(s)
- Alasdair R Gunn
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Benito Banos-Pinero
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Peggy Paschke
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Luis Sanchez-Pulido
- MRC Human Genetics Unit, The MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK
| | - Antonio Ariza
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Joseph Day
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - Mehera Emrich
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
| | - David Leys
- Manchester Institute of Biotechnology, University of Manchester, Princess Street 131, Manchester, M1 7DN, UK
| | - Chris P Ponting
- MRC Human Genetics Unit, The MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK
| | - Ivan Ahel
- Dunn School of Pathology, University of Oxford, South Parks Road, Oxford, OX1 3RE, UK
| | - Nicholas D Lakin
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, UK
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16
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Thongthip S, Bellani M, Gregg SQ, Sridhar S, Conti BA, Chen Y, Seidman MM, Smogorzewska A. Fan1 deficiency results in DNA interstrand cross-link repair defects, enhanced tissue karyomegaly, and organ dysfunction. Genes Dev 2016; 30:645-59. [PMID: 26980189 PMCID: PMC4803051 DOI: 10.1101/gad.276261.115] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Thongthip et al. describe a FANCD2/FANCI-associated nuclease 1 (Fan1)-deficient mouse and show that FAN1 is required for cellular and organismal resistance to DNA interstrand cross-links. Karyomegaly becomes prominent in the kidneys and livers of Fan1-deficient mice with age, and mice develop liver dysfunction. Deficiency of FANCD2/FANCI-associated nuclease 1 (FAN1) in humans leads to karyomegalic interstitial nephritis (KIN), a rare hereditary kidney disease characterized by chronic renal fibrosis, tubular degeneration, and characteristic polyploid nuclei in multiple tissues. The mechanism of how FAN1 protects cells is largely unknown but is thought to involve FAN1's function in DNA interstrand cross-link (ICL) repair. Here, we describe a Fan1-deficient mouse and show that FAN1 is required for cellular and organismal resistance to ICLs. We show that the ubiquitin-binding zinc finger (UBZ) domain of FAN1, which is needed for interaction with FANCD2, is not required for the initial rapid recruitment of FAN1 to ICLs or for its role in DNA ICL resistance. Epistasis analyses reveal that FAN1 has cross-link repair activities that are independent of the Fanconi anemia proteins and that this activity is redundant with the 5′–3′ exonuclease SNM1A. Karyomegaly becomes prominent in kidneys and livers of Fan1-deficient mice with age, and mice develop liver dysfunction. Treatment of Fan1-deficient mice with ICL-inducing agents results in pronounced thymic and bone marrow hypocellularity and the disappearance of c-kit+ cells. Our results provide insight into the mechanism of FAN1 in ICL repair and demonstrate that the Fan1 mouse model effectively recapitulates the pathological features of human FAN1 deficiency.
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Affiliation(s)
- Supawat Thongthip
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Marina Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Siobhan Q Gregg
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Sunandini Sridhar
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Brooke A Conti
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Yanglu Chen
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, USA
| | - Agata Smogorzewska
- Laboratory of Genome Maintenance, The Rockefeller University, New York, New York 10065, USA
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17
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Allerston CK, Lee SY, Newman JA, Schofield CJ, McHugh PJ, Gileadi O. The structures of the SNM1A and SNM1B/Apollo nuclease domains reveal a potential basis for their distinct DNA processing activities. Nucleic Acids Res 2015; 43:11047-60. [PMID: 26582912 PMCID: PMC4678830 DOI: 10.1093/nar/gkv1256] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/30/2015] [Indexed: 11/30/2022] Open
Abstract
The human SNM1A and SNM1B/Apollo proteins are members of an extended family of eukaryotic nuclease containing a motif related to the prokaryotic metallo-β-lactamase (MBL) fold. SNM1A is a key exonuclease during replication-dependent and transcription-coupled interstrand crosslink repair, while SNM1B/Apollo is required for maintaining telomeric overhangs. Here, we report the crystal structures of SNM1A and SNM1B at 2.16 Å. While both proteins contain a typical MBL-β-CASP domain, a region of positive charge surrounds the active site of SNM1A, which is absent in SNM1B and explains the greater apparent processivity of SNM1A. The structures of both proteins also reveal a putative, wide DNA-binding groove. Extensive mutagenesis of this groove, coupled with detailed biochemical analysis, identified residues that did not impact on SNM1A catalytic activity, but drastically reduced its processivity. Moreover, we identified a key role for this groove for efficient digestion past DNA interstrand crosslinks, facilitating the key DNA repair reaction catalysed by SNM1A. Together, the architecture and dimensions of this groove, coupled to the surrounding region of high positive charge, explain the remarkable ability of SNM1A to accommodate and efficiently digest highly distorted DNA substrates, such as those containing DNA lesions.
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Affiliation(s)
- Charles K Allerston
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK
| | - Sook Y Lee
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford, OX1 3TA, UK Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Joseph A Newman
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Opher Gileadi
- Structural Genomics Consortium, Old Road Campus Research Building, Roosevelt Drive, University of Oxford, Oxford OX3 7DQ, UK
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18
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Glanzer JG, Liu S, Wang L, Mosel A, Peng A, Oakley GG. RPA inhibition increases replication stress and suppresses tumor growth. Cancer Res 2014; 74:5165-72. [PMID: 25070753 DOI: 10.1158/0008-5472.can-14-0306] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The ATR/Chk1 pathway is a critical surveillance network that maintains genomic integrity during DNA replication by stabilizing the replication forks during normal replication to avoid replication stress. One of the many differences between normal cells and cancer cells is the amount of replication stress that occurs during replication. Cancer cells with activated oncogenes generate increased levels of replication stress. This creates an increased dependency on the ATR/Chk1 pathway in cancer cells and opens up an opportunity to preferentially kill cancer cells by inhibiting this pathway. In support of this idea, we have identified a small molecule termed HAMNO ((1Z)-1-[(2-hydroxyanilino)methylidene]naphthalen-2-one), a novel protein interaction inhibitor of replication protein A (RPA), a protein involved in the ATR/Chk1 pathway. HAMNO selectively binds the N-terminal domain of RPA70, effectively inhibiting critical RPA protein interactions that rely on this domain. HAMNO inhibits both ATR autophosphorylation and phosphorylation of RPA32 Ser33 by ATR. By itself, HAMNO treatment creates DNA replication stress in cancer cells that are already experiencing replication stress, but not in normal cells, and it acts synergistically with etoposide to kill cancer cells in vitro and slow tumor growth in vivo. Thus, HAMNO illustrates how RPA inhibitors represent candidate therapeutics for cancer treatment, providing disease selectivity in cancer cells by targeting their differential response to replication stress. Cancer Res; 74(18); 5165-72. ©2014 AACR.
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Affiliation(s)
- Jason G Glanzer
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Shengqin Liu
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Ling Wang
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Adam Mosel
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska
| | - Aimin Peng
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska. Eppley Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska
| | - Greg G Oakley
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, Nebraska. Eppley Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska.
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19
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Klein Douwel D, Boonen RACM, Long DT, Szypowska AA, Räschle M, Walter JC, Knipscheer P. XPF-ERCC1 acts in Unhooking DNA interstrand crosslinks in cooperation with FANCD2 and FANCP/SLX4. Mol Cell 2014; 54:460-71. [PMID: 24726325 DOI: 10.1016/j.molcel.2014.03.015] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 01/17/2014] [Accepted: 02/28/2014] [Indexed: 12/26/2022]
Abstract
DNA interstrand crosslinks (ICLs), highly toxic lesions that covalently link the Watson and Crick strands of the double helix, are repaired by a complex, replication-coupled pathway in higher eukaryotes. The earliest DNA processing event in ICL repair is the incision of parental DNA on either side of the ICL ("unhooking"), which allows lesion bypass. Incisions depend critically on the Fanconi anemia pathway, whose activation involves ubiquitylation of the FANCD2 protein. Using Xenopus egg extracts, which support replication-coupled ICL repair, we show that the 3' flap endonuclease XPF-ERCC1 cooperates with SLX4/FANCP to carry out the unhooking incisions. Efficient recruitment of XPF-ERCC1 and SLX4 to the ICL depends on FANCD2 and its ubiquitylation. These data help define the molecular mechanism by which the Fanconi anemia pathway promotes a key event in replication-coupled ICL repair.
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Affiliation(s)
- Daisy Klein Douwel
- Hubrecht Institute-KNAW, University Medical Center Utrecht and Cancer Genomics Netherlands, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Rick A C M Boonen
- Hubrecht Institute-KNAW, University Medical Center Utrecht and Cancer Genomics Netherlands, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - David T Long
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Anna A Szypowska
- Hubrecht Institute-KNAW, University Medical Center Utrecht and Cancer Genomics Netherlands, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands
| | - Markus Räschle
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
| | - Puck Knipscheer
- Hubrecht Institute-KNAW, University Medical Center Utrecht and Cancer Genomics Netherlands, Uppsalalaan 8, 3584 CT Utrecht, the Netherlands.
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20
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Li S, Chang HH, Niewolik D, Hedrick MP, Pinkerton AB, Hassig CA, Schwarz K, Lieber MR. Evidence that the DNA endonuclease ARTEMIS also has intrinsic 5'-exonuclease activity. J Biol Chem 2014; 289:7825-34. [PMID: 24500713 DOI: 10.1074/jbc.m113.544874] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
ARTEMIS is a member of the metallo-β-lactamase protein family. ARTEMIS has endonuclease activity at DNA hairpins and at 5'- and 3'-DNA overhangs of duplex DNA, and this endonucleolytic activity is dependent upon DNA-PKcs. There has been uncertainty about whether ARTEMIS also has 5'-exonuclease activity on single-stranded DNA and 5'-overhangs, because this 5'-exonuclease is not dependent upon DNA-PKcs. Here, we show that the 5'-exonuclease and the endonuclease activities co-purify. Second, we show that a point mutant of ARTEMIS at a putative active site residue (H115A) markedly reduces both the endonuclease activity and the 5'-exonuclease activity. Third, divalent cation effects on the 5'-exonuclease and the endonuclease parallel one another. Fourth, both the endonuclease activity and 5'-exonuclease activity of ARTEMIS can be blocked in parallel by small molecule inhibitors, which do not block unrelated nucleases. We conclude that the 5'-exonuclease is intrinsic to ARTEMIS, making it relevant to the role of ARTEMIS in nonhomologous DNA end joining.
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Affiliation(s)
- Sicong Li
- From the Departments of Pathology, Biochemistry and Molecular Biology, Biological Sciences, and Molecular Microbiology and Immunology, University of Southern California Keck School of Medicine, Norris Comprehensive Cancer Center, Los Angeles, California 90089-9176
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21
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Munari FM, Guecheva TN, Bonatto D, Henriques JAP. New features on Pso2 protein family in DNA interstrand cross-link repair and in the maintenance of genomic integrity in Saccharomyces cerevisiae. Fungal Genet Biol 2013; 60:122-32. [PMID: 24076078 DOI: 10.1016/j.fgb.2013.09.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 09/11/2013] [Accepted: 09/15/2013] [Indexed: 11/27/2022]
Abstract
Pso2 protein, a member of the highly conserved metallo-β-lactamase (MBL) super family of nucleases, plays a central role in interstrand crosslink repair (ICL) in yeast. Pso2 protein is the founder member of a distinct group within the MBL superfamily, called β-CASP family. Three mammalian orthologs of this protein that act on DNA were identified: SNM1A, SNM1B/Apollo and SNM1C/Artemis. Yeast Pso2 and all three mammalian orthologs proteins have been shown to possess nuclease activity. Besides Pso2, ICL repair involves proteins of several DNA repair pathways. Over the last years, new homologs for human proteins have been identified in yeast. In this review, we will focus on studies clarifying the function of Pso2 protein during ICL repair in yeast, emphasizing the contribution of Brazilian research groups in this topic. New sub-pathways in the mechanisms of ICL repair, such as recently identified conserved Fanconi Anemia pathway in yeast as well as a contribution of non-homologous end joining are discussed.
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Affiliation(s)
- Fernanda Mosena Munari
- Biotechnology Center, Federal University of Rio Grande do Sul (UFRGS), 91507-970 Porto Alegre, RS, Brazil
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22
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Lee PP, Woodbine L, Gilmour KC, Bibi S, Cale CM, Amrolia PJ, Veys PA, Davies EG, Jeggo PA, Jones A. The many faces of Artemis-deficient combined immunodeficiency - Two patients with DCLRE1C mutations and a systematic literature review of genotype-phenotype correlation. Clin Immunol 2013; 149:464-74. [PMID: 24230999 DOI: 10.1016/j.clim.2013.08.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 08/04/2013] [Accepted: 08/07/2013] [Indexed: 12/31/2022]
Abstract
Defective V(D)J recombination and DNA double-strand break (DSB) repair severely impair the development of T-lymphocytes and B-lymphocytes. Most patients manifest a severe combined immunodeficiency during infancy. We report 2 siblings with combined immunodeficiency (CID) and immunodysregulation caused by compound heterozygous Artemis mutations, including an exon 1-3 deletion generating a null allele, and a missense change (p.T71P). Skin fibroblasts demonstrated normal DSB repair by gamma-H2AX analysis, supporting the predicted hypomorphic nature of the p.T71P allele. In addition to these two patients, 12 patients with Artemis-deficient CID were previously reported. All had significant morbidities including recurrent infections, autoimmunity, EBV-associated lymphoma, and carcinoma despite having hypomorphic mutants with residual Artemis expression, V(D)J recombination or DSB repair capacity. Nine patients underwent stem cell transplant and six survived, while four patients who did not receive transplant died. The progressive nature of immunodeficiency and genomic instability accounts for poor survival, and early HSCT should be considered.
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Affiliation(s)
- Pamela P Lee
- Department of Immunology, Great Ormond Street Hospital NHS Foundation Trust, London, UK
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23
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Abstract
The protein Snm1B plays a key role in interstrand crosslink (ICL) repair. In a yeast two-hybrid screen we identified the protein PSF2 to bind Snm1B. PSF2 is a member of the GINS complex involved in replication initiation and elongation, and is known to play a role in ICL repair. Snm1B was shown to bind PSF2 in human cells through two regions, strongly to a 144 amino acid N-terminal region and weakly to a second smaller 37 amino acid C-terminal region. Ectopic expression of PSF2 increased the amount of Mus81, a protein component of the endonucleolytic complex involved in ICL repair, co-immunoprecipitating with Snm1B. Moreover, deleting the N-terminal, but not C-terminal region of Snm1B reduced the amount of co-immunoprecipitated Mus81. Conversely, the telomere-binding protein TRF2 competed with PSF2 for binding to the C-terminus of Snm1B, and deletion of this region, but not the N-terminal region, reduced Snm1B chromatin association. We speculate that the N-terminal region of Snm1B forms a complex containing PSF2 and Mus81, while the C-terminal region is important for PSF2-mediated chromatin association.
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Affiliation(s)
- Jay R. Stringer
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Christopher M. Counter
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina, United States of America
- * E-mail:
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24
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McHugh PJ, Ward TA, Chovanec M. A prototypical Fanconi anemia pathway in lower eukaryotes? Cell Cycle 2012; 11:3739-44. [PMID: 22895051 DOI: 10.4161/cc.21727] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
DNA interstrand cross-links (ICLs) present a major challenge to cells, preventing separation of the two strands of duplex DNA and blocking major chromosome transactions, including transcription and replication. Due to the complexity of removing this form of DNA damage, no single DNA repair pathway has been shown to be capable of eradicating ICLs. In eukaryotes, ICL repair is a complex process, principally because several repair pathways compete for ICL repair intermediates in a strictly cell cycle-dependent manner. Yeast cells require a combination of nucleotide excision repair, homologous recombination repair and postreplication repair/translesion DNA synthesis to remove ICLs. There are also a number of additional ICL repair factors originally identified in the budding yeast Saccharomyces cerevisiae, called Pso1 though 10, of which Pso2 has an apparently dedicated role in ICL repair. Mammalian cells respond to ICLs by a complex network guided by factors mutated in the inherited cancer-prone disorder Fanconi anemia (FA). Although enormous progress has been made over recent years in identifying and characterizing FA factors as well as in elucidating certain aspects of the biology of FA, the mechanistic details of the ICL repair defects in FA patients remain unknown. Dissection of the FA DNA damage response pathway has, in part, been limited by the absence of FA-like pathways in highly tractable model organisms, such as yeast. Although S. cerevisiae possesses putative homologs of the FA factors FANCM, FANCJ and FANCP (Mph1, Chl1 and Slx4, respectively) as well as of the FANCM-associated proteins MHF1 and MHF2 (Mhf1 and Mhf2), the corresponding mutants display no significant increase in sensitivity to ICLs. Nevertheless, we and others have recently shown that these FA homologs, along with several other factors, control an ICL repair pathway, which has an overlapping or redundant role with a Pso2-controlled pathway. This pathway acts in S-phase and serves to prevent ICL-stalled replication forks from collapsing into DNA double-strand breaks.
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Affiliation(s)
- Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford, UK
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25
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Thompson LH. Recognition, signaling, and repair of DNA double-strand breaks produced by ionizing radiation in mammalian cells: the molecular choreography. Mutat Res 2012; 751:158-246. [PMID: 22743550 DOI: 10.1016/j.mrrev.2012.06.002] [Citation(s) in RCA: 261] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2011] [Revised: 06/09/2012] [Accepted: 06/16/2012] [Indexed: 12/15/2022]
Abstract
The faithful maintenance of chromosome continuity in human cells during DNA replication and repair is critical for preventing the conversion of normal diploid cells to an oncogenic state. The evolution of higher eukaryotic cells endowed them with a large genetic investment in the molecular machinery that ensures chromosome stability. In mammalian and other vertebrate cells, the elimination of double-strand breaks with minimal nucleotide sequence change involves the spatiotemporal orchestration of a seemingly endless number of proteins ranging in their action from the nucleotide level to nucleosome organization and chromosome architecture. DNA DSBs trigger a myriad of post-translational modifications that alter catalytic activities and the specificity of protein interactions: phosphorylation, acetylation, methylation, ubiquitylation, and SUMOylation, followed by the reversal of these changes as repair is completed. "Superfluous" protein recruitment to damage sites, functional redundancy, and alternative pathways ensure that DSB repair is extremely efficient, both quantitatively and qualitatively. This review strives to integrate the information about the molecular mechanisms of DSB repair that has emerged over the last two decades with a focus on DSBs produced by the prototype agent ionizing radiation (IR). The exponential growth of molecular studies, heavily driven by RNA knockdown technology, now reveals an outline of how many key protein players in genome stability and cancer biology perform their interwoven tasks, e.g. ATM, ATR, DNA-PK, Chk1, Chk2, PARP1/2/3, 53BP1, BRCA1, BRCA2, BLM, RAD51, and the MRE11-RAD50-NBS1 complex. Thus, the nature of the intricate coordination of repair processes with cell cycle progression is becoming apparent. This review also links molecular abnormalities to cellular pathology as much a possible and provides a framework of temporal relationships.
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Affiliation(s)
- Larry H Thompson
- Biology & Biotechnology Division, L452, Lawrence Livermore National Laboratory, P.O. Box 808, Livermore, CA 94551-0808, United States.
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26
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Paz MM, Pritsos CA. The Molecular Toxicology of Mitomycin C. ADVANCES IN MOLECULAR TOXICOLOGY VOLUME 6 2012. [DOI: 10.1016/b978-0-444-59389-4.00007-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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27
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Sengerová B, Wang AT, McHugh PJ. Orchestrating the nucleases involved in DNA interstrand cross-link (ICL) repair. Cell Cycle 2011; 10:3999-4008. [PMID: 22101340 DOI: 10.4161/cc.10.23.18385] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
DNA interstrand cross-links (ICLs) pose a significant threat to genomic and cellular integrity by blocking essential cellular processes, including replication and transcription. In mammalian cells, much ICL repair occurs in association with DNA replication during S phase, following the stalling of a replication fork at the block caused by an ICL lesion. Here, we review recent work showing that the XPF-ERCC1 endonuclease and the hSNM1A exonuclease act in the same pathway, together with SLX4, to initiate ICL repair, with the MUS81-EME1 fork incision activity becoming important in the absence of the XPF-SNM1A-SLX4-dependent pathway. Another nuclease, the Fanconi anemia-associated nuclease (FAN1), has recently been implicated in the repair of ICLs, and we discuss the possible ways in which the activities of different nucleases at the ICL-stalled replication fork may be coordinated. In relation to this, we briefly speculate on the possible role of SLX4, which contains XPF and MUS81- interacting domains, in the coordination of ICL repair nucleases.
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Affiliation(s)
- Blanka Sengerová
- Department of Oncology, Weatherall Institute of Molecular Medicine,University of Oxford, John Radcliffe Hospital, Oxford, UK
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28
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Wang AT, Sengerová B, Cattell E, Inagawa T, Hartley JM, Kiakos K, Burgess-Brown NA, Swift LP, Enzlin JH, Schofield CJ, Gileadi O, Hartley JA, McHugh PJ. Human SNM1A and XPF-ERCC1 collaborate to initiate DNA interstrand cross-link repair. Genes Dev 2011; 25:1859-70. [PMID: 21896658 PMCID: PMC3175721 DOI: 10.1101/gad.15699211] [Citation(s) in RCA: 108] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Accepted: 07/20/2011] [Indexed: 12/24/2022]
Abstract
One of the major DNA interstrand cross-link (ICL) repair pathways in mammalian cells is coupled to replication, but the mechanistic roles of the critical factors involved remain largely elusive. Here, we show that purified human SNM1A (hSNM1A), which exhibits a 5'-3' exonuclease activity, can load from a single DNA nick and digest past an ICL on its substrate strand. hSNM1A-depleted cells are ICL-sensitive and accumulate replication-associated DNA double-strand breaks (DSBs), akin to ERCC1-depleted cells. These DSBs are Mus81-induced, indicating that replication fork cleavage by Mus81 results from the failure of the hSNM1A- and XPF-ERCC1-dependent ICL repair pathway. Our results reveal how collaboration between hSNM1A and XPF-ERCC1 is necessary to initiate ICL repair in replicating human cells.
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Affiliation(s)
- Anderson T. Wang
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Blanka Sengerová
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Emma Cattell
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Takabumi Inagawa
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Janet M. Hartley
- Cancer Research UK Drug–DNA Interactions Research Group, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Konstantinos Kiakos
- Cancer Research UK Drug–DNA Interactions Research Group, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | | | - Lonnie P. Swift
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | - Jacqueline H. Enzlin
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
| | | | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, United Kingdom
| | - John A. Hartley
- Cancer Research UK Drug–DNA Interactions Research Group, UCL Cancer Institute, University College London, London WC1E 6BT, United Kingdom
| | - Peter J. McHugh
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom
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29
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Mason JM, Sekiguchi JM. Snm1B/Apollo functions in the Fanconi anemia pathway in response to DNA interstrand crosslinks. Hum Mol Genet 2011; 20:2549-59. [PMID: 21478198 DOI: 10.1093/hmg/ddr153] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Fanconi anemia (FA) is an inherited chromosomal instability disorder characterized by childhood aplastic anemia, developmental abnormalities and cancer predisposition. One of the hallmark phenotypes of FA is cellular hypersensitivity to agents that induce DNA interstrand crosslinks (ICLs), such as mitomycin C (MMC). FA is caused by mutation in at least 14 genes which function in the resolution of ICLs during replication. The FA proteins act within the context of a protein network in coordination with multiple repair factors that function in distinct pathways. SNM1B/Apollo is a member of metallo-β-lactamase/βCASP family of nucleases and has been demonstrated to function in ICL repair. However, the relationship between SNM1B and the FA protein network is not known. In the current study, we establish that SNM1B functions epistatically to the central FA factor, FANCD2, in cellular survival after ICL damage and homology-directed repair of DNA double-strand breaks. We also demonstrate that MMC-induced chromosomal anomalies are increased in SNM1B-depleted cells, and this phenotype is not further exacerbated upon depletion of either FANCD2 or another key FA protein, FANCI. Furthermore, we find that SNM1B is required for proper localization of critical repair factors, including FANCD2, BRCA1 and RAD51, to MMC-induced subnuclear foci. Our findings demonstrate that SNM1B functions within the FA pathway during the repair of ICL damage.
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Affiliation(s)
- Jennifer M Mason
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI 48109, USA
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30
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Akhter S, Lam YC, Chang S, Legerski RJ. The telomeric protein SNM1B/Apollo is required for normal cell proliferation and embryonic development. Aging Cell 2010; 9:1047-56. [PMID: 20854421 DOI: 10.1111/j.1474-9726.2010.00631.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Conserved metallo β-Lactamase and β-CASP (CPSF-Artemis-Snm1-Pso2) domain nuclease family member SNM1B/Apollo is a shelterin-associated protein that localizes to telomeres through its interaction with TRF2. To study its in vivo role, we generated a knockout of SNM1B/Apollo in a mouse model. Snm1B/Apollo homozygous null mice die at birth with developmental delay and defects in multiple organ systems. Cell proliferation defects were observed in Snm1B/Apollo mutant mouse embryonic fibroblasts (MEFs) owing to high levels of telomeric end-to-end fusions. Deficiency of the nonhomologous end-joining (NHEJ) factor Ku70, but not p53, rescued the developmental defects and lethality observed in Snm1B/Apollo mutant mice as well as the impaired proliferation of Snm1B/Apollo-deficient MEFs. These findings demonstrate that SNM1B/Apollo is required to protect telomeres against NHEJ-mediated repair, which results in genomic instability and the consequent multi-organ developmental failure. Although Snm1B/Apollo-deficient MEFs exhibited high levels of apoptosis, abrogation of p53-dependent programmed cell death did not rescue the multi-organ developmental failure in the mice.
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Affiliation(s)
- Shamima Akhter
- Department of Genetics, The UT MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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31
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Yan Y, Akhter S, Zhang X, Legerski R. The multifunctional SNM1 gene family: not just nucleases. Future Oncol 2010; 6:1015-29. [PMID: 20528238 DOI: 10.2217/fon.10.47] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The archetypical member of the SNM1 gene family was discovered 30 years ago in the budding yeast Saccharomyces cerevisiae. This small but ubiquitous gene family is characterized by metallo-beta-lactamase and beta-CASP domains, which together have been demonstrated to comprise a nuclease activity. Three mammalian members of this family, SNM1A, SNM1B/Apollo and Artemis, have been demonstrated to play surprisingly divergent roles in cellular metabolism. These pathways include variable (diversity) joining recombination, nonhomologous end-joining of double-strand breaks, DNA damage and mitotic cell cycle checkpoints, telomere maintenance and protein ubiquitination. Not all of these functions are consistent with a model in which these proteins act only as nucleases, and indicate that the SNM1 gene family encodes multifunctional products that can act in diverse biochemical pathways. In this article we discuss the various functions of SNM1A, SNM1B/Apollo and Artemis.
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Affiliation(s)
- Yiyi Yan
- Department of Genetics, University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
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32
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Abstract
To cope with the life-threatening crisis of a DNA interstrand cross-link (ICL), human cells must invoke the Fanconi anemia (FA) DNA repair pathway. The FA pathway is a multistep repair process, requiring multiple nucleolytic incisions and translesion DNA synthesis. Recent work from four laboratories has identified a novel FA-associated nuclease, FAN1, that binds directly to monoubiquitinated FANCD2, resolving a decade-long puzzle regarding the function of this FANCD2 modification.
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33
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Dominski Z. The hunt for the 3' endonuclease. WILEY INTERDISCIPLINARY REVIEWS-RNA 2010; 1:325-40. [PMID: 21935893 DOI: 10.1002/wrna.33] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Pre-mRNAs are typically processed at the 3(') end by cleavage/polyadenylation. This is a two-step processing reaction initiated by endonucleolytic cleavage of pre-mRNAs downstream of the AAUAAA sequence or its variant, followed by extension of the newly generated 3(') end with a poly(A) tail. In metazoans, replication-dependent histone transcripts are cleaved by a different 3(') end processing mechanism that depends on the U7 small nuclear ribonucleoprotein and the polyadenylation step is omitted. Each of the two mechanisms occurs in a macromolecular assembly that primarily functions to juxtapose the scissile bond with the 3(') endonuclease. Remarkably, despite characterizing a number of processing factors, the identity of this most critical component remained elusive until recently. For cleavage coupled to polyadenylation, much needed help was offered by bioinformatics, which pointed to CPSF-73, a known processing factor required for both cleavage and polyadenylation, as the possible 3(') endonuclease. In silico structural analysis indicated that this protein is a member of the large metallo-β-lactamase family of hydrolytic enzymes and belongs to the β-CASP subfamily that includes several RNA and DNA-specific nucleases. Subsequent experimental studies supported the notion that CPSF-73 does function as the endonuclease in the formation of polyadenylated mRNAs, but some controversy still remains as a different cleavage and polyadenylation specificity factor (CPSF) subunit, CPSF-30, displays an endonuclease activity in vitro while recombinant CPSF-73 is inactive. Unexpectedly, CPSF-73 as the 3(') endonuclease in cleavage coupled to polyadenylation found a strong ally in U7-dependent processing of histone pre-mRNAs, which was shown to utilize the same protein as the cleaving enzyme. It thus seems likely that these two processing reactions evolved from a common mechanism, with CPSF-73 as the endonuclease.
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Affiliation(s)
- Zbigniew Dominski
- Department of Biochemistry and Biophysics and Program in Molecular Biology and Biotechnology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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34
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Apollo contributes to G overhang maintenance and protects leading-end telomeres. Mol Cell 2010; 39:606-17. [PMID: 20619712 DOI: 10.1016/j.molcel.2010.06.031] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Revised: 06/14/2010] [Accepted: 06/24/2010] [Indexed: 12/19/2022]
Abstract
Mammalian telomeres contain a single-stranded 3' overhang that is thought to mediate telomere protection. Here we identify the TRF2-interacting factor Apollo as a nuclease that contributes to the generation/maintenance of this overhang. The function of mouse Apollo was determined using Cre-mediated gene deletion, complementation with Apollo mutants, and the TRF2-F120A mutant that cannot bind Apollo. Cells lacking Apollo activated the ATM kinase at their telomeres in S phase and showed leading-end telomere fusions. These telomere dysfunction phenotypes were accompanied by a reduction in the telomeric overhang signal. The telomeric functions of Apollo required its TRF2-interaction and nuclease motifs. Thus, TRF2 recruits the Apollo nuclease to process telomere ends synthesized by leading-strand DNA synthesis, thereby creating a terminal structure that avoids ATM activation and resists end-joining. These data establish that the telomeric overhang is required for the protection of telomeres from the DNA damage response.
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35
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Cattell E, Sengerová B, McHugh PJ. The SNM1/Pso2 family of ICL repair nucleases: from yeast to man. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2010; 51:635-645. [PMID: 20175117 DOI: 10.1002/em.20556] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Efficient interstrand crosslink (ICL) repair in yeast depends on the Pso2/Snm1 protein. Pso2 is a member of the highly conserved metallo-beta-lactamase structural family of nucleases. Mammalian cells possess three SNM1/Pso2 related proteins, SNM1A, SNM1B/Apollo, and SNM1C/Artemis. Evidence that SNM1A and SNM1B contribute to ICL repair is mounting, whereas Artemis appears to primarily contribute to non-ICL repair pathways, particularly some double-strand break repair events. Yeast Pso2 and all three mammalian SNM1-family proteins have been shown to possess nuclease activity. Here, we review the biochemical, genetic, and cellular evidence for the SNM1 family as DNA repair factors, focusing on ICL repair.
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Affiliation(s)
- Emma Cattell
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
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36
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SNMIB/Apollo protects leading-strand telomeres against NHEJ-mediated repair. EMBO J 2010; 29:2230-41. [PMID: 20551906 DOI: 10.1038/emboj.2010.58] [Citation(s) in RCA: 90] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2010] [Accepted: 05/19/2010] [Indexed: 11/08/2022] Open
Abstract
Progressive telomere attrition or deficiency of the protective shelterin complex elicits a DNA damage response as a result of a cell's inability to distinguish dysfunctional telomeric ends from DNA double-strand breaks. SNMIB/Apollo is a shelterin-associated protein and a member of the SMN1/PSO2 nuclease family that localizes to telomeres through its interaction with TRF2. Here, we generated SNMIB/Apollo knockout mouse embryo fibroblasts (MEFs) to probe the function of SNMIB/Apollo at mammalian telomeres. SNMIB/Apollo null MEFs exhibit an increased incidence of G2 chromatid-type fusions involving telomeres created by leading-strand DNA synthesis, reflective of a failure to protect these telomeres after DNA replication. Mutations within SNMIB/Apollo's conserved nuclease domain failed to suppress this phenotype, suggesting that its nuclease activity is required to protect leading-strand telomeres. SNMIB/Apollo(-/-)ATM(-/-) MEFs display robust telomere fusions when Trf2 is depleted, indicating that ATM is dispensable for repair of uncapped telomeres in this setting. Our data implicate the 5'-3' exonuclease function of SNM1B/Apollo in the generation of 3' single-stranded overhangs at newly replicated leading-strand telomeres to protect them from engaging the non-homologous end-joining pathway.
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37
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Yang K, Moldovan GL, D'Andrea AD. RAD18-dependent recruitment of SNM1A to DNA repair complexes by a ubiquitin-binding zinc finger. J Biol Chem 2010; 285:19085-91. [PMID: 20385554 DOI: 10.1074/jbc.m109.100032] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
SNM1A is a member of the SNM1 family of nucleases required for cellular processing of interstrand DNA crosslinks (ICLs). Little is known about the molecular function of SNM1A, in terms of its recruitment to ICL lesions or its DNA damage processing activity. Here we show that SNM1A contains a functional PIP box (PCNA-interacting protein box) and a UBZ (ubiquitin binding zinc finger), required for assembly of SNM1A into nuclear focus. Moreover, RAD18-dependent monoubiquitination of PCNA is required for Mitomycin C and Ultraviolet Light inducible SNM1A nuclear focus assembly. Taken together, our results identify a novel RAD18-PCNA(Ub)-SNM1A pathway required for nuclear focus formation and ICL resistance.
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Affiliation(s)
- Kailin Yang
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
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38
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Muniandy PA, Liu J, Majumdar A, Liu ST, Seidman MM. DNA interstrand crosslink repair in mammalian cells: step by step. Crit Rev Biochem Mol Biol 2010; 45:23-49. [PMID: 20039786 PMCID: PMC2824768 DOI: 10.3109/10409230903501819] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Interstrand DNA crosslinks (ICLs) are formed by natural products of metabolism and by chemotherapeutic reagents. Work in E. coli identified a two cycle repair scheme involving incisions on one strand on either side of the ICL (unhooking) producing a gapped intermediate with the incised oligonucleotide attached to the intact strand. The gap is filled by recombinational repair or lesion bypass synthesis. The remaining monoadduct is then removed by nucleotide excision repair (NER). Despite considerable effort, our understanding of each step in mammalian cells is still quite limited. In part this reflects the variety of crosslinking compounds, each with distinct structural features, used by different investigators. Also, multiple repair pathways are involved, variably operative during the cell cycle. G(1) phase repair requires functions from NER, although the mechanism of recognition has not been determined. Repair can be initiated by encounters with the transcriptional apparatus, or a replication fork. In the case of the latter, the reconstruction of a replication fork, stalled or broken by collision with an ICL, adds to the complexity of the repair process. The enzymology of unhooking, the identity of the lesion bypass polymerases required to fill the first repair gap, and the functions involved in the second repair cycle are all subjects of active inquiry. Here we will review current understanding of each step in ICL repair in mammalian cells.
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Affiliation(s)
- Parameswary A Muniandy
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
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39
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Bhagwat N, Olsen AL, Wang AT, Hanada K, Stuckert P, Kanaar R, D'Andrea A, Niedernhofer LJ, McHugh PJ. XPF-ERCC1 participates in the Fanconi anemia pathway of cross-link repair. Mol Cell Biol 2009; 29:6427-37. [PMID: 19805513 PMCID: PMC2786876 DOI: 10.1128/mcb.00086-09] [Citation(s) in RCA: 108] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2009] [Revised: 02/28/2009] [Accepted: 09/26/2009] [Indexed: 11/20/2022] Open
Abstract
Interstrand cross-links (ICLs) prevent DNA strand separation and, therefore, transcription and replication, making them extremely cytotoxic. The precise mechanism by which ICLs are removed from mammalian genomes largely remains elusive. Genetic evidence implicates ATR, the Fanconi anemia proteins, proteins required for homologous recombination, translesion synthesis, and at least two endonucleases, MUS81-EME1 and XPF-ERCC1. ICLs cause replication-dependent DNA double-strand breaks (DSBs), and MUS81-EME1 facilitates DSB formation. The subsequent repair of these DSBs occurs via homologous recombination after the ICL is unhooked by XPF-ERCC1. Here, we examined the effect of the loss of either nuclease on FANCD2 monoubiquitination to determine if the nucleolytic processing of ICLs is required for the activation of the Fanconi anemia pathway. FANCD2 was monoubiquitinated in Mus81(-/-), Ercc1(-/-), and XPF-deficient human, mouse, and hamster cells exposed to cross-linking agents. However, the monoubiquitinated form of FANCD2 persisted longer in XPF-ERCC1-deficient cells than in wild-type cells. Moreover, the levels of chromatin-bound FANCD2 were dramatically reduced and the number of ICL-induced FANCD2 foci significantly lower in XPF-ERCC1-deficient cells. These data demonstrate that the unhooking of an ICL by XPF-ERCC1 is necessary for the stable localization of FANCD2 to the chromatin and subsequent homologous recombination-mediated DSB repair.
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Affiliation(s)
- Nikhil Bhagwat
- Department of Human Genetics, University of Pittsburgh School of Public Health, A300 Crabtree Hall, 130 Desoto St., Pittsburgh, Pennsylvania 15261, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion 2.6, 5117 Centre Ave., Pittsburgh, Pennsylvania 15213-1863, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom, Department of Cell Biology & Genetics, Cancer Genomics Center, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, Department of Radiation Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, E1240 BSTWR, 200 Lothrop St., Pittsburgh, Pennsylvania 15261
| | - Anna L. Olsen
- Department of Human Genetics, University of Pittsburgh School of Public Health, A300 Crabtree Hall, 130 Desoto St., Pittsburgh, Pennsylvania 15261, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion 2.6, 5117 Centre Ave., Pittsburgh, Pennsylvania 15213-1863, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom, Department of Cell Biology & Genetics, Cancer Genomics Center, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, Department of Radiation Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, E1240 BSTWR, 200 Lothrop St., Pittsburgh, Pennsylvania 15261
| | - Anderson T. Wang
- Department of Human Genetics, University of Pittsburgh School of Public Health, A300 Crabtree Hall, 130 Desoto St., Pittsburgh, Pennsylvania 15261, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion 2.6, 5117 Centre Ave., Pittsburgh, Pennsylvania 15213-1863, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom, Department of Cell Biology & Genetics, Cancer Genomics Center, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, Department of Radiation Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, E1240 BSTWR, 200 Lothrop St., Pittsburgh, Pennsylvania 15261
| | - Katsuhiro Hanada
- Department of Human Genetics, University of Pittsburgh School of Public Health, A300 Crabtree Hall, 130 Desoto St., Pittsburgh, Pennsylvania 15261, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion 2.6, 5117 Centre Ave., Pittsburgh, Pennsylvania 15213-1863, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom, Department of Cell Biology & Genetics, Cancer Genomics Center, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, Department of Radiation Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, E1240 BSTWR, 200 Lothrop St., Pittsburgh, Pennsylvania 15261
| | - Patricia Stuckert
- Department of Human Genetics, University of Pittsburgh School of Public Health, A300 Crabtree Hall, 130 Desoto St., Pittsburgh, Pennsylvania 15261, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion 2.6, 5117 Centre Ave., Pittsburgh, Pennsylvania 15213-1863, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom, Department of Cell Biology & Genetics, Cancer Genomics Center, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, Department of Radiation Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, E1240 BSTWR, 200 Lothrop St., Pittsburgh, Pennsylvania 15261
| | - Roland Kanaar
- Department of Human Genetics, University of Pittsburgh School of Public Health, A300 Crabtree Hall, 130 Desoto St., Pittsburgh, Pennsylvania 15261, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion 2.6, 5117 Centre Ave., Pittsburgh, Pennsylvania 15213-1863, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom, Department of Cell Biology & Genetics, Cancer Genomics Center, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, Department of Radiation Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, E1240 BSTWR, 200 Lothrop St., Pittsburgh, Pennsylvania 15261
| | - Alan D'Andrea
- Department of Human Genetics, University of Pittsburgh School of Public Health, A300 Crabtree Hall, 130 Desoto St., Pittsburgh, Pennsylvania 15261, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion 2.6, 5117 Centre Ave., Pittsburgh, Pennsylvania 15213-1863, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom, Department of Cell Biology & Genetics, Cancer Genomics Center, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, Department of Radiation Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, E1240 BSTWR, 200 Lothrop St., Pittsburgh, Pennsylvania 15261
| | - Laura J. Niedernhofer
- Department of Human Genetics, University of Pittsburgh School of Public Health, A300 Crabtree Hall, 130 Desoto St., Pittsburgh, Pennsylvania 15261, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion 2.6, 5117 Centre Ave., Pittsburgh, Pennsylvania 15213-1863, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom, Department of Cell Biology & Genetics, Cancer Genomics Center, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, Department of Radiation Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, E1240 BSTWR, 200 Lothrop St., Pittsburgh, Pennsylvania 15261
| | - Peter J. McHugh
- Department of Human Genetics, University of Pittsburgh School of Public Health, A300 Crabtree Hall, 130 Desoto St., Pittsburgh, Pennsylvania 15261, University of Pittsburgh Cancer Institute, Hillman Cancer Center, Research Pavilion 2.6, 5117 Centre Ave., Pittsburgh, Pennsylvania 15213-1863, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, United Kingdom, Department of Cell Biology & Genetics, Cancer Genomics Center, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, Department of Radiation Oncology, Erasmus Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands, Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, E1240 BSTWR, 200 Lothrop St., Pittsburgh, Pennsylvania 15261
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Ma S, Huang J, Moran MS. Identification of genes associated with multiple cancers via integrative analysis. BMC Genomics 2009; 10:535. [PMID: 19919702 PMCID: PMC2785840 DOI: 10.1186/1471-2164-10-535] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2009] [Accepted: 11/17/2009] [Indexed: 12/03/2022] Open
Abstract
Background Advancement in gene profiling techniques makes it possible to measure expressions of thousands of genes and identify genes associated with development and progression of cancer. The identified cancer-associated genes can be used for diagnosis, prognosis prediction, and treatment selection. Most existing cancer microarray studies have been focusing on the identification of genes associated with a specific type of cancer. Recent biomedical studies suggest that different cancers may share common susceptibility genes. A comprehensive description of the associations between genes and cancers requires identification of not only multiple genes associated with a specific type of cancer but also genes associated with multiple cancers. Results In this article, we propose the Mc.TGD (Multi-cancer Threshold Gradient Descent), an integrative analysis approach capable of analyzing multiple microarray studies on different cancers. The Mc.TGD is the first regularized approach to conduct "two-dimensional" selection of genes with joint effects on cancer development. Simulation studies show that the Mc.TGD can more accurately identify genes associated with multiple cancers than meta analysis based on "one-dimensional" methods. As a byproduct, identification accuracy of genes associated with only one type of cancer may also be improved. We use the Mc.TGD to analyze seven microarray studies investigating development of seven different types of cancers. We identify one gene associated with six types of cancers and four genes associated with five types of cancers. In addition, we also identify 11, 9, 18, and 17 genes associated with 4 to 1 types of cancers, respectively. We evaluate prediction performance using a Leave-One-Out cross validation approach and find that only 4 (out of 570) subjects cannot be properly predicted. Conclusion The Mc.TGD can identify a short list of genes associated with one or multiple types of cancers. The identified genes are considerably different from those identified using meta analysis or analysis of marginal effects.
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Affiliation(s)
- Shuangge Ma
- School of Public Health, Yale University, New Haven, CT 06520, USA.
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Meier B, Barber LJ, Liu Y, Shtessel L, Boulton SJ, Gartner A, Ahmed S. The MRT-1 nuclease is required for DNA crosslink repair and telomerase activity in vivo in Caenorhabditis elegans. EMBO J 2009; 28:3549-63. [PMID: 19779462 DOI: 10.1038/emboj.2009.278] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2008] [Accepted: 08/24/2009] [Indexed: 12/26/2022] Open
Abstract
The telomerase reverse transcriptase adds de novo DNA repeats to chromosome termini. Here we define Caenorhabditis elegans MRT-1 as a novel factor required for telomerase-mediated telomere replication and the DNA-damage response. MRT-1 is composed of an N-terminal domain homologous to the second OB-fold of POT1 telomere-binding proteins and a C-terminal SNM1 family nuclease domain, which confer single-strand DNA-binding and processive 3'-to-5' exonuclease activity, respectively. Furthermore, telomerase activity in vivo depends on a functional MRT-1 OB-fold. We show that MRT-1 acts in the same telomere replication pathway as telomerase and the 9-1-1 DNA-damage response complex. MRT-1 is dispensable for DNA double-strand break repair, but functions with the 9-1-1 complex to promote DNA interstrand cross-link (ICL) repair. Our data reveal MRT-1 as a dual-domain protein required for telomerase function and ICL repair, which raises the possibility that telomeres and ICL lesions may share a common feature that plays a critical role in de novo telomere repeat addition.
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Affiliation(s)
- Bettina Meier
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
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de Villartay JP, Shimazaki N, Charbonnier JB, Fischer A, Mornon JP, Lieber MR, Callebaut I. A histidine in the β-CASP domain of Artemis is critical for its full in vitro and in vivo functions. DNA Repair (Amst) 2009; 8:202-8. [DOI: 10.1016/j.dnarep.2008.10.010] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2008] [Revised: 09/30/2008] [Accepted: 10/08/2008] [Indexed: 01/03/2023]
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Akhter S, Legerski RJ. SNM1A acts downstream of ATM to promote the G1 cell cycle checkpoint. Biochem Biophys Res Commun 2008; 377:236-41. [PMID: 18848520 DOI: 10.1016/j.bbrc.2008.09.130] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2008] [Accepted: 09/24/2008] [Indexed: 01/16/2023]
Abstract
We have shown previously that SNM1A colocalizes with 53BP1 at sites of double-strand breaks (DSBs) induced by IR, and that these proteins interact with or without DNA damage. However, the role of SNM1A in the DNA damage response has not been elucidated. Here, we show that SNM1A is required for an efficient G1 checkpoint arrest after IR exposure. Interestingly, the localization of SNM1A to sites of DSBs does not require either 53BP1 or H2AX, nor does the localization of 53BP1 require SNM1A. However, the localization of SNM1A does require ATM. Furthermore, SNM1A is shown to be a phosphorylation substrate of ATM in vitro, and to interact with ATM in vivo particularly after exposure of cells to IR. In addition, in the absence of SNM1A the activation of the downstream ATM target p53 is reduced. These findings suggest that SNM1A acts with ATM to promote the G1 cell cycle checkpoint.
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Affiliation(s)
- Shamima Akhter
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Bae JB, Mukhopadhyay SS, Liu L, Zhang N, Tan J, Akhter S, Liu X, Shen X, Li L, Legerski RJ. Snm1B/Apollo mediates replication fork collapse and S Phase checkpoint activation in response to DNA interstrand cross-links. Oncogene 2008; 27:5045-56. [PMID: 18469862 PMCID: PMC2805112 DOI: 10.1038/onc.2008.139] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2007] [Revised: 03/10/2008] [Accepted: 03/31/2008] [Indexed: 12/13/2022]
Abstract
The removal of DNA interstrand cross-links (ICLs) has proven to be notoriously complicated due to the involvement of multiple pathways of DNA repair, which include the Fanconi anemia/BRCA pathway, homologous recombination and components of the nucleotide excision and mismatch repair pathways. Members of the SNM1 gene family have also been shown to have a role in mediating cellular resistance to ICLs, although their precise function has remained elusive. Here, we show that knockdown of Snm1B/Apollo in human cells results in hypersensitivity to mitomycin C (MMC), but not to IR. We also show that Snm1B-deficient cells exhibit a defective S phase checkpoint in response to MMC, but not to IR, and this finding may account for the specific sensitivity to the cross-linking drug. Interestingly, although previous studies have largely implicated ATR as the major kinase activated in response to ICLs, we show that it is activation of the ATM-mediated checkpoint that is defective in Snm1B-deficient cells. The requirement for Snm1B in ATM checkpoint activation specifically after ICL damage is correlated with its role in promoting double-strand break formation, and thus replication fork collapse. Consistent with this result Snm1B was found to interact directly with Mus81-Eme1, an endonuclease previously implicated in fork collapse. In addition, we also show that Snm1B interacts with the Mre11-Rad50-Nbs1 (MRN) complex and with FancD2 further substantiating its role as a checkpoint/DNA repair protein.
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Affiliation(s)
- Jae-Bum Bae
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Sudit S. Mukhopadhyay
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Lingling Liu
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Nianxiang Zhang
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Jeff Tan
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Shamimi Akhter
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Xiaojun Liu
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Xi Shen
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Randy J. Legerski
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
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Freibaum BD, Counter CM. The protein hSnm1B is stabilized when bound to the telomere-binding protein TRF2. J Biol Chem 2008; 283:23671-6. [PMID: 18593705 DOI: 10.1074/jbc.m800388200] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
hSnm1B is member of the SNM family of exonucleases involved in DNA processing and is known to be localized to telomeres via binding to the telomere-binding protein TRF2. Here we demonstrate that the C terminus of hSnm1B facilitates the concentration of hSnm1B on telomeres by promoting ubiquitin-mediated degradation of hSnm1B that is not localized to telomeres, as well as by blocking protein degradation and fostering localization to telomeres via binding of TRF2. Finally, a mutant of hSnm1B stabilized independently of exogenous TRF2-induced cell death. Taken together, we speculate that sequestering hSnm1B at telomeres by a combination of stabilizing the protein when bound to telomeres and degrading it when not bound to telomeres may be a means to prevent potentially lethal effects of unregulated hSnm1B activity.
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Affiliation(s)
- Brian D Freibaum
- Departments of Pharmacology and Cancer Biology and Radiation Oncology, Duke University Medical Center, Durham, NC 27710, USA
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Endogenous hSNM1B/Apollo interacts with TRF2 and stimulates ATM in response to ionizing radiation. DNA Repair (Amst) 2008; 7:1192-201. [PMID: 18468965 DOI: 10.1016/j.dnarep.2008.03.020] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2007] [Revised: 03/20/2008] [Accepted: 03/27/2008] [Indexed: 01/07/2023]
Abstract
Human SNM1B/Apollo is involved in the cellular response to DNA-damage, however, its precise role is unknown. Recent reports have implicated hSNM1B in the protection of telomeres. We have found hSNM1B to interact with TRF2, a protein which functions in telomere protection and in an early response to ionizing radiation. Here we show that endogenous hSNM1B forms foci which colocalize at telomeres with TRF1 and TRF2. However, we observed that additional hSNM1B foci could be induced upon exposure to ionizing radiation (IR). In live-cell-imaging experiments, hSNM1B localized to photo-induced double-strand breaks (DSBs) within 10s post-induction. Further supporting a role for hSNM1B in the early stages of the cellular response to DSBs, we observed that autophosphorylation of ATM, as well as the phosphorylation of ATM target proteins in response to IR, was attenuated in cells depleted of hSNM1B. These observations suggest an important role for hSNM1B in the response to IR damage, a role that may be, in part, upstream of the central player in maintenance of genome integrity, ATM.
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Hemphill AW, Bruun D, Thrun L, Akkari Y, Torimaru Y, Hejna K, Jakobs P, Hejna J, Jones S, Olson S, Moses R. Mammalian SNM1 is required for genome stability. Mol Genet Metab 2008; 94:38-45. [PMID: 18180189 PMCID: PMC2413150 DOI: 10.1016/j.ymgme.2007.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2007] [Revised: 11/21/2007] [Accepted: 11/22/2007] [Indexed: 12/30/2022]
Abstract
The protein encoded by SNM1 in Saccharomyces cerevisiae has been shown to act specifically in DNA interstrand crosslinks (ICL) repair. There are five mammalian homologs of SNM1, including Artemis, which is involved in V(D)J recombination. Cells from mice constructed with a disruption in the Snm1 gene are sensitive to the DNA interstrand crosslinker, mitomycin (MMC), as indicated by increased radial formation following exposure. The mice reproduce normally and have normal life spans. However, a partial perinatal lethality, not seen in either homozygous mutant alone, can be noted when the Snm1 disruption is combined with a Fancd2 disruption. To explore the role of hSNM1 and its homologs in ICL repair in human cells, we used siRNA depletion in human fibroblasts, with cell survival and chromosome radials as the end points for sensitivity following treatment with MMC. Depletion of hSNM1 increases sensitivity to ICLs as detected by both end points, while depletion of Artemis does not. Thus hSNM1 is active in maintenance of genome stability following ICL formation. To evaluate the epistatic relationship between hSNM1 and other ICL repair pathways, we depleted hSNM1 in Fanconi anemia (FA) cells, which are inherently sensitive to ICLs. Depletion of hSNM1 in an FA cell line produces additive sensitivity for MMC. Further, mono-ubiquitination of FANCD2, an endpoint of the FA pathway, is not disturbed by depletion of hSNM1 in normal cells. Thus, hSNM1 appears to represent a second pathway for genome stability, distinct from the FA pathway.
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Affiliation(s)
- A. W. Hemphill
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
| | - D. Bruun
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
| | - L. Thrun
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
| | - Y. Akkari
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
| | - Y. Torimaru
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
| | - K. Hejna
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
| | - P.M. Jakobs
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
| | - J. Hejna
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
| | - S. Jones
- Department of Cell Biology, University of Massachusetts Medical School, 55 Lake Ave. North, Worcester, MA 01655
| | - S.B. Olson
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
| | - R.E. Moses
- Department of Molecular and Medical Genetics, Oregon Health & Sciences University, 3181 Sam Jackson Park Road, Portland, OR 97239
- Mailing address for corresponding author: Department of Molecular and Medical Genetics, L103, OHSU, 3181 SW Sam Jackson Park Road, Portland, OR 97239, Telephone: 503-494-6881, FAX: 503-494-6882, e-mail:
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Chen YC, Giovannucci E, Kraft P, J Hunter D. Sequence variants of elaC homolog 2 (Escherichia coli) (ELAC2) gene and susceptibility to prostate cancer in the Health Professionals Follow-Up Study. Carcinogenesis 2008; 29:999-1004. [PMID: 18375959 DOI: 10.1093/carcin/bgn081] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Two non-synonymous single-nucleotide polymorphisms (SNPs), Ser217Leu and Ala541Thr, in the elaC homolog 2 (Escherichia coli) (ELAC2) gene have been related to prostate cancer risk in previous studies, though with inconsistent results. The association of ELAC2 haplotypes with prostate cancer risk has not yet been explored. We assessed whether sequence variants in ELAC2 were associated with the risk of total or aggressive prostate cancer. In a nested case-control design within the Health Professionals Follow-Up Study, we identified 659 participants with prostate cancer diagnosed after they provided a blood specimen in 1993 and before January 2000. Controls were 656 age-matched men without prostate cancer who had had a prostate-specific antigen test after providing a blood specimen. We genotyped eight tagging SNPs in ELAC2 to test for the association between sequence variances in ELAC2 and prostate cancer. No individual SNP (including Ser217Leu) was associated with the risk of prostate cancer. Ala541Thr is a rare SNP in this population. One common haplotype (hap4) was statistically significantly associated with an increased risk of prostate cancer [odds ratio (OR) = 1.39, 95% confidence interval = 1.05-1.85]. Two common promoter SNPs and three common haplotypes were statistically significantly associated with aggressive prostate cancer (carriers versus non-carriers-snp2: OR = 1.43, snp3: OR = 0.69, hap1: OR = 1.47, hap2: OR = 0.72, hap4: OR = 1.51; global P-value for all common haplotypes = 0.11). Common SNPs and haplotypes of ELAC2 were associated with risk of aggressive prostate cancer.
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Affiliation(s)
- Yen-Ching Chen
- Department of Medicine, Channing Laboratory, Brigham and Women's Hospital, Harvard Medical School, 181 Longwood Avenue, Boston, MA 02115, USA.
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Else T, Theisen BK, Wu Y, Hutz JE, Keegan CE, Hammer GD, Ferguson DO. Tpp1/Acd maintains genomic stability through a complex role in telomere protection. Chromosome Res 2008; 15:1001-13. [PMID: 18185984 DOI: 10.1007/s10577-007-1175-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Revised: 09/05/2007] [Accepted: 09/05/2007] [Indexed: 11/29/2022]
Abstract
Telomeres serve to protect the ends of chromosomes, and failure to maintain telomeres can lead to dramatic genomic instability. Human TPP1 was identified as a protein which interacts with components of a telomere cap complex, but does not directly bind to telomeric DNA. While biochemical interactions indicate a function in telomere biology, much remains to be learned regarding the roles of TPP1 in vivo. We previously reported the positional cloning of the gene responsible for the adrenocortical dysplasia (acd) mouse phenotype, which revealed a mutation in the mouse homologue encoding TPP1. We find that cells from homozygous acd mice harbor chromosomes fused at telomere sequences, demonstrating a role in telomere protection in vivo. Surprisingly, our studies also reveal fusions and radial structures lacking internal telomere sequences, which are not anticipated from a simple deficiency in telomere protection. Employing spectral karyotyping and telomere FISH in a combined approach, we have uncovered a striking pattern; fusions with telomeric sequences involve nonhomologous chromosomes while those lacking telomeric sequences involve homologues. Together, these studies show that Tpp1/Acd plays a vital role in telomere protection, but likely has additional functions yet to be defined.
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Affiliation(s)
- Tobias Else
- Department of Internal Medicine, Division of Endocrinology and Metabolism, The University of Michigan, Ann Arbor, MI 48109, USA
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Abstract
Homologous recombination (HR) comprises a series of interrelated pathways that function in the repair of DNA double-stranded breaks (DSBs) and interstrand crosslinks (ICLs). In addition, recombination provides critical support for DNA replication in the recovery of stalled or broken replication forks, contributing to tolerance of DNA damage. A central core of proteins, most critically the RecA homolog Rad51, catalyzes the key reactions that typify HR: homology search and DNA strand invasion. The diverse functions of recombination are reflected in the need for context-specific factors that perform supplemental functions in conjunction with the core proteins. The inability to properly repair complex DNA damage and resolve DNA replication stress leads to genomic instability and contributes to cancer etiology. Mutations in the BRCA2 recombination gene cause predisposition to breast and ovarian cancer as well as Fanconi anemia, a cancer predisposition syndrome characterized by a defect in the repair of DNA interstrand crosslinks. The cellular functions of recombination are also germane to DNA-based treatment modalities of cancer, which target replicating cells by the direct or indirect induction of DNA lesions that are substrates for recombination pathways. This review focuses on mechanistic aspects of HR relating to DSB and ICL repair as well as replication fork support.
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Affiliation(s)
- Xuan Li
- Section of Microbiology University of California, Davis, Davis CA 95616-8665, USA
| | - Wolf-Dietrich Heyer
- Section of Microbiology University of California, Davis, Davis CA 95616-8665, USA
- Section of Molecular and Cellular Biology, University of California, Davis, Davis CA 95616-8665, USA
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