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Bellani MA, Shaik A, Majumdar I, Ling C, Seidman MM. Repair of genomic interstrand crosslinks. DNA Repair (Amst) 2024; 141:103739. [PMID: 39106540 DOI: 10.1016/j.dnarep.2024.103739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 07/11/2024] [Accepted: 07/25/2024] [Indexed: 08/09/2024]
Abstract
Genomic interstrand crosslinks (ICLs) are formed by reactive species generated during normal cellular metabolism, produced by the microbiome, and employed in cancer chemotherapy. While there are multiple options for replication dependent and independent ICL repair, the crucial step for each is unhooking one DNA strand from the other. Much of our insight into mechanisms of unhooking comes from powerful model systems based on plasmids with defined ICLs introduced into cells or cell free extracts. Here we describe the properties of exogenous and endogenous ICL forming compounds and provide an historical perspective on early work on ICL repair. We discuss the modes of unhooking elucidated in the model systems, the concordance or lack thereof in drug resistant tumors, and the evolving view of DNA adducts, including ICLs, formed by metabolic aldehydes.
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Affiliation(s)
- Marina A Bellani
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Althaf Shaik
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Ishani Majumdar
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Chen Ling
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Michael M Seidman
- Laboratory of Molecular Biology and Immunology, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA.
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2
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Muniesa-Vargas A, Davó-Martínez C, Ribeiro-Silva C, van der Woude M, Thijssen KL, Haspels B, Häckes D, Kaynak ÜU, Kanaar R, Marteijn JA, Theil AF, Kuijten MMP, Vermeulen W, Lans H. Persistent TFIIH binding to non-excised DNA damage causes cell and developmental failure. Nat Commun 2024; 15:3490. [PMID: 38664429 PMCID: PMC11045817 DOI: 10.1038/s41467-024-47935-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Accepted: 04/12/2024] [Indexed: 04/28/2024] Open
Abstract
Congenital nucleotide excision repair (NER) deficiency gives rise to several cancer-prone and/or progeroid disorders. It is not understood how defects in the same DNA repair pathway cause different disease features and severity. Here, we show that the absence of functional ERCC1-XPF or XPG endonucleases leads to stable and prolonged binding of the transcription/DNA repair factor TFIIH to DNA damage, which correlates with disease severity and induces senescence features in human cells. In vivo, in C. elegans, this prolonged TFIIH binding to non-excised DNA damage causes developmental arrest and neuronal dysfunction, in a manner dependent on transcription-coupled NER. NER factors XPA and TTDA both promote stable TFIIH DNA binding and their depletion therefore suppresses these severe phenotypical consequences. These results identify stalled NER intermediates as pathogenic to cell functionality and organismal development, which can in part explain why mutations in XPF or XPG cause different disease features than mutations in XPA or TTDA.
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Affiliation(s)
- Alba Muniesa-Vargas
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Carlota Davó-Martínez
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Melanie van der Woude
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Karen L Thijssen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ben Haspels
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - David Häckes
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Ülkem U Kaynak
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Roland Kanaar
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Jurgen A Marteijn
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Maayke M P Kuijten
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Oncode Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, 3015 GD, Rotterdam, The Netherlands.
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3
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Hill RJ, Bona N, Smink J, Webb HK, Crisp A, Garaycoechea JI, Crossan GP. p53 regulates diverse tissue-specific outcomes to endogenous DNA damage in mice. Nat Commun 2024; 15:2518. [PMID: 38514641 PMCID: PMC10957910 DOI: 10.1038/s41467-024-46844-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
DNA repair deficiency can lead to segmental phenotypes in humans and mice, in which certain tissues lose homeostasis while others remain seemingly unaffected. This may be due to different tissues facing varying levels of damage or having different reliance on specific DNA repair pathways. However, we find that the cellular response to DNA damage determines different tissue-specific outcomes. Here, we use a mouse model of the human XPF-ERCC1 progeroid syndrome (XFE) caused by loss of DNA repair. We find that p53, a central regulator of the cellular response to DNA damage, regulates tissue dysfunction in Ercc1-/- mice in different ways. We show that ablation of p53 rescues the loss of hematopoietic stem cells, and has no effect on kidney, germ cell or brain dysfunction, but exacerbates liver pathology and polyploidisation. Mechanistically, we find that p53 ablation led to the loss of cell-cycle regulation in the liver, with reduced p21 expression. Eventually, p16/Cdkn2a expression is induced, serving as a fail-safe brake to proliferation in the absence of the p53-p21 axis. Taken together, our data show that distinct and tissue-specific functions of p53, in response to DNA damage, play a crucial role in regulating tissue-specific phenotypes.
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Affiliation(s)
- Ross J Hill
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Nazareno Bona
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Job Smink
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands
| | - Hannah K Webb
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Alastair Crisp
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK
| | - Juan I Garaycoechea
- Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW), Utrecht, the Netherlands.
| | - Gerry P Crossan
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, UK.
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4
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Liu H, Xu Y, Sun Y, Wu H, Hou J. Tissue-specific toxic effects of nano-copper on zebrafish. ENVIRONMENTAL RESEARCH 2024; 242:117717. [PMID: 37993046 DOI: 10.1016/j.envres.2023.117717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/23/2023] [Accepted: 11/15/2023] [Indexed: 11/24/2023]
Abstract
Understanding the behavior and potential toxicity of copper nanoparticles (nano-Cu) in the aquatic environment is a primary way to assess their environmental risks. In this study, RNA-seq was performed on three different tissues (gills, intestines, and muscles) of zebrafish exposed to nano-Cu, to explore the potential toxic mechanism of nano-Cu on zebrafish. The results indicated that the toxic mechanism of nano-Cu on zebrafish was tissue-specific. Nano-Cu enables the CB1 receptor of the presynaptic membrane of gill cells to affect short-term synaptic plasticity or long-term synaptic changes (ECB-LTD) through DSI and DSE, causing dysfunction of intercellular signal transmission. Imbalance of de novo synthesis of UMP in intestinal cells and its transformation to UDP, UTP, uridine, and uracil, resulted in many functions involved in the pyrimidine metabolic pathway being blocked. Meanwhile, the toxicity of nano-Cu caused abnormal expression of RAD51 gene in muscle cells, which affects the repair of damaged DNA through Fanconi anemia and homologous recombination pathway, thus causing cell cycle disorder. These results provide insights for us to better understand the differences in toxicity of nano-Cu on zebrafish tissues and are helpful for a comprehensive assessment of nano-Cu's effects on aquatic organisms.
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Affiliation(s)
- Haiqiang Liu
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China; College of Life and Environmental Sciences, Minzu University of China, Beijing 100081, China; Key Laboratory of Mass Spectrometry Imaging and Metabolomics (State Ethnic Affairs Commission), Centre for Imaging & Systems Biology, Minzu University of China, Beijing, 100081, China
| | - Yanli Xu
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
| | - Yuqiong Sun
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
| | - Haodi Wu
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China
| | - Jing Hou
- MOE Key Laboratory of Resources and Environmental Systems Optimization, College of Environmental Science and Engineering, North China Electric Power University, Beijing, 102206, China.
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Wynen F, Krautstrunk J, Müller LM, Graf V, Brinkmann V, Fritz G. Cisplatin-induced DNA crosslinks trigger neurotoxicity in C. elegans. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119591. [PMID: 37730131 DOI: 10.1016/j.bbamcr.2023.119591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 09/14/2023] [Accepted: 09/14/2023] [Indexed: 09/22/2023]
Abstract
The anticancer drug cisplatin (CisPt) injures post-mitotic neuronal cells, leading to neuropathy. Furthermore, CisPt triggers cell death in replicating cells. Here, we aim to unravel the relevance of different types of CisPt-induced DNA lesions for evoking neurotoxicity. To this end, we comparatively analyzed wild-type and loss of function mutants of C. elegans lacking key players of specific DNA repair pathways. Deficiency in ercc-1, which is essential for nucleotide excision repair (NER) and interstrand crosslink (ICL) repair, revealed the most pronounced enhancement in CisPt-induced neurotoxicity with respect to the functionality of post-mitotic chemosensory AWA neurons, without inducing neuronal cell death. Potentiation of CisPt-triggered neurotoxicity in ercc-1 mutants was accompanied by complex alterations in both basal and CisPt-stimulated mRNA expression of genes involved in the regulation of neurotransmission, including cat-4, tph-1, mod-1, glr-1, unc-30 and eat-18. Moreover, xpf-1, csb-1, csb-1;xpc-1 and msh-6 mutants were significantly more sensitive to CisPt-induced neurotoxicity than the wild-type, whereas xpc-1, msh-2, brc-1 and dog-1 mutants did not distinguish from the wild-type. The majority of DNA repair mutants also revealed increased basal germline apoptosis, which was analyzed for control. Yet, only xpc-1, xpc-1;csb-1 and dog-1 mutants showed elevated apoptosis in the germline following CisPt treatment. To conclude, we provide evidence that neurotoxicity, including sensory neurotoxicity, is triggered by CisPt-induced DNA intra- and interstrand crosslinks that are subject of repair by NER and ICL repair. We hypothesize that especially ERCC1/XPF, CSB and MSH6-related DNA repair protects from chemotherapy-induced neuropathy in the context of CisPt-based anticancer therapy.
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Affiliation(s)
- Fabian Wynen
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Johannes Krautstrunk
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Lisa Marie Müller
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Viktoria Graf
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany
| | - Vanessa Brinkmann
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany.
| | - Gerhard Fritz
- Heinrich Heine University Düsseldorf, Medical Faculty, Institute of Toxicology, Moorenstraße 5, 40225 Düsseldorf, Germany.
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Association between ERCC1 Gene Polymorphism (rs11615) and Colorectal Cancer Susceptibility: A Meta-Analysis of Medical Image Fusion and Safety Applications. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:9988513. [PMID: 36277013 PMCID: PMC9586779 DOI: 10.1155/2022/9988513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 09/19/2022] [Accepted: 09/24/2022] [Indexed: 11/29/2022]
Abstract
Colorectal cancer (CRC) is a malignant tumor of the colorectal mucosa epithelial tissue transformed. The fusion of data for medical imaging has become a central issue in such biomedical applications as image-guided surgery and radiotherapy. Currently, CRC has been one of the most threatening tumors affecting people's health worldwide. The excision repair cross-complementation group 1 (ERCC1) is a key enzyme for nucleotide excision repair (NER). Emerging epidemiological studies have indicated that the presence of colorectal cancer (CRC) may be relevant to the ERCC1 rs11615 genetic polymorphism. However, the results of ERCC1 rs11615 on CRC in these studies are controversial. We searched PubMed, Web of Science, Embase, CNKI, and CBM databases for the effects of ERCC1 rs11615 variant on CRC development. There was no meta-analysis focused on the diagnosis of colorectal cancer with ERCC1 rs11615 variant. We creatively carried out a meta-analysis of nine case-control studies and used Stata (version 12.0) software to integrate the pooled odds ratios (ORs) corresponding to a 95% confidence interval (CI) of overall and subgroup analysis. Our results suggest that a significant correlation was observed between rs11615 and the susceptibility of CRC OR 95% CI = 1.13 (1.04-1.23) under an allele genetic model and OR 95% CI = 1.14 (1.01-1.30) under a dominant genetic model for overall CRC. Significant statistical difference was also noted in Asians rather than Caucasians based on the ethnicity subgroups. These results suggested that there is a certain association between rs11615 and the susceptibility of colorectal cancer in the Asian populations.
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7
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Zhang X, Yin M, Hu J. Nucleotide excision repair: a versatile and smart toolkit. Acta Biochim Biophys Sin (Shanghai) 2022; 54:807-819. [PMID: 35975604 PMCID: PMC9828404 DOI: 10.3724/abbs.2022054] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Nucleotide excision repair (NER) is a major pathway to deal with bulky adducts induced by various environmental toxins in all cellular organisms. The two sub-pathways of NER, global genome repair (GGR) and transcription-coupled repair (TCR), differ in the damage recognition modes. In this review, we describe the molecular mechanism of NER in mammalian cells, especially the details of damage recognition steps in both sub-pathways. We also introduce new sequencing methods for genome-wide mapping of NER, as well as recent advances about NER in chromatin by these methods. Finally, the roles of NER factors in repairing oxidative damages and resolving R-loops are discussed.
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Affiliation(s)
| | | | - Jinchuan Hu
- Correspondence address. Tel: +86-21-54237702; E-mail:
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8
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Weilbeer C, Jay D, Donnelly JC, Gentile F, Karimi-Busheri F, Yang X, Mani RS, Yu Y, Elmenoufy AH, Barakat KH, Tuszynski JA, Weinfeld M, West FG. Modulation of ERCC1-XPF Heterodimerization Inhibition via Structural Modification of Small Molecule Inhibitor Side-Chains. Front Oncol 2022; 12:819172. [PMID: 35372043 PMCID: PMC8968952 DOI: 10.3389/fonc.2022.819172] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
Inhibition of DNA repair enzymes is an attractive target for increasing the efficacy of DNA damaging chemotherapies. The ERCC1-XPF heterodimer is a key endonuclease in numerous single and double strand break repair processes, and inhibition of the heterodimerization has previously been shown to sensitize cancer cells to DNA damage. In this work, the previously reported ERCC1-XPF inhibitor 4 was used as the starting point for an in silico study of further modifications of the piperazine side-chain. A selection of the best scoring hits from the in silico screen were synthesized using a late stage functionalization strategy which should allow for further iterations of this class of inhibitors to be readily synthesized. Of the synthesized compounds, compound 6 performed the best in the in vitro fluorescence based endonuclease assay. The success of compound 6 in inhibiting ERCC1-XPF endonuclease activity in vitro translated well to cell-based assays investigating the inhibition of nucleotide excision repair and disruption of heterodimerization. Subsequently compound 6 was shown to sensitize HCT-116 cancer cells to treatment with UVC, cyclophosphamide, and ionizing radiation. This work serves as an important step towards the synergistic use of DNA repair inhibitors with chemotherapeutic drugs.
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Affiliation(s)
- Claudia Weilbeer
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - David Jay
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - James C. Donnelly
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | | | | | - Xiaoyan Yang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - Rajam S. Mani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - Yaping Yu
- Centre for Genome Engineering, University of Calgary, Calgary, AB, Canada
| | - Ahmed H. Elmenoufy
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Pharmaceutical Chemistry, College of Pharmacy, Misr University for Science and Technology, 6th of October City, Egypt
| | - Khaled H. Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Jack A. Tuszynski
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
- Department of Physics, University of Alberta, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Michael Weinfeld
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Michael Weinfeld, ; Frederick G. West,
| | - Frederick G. West
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Michael Weinfeld, ; Frederick G. West,
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Huang D, Chowdhury S, Wang H, Savage SR, Ivey RG, Kennedy JJ, Whiteaker JR, Lin C, Hou X, Oberg AL, Larson MC, Eskandari N, Delisi DA, Gentile S, Huntoon CJ, Voytovich UJ, Shire ZJ, Yu Q, Gygi SP, Hoofnagle AN, Herbert ZT, Lorentzen TD, Calinawan A, Karnitz LM, Weroha SJ, Kaufmann SH, Zhang B, Wang P, Birrer MJ, Paulovich AG. Multiomic analysis identifies CPT1A as a potential therapeutic target in platinum-refractory, high-grade serous ovarian cancer. Cell Rep Med 2021; 2:100471. [PMID: 35028612 PMCID: PMC8714940 DOI: 10.1016/j.xcrm.2021.100471] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 09/24/2021] [Accepted: 11/19/2021] [Indexed: 12/14/2022]
Abstract
Resistance to platinum compounds is a major determinant of patient survival in high-grade serous ovarian cancer (HGSOC). To understand mechanisms of platinum resistance and identify potential therapeutic targets in resistant HGSOC, we generated a data resource composed of dynamic (±carboplatin) protein, post-translational modification, and RNA sequencing (RNA-seq) profiles from intra-patient cell line pairs derived from 3 HGSOC patients before and after acquiring platinum resistance. These profiles reveal extensive responses to carboplatin that differ between sensitive and resistant cells. Higher fatty acid oxidation (FAO) pathway expression is associated with platinum resistance, and both pharmacologic inhibition and CRISPR knockout of carnitine palmitoyltransferase 1A (CPT1A), which represents a rate limiting step of FAO, sensitize HGSOC cells to platinum. The results are further validated in patient-derived xenograft models, indicating that CPT1A is a candidate therapeutic target to overcome platinum resistance. All multiomic data can be queried via an intuitive gene-query user interface (https://sites.google.com/view/ptrc-cell-line).
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Affiliation(s)
- Dongqing Huang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Hong Wang
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Sara R. Savage
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard G. Ivey
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xiaonan Hou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ann L. Oberg
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Melissa C. Larson
- Department of Quantitative Health Sciences, Division of Clinical Trials and Biostatistics, Mayo Clinic, Rochester, MN 55905, USA
| | - Najmeh Eskandari
- Division of Hematology and Oncology, Department of Medicine, University of Illinois, Chicago, IL 60612, USA
| | - Davide A. Delisi
- Division of Hematology and Oncology, Department of Medicine, University of Illinois, Chicago, IL 60612, USA
| | - Saverio Gentile
- Division of Hematology and Oncology, Department of Medicine, University of Illinois, Chicago, IL 60612, USA
| | | | - Uliana J. Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Zahra J. Shire
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Qing Yu
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Steven P. Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Andrew N. Hoofnagle
- Department of Lab Medicine, University of Washington, Seattle, WA 98195, USA
| | - Zachary T. Herbert
- Molecular Biology Core Facilities, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Travis D. Lorentzen
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - S. John Weroha
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Michael J. Birrer
- University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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10
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Murashko MM, Stasevich EM, Schwartz AM, Kuprash DV, Uvarova AN, Demin DE. The Role of RNA in DNA Breaks, Repair and Chromosomal Rearrangements. Biomolecules 2021; 11:biom11040550. [PMID: 33918762 PMCID: PMC8069526 DOI: 10.3390/biom11040550] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 03/31/2021] [Accepted: 04/07/2021] [Indexed: 12/28/2022] Open
Abstract
Incorrect reparation of DNA double-strand breaks (DSB) leading to chromosomal rearrangements is one of oncogenesis's primary causes. Recently published data elucidate the key role of various types of RNA in DSB formation, recognition and repair. With growing interest in RNA biology, increasing RNAs are classified as crucial at the different stages of the main pathways of DSB repair in eukaryotic cells: nonhomologous end joining (NHEJ) and homology-directed repair (HDR). Gene mutations or variation in expression levels of such RNAs can lead to local DNA repair defects, increasing the chromosome aberration frequency. Moreover, it was demonstrated that some RNAs could stimulate long-range chromosomal rearrangements. In this review, we discuss recent evidence demonstrating the role of various RNAs in DSB formation and repair. We also consider how RNA may mediate certain chromosomal rearrangements in a sequence-specific manner.
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Affiliation(s)
- Matvey Mikhailovich Murashko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Ekaterina Mikhailovna Stasevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Anton Markovich Schwartz
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
- Moscow Institute of Physics and Technology, Department of Molecular and Biological Physics, 141701 Moscow, Russia
| | - Dmitriy Vladimirovich Kuprash
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Aksinya Nicolaevna Uvarova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
| | - Denis Eriksonovich Demin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia; (M.M.M.); (E.M.S.); (A.M.S.); (D.V.K.); (A.N.U.)
- Correspondence:
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11
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de Almeida LC, Calil FA, Machado-Neto JA, Costa-Lotufo LV. DNA damaging agents and DNA repair: From carcinogenesis to cancer therapy. Cancer Genet 2021; 252-253:6-24. [DOI: 10.1016/j.cancergen.2020.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/30/2020] [Accepted: 12/02/2020] [Indexed: 02/09/2023]
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12
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Yousefzadeh M, Henpita C, Vyas R, Soto-Palma C, Robbins P, Niedernhofer L. DNA damage-how and why we age? eLife 2021; 10:62852. [PMID: 33512317 PMCID: PMC7846274 DOI: 10.7554/elife.62852] [Citation(s) in RCA: 184] [Impact Index Per Article: 61.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 01/15/2021] [Indexed: 12/16/2022] Open
Abstract
Aging is a complex process that results in loss of the ability to reattain homeostasis following stress, leading, thereby, to increased risk of morbidity and mortality. Many factors contribute to aging, such as the time-dependent accumulation of macromolecular damage, including DNA damage. The integrity of the nuclear genome is essential for cellular, tissue, and organismal health. DNA damage is a constant threat because nucleic acids are chemically unstable under physiological conditions and vulnerable to attack by endogenous and environmental factors. To combat this, all organisms possess highly conserved mechanisms to detect and repair DNA damage. Persistent DNA damage (genotoxic stress) triggers signaling cascades that drive cells into apoptosis or senescence to avoid replicating a damaged genome. The drawback is that these cancer avoidance mechanisms promote aging. Here, we review evidence that DNA damage plays a causal role in aging. We also provide evidence that genotoxic stress is linked to other cellular processes implicated as drivers of aging, including mitochondrial and metabolic dysfunction, altered proteostasis and inflammation. These links between damage to the genetic code and other pillars of aging support the notion that DNA damage could be the root of aging.
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Affiliation(s)
- Matt Yousefzadeh
- Institute on the Biology of Aging and Metabolism Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Chathurika Henpita
- Institute on the Biology of Aging and Metabolism Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Rajesh Vyas
- Institute on the Biology of Aging and Metabolism Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Carolina Soto-Palma
- Institute on the Biology of Aging and Metabolism Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Paul Robbins
- Institute on the Biology of Aging and Metabolism Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
| | - Laura Niedernhofer
- Institute on the Biology of Aging and Metabolism Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, United States
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13
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Schweer D, McCorkle JR, Rohr J, Tsodikov OV, Ueland F, Kolesar J. Mithramycin and Analogs for Overcoming Cisplatin Resistance in Ovarian Cancer. Biomedicines 2021; 9:70. [PMID: 33445667 PMCID: PMC7828137 DOI: 10.3390/biomedicines9010070] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 12/12/2022] Open
Abstract
Ovarian cancer is a highly deadly malignancy in which recurrence is considered incurable. Resistance to platinum-based chemotherapy bodes a particularly abysmal prognosis, underscoring the need for novel therapeutic agents and strategies. The use of mithramycin, an antineoplastic antibiotic, has been previously limited by its narrow therapeutic window. Recent advances in semisynthetic methods have led to mithramycin analogs with improved pharmacological profiles. Mithramycin inhibits the activity of the transcription factor Sp1, which is closely linked with ovarian tumorigenesis and platinum-resistance. This article summarizes recent clinical developments related to mithramycin and postulates a role for the use of mithramycin, or its analog, in the treatment of platinum-resistant ovarian cancer.
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Affiliation(s)
- David Schweer
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Lexington, University of Kentucky Markey Cancer Center, Lexington, KY 40536, USA; (D.S.); (F.U.)
| | - J. Robert McCorkle
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA; (J.R.M.); (J.R.); (O.V.T.)
| | - Jurgen Rohr
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA; (J.R.M.); (J.R.); (O.V.T.)
| | - Oleg V. Tsodikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536, USA; (J.R.M.); (J.R.); (O.V.T.)
| | - Frederick Ueland
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Lexington, University of Kentucky Markey Cancer Center, Lexington, KY 40536, USA; (D.S.); (F.U.)
| | - Jill Kolesar
- Department of Obstetrics and Gynecology, Division of Gynecologic Oncology Lexington, University of Kentucky Markey Cancer Center, Lexington, KY 40536, USA; (D.S.); (F.U.)
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14
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DNA polymerase ι compensates for Fanconi anemia pathway deficiency by countering DNA replication stress. Proc Natl Acad Sci U S A 2020; 117:33436-33445. [PMID: 33376220 DOI: 10.1073/pnas.2008821117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Fanconi anemia (FA) is caused by defects in cellular responses to DNA crosslinking damage and replication stress. Given the constant occurrence of endogenous DNA damage and replication fork stress, it is unclear why complete deletion of FA genes does not have a major impact on cell proliferation and germ-line FA patients are able to progress through development well into their adulthood. To identify potential cellular mechanisms that compensate for the FA deficiency, we performed dropout screens in FA mutant cells with a whole genome guide RNA library. This uncovered a comprehensive genome-wide profile of FA pathway synthetic lethality, including POLI and CDK4 As little is known of the cellular function of DNA polymerase iota (Pol ι), we focused on its role in the loss-of-function FA knockout mutants. Loss of both FA pathway function and Pol ι leads to synthetic defects in cell proliferation and cell survival, and an increase in DNA damage accumulation. Furthermore, FA-deficient cells depend on the function of Pol ι to resume replication upon replication fork stalling. Our results reveal a critical role for Pol ι in DNA repair and replication fork restart and suggest Pol ι as a target for therapeutic intervention in malignancies carrying an FA gene mutation.
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15
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Patterson-Fortin J, D'Andrea AD. Exploiting the Microhomology-Mediated End-Joining Pathway in Cancer Therapy. Cancer Res 2020; 80:4593-4600. [PMID: 32651257 PMCID: PMC7641946 DOI: 10.1158/0008-5472.can-20-1672] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 06/13/2020] [Accepted: 07/07/2020] [Indexed: 01/16/2023]
Abstract
Repair of DNA double-strand breaks (DSB) is performed by two major pathways, homology-dependent repair and classical nonhomologous end-joining. Recent studies have identified a third pathway, microhomology-mediated end-joining (MMEJ). MMEJ has similarities to homology-dependent repair, in that repair is initiated with end resection, leading to single-stranded 3' ends, which require microhomology upstream and downstream of the DSB. Importantly, the MMEJ pathway is commonly upregulated in cancers, especially in homologous recombination-deficient cancers, which display a distinctive mutational signature. Here, we review the molecular process of MMEJ as well as new targets and approaches exploiting the MMEJ pathway in cancer therapy.
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Affiliation(s)
| | - Alan D D'Andrea
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts.
- Center for DNA Damage and Repair, Dana-Farber Cancer Institute, Boston, Massachusetts
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16
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Sabatella M, Pines A, Slyskova J, Vermeulen W, Lans H. ERCC1-XPF targeting to psoralen-DNA crosslinks depends on XPA and FANCD2. Cell Mol Life Sci 2020; 77:2005-2016. [PMID: 31392348 PMCID: PMC7228994 DOI: 10.1007/s00018-019-03264-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 07/19/2019] [Accepted: 07/31/2019] [Indexed: 01/02/2023]
Abstract
The effectiveness of many DNA-damaging chemotherapeutic drugs depends on their ability to form monoadducts, intrastrand crosslinks and/or interstrand crosslinks (ICLs) that interfere with transcription and replication. The ERCC1-XPF endonuclease plays a critical role in removal of these lesions by incising DNA either as part of nucleotide excision repair (NER) or interstrand crosslink repair (ICLR). Engagement of ERCC1-XPF in NER is well characterized and is facilitated by binding to the XPA protein. However, ERCC1-XPF recruitment to ICLs is less well understood. Moreover, specific mutations in XPF have been found to disrupt its function in ICLR but not in NER, but whether this involves differences in lesion targeting is unknown. Here, we imaged GFP-tagged ERCC1, XPF and ICLR-defective XPF mutants to investigate how in human cells ERCC1-XPF is localized to different types of psoralen-induced DNA lesions, repaired by either NER or ICLR. Our results confirm its dependence on XPA in NER and furthermore show that its engagement in ICLR is dependent on FANCD2. Interestingly, we find that two ICLR-defective XPF mutants (R689S and S786F) are less well recruited to ICLs. These studies highlight the differential mechanisms that regulate ERCC1-XPF activity in DNA repair.
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Affiliation(s)
- Mariangela Sabatella
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Alex Pines
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
| | - Jana Slyskova
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands
- CeMM Research Centre for Molecular Medicine of the Austrian Academy of Sciences, 1090, Vienna, Austria
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands.
- Oncode Institute, Erasmus MC, 3015 GE, Rotterdam, The Netherlands.
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC, 3015 GE, Rotterdam, The Netherlands.
- Oncode Institute, Erasmus MC, 3015 GE, Rotterdam, The Netherlands.
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17
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Liu W, Palovcak A, Li F, Zafar A, Yuan F, Zhang Y. Fanconi anemia pathway as a prospective target for cancer intervention. Cell Biosci 2020; 10:39. [PMID: 32190289 PMCID: PMC7075017 DOI: 10.1186/s13578-020-00401-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fanconi anemia (FA) is a recessive genetic disorder caused by biallelic mutations in at least one of 22 FA genes. Beyond its pathological presentation of bone marrow failure and congenital abnormalities, FA is associated with chromosomal abnormality and genomic instability, and thus represents a genetic vulnerability for cancer predisposition. The cancer relevance of the FA pathway is further established with the pervasive occurrence of FA gene alterations in somatic cancers and observations of FA pathway activation-associated chemotherapy resistance. In this article we describe the role of the FA pathway in canonical interstrand crosslink (ICL) repair and possible contributions of FA gene alterations to cancer development. We also discuss the perspectives and potential of targeting the FA pathway for cancer intervention.
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Affiliation(s)
- Wenjun Liu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Anna Palovcak
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fang Li
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Alyan Zafar
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fenghua Yuan
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Yanbin Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
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18
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Abstract
Exposure to arsenic in contaminated drinking water is an emerging public health problem that impacts more than 200 million people worldwide. Accumulating lines of evidence from epidemiological studies revealed that chronic exposure to arsenic can result in various human diseases including cancer, type 2 diabetes, and neurodegenerative disorders. Arsenic is also classified as a Group I human carcinogen. In this review, we survey extensively different modes of action for arsenic-induced carcinogenesis, with focus being placed on arsenic-mediated impairment of DNA repair pathways. Inorganic arsenic can be bioactivated by methylation, and the ensuing products are highly genotoxic. Bioactivation of arsenicals also elicits the production of reactive oxygen and nitrogen species (ROS and RNS), which can directly damage DNA and modify cysteine residues in proteins. Results from recent studies suggest zinc finger proteins as crucial molecular targets for direct binding to As3+ or for modifications by arsenic-induced ROS/RNS, which may constitute a common mechanism underlying arsenic-induced perturbations of DNA repair.
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19
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Mukherjee A, Vasquez KM. Targeting Chromosomal Architectural HMGB Proteins Could Be the Next Frontier in Cancer Therapy. Cancer Res 2020; 80:2075-2082. [PMID: 32152151 DOI: 10.1158/0008-5472.can-19-3066] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/24/2020] [Accepted: 03/04/2020] [Indexed: 12/18/2022]
Abstract
Chromatin-associated architectural proteins are part of a fundamental support system for cellular DNA-dependent processes and can maintain/modulate the efficiency of DNA replication, transcription, and DNA repair. Interestingly, prognostic outcomes of many cancer types have been linked with the expression levels of several of these architectural proteins. The high mobility group box (HMGB) architectural protein family has been well studied in this regard. The differential expression levels of HMGB proteins and/or mRNAs and their implications in cancer etiology and prognosis present the potential of novel targets that can be explored to increase the efficacy of existing cancer therapies. HMGB1, the most studied member of the HMGB protein family, has pleiotropic roles in cells including an association with nucleotide excision repair, base excision repair, mismatch repair, and DNA double-strand break repair. Moreover, the HMGB proteins have been identified in regulating DNA damage responses and cell survival following treatment with DNA-damaging agents and, as such, may play roles in modulating the efficacy of chemotherapeutic drugs by modulating DNA repair pathways. Here, we discuss the functions of HMGB proteins in DNA damage processing and their potential roles in cancer etiology, prognosis, and therapeutics.
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Affiliation(s)
- Anirban Mukherjee
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, Texas
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, Austin, Texas.
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20
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Abstract
Gel electrophoresis of DNA is one of the most frequently used techniques in molecular biology. Typically, it is used in the following: the analysis of in vitro reactions and purification of DNA fragments, analysis of PCR reactions, characterization of enzymes involved in DNA reactions, and sequencing. With some ingenuity gel electrophoresis of DNA is also used for the analysis of cellular biochemical reactions. For example, DNA breaks that accumulate in cells are analyzed by the comet assay and pulsed-field gel electrophoresis (PFGE). Furthermore, DNA replication intermediates are analyzed with two-dimensional (2D) gel electrophoresis. Moreover, several new methods for analyzing various chromosomal functions in cells have been developed. In this chapter, a brief introduction to these is given.
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Affiliation(s)
- Katsuhiro Hanada
- Clinical Engineering Research Center, Faculty of Medicine, Oita University, Yufu, Oita, Japan.
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21
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Swift LP, Castle L, McHugh PJ. Analysis of DNA Interstrand Cross-Links and their Repair by Modified Comet Assay. Methods Mol Biol 2020; 2119:79-88. [PMID: 31989516 DOI: 10.1007/978-1-0716-0323-9_7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
DNA interstrand cross-links (ICLs) are an extremely toxic form of DNA damage that cells experience upon exposure to natural metabolites. Moreover, ICLs are cytotoxic lesions produced by a range of clinically important anticancer agents. Therefore, improving our understanding of ICL induction and processing has important implications in biology and medicine. The sensitive detection of ICLs in mammalian cells is challenging but has been aided by the development of a modified form of the single-cell gel electrophoresis (SCGE) assay, also known as the "comet assay." Here we describe this method and how it can be used to sensitively monitor the induction and removal of ICLs in single mammalian cells.
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Affiliation(s)
- Lonnie P Swift
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
| | - Lianne Castle
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Peter J McHugh
- Department of Oncology, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.
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22
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Gaur V, Ziajko W, Nirwal S, Szlachcic A, Gapińska M, Nowotny M. Recognition and processing of branched DNA substrates by Slx1-Slx4 nuclease. Nucleic Acids Res 2019; 47:11681-11690. [PMID: 31584081 PMCID: PMC6902002 DOI: 10.1093/nar/gkz842] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 09/16/2019] [Accepted: 10/01/2019] [Indexed: 12/11/2022] Open
Abstract
Structure-selective endonucleases cleave branched DNA substrates. Slx1 is unique among structure-selective nucleases because it can cleave all branched DNA structures at multiple sites near the branch point. The mechanism behind this broad range of activity is unknown. The present study structurally and biochemically investigated fungal Slx1 to define a new protein interface that binds the non-cleaved arm of branched DNAs. The DNA arm bound at this new site was positioned at a sharp angle relative to the arm that was modeled to interact with the active site, implying that Slx1 uses DNA bending to localize the branch point as a flexible discontinuity in DNA. DNA binding at the new interface promoted a disorder-order transition in a region of the protein that was located in the vicinity of the active site, potentially participating in its formation. This appears to be a safety mechanism that ensures that DNA cleavage occurs only when the new interface is occupied by the non-cleaved DNA arm. Models of Slx1 that interacted with various branched DNA substrates were prepared. These models explain the way in which Slx1 cuts DNA toward the 3' end away from the branch point and elucidate the unique ability of Slx1 to cleave various DNA structures.
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Affiliation(s)
- Vineet Gaur
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland
| | - Weronika Ziajko
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland
| | - Shivlee Nirwal
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland
| | - Aleksandra Szlachcic
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland
| | - Marta Gapińska
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland
| | - Marcin Nowotny
- Laboratory of Protein Structure, International Institute of Molecular and Cell Biology, 4 Trojdena St., 02-109 Warsaw, Poland
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23
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Slyskova J, Sabatella M, Ribeiro-Silva C, Stok C, Theil AF, Vermeulen W, Lans H. Base and nucleotide excision repair facilitate resolution of platinum drugs-induced transcription blockage. Nucleic Acids Res 2019; 46:9537-9549. [PMID: 30137419 PMCID: PMC6182164 DOI: 10.1093/nar/gky764] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/20/2018] [Indexed: 12/21/2022] Open
Abstract
Sensitivity and resistance of cells to platinum drug chemotherapy are to a large extent determined by activity of the DNA damage response (DDR). Combining chemotherapy with inhibition of specific DDR pathways could therefore improve treatment efficacy. Multiple DDR pathways have been implicated in removal of platinum-DNA lesions, but it is unclear which exact pathways are most important to cellular platinum drug resistance. Here, we used CRISPR/Cas9 screening to identify DDR proteins that protect colorectal cancer cells against the clinically applied platinum drug oxaliplatin. We find that besides the expected homologous recombination, Fanconi anemia and translesion synthesis pathways, in particular also transcription-coupled nucleotide excision repair (TC-NER) and base excision repair (BER) protect against platinum-induced cytotoxicity. Both repair pathways are required to overcome oxaliplatin- and cisplatin-induced transcription arrest. In addition to the generation of DNA crosslinks, exposure to platinum drugs leads to reactive oxygen species production that induces oxidative DNA lesions, explaining the requirement for BER. Our findings highlight the importance of transcriptional integrity in cells exposed to platinum drugs and suggest that both TC-NER and BER should be considered as targets for novel combinatorial treatment strategies.
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Affiliation(s)
- Jana Slyskova
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Mariangela Sabatella
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Colin Stok
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- Oncode Institute, Erasmus MC, Erasmus University Medical Center Rotterdam, 3000 CA Rotterdam, The Netherlands
- To whom correspondence should be addressed. Tel: +31 10 7038169; Fax: +31 10 7044743;
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24
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Buzon B, Grainger R, Huang S, Rzadki C, Junop MS. Structure-specific endonuclease activity of SNM1A enables processing of a DNA interstrand crosslink. Nucleic Acids Res 2019; 46:9057-9066. [PMID: 30165656 PMCID: PMC6158701 DOI: 10.1093/nar/gky759] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 08/20/2018] [Indexed: 01/09/2023] Open
Abstract
DNA interstrand crosslinks (ICLs) covalently join opposing strands, blocking both replication and transcription, therefore making ICL-inducing compounds highly toxic and ideal anti-cancer agents. While incisions surrounding the ICL are required to remove damaged DNA, it is currently unclear which endonucleases are needed for this key event. SNM1A has been shown to play an important function in human ICL repair, however its suggested role has been limited to exonuclease activity and not strand incision. Here we show that SNM1A has endonuclease activity, having the ability to cleave DNA structures that arise during the initiation of ICL repair. In particular, this endonuclease activity cleaves single-stranded DNA. Given that unpaired DNA regions occur 5′ to an ICL, these findings suggest SNM1A may act as either an endonuclease and/or exonuclease during ICL repair. This finding is significant as it expands the potential role of SNM1A in ICL repair.
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Affiliation(s)
- Beverlee Buzon
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster, University, Hamilton, Ontario L8N 3Z5, Canada.,Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Ryan Grainger
- Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada
| | - Simon Huang
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster, University, Hamilton, Ontario L8N 3Z5, Canada
| | - Cameron Rzadki
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster, University, Hamilton, Ontario L8N 3Z5, Canada
| | - Murray S Junop
- Department of Biochemistry and Biomedical Sciences, Faculty of Health Sciences, McMaster, University, Hamilton, Ontario L8N 3Z5, Canada.,Department of Biochemistry, Schulich School of Medicine & Dentistry, Western University, London, Ontario N6A 5C1, Canada
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25
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Guyon-Debast A, Rossetti P, Charlot F, Epert A, Neuhaus JM, Schaefer DG, Nogué F. The XPF-ERCC1 Complex Is Essential for Genome Stability and Is Involved in the Mechanism of Gene Targeting in Physcomitrella patens. FRONTIERS IN PLANT SCIENCE 2019; 10:588. [PMID: 31143199 PMCID: PMC6521618 DOI: 10.3389/fpls.2019.00588] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/18/2019] [Indexed: 06/09/2023]
Abstract
The XPF-ERCC1 complex, a highly conserved structure-specific endonuclease, functions in multiple DNA repair pathways that are pivotal for maintaining genome stability, including nucleotide excision repair, interstrand crosslink repair, and homologous recombination. XPF-ERCC1 incises double-stranded DNA at double-strand/single-strand junctions, making it an ideal enzyme for processing DNA structures that contain partially unwound strands. Here, we have examined the role of the XPF-ERCC1 complex in the model bryophyte Physcomitrella patens which exhibits uniquely high gene targeting frequencies. We undertook targeted knockout of the Physcomitrella ERCC1 and XPF genes. Mutant analysis shows that the endonuclease complex is essential for resistance to UV-B and to the alkylating agent MMS, and contributes to the maintenance of genome integrity but is also involved in gene targeting in this model plant. Using different constructs we determine whether the function of the XPF-ERCC1 endonuclease complex in gene targeting was removal of 3' non-homologous termini, similar to SSA, or processing of looped-out heteroduplex intermediates. Interestingly, our data suggest a role of the endonuclease in both pathways and have implications for the mechanism of targeted gene replacement in plants and its specificities compared to yeast and mammalian cells.
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Affiliation(s)
- Anouchka Guyon-Debast
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Patricia Rossetti
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Florence Charlot
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Aline Epert
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
| | - Jean-Marc Neuhaus
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Didier G. Schaefer
- Laboratoire de Biologie Moléculaire et Cellulaire, Institut de Biologie, Université de Neuchâtel, Neuchâtel, Switzerland
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Versailles, France
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26
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Huang J, Zhang J, Bellani MA, Pokharel D, Gichimu J, James RC, Gali H, Ling C, Yan Z, Xu D, Chen J, Meetei AR, Li L, Wang W, Seidman MM. Remodeling of Interstrand Crosslink Proximal Replisomes Is Dependent on ATR, FANCM, and FANCD2. Cell Rep 2019; 27:1794-1808.e5. [PMID: 31067464 PMCID: PMC6676478 DOI: 10.1016/j.celrep.2019.04.032] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 12/19/2018] [Accepted: 04/04/2019] [Indexed: 11/23/2022] Open
Abstract
Eukaryotic replisomes are driven by the mini chromosome maintenance (MCM [M]) helicase complex, an offset ring locked around the template for leading strand synthesis by CDC45 (C) and GINS (G) proteins. Although the CDC45 MCM GINS (CMG) structure implies that interstrand crosslinks (ICLs) are absolute blocks to replisomes, recent studies indicate that cells can restart DNA synthesis on the side of the ICL distal to the initial encounter. Here, we report that restart requires ATR and is promoted by FANCD2 and phosphorylated FANCM. Following introduction of genomic ICLs and dependent on ATR and FANCD2 but not on the Fanconi anemia core proteins or FAAP24, FANCM binds the replisome complex, with concomitant release of the GINS proteins. In situ analysis of replisomes proximal to ICLs confirms the ATR-dependent release of GINS proteins while CDC45 is retained on the remodeled replisome. The results demonstrate the plasticity of CMG composition in response to replication stress.
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Affiliation(s)
- Jing Huang
- Institute of Chemical Biology and Nanomedicine, State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Biology, Hunan University, Changsha 410082, China.
| | - Jing Zhang
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA
| | - Marina A Bellani
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA
| | - Durga Pokharel
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA
| | - Julia Gichimu
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA
| | - Ryan C James
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA
| | - Himabindu Gali
- Department of Pharmacology & Experimental Therapeutics and Medicine, Boston University School of Medicine, 72 East Concord St., K-712D, Boston, MA 02118-2526
| | - Chen Ling
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA
| | - Zhijiang Yan
- Institute of DNA Repair Diseases, School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, China
| | - Dongyi Xu
- Peking University, Beijing 100871, China
| | - Junjie Chen
- Department Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77225-0334, USA
| | - Amom Ruhikanta Meetei
- Division of Experimental Hematology and Cancer Biology and Cancer & Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH 45229, USA
| | - Lei Li
- Department Experimental Radiation Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77225-0334, USA
| | - Weidong Wang
- Laboratory of Genetics and Genomics, National Institute on Aging, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA
| | - Michael M Seidman
- Laboratory of Molecular Gerontology, National Institute on Aging, NIH, 251 Bayview Blvd., Baltimore, MD 21224, USA.
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27
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Dorn A, Feller L, Castri D, Röhrig S, Enderle J, Herrmann NJ, Block-Schmidt A, Trapp O, Köhler L, Puchta H. An Arabidopsis FANCJ helicase homologue is required for DNA crosslink repair and rDNA repeat stability. PLoS Genet 2019; 15:e1008174. [PMID: 31120885 PMCID: PMC6550410 DOI: 10.1371/journal.pgen.1008174] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 06/05/2019] [Accepted: 05/03/2019] [Indexed: 11/18/2022] Open
Abstract
Proteins of the Fanconi Anemia (FA) complementation group are required for crosslink (CL) repair in humans and their loss leads to severe pathological phenotypes. Here we characterize a homolog of the Fe-S cluster helicase FANCJ in the model plant Arabidopsis, AtFANCJB, and show that it is involved in interstrand CL repair. It acts at a presumably early step in concert with the nuclease FAN1 but independently of the nuclease AtMUS81, and is epistatic to both error-prone and error-free post-replicative repair in Arabidopsis. The simultaneous knock out of FANCJB and the Fe-S cluster helicase RTEL1 leads to induced cell death in root meristems, indicating an important role of the enzymes in replicative DNA repair. Surprisingly, we found that AtFANCJB is involved in safeguarding rDNA stability in plants. In the absence of AtRTEL1 and AtFANCJB, we detected a synergetic reduction to about one third of the original number of 45S rDNA copies. It is tempting to speculate that the detected rDNA instability might be due to deficiencies in G-quadruplex structure resolution and might thus contribute to pathological phenotypes of certain human genetic diseases.
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Affiliation(s)
- Annika Dorn
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Laura Feller
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Dominique Castri
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sarah Röhrig
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Janina Enderle
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Natalie J. Herrmann
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Astrid Block-Schmidt
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Oliver Trapp
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Laura Köhler
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Holger Puchta
- Botanical Institute, Molecular Biology and Biochemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
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28
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JMJD2 promotes acquired cisplatin resistance in non-small cell lung carcinoma cells. Oncogene 2019; 38:5643-5657. [PMID: 30967636 DOI: 10.1038/s41388-019-0814-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 02/19/2019] [Accepted: 03/23/2019] [Indexed: 12/11/2022]
Abstract
Platinum-based drugs such as cisplatin (CP) are the first-line chemotherapy for non-small-cell lung carcinoma (NSCLC). Unfortunately, NSCLC has a low response rate to CP and acquired resistance always occurs. Histone methylation regulates chromatin structure and is implicated in DNA repair. We hypothesize histone methylation regulators are involved in CP resistance. We therefore screened gene expression of known histone methyltransferases and demethylases in three NSCLC cell lines with or without acquired resistance to CP. JMJD2s are a family of histone demethylases that remove tri-methyl groups from H3K9 and H3K36. We found expression of several JMJD2 family genes upregulated in CP-resistant cells, with JMJD2B expression being upregulated in all three CP-resistant NSCLC cell lines. Further analysis showed increased JMJD2 protein expression coincided with decreased H3K9me3 and H3K36me3. Chemical inhibitors of JMJD2-family proteins increased H3K9me3 and H3K36me3 levels and sensitized resistant cells to CP. Mechanistic studies showed that JMJD2 inhibition decreased chromatin association of ATR and Chk1 and inhibited the ATR-Chk1 replication checkpoint. Our results reveal that JMJD2 demethylases are potential therapeutic targets to overcome CP resistance in NSCLC.
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29
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Faridounnia M, Folkers GE, Boelens R. Function and Interactions of ERCC1-XPF in DNA Damage Response. Molecules 2018; 23:E3205. [PMID: 30563071 PMCID: PMC6320978 DOI: 10.3390/molecules23123205] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/27/2018] [Accepted: 12/01/2018] [Indexed: 12/28/2022] Open
Abstract
Numerous proteins are involved in the multiple pathways of the DNA damage response network and play a key role to protect the genome from the wide variety of damages that can occur to DNA. An example of this is the structure-specific endonuclease ERCC1-XPF. This heterodimeric complex is in particular involved in nucleotide excision repair (NER), but also in double strand break repair and interstrand cross-link repair pathways. Here we review the function of ERCC1-XPF in various DNA repair pathways and discuss human disorders associated with ERCC1-XPF deficiency. We also overview our molecular and structural understanding of XPF-ERCC1.
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Affiliation(s)
- Maryam Faridounnia
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Gert E Folkers
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
| | - Rolf Boelens
- Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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30
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Sharma K, Darvas M, Keene CD, Niedernhofer LJ, Ladiges W. Modeling Alzheimer's disease in progeria mice. An age-related concept. PATHOBIOLOGY OF AGING & AGE RELATED DISEASES 2018; 8:1524815. [PMID: 30319737 PMCID: PMC6179061 DOI: 10.1080/20010001.2018.1524815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The prevalence of Alzheimer’s disease (AD) is expected to dramatically increase in older people worldwide. Efforts to find disease-modifying treatments have been largely unsuccessful because of the focus on disease-specific pathogenesis, and lack of animal models to study AD in the context of aging and age-related co-morbidities. The geroscience approach to studying AD would suggest that modulation of aging per se would be a useful strategy, but a mammalian model system that combines both aging and AD is not available. One approach to study old age and AD is to utilize murine models of progeroid syndrome, which can provide a number of advantages not only for basic aging biology but also for preclinical drug testing. A progeria background, such as the Ercc1 mutant mouse (Ercc1−/Δ), provides an aging component not seen in current murine models of AD that lack age-related co-morbidities typical of AD patients. Ercc1−/Δ mice experience the same types of stochastic endogenous DNA damage as WT mice, but accumulate lesions faster due to impaired DNA repair, which accelerates the normal aging process by 6-fold. These mice do not show frank AD pathology but represent a predisposed or hypersensitive environment for AD pathology, where pathogenic elements of AD can be introduced, either by crossing with well-established AD transgenic mouse lines, or transcranial stereotaxic delivery directly into the brain. Since Ercc1−/Δ mice age five to six times faster than WT mice, very rapid characterization and testing of therapeutic interventions is possible. Studies are urgently needed to capitalize on the highly informative potential of this novel AD mouse model.
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Affiliation(s)
- Kavita Sharma
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA, USA
| | - Martin Darvas
- Department of Pathology, Division of Neuropathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - C Dirk Keene
- Department of Pathology, Division of Neuropathology, School of Medicine, University of Washington, Seattle, WA, USA
| | - Laura J Niedernhofer
- Institute on the Biology of Aging and Metabolism, Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN, USA
| | - Warren Ladiges
- Department of Comparative Medicine, School of Medicine, University of Washington, Seattle, WA, USA
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31
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Sabatella M, Theil AF, Ribeiro-Silva C, Slyskova J, Thijssen K, Voskamp C, Lans H, Vermeulen W. Repair protein persistence at DNA lesions characterizes XPF defect with Cockayne syndrome features. Nucleic Acids Res 2018; 46:9563-9577. [PMID: 30165384 PMCID: PMC6182131 DOI: 10.1093/nar/gky774] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 07/19/2018] [Accepted: 08/16/2018] [Indexed: 12/28/2022] Open
Abstract
The structure-specific ERCC1-XPF endonuclease plays a key role in DNA damage excision by nucleotide excision repair (NER) and interstrand crosslink repair. Mutations in this complex can either cause xeroderma pigmentosum (XP) or XP combined with Cockayne syndrome (XPCS-complex) or Fanconi anemia. However, most patients carry compound heterozygous mutations, which confounds the dissection of the phenotypic consequences for each of the identified XPF alleles. Here, we analyzed the functional impact of individual pathogenic XPF alleles on NER. We show that XP-causing mutations diminish XPF recruitment to DNA damage and only mildly affect global genome NER. In contrast, an XPCS-complex-specific mutation causes persistent recruitment of XPF and the upstream core NER machinery to DNA damage and severely impairs both global genome and transcription-coupled NER. Remarkably, persistence of NER factors at DNA damage appears to be a common feature of XPCS-complex cells, suggesting that this could be a determining factor contributing to the development of additional developmental and/or neurodegenerative features in XP patients.
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Affiliation(s)
- Mariangela Sabatella
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Arjan F Theil
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Cristina Ribeiro-Silva
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Jana Slyskova
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Karen Thijssen
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Chantal Voskamp
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Hannes Lans
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
| | - Wim Vermeulen
- Department of Molecular Genetics, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
- Oncode Institute, Erasmus MC, University Erasmus Medical Center Rotterdam, 3000 CA, The Netherlands
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32
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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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33
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Czerwińska J, Nowak M, Wojtczak P, Dziuban-Lech D, Cieśla JM, Kołata D, Gajewska B, Barańczyk-Kuźma A, Robinson AR, Shane HL, Gregg SQ, Rigatti LH, Yousefzadeh MJ, Gurkar AU, McGowan SJ, Kosicki K, Bednarek M, Zarakowska E, Gackowski D, Oliński R, Speina E, Niedernhofer LJ, Tudek B. ERCC1-deficient cells and mice are hypersensitive to lipid peroxidation. Free Radic Biol Med 2018; 124:79-96. [PMID: 29860127 PMCID: PMC6098728 DOI: 10.1016/j.freeradbiomed.2018.05.088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/28/2018] [Accepted: 05/29/2018] [Indexed: 01/01/2023]
Abstract
Lipid peroxidation (LPO) products are relatively stable and abundant metabolites, which accumulate in tissues of mammals with aging, being able to modify all cellular nucleophiles, creating protein and DNA adducts including crosslinks. Here, we used cells and mice deficient in the ERCC1-XPF endonuclease required for nucleotide excision repair and the repair of DNA interstrand crosslinks to ask if specifically LPO-induced DNA damage contributes to loss of cell and tissue homeostasis. Ercc1-/- mouse embryonic fibroblasts were more sensitive than wild-type (WT) cells to the LPO products: 4-hydroxy-2-nonenal (HNE), crotonaldehyde and malondialdehyde. ERCC1-XPF hypomorphic mice were hypersensitive to CCl4 and a diet rich in polyunsaturated fatty acids, two potent inducers of endogenous LPO. To gain insight into the mechanism of how LPO influences DNA repair-deficient cells, we measured the impact of the major endogenous LPO product, HNE, on WT and Ercc1-/- cells. HNE inhibited proliferation, stimulated ROS and LPO formation, induced DNA base damage, strand breaks, error-prone translesion DNA synthesis and cellular senescence much more potently in Ercc1-/- cells than in DNA repair-competent control cells. HNE also deregulated base excision repair and energy production pathways. Our observations that ERCC1-deficient cells and mice are hypersensitive to LPO implicates LPO-induced DNA damage in contributing to cellular demise and tissue degeneration, notably even when the source of LPO is dietary polyunsaturated fats.
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Affiliation(s)
- Jolanta Czerwińska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Małgorzata Nowak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Patrycja Wojtczak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Dorota Dziuban-Lech
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Jarosław M Cieśla
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Daria Kołata
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Beata Gajewska
- Department of Biochemistry, Medical University of Warsaw, Warsaw, Poland.
| | | | - Andria R Robinson
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Hillary L Shane
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Siobhán Q Gregg
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA; Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
| | - Lora H Rigatti
- University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA.
| | - Matthew J Yousefzadeh
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Aditi U Gurkar
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Sara J McGowan
- Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Konrad Kosicki
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Małgorzata Bednarek
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
| | - Ewelina Zarakowska
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
| | - Daniel Gackowski
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
| | - Ryszard Oliński
- Department of Clinical Biochemistry, Faculty of Pharmacy, Collegium Medicum, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland.
| | - Elżbieta Speina
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.
| | - Laura J Niedernhofer
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA; University of Pittsburgh Medical Center Hillman Cancer Center, Pittsburgh, PA, USA; Department of Molecular Medicine, Center on Aging, The Scripps Research Institute, Jupiter, FL, USA.
| | - Barbara Tudek
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland; Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.
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34
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Liu JL, Huang WS, Lee KC, Tung SY, Chen CN, Chang SF. Effect of 5-fluorouracil on excision repair cross-complementing 1 expression and consequent cytotoxicity regulation in human gastric cancer cells. J Cell Biochem 2018; 119:8472-8480. [PMID: 30011079 DOI: 10.1002/jcb.27073] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 04/26/2018] [Indexed: 11/11/2022]
Abstract
Gastric cancer is the third leading cause of cancer mortality all over the world. The combination therapy of surgery with chemotherapy, that is, 5-fluorouracil (5-FU) and platinum-containing anticancer drugs, is becoming a current clinical strategy for patients with gastric cancer because of the lower curative rate and higher cancer recurrence rate of patients treated with only surgery. However, the development of drug resistance in cancer cells is still the most challenge in clinical chemotherapy. Excision repair cross-complementing 1 (ERCC1), an essential member of nucleotide excision repair system, recently has been suggested to be a predictive biomarker of treatment evaluation and might affect the outcomes of chemotherapy. Thus, this study was aimed to investigate whether ERCC1 expression could be regulated, and its role in gastric cancer cells treated with 5-FU and the underlying mechanism. Human AGS gastric cancer cells were used in this study. It was shown that ERCC1 expression could be upregulated in AGS cells treated with 5-FU and this upregulation could subsequently attenuate the cytotoxicity of 5-FU in AGS cells. Moreover, 5-FU-upregulated ERCC1 expression was regulated by extracellular signal-regulated kinase (ERK) 1/2 and p38 signaling through activating the transcription factor c-jun/activator protein (AP)-1. These results indicated the role of ERCC1 in the development of drug resistance to 5-FU in AGS cells. The mechanism elucidation concerning the ERK1/2 and p38 kinases and transcription factor c-jun/AP-1 might contribute another idea to the development of chemotherapy strategy for the gastric cancers in the future.
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Affiliation(s)
- Jing-Lan Liu
- Department of Pathology, Chang Gung Memorial Hospital Chiayi Branch, Chiayi, Taiwan
| | - Wen-Shih Huang
- Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Division of Colon and Rectal Surgery, Department of Surgery, Chang Gung Memorial Hospital, Chiayi, Taiwan
| | - Ko-Chao Lee
- Department of Colorectal Surgery, Department of Surgery, Chang Gung Memorial Hospital, Kaohsiung Medical Center, Kaohsiung, Taiwan
| | - Shui-Yi Tung
- Department of Hepato-Gastroenterology, Chang Gung Memorial Hospital Chiayi Branch, Chiayi, Taiwan.,Chang Gung University College of Medicine, Taoyuan, Taiwan
| | - Cheng-Nan Chen
- Department of Biochemical Science and Technology, National Chiayi University, Chiayi, Taiwan
| | - Shun-Fu Chang
- Department of Medical Research and Development, Chang Gung Memorial Hospital Chiayi Branch, Chiayi, Taiwan
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35
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Distinct roles of XPF-ERCC1 and Rad1-Rad10-Saw1 in replication-coupled and uncoupled inter-strand crosslink repair. Nat Commun 2018; 9:2025. [PMID: 29795289 PMCID: PMC5966407 DOI: 10.1038/s41467-018-04327-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 04/20/2018] [Indexed: 01/17/2023] Open
Abstract
Yeast Rad1-Rad10 (XPF-ERCC1 in mammals) incises UV, oxidation, and cross-linking agent-induced DNA lesions, and contributes to multiple DNA repair pathways. To determine how Rad1-Rad10 catalyzes inter-strand crosslink repair (ICLR), we examined sensitivity to ICLs from yeast deleted for SAW1 and SLX4, which encode proteins that interact physically with Rad1-Rad10 and bind stalled replication forks. Saw1, Slx1, and Slx4 are critical for replication-coupled ICLR in mus81 deficient cells. Two rad1 mutations that disrupt interactions between Rpa1 and Rad1-Rad10 selectively disable non-nucleotide excision repair (NER) function, but retain UV lesion repair. Mutations in the analogous region of XPF also compromised XPF interactions with Rpa1 and Slx4, and are proficient in NER but deficient in ICLR and direct repeat recombination. We propose that Rad1-Rad10 makes distinct contributions to ICLR depending on cell cycle phase: in G1, Rad1-Rad10 removes ICL via NER, whereas in S/G2, Rad1-Rad10 facilitates NER-independent replication-coupled ICLR.
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36
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Kuo MS, Adam J, Dorvault N, Robin A, Friboulet L, Soria JC, Olaussen KA. A novel antibody-based approach to detect the functional ERCC1-202 isoform. DNA Repair (Amst) 2018; 64:34-44. [PMID: 29482102 DOI: 10.1016/j.dnarep.2018.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 10/26/2017] [Accepted: 02/06/2018] [Indexed: 12/16/2022]
Abstract
ERCC1/XPF endonuclease plays an important role in multiple DNA repair pathways and stands as a potential prognostic and predictive biomarker for cisplatin-based chemotherapy. Four distinct ERCC1 isoforms arising from alternative splicing have been described (201, 202, 203 and 204) but only the 202 isoform is functional in DNA excision repair, when interacting with its obligate partner XPF. Currently, there is no tool to assess specifically the expression of ERCC1-202 due to high sequence homology between the four isoforms. Here, we generated monoclonal antibodies directed against the heterodimer of ERCC1 and its obligate interacting partner XPF by genetic immunization. We obtained three monoclonal antibodies (2C11, 7C3 and 10D10) recognizing specifically the heterodimer ERCC1-202/XPF as well as the ERCC1-204/XPF with no affinity to ERCC1 or XPF monomers. By combining one of these three heterodimer-specific antibodies with a commercial anti-ERCC1 antibody (clone 4F9) unable to recognize the 204 isoform in a proximity ligation assay (PLA), we managed to specifically detect the functional ERCC1-202 isoform. This methodological breakthrough can constitute a basis for the development of clinical tests to evaluate ERCC1 functional proficiency.
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Affiliation(s)
- Mei-Shiue Kuo
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Julien Adam
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Nicolas Dorvault
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Angélique Robin
- UF de Pharmacologie Biologie, Saint Louis Hopital, Institut de Génétique Moléculaire, 75010, Paris, France
| | - Luc Friboulet
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France
| | - Jean-Charles Soria
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France; Gustave Roussy, Université Paris-Saclay, Drug Development Department (DITEP), 94805, Villejuif, France
| | - Ken A Olaussen
- INSERM U981, Gustave Roussy, 94805, Villejuif, France; Faculté de médecine, Université Paris-Sud, 94270, Kremlin-Bicêtre, France.
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37
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Tian Y, Shen X, Wang R, Klages-Mundt NL, Lynn EJ, Martin SK, Ye Y, Gao M, Chen J, Schlacher K, Li L. Constitutive role of the Fanconi anemia D2 gene in the replication stress response. J Biol Chem 2017; 292:20184-20195. [PMID: 29021208 DOI: 10.1074/jbc.m117.814780] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/29/2017] [Indexed: 12/12/2022] Open
Abstract
In response to DNA cross-linking damage, the Fanconi anemia (FA) core complex activates the FA pathway by monoubiquitinating Fanconi anemia complementation group D2 (FANCD2) for the initiation of the nucleolytic processing of the DNA cross-links and stabilization of stalled replication forks. Given that all the classic FA proteins coordinately monoubiquitinate FANCD2, it is unclear why losses of individual classic FA genes yield varying cellular sensitivities to cross-linking damage. To address this question, we generated cellular knock-out models of FA core complex components and FANCD2 and found that FANCD2-null mutants display higher levels of spontaneous chromosomal damage and hypersensitivity to replication-blocking lesions than Fanconi anemia complementation group L (FANCL)-null mutants, suggesting that FANCD2 provides a basal level of DNA protection countering endogenous lesions in the absence of monoubiquitination. FANCD2's ubiquitination-independent function is likely involved in optimized recruitment of nucleolytic activities for the processing and protection of stressed replication forks. Our results reveal that FANCD2 has a ubiquitination-independent role in countering endogenous levels of replication stress, a function that is critical for the maintenance of genomic stability.
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Affiliation(s)
- Yanyan Tian
- Departments of Experimental Radiation Biology, Houston, Texas 77030
| | - Xi Shen
- Departments of Experimental Radiation Biology, Houston, Texas 77030
| | - Rui Wang
- Departments of Experimental Radiation Biology, Houston, Texas 77030
| | - Naeh L Klages-Mundt
- Departments of Experimental Radiation Biology, Houston, Texas 77030; Programs in Genetics and Epigenetics, Houston, Texas 77030
| | - Erica J Lynn
- Departments of Experimental Radiation Biology, Houston, Texas 77030
| | - Sara K Martin
- Departments of Experimental Radiation Biology, Houston, Texas 77030; Programs in Genetics and Epigenetics, Houston, Texas 77030
| | - Yin Ye
- Departments of Experimental Radiation Biology, Houston, Texas 77030
| | - Min Gao
- Departments of Experimental Radiation Biology, Houston, Texas 77030
| | - Junjie Chen
- Departments of Experimental Radiation Biology, Houston, Texas 77030; Programs in Genetics and Epigenetics, Houston, Texas 77030
| | - Katharina Schlacher
- Cancer Biology, University of Texas M. D. Anderson Cancer Center, Houston, Texas 77030; Cancer Biology, M. D. Anderson Cancer Center University of Texas Health Graduate School of Biomedical Sciences, Houston, Texas 77030
| | - Lei Li
- Departments of Experimental Radiation Biology, Houston, Texas 77030; Programs in Genetics and Epigenetics, Houston, Texas 77030.
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38
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39
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Jiang J, Bellani M, Li L, Wang P, Seidman MM, Wang Y. Arsenite Binds to the RING Finger Domain of FANCL E3 Ubiquitin Ligase and Inhibits DNA Interstrand Crosslink Repair. ACS Chem Biol 2017; 12:1858-1866. [PMID: 28535027 DOI: 10.1021/acschembio.6b01135] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Human exposure to arsenic in drinking water is known to be associated with the development of bladder, lung, kidney, and skin cancers. The molecular mechanisms underlying the carcinogenic effects of arsenic species remain incompletely understood. DNA interstrand cross-links (ICLs) are among the most cytotoxic type of DNA lesions that block DNA replication and transcription, and these lesions can be induced by endogenous metabolism and by exposure to exogenous agents. Fanconi anemia (FA) is a congenital disorder manifested with elevated sensitivity toward DNA interstrand cross-linking agents, and monoubiquitination of FANCD2 by FANCL is a crucial step in FA-mediated DNA repair. Here, we demonstrated that As3+ could bind to the PHD/RING finger domain of FANCL in vitro and in cells. This binding led to compromised ubiquitination of FANCD2 in cells and diminished recruitment of FANCD2 to chromatin and DNA damage sites induced by 4,5',8-trimethylpsoralen plus UVA irradiation. Furthermore, clonogenic survival assay results showed that arsenite coexposure rendered cells more sensitive toward DNA interstrand cross-linking agents. Together, our study suggested that arsenite may compromise genomic stability via perturbation of the Fanconi anemia pathway, thereby conferring its carcinogenic effect.
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Affiliation(s)
| | - Marina Bellani
- Laboratory
of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
| | | | | | - Michael M. Seidman
- Laboratory
of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224, United States
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40
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Abdullah UB, McGouran JF, Brolih S, Ptchelkine D, El-Sagheer AH, Brown T, McHugh PJ. RPA activates the XPF-ERCC1 endonuclease to initiate processing of DNA interstrand crosslinks. EMBO J 2017; 36:2047-2060. [PMID: 28607004 PMCID: PMC5510000 DOI: 10.15252/embj.201796664] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 04/13/2017] [Accepted: 05/19/2017] [Indexed: 12/11/2022] Open
Abstract
During replication-coupled DNA interstrand crosslink (ICL) repair, the XPF-ERCC1 endonuclease is required for the incisions that release, or "unhook", ICLs, but the mechanism of ICL unhooking remains largely unknown. Incisions are triggered when the nascent leading strand of a replication fork strikes the ICL Here, we report that while purified XPF-ERCC1 incises simple ICL-containing model replication fork structures, the presence of a nascent leading strand, modelling the effects of replication arrest, inhibits this activity. Strikingly, the addition of the single-stranded DNA (ssDNA)-binding replication protein A (RPA) selectively restores XPF-ERCC1 endonuclease activity on this structure. The 5'-3' exonuclease SNM1A can load from the XPF-ERCC1-RPA-induced incisions and digest past the crosslink to quantitatively complete the unhooking reaction. We postulate that these collaborative activities of XPF-ERCC1, RPA and SNM1A might explain how ICL unhooking is achieved in vivo.
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Affiliation(s)
- Ummi B Abdullah
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Sanja Brolih
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Denis Ptchelkine
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK.,Research Complex at Harwell, Rutherford Appleton Laboratory, Oxford, UK
| | | | - Tom Brown
- Department of Chemistry, University of Oxford, Oxford, UK.,Department of Oncology, University of Oxford, Oxford, UK
| | - Peter J McHugh
- Department of Oncology, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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41
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Woodrick J, Gupta S, Camacho S, Parvathaneni S, Choudhury S, Cheema A, Bai Y, Khatkar P, Erkizan HV, Sami F, Su Y, Schärer OD, Sharma S, Roy R. A new sub-pathway of long-patch base excision repair involving 5' gap formation. EMBO J 2017; 36:1605-1622. [PMID: 28373211 DOI: 10.15252/embj.201694920] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 02/21/2017] [Accepted: 03/09/2017] [Indexed: 02/06/2023] Open
Abstract
Base excision repair (BER) is one of the most frequently used cellular DNA repair mechanisms and modulates many human pathophysiological conditions related to DNA damage. Through live cell and in vitro reconstitution experiments, we have discovered a major sub-pathway of conventional long-patch BER that involves formation of a 9-nucleotide gap 5' to the lesion. This new sub-pathway is mediated by RECQ1 DNA helicase and ERCC1-XPF endonuclease in cooperation with PARP1 poly(ADP-ribose) polymerase and RPA The novel gap formation step is employed during repair of a variety of DNA lesions, including oxidative and alkylation damage. Moreover, RECQ1 regulates PARP1 auto-(ADP-ribosyl)ation and the choice between long-patch and single-nucleotide BER, thereby modulating cellular sensitivity to DNA damage. Based on these results, we propose a revised model of long-patch BER and a new key regulation point for pathway choice in BER.
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Affiliation(s)
- Jordan Woodrick
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Suhani Gupta
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Sharon Camacho
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Swetha Parvathaneni
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC, USA
| | - Sujata Choudhury
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Amrita Cheema
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Yi Bai
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Pooja Khatkar
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Hayriye Verda Erkizan
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Furqan Sami
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC, USA
| | - Yan Su
- Department of Pharmacological Sciences & Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Orlando D Schärer
- Department of Pharmacological Sciences & Department of Chemistry, Stony Brook University, Stony Brook, NY, USA
| | - Sudha Sharma
- Department of Biochemistry and Molecular Biology, College of Medicine, Howard University, Washington, DC, USA
| | - Rabindra Roy
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
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42
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Yang Z, Nejad MI, Varela JG, Price NE, Wang Y, Gates KS. A role for the base excision repair enzyme NEIL3 in replication-dependent repair of interstrand DNA cross-links derived from psoralen and abasic sites. DNA Repair (Amst) 2017; 52:1-11. [PMID: 28262582 PMCID: PMC5424475 DOI: 10.1016/j.dnarep.2017.02.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2017] [Accepted: 02/13/2017] [Indexed: 12/23/2022]
Abstract
Interstrand DNA-DNA cross-links are highly toxic lesions that are important in medicinal chemistry, toxicology, and endogenous biology. In current models of replication-dependent repair, stalling of a replication fork activates the Fanconi anemia pathway and cross-links are "unhooked" by the action of structure-specific endonucleases such as XPF-ERCC1 that make incisions flanking the cross-link. This process generates a double-strand break, which must be subsequently repaired by homologous recombination. Recent work provided evidence for a new, incision-independent unhooking mechanism involving intrusion of a base excision repair (BER) enzyme, NEIL3, into the world of cross-link repair. The evidence suggests that the glycosylase action of NEIL3 unhooks interstrand cross-links derived from an abasic site or the psoralen derivative trioxsalen. If the incision-independent NEIL3 pathway is blocked, repair reverts to the incision-dependent route. In light of the new model invoking participation of NEIL3 in cross-link repair, we consider the possibility that various BER glycosylases or other DNA-processing enzymes might participate in the unhooking of chemically diverse interstrand DNA cross-links.
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Affiliation(s)
- Zhiyu Yang
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Maryam Imani Nejad
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Jacqueline Gamboa Varela
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States
| | - Nathan E Price
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Yinsheng Wang
- University of California-Riverside, Department of Chemistry, 501 Big Springs Road Riverside, CA 92521-0403, United States
| | - Kent S Gates
- University of Missouri Department of Chemistry, 125 Chemistry Building Columbia, MO 65211, United States; University of Missouri Department of Biochemistry, 125 Chemistry Building Columbia, MO 65211, United States.
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43
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Palovcak A, Liu W, Yuan F, Zhang Y. Maintenance of genome stability by Fanconi anemia proteins. Cell Biosci 2017; 7:8. [PMID: 28239445 PMCID: PMC5320776 DOI: 10.1186/s13578-016-0134-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 12/07/2016] [Indexed: 12/20/2022] Open
Abstract
Persistent dysregulation of the DNA damage response and repair in cells causes genomic instability. The resulting genetic changes permit alterations in growth and proliferation observed in virtually all cancers. However, an unstable genome can serve as a double-edged sword by providing survival advantages in the ability to evade checkpoint signaling, but also creating vulnerabilities through dependency on alternative genomic maintenance factors. The Fanconi anemia pathway comprises an intricate network of DNA damage signaling and repair that are critical for protection against genomic instability. The importance of this pathway is underlined by the severity of the cancer predisposing syndrome Fanconi anemia which can be caused by biallelic mutations in any one of the 21 genes known thus far. This review delineates the roles of the Fanconi anemia pathway and the molecular actions of Fanconi anemia proteins in confronting replicative, oxidative, and mitotic stress.
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Affiliation(s)
- Anna Palovcak
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Wenjun Liu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fenghua Yuan
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Yanbin Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
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44
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Wan J, Chao L, Lee AC, Chen Q. Higher Expression of ERCC1 May Be Associated with Resistance to Adjuvant Platinum-Based Chemotherapy in Gastric Cancer. Cancer Invest 2017; 35:85-91. [PMID: 28102711 DOI: 10.1080/07357907.2016.1267741] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Potential predictive biomarker(s) to respond to chemotherapy in gastric cancer are unclear. Excision repair cross-complementing 1 (ERCC1), a DNA repair enzyme, is associated with clinical outcomes in gastric cancer. Here, we investigated the expression of ERCC1 in gastric cancer with platinum-based chemotherapy after surgery, and the association between ERCC1 expression and clinical parameters was analyzed. Our data showed that high levels of ERCC1 expression were positively associated with resistance to platinum-based chemotherapy but not with lymph node metastasis and pathological stage. In addition, patients with resistance to platinum-based chemotherapy probably had lymph node metastasis and pathological stage.
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Affiliation(s)
- Jiayi Wan
- a Department of Pathology , Wuxi No. 2 People's Hospital, Nanjing Medical University , Wuxi , China
| | - Lin Chao
- b Department of General Surgery , Wuxi No. 2 People's Hospital, Nanjing Medical University , Wuxi , China
| | - Arier C Lee
- c Section of Epidemiology and Biostatistics, School of Population Health , The University of Auckland , Auckland , New Zealand
| | - Qi Chen
- d The Hospital of Obstetrics & Gynaecology , Fudan University , Shanghai , China.,e Department of Obstetrics & Gynaecology , The University of Auckland , Auckland , New Zealand
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45
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Zhang Q, Shi J, Yuan F, Wang H, Fu W, Pan J, Huang Y, Yu J, Yang J, Chen Z. Higher expression of XPF is a critical factor in intrinsic chemotherapy resistance of human renal cell carcinoma. Int J Cancer 2016; 139:2827-2837. [PMID: 27542841 DOI: 10.1002/ijc.30396] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 07/26/2016] [Accepted: 08/08/2016] [Indexed: 02/03/2023]
Abstract
Human renal cancer is extremely resistant to chemotherapy and radiation therapy. This clinical characteristic reduces the efficacy of chemotherapeutic agents in the treatment of recurrence or metastasis following surgical resection. Understanding the mechanism of chemotherapy resistance in renal cell carcinoma remains a significant challenge. In this study, we have shown that varied level of XPF expression was organ-tissue specific by comparing human renal cancer, bladder cancer, testicular cancer and their normal tissue counterparts, respectively. The expression of XPF was significantly higher in renal cancer than in bladder cancer and testicular cancer and correlated with the clinical characteristic of their chemotherapeutics sensitivity. These novel findings proposed that the intrinsic chemoresistance of human renal cell carcinomas might be derived from the high level of XPF expression. In a panel of five cancer cell lines, decreasing cisplatin sensitivity correlated with increasing levels of XPF expression. Knockdown of XPF expression not only increased sensitivity of renal carcinoma cells to cisplatin treatment by affecting the DNA damage response, including DNA repair, cell cycle regulation and apoptosis, but also increased senescence of renal cancer cell. Furthermore, experiment in vivo confirmed that silenced XPF significantly increased the sensitivity and survival following treatment with cisplatin in xenograft mice bearing renal cell tumor. These findings firstly uncover a partial mechanism of intrinsic chemoresistance in renal cancer and may provide a new approach to break through the obstacle of intrinsic chemoresistance by targeting the XPF protein with a potential new inhibitor.
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Affiliation(s)
- Qiao Zhang
- Department of Cell Biology, The Third Military Medical University, Chongqing, China
| | - Jiazhong Shi
- Department of Cell Biology, The Third Military Medical University, Chongqing, China
| | - Fang Yuan
- Department of Urology, Chongqing Oncology Hospital, Chongqing, China
| | - Huanhuan Wang
- Department of Cell Biology, The Third Military Medical University, Chongqing, China
| | - Weihua Fu
- Urology Institute of PLA, Southwest Hospital, The Third Military Medical University, Chongqing, China
| | - Jinhong Pan
- Urology Institute of PLA, Southwest Hospital, The Third Military Medical University, Chongqing, China
| | - Yaqin Huang
- Department of Cell Biology, The Third Military Medical University, Chongqing, China
| | - Jin Yu
- Department of Cell Biology, The Third Military Medical University, Chongqing, China
| | - Jin Yang
- Department of Cell Biology, The Third Military Medical University, Chongqing, China.
| | - Zhiwen Chen
- Urology Institute of PLA, Southwest Hospital, The Third Military Medical University, Chongqing, China. .,Southwest Cancer Center, Southwest Hospital, The Third Military Medical University, Chongqing, China.
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46
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Lambert MW. Nuclear alpha spectrin: Critical roles in DNA interstrand cross-link repair and genomic stability. Exp Biol Med (Maywood) 2016; 241:1621-38. [PMID: 27480253 PMCID: PMC4999628 DOI: 10.1177/1535370216662714] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Non-erythroid alpha spectrin (αIISp) is a structural protein which we have shown is present in the nucleus of human cells. It interacts with a number of nuclear proteins such as actin, lamin, emerin, chromatin remodeling factors, and DNA repair proteins. αIISp's interaction with DNA repair proteins has been extensively studied. We have demonstrated that nuclear αIISp is critical in DNA interstrand cross-link (ICL) repair in S phase, in both genomic (non-telomeric) and telomeric DNA, and in maintenance of genomic stability following ICL damage to DNA. We have proposed that αIISp acts as a scaffold aiding to recruit repair proteins to sites of damage. This involvement of αIISp in ICL repair and telomere maintenance after ICL damage represents new and critical functions for αIISp. These studies have led to development of a model for the role of αIISp in DNA ICL repair. They have been aided by examination of cells from patients with Fanconi anemia (FA), a repair-deficient genetic disorder in which a deficiency in αIISp leads to defective ICL repair in genomic and telomeric DNA, telomere dysfunction, and chromosome instability following DNA ICL damage. We have shown that loss of αIISp in FA cells is due to increased breakdown by the protease, µ-calpain. Importantly, we have demonstrated that this deficiency can be corrected by knockdown of µ-calpain and restoring αIISp levels to normal. This corrects a number of the phenotypic deficiencies in FA after ICL damage. These studies suggest a new and unexplored direction for therapeutically restoring genomic stability in FA cells and for correcting numerous phenotypic deficiencies occurring after ICL damage. Developing a more in-depth understanding of the importance of the interaction of αIISp with other nuclear proteins could significantly enhance our knowledge of the consequences of loss of αIISp on critical nuclear processes.
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Affiliation(s)
- Muriel W Lambert
- Department of Pathology and Laboratory Medicine, New Jersey Medical School, Rutgers, The State University of New Jersey, Newark, NJ 07103, USA
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47
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The functional status of DNA repair pathways determines the sensitization effect to cisplatin in non-small cell lung cancer cells. Cell Oncol (Dordr) 2016; 39:511-522. [PMID: 27473273 DOI: 10.1007/s13402-016-0291-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2016] [Indexed: 12/29/2022] Open
Abstract
PURPOSE Cisplatin can cause a variety of DNA crosslink lesions including intra-strand and inter-strand crosslinks (ICLs), which are associated with the sensitivity of cancer cells to cisplatin. Here, we aimed to assess the contribution of the Fanconi anemia (FA), homologous recombination (HR) and nucleotide excision repair (NER) pathways to cisplatin resistance in non-small cell lung cancer (NSCLC)-derived cells. METHODS The expression of FA, HR and NER pathway-associated genes was assessed by RT-qPCR and Western blotting. siRNAs were used to knock down the expression of these genes. CCK-8 and flow cytometry assays were used to assess the viability and apoptotic rate of NSCLC-derived cells, respectively. Immunofluorescence and alkaline comet assays were used to assess the repair of ICLs. RESULTS We found that acquired cisplatin-resistant NSCLC-derived A549/DR cells exhibited markedly enhanced FA and HR repair pathway capacities compared to its parental A549 cells and another independent NSCLC-derived cell line, Calu-1, which possesses a moderate innate resistance to cisplatin. siRNA-mediated silencing of the FA-associated genes FANCL and RAD18 and the HR-associated genes BRCA1 and BRCA2 significantly potentiated the sensitivity of A549/DR cells to cisplatin compared to A549 and Calu-1 cells, suggesting that the acquired cisplatin resistance in A549/DR cells may be attributed to enhanced FA and HR pathway capacities responsible for ICL repair. Although we found that expression knockdown of the NER-associated genes XPA and ERCC1 sensitized the three NSCLC-derived cell lines to cisplatin, the sensitization effect was more significant in Calu-1 cells than in A549 and A549/DR cells, implying that the innate cisplatin resistance in Calu-1 cells may result from an increased NER activity. CONCLUSIONS Our results indicate that the functional status of DNA repair pathways determine the sensitivity of NSCLC cells to cisplatin. Direct targeting of the pathway that is involved in cisplatin resistance may be an effective strategy to surmount cisplatin resistance in NSCLC.
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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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Fanconi anemia cells with unrepaired DNA damage activate components of the checkpoint recovery process. Theor Biol Med Model 2015; 12:19. [PMID: 26385365 PMCID: PMC4575447 DOI: 10.1186/s12976-015-0011-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 08/12/2015] [Indexed: 12/30/2022] Open
Abstract
Background The FA/BRCA pathway repairs DNA interstrand crosslinks. Mutations in this pathway cause Fanconi anemia (FA), a chromosome instability syndrome with bone marrow failure and cancer predisposition. Upon DNA damage, normal and FA cells inhibit the cell cycle progression, until the G2/M checkpoint is turned off by the checkpoint recovery, which becomes activated when the DNA damage has been repaired. Interestingly, highly damaged FA cells seem to override the G2/M checkpoint. In this study we explored with a Boolean network model and key experiments whether checkpoint recovery activation occurs in FA cells with extensive unrepaired DNA damage. Methods We performed synchronous/asynchronous simulations of the FA/BRCA pathway Boolean network model. FA-A and normal lymphoblastoid cell lines were used to study checkpoint and checkpoint recovery activation after DNA damage induction. The experimental approach included flow cytometry cell cycle analysis, cell division tracking, chromosome aberration analysis and gene expression analysis through qRT-PCR and western blot. Results Computational simulations suggested that in FA mutants checkpoint recovery activity inhibits the checkpoint components despite unrepaired DNA damage, a behavior that we did not observed in wild-type simulations. This result implies that FA cells would eventually reenter the cell cycle after a DNA damage induced G2/M checkpoint arrest, but before the damage has been fixed. We observed that FA-A cells activate the G2/M checkpoint and arrest in G2 phase, but eventually reach mitosis and divide with unrepaired DNA damage, thus resolving the initial checkpoint arrest. Based on our model result we look for ectopic activity of checkpoint recovery components. We found that checkpoint recovery components, such as PLK1, are expressed to a similar extent as normal undamaged cells do, even though FA-A cells harbor highly damaged DNA. Conclusions Our results show that FA cells, despite extensive DNA damage, do not loss the capacity to express the transcriptional and protein components of checkpoint recovery that might eventually allow their division with unrepaired DNA damage. This might allow cell survival but increases the genomic instability inherent to FA individuals and promotes cancer.
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Zhang P, Sridharan D, Lambert MW. Nuclear α Spectrin Differentially Affects Monoubiquitinated Versus Non-Ubiquitinated FANCD2 Function After DNA Interstrand Cross-Link Damage. J Cell Biochem 2015; 117:671-83. [PMID: 26297932 DOI: 10.1002/jcb.25352] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 08/19/2015] [Indexed: 01/21/2023]
Abstract
Nonerythroid α spectrin (αIISp) and the Fanconi anemia (FA) protein, FANCD2, play critical roles in DNA interstrand cross-link (ICL) repair during S phase. Both are needed for recruitment of repair proteins, such as XPF, to sites of damage and repair of ICLs. However, the relationship between them in ICL repair and whether αIISp is involved in FANCD2's function in repair is unclear. The present studies show that, after ICL formation, FANCD2 disassociates from αIISp and localizes, before αIISp, at sites of damage in nuclear foci. αIISp and FANCD2 foci do not co-localize, in contrast to our previous finding that αIISp and the ICL repair protein, XPF, co-localize and follow a similar time course for formation. Knock-down of αIISp has no effect on monoubiquitination of FANCD2 (FANCD2-Ub) or its localization to chromatin or foci, though it leads to decreased ICL repair. Studies using cells from FA patients, defective in ICL repair and αIISp, have elucidated an important role for αIISp in the function of non-Ub FANCD2. In FA complementation group A (FA-A) cells, in which FANCD2 is not monoubiquitinated and does not form damage-induced foci, we demonstrate that restoration of αIISp levels to normal, by knocking down the protease μ-calpain, leads to formation of non-Ub FANCD2 foci after ICL damage. Since restoration of αIISp levels in FA-A cells restores DNA repair and cell survival, we propose that αIISp is critical for recruitment of non-Ub FANCD2 to sites of damage, which has an important role in the repair response and ICL repair.
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Affiliation(s)
- Pan Zhang
- Department of Pathology and Laboratory Medicine, Rutgers New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey, 07103, USA
| | - Deepa Sridharan
- Department of Pathology and Laboratory Medicine, Rutgers New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey, 07103, USA
| | - Muriel W Lambert
- Department of Pathology and Laboratory Medicine, Rutgers New Jersey Medical School, 185 South Orange Avenue, Newark, New Jersey, 07103, USA
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