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Mohajeri Khorasani A, Raghibi A, Haj Mohammad Hassani B, Bolbolizadeh P, Amali A, Sadeghi M, Farshidi N, Dehghani A, Mousavi P. Decoding the Role of NEIL1 Gene in DNA Repair and Lifespan: A Literature Review with Bioinformatics Analysis. Adv Biol (Weinh) 2024:e2300708. [PMID: 39164210 DOI: 10.1002/adbi.202300708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 06/21/2024] [Indexed: 08/22/2024]
Abstract
Longevity, the length of an organism's lifespan, is impacted by environmental factors, metabolic processes, and genetic determinants. The base excision repair (BER) pathway is crucial for maintaining genomic integrity by repairing oxidatively modified base lesions. Nei-like DNA Glycosylase 1 (NEIL1), part of the BER pathway, is vital in repairing oxidative bases in G-rich DNA regions, such as telomeres and promoters. Hence, in this comprehensive review, it have undertaken a meticulous investigation of the intricate association between NEIL1 and longevity. The analysis delves into the multifaceted aspects of the NEIL1 gene, its various RNA transcripts, and the diverse protein isoforms. In addition, a combination of bioinformatic analysis is conducted to identify NEIL1 mutations, transcription factors, and epigenetic modifications, as well as its lncRNA/pseudogene/circRNA-miRNA-mRNA regulatory network. The findings suggest that the normal function of NEIL1 is a significant factor in human health and longevity, with defects in NEIL1 potentially leading to various cancers and related syndromes, Alzheimer's disease, obesity, and diabetes.
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Affiliation(s)
- Amirhossein Mohajeri Khorasani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Alireza Raghibi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, 1416634793, Iran
| | - Behzad Haj Mohammad Hassani
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Pedram Bolbolizadeh
- Student Research Committee, Faculty of Para-Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Arian Amali
- School of Infection & Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Mahboubeh Sadeghi
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- Student Research Committee, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Narges Farshidi
- Department of Pharmaceutics, Faculty of Pharmacy, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
- USERN Office, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Aghdas Dehghani
- Endocrinology and Metabolism Research Center, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
| | - Pegah Mousavi
- Molecular Medicine Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, 7916613885, Iran
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2
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Hu ML, Pan YR, Yong YY, Liu Y, Yu L, Qin DL, Qiao G, Law BYK, Wu JM, Zhou XG, Wu AG. Poly (ADP-ribose) polymerase 1 and neurodegenerative diseases: Past, present, and future. Ageing Res Rev 2023; 91:102078. [PMID: 37758006 DOI: 10.1016/j.arr.2023.102078] [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: 02/13/2023] [Revised: 08/30/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
Abstract
Poly (ADP-ribose) polymerase 1 (PARP1) is a first responder that recognizes DNA damage and facilitates its repair. Neurodegenerative diseases, characterized by progressive neuron loss driven by various risk factors, including DNA damage, have increasingly shed light on the pivotal involvement of PARP1. During the early phases of neurodegenerative diseases, PARP1 experiences controlled activation to swiftly address mild DNA damage, thereby contributing to maintain brain homeostasis. However, in late stages, exacerbated PARP1 activation precipitated by severe DNA damage exacerbates the disease condition. Consequently, inhibition of PARP1 overactivation emerges as a promising therapeutic approach for neurodegenerative diseases. In this review, we comprehensively synthesize and explore the multifaceted role of PARP1 in neurodegenerative diseases, with a particular emphasis on its over-activation in the aggregation of misfolded proteins, dysfunction of the autophagy-lysosome pathway, mitochondrial dysfunction, neuroinflammation, and blood-brain barrier (BBB) injury. Additionally, we encapsulate the therapeutic applications and limitations intrinsic of PARP1 inhibitors, mainly including limited specificity, intricate pathway dynamics, constrained clinical translation, and the heterogeneity of patient cohorts. We also explore and discuss the potential synergistic implementation of these inhibitors alongside other agents targeting DNA damage cascades within neurodegenerative diseases. Simultaneously, we propose several recommendations for the utilization of PARP1 inhibitors within the realm of neurodegenerative disorders, encompassing factors like the disease-specific roles of PARP1, combinatorial therapeutic strategies, and personalized medical interventions. Lastly, the encompassing review presents a forward-looking perspective along with strategic recommendations that could guide future research endeavors in this field.
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Affiliation(s)
- Meng-Ling Hu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yi-Ru Pan
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yuan-Yuan Yong
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Yi Liu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Lu Yu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Da-Lian Qin
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Gan Qiao
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China
| | - Betty Yuen-Kwan Law
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China
| | - Jian-Ming Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China.
| | - Xiao-Gang Zhou
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China.
| | - An-Guo Wu
- Sichuan Key Medical Laboratory of New Drug Discovery and Drugability Evaluation, Luzhou Key Laboratory of Activity Screening and Druggability Evaluation for Chinese Materia Medica, Key Laboratory of Medical Electrophysiology of Ministry of Education, School of Pharmacy, School of Basic Medical Sciences, Southwest Medical University, Luzhou 646000, China; State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau 999078, China.
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3
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SenGupta T, Palikaras K, Esbensen YQ, Konstantinidis G, Galindo FJN, Achanta K, Kassahun H, Stavgiannoudaki I, Bohr VA, Akbari M, Gaare J, Tzoulis C, Tavernarakis N, Nilsen H. Base excision repair causes age-dependent accumulation of single-stranded DNA breaks that contribute to Parkinson disease pathology. Cell Rep 2021; 36:109668. [PMID: 34496255 PMCID: PMC8441048 DOI: 10.1016/j.celrep.2021.109668] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 05/26/2021] [Accepted: 08/13/2021] [Indexed: 01/24/2023] Open
Abstract
Aging, genomic stress, and mitochondrial dysfunction are risk factors for neurodegenerative pathologies, such as Parkinson disease (PD). Although genomic instability is associated with aging and mitochondrial impairment, the underlying mechanisms are poorly understood. Here, we show that base excision repair generates genomic stress, promoting age-related neurodegeneration in a Caenorhabditis elegans PD model. A physiological level of NTH-1 DNA glycosylase mediates mitochondrial and nuclear genomic instability, which promote degeneration of dopaminergic neurons in older nematodes. Conversely, NTH-1 deficiency protects against α-synuclein-induced neurotoxicity, maintaining neuronal function with age. This apparent paradox is caused by modulation of mitochondrial transcription in NTH-1-deficient cells, and this modulation activates LMD-3, JNK-1, and SKN-1 and induces mitohormesis. The dependance of neuroprotection on mitochondrial transcription highlights the integration of BER and transcription regulation during physiological aging. Finally, whole-exome sequencing of genomic DNA from patients with idiopathic PD suggests that base excision repair might modulate susceptibility to PD in humans. Incomplete base excision repair is a source of genomic stress during aging The NTH-1 DNA glycosylase is a key mediator of age-dependent genomic instability Compromised NTH-1 activity promotes neuroprotection in PD nematodes NTH-1 deficiency triggers LMD-3/JNK-1/SKN-1-dependent mitohormetic response
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Affiliation(s)
- Tanima SenGupta
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Konstantinos Palikaras
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Hellas, Greece; Department of Physiology, School of Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Ying Q Esbensen
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Georgios Konstantinidis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Hellas, Greece
| | - Francisco Jose Naranjo Galindo
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway
| | - Kavya Achanta
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, SUND, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Henok Kassahun
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway
| | - Ioanna Stavgiannoudaki
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Hellas, Greece
| | - Vilhelm A Bohr
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, SUND, University of Copenhagen, 2200 Copenhagen, Denmark; DNA Repair Section, National Institute on Aging, 251 Bayview Boulevard, Baltimore, MD, USA
| | - Mansour Akbari
- Center for Healthy Aging, Department of Cellular and Molecular Medicine, SUND, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Johannes Gaare
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway; Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Charalampos Tzoulis
- Neuro-SysMed, Department of Neurology, Haukeland University Hospital, 5021 Bergen, Norway; Department of Clinical Medicine, University of Bergen, Pb 7804, 5020 Bergen, Norway
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Hellas, Greece; Department of Basic Sciences, Faculty of Medicine, University of Crete, Heraklion, 70013 Crete, Greece.
| | - Hilde Nilsen
- Department of Clinical Molecular Biology, University of Oslo, Oslo, Norway; Department of Clinical Molecular Biology, Akershus University Hospital, Lørenskog, Norway.
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4
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Saad AM, Abdel-Megied AES, Elbaz RA, Hassab El-Nabi SE, Elshazli RM. Genetic variants of APEX1 p.Asp148Glu and XRCC1 p.Gln399Arg with the susceptibility of hepatocellular carcinoma. J Med Virol 2021; 93:6278-6291. [PMID: 34289138 DOI: 10.1002/jmv.27217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 07/17/2021] [Indexed: 12/30/2022]
Abstract
The DNA repair genes have a crucial function in the base excision repair (BER) mechanism among different cancerous disorders, particularly hepatocellular carcinoma (HCC). The foremost objective of this study is to explore the association of genetic variants of the APEX1 p.Asp148Glu and the XRCC1 p.Gln399Arg with the susceptibility of HCC and to identify the computational bioinformatics frameworks of these missense variants. A total of 250 participants were enrolled in this study, including 150 HCC patients and 100 cancer-free controls. The genomic DNA was characterized and genotyped by applying the PCR-CTPP method. The frequency of the APEX1 (rs1130409*Glu) allele was statistically significant with increased risk of HCC (OR = 1.66, 95% CI = 1.12-2.45), while the XRCC1 (rs25487*Gln) allele conferred a protection against the progression of HCC (OR = 0.64, 95% CI = 0.42-0.96). Furthermore, HCC patients carrying the APEX1 p.Asp148Glu and the XRCC1 p.Gln399Arg variants indicated no significant difference with the clinical, and laboratory parameters (p > .05). Our findings confirmed that the APEX1 p.Asp148Glu variant was associated with increased risk of HCC, while the XRCC1 p.Gln399Arg variant revealed protection against the development of HCC.
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Affiliation(s)
- Ahmad M Saad
- Biochemistry Section, Department of Chemistry, Faculty of Science, Menoufia University, Menoufia, Egypt
| | | | - Rizk A Elbaz
- Genetic Unit, Children Hospital, Mansoura University, Mansoura, Egypt
| | | | - Rami M Elshazli
- Biochemistry and Molecular Genetics Unit, Department of Basic Sciences, Faculty of Physical Therapy, Horus University-Egypt, New Damietta, Egypt
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5
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Toprani SM, Bitounis D, Qiansheng H, Oliveira N, Ng KW, Tay CY, Nagel ZD, Demokritou P. High-Throughput Screening Platform for Nanoparticle-Mediated Alterations of DNA Repair Capacity. ACS NANO 2021; 15:4728-4746. [PMID: 33710878 PMCID: PMC8111687 DOI: 10.1021/acsnano.0c09254] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The potential genotoxic effects of engineered nanomaterials (ENMs) may occur through the induction of DNA damage or the disruption of DNA repair processes. Inefficient DNA repair may lead to the accumulation of DNA lesions and has been linked to various diseases, including cancer. Most studies so far have focused on understanding the nanogenotoxicity of ENM-induced damages to DNA, whereas the effects on DNA repair have been widely overlooked. The recently developed fluorescence multiplex-host-cell reactivation (FM-HCR) assay allows for the direct quantification of multiple DNA repair pathways in living cells and offers a great opportunity to address this methodological gap. Herein an FM-HCR-based method is developed to screen the impact of ENMs on six major DNA repair pathways using suspended or adherent cells. The sensitivity and efficiency of this DNA repair screening method were demonstrated in case studies using primary human small airway epithelial cells and TK6 cells exposed to various model ENMs (CuO, ZnO, and Ga2O3) at subcytotoxic doses. It was shown that ENMs may inhibit nucleotide-excision repair, base-excision repair, and the repair of oxidative damage by DNA glycosylases in TK6 cells, even in the absence of significant genomic DNA damage. It is of note that the DNA repair capacity was increased by some ENMs, whereas it was suppressed by others. Overall, this method can be part of a multitier, in vitro hazard assessment of ENMs as a functional, high-throughput platform that provides insights into the interplay of the properties of ENMs, the DNA repair efficiency, and the genomic stability.
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Affiliation(s)
- Sneh M Toprani
- John B Little Center of Radiation Sciences, Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Dimitrios Bitounis
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
| | - Huang Qiansheng
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
- Center for Excellence in Regional Atmospheric Environment, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Nathalia Oliveira
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
| | - Kee Woei Ng
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- Environmental Chemistry and Materials Centre, Nanyang Environment and Water Research Institution, 1 Cleantech Loop, CleanTech One, Singapore 637141, Singapore
| | - Chor Yong Tay
- School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore
- School of Biological Sciences, Nanyang Technological University, 637551, Singapore
| | - Zachary D Nagel
- John B Little Center of Radiation Sciences, Department of Environmental Health, Harvard T H Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Philip Demokritou
- Center for Nanotechnology and Nanotoxicology, Department of Environmental Health, T.H. Chan School of Public Health, Harvard University, 655 Huntington Ave Boston, MA 02115, USA
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Zhang Y, Zhang Q, Li L, Mu D, Hua K, Ci S, Shen L, Zheng L, Shen B, Guo Z. Arginine methylation of APE1 promotes its mitochondrial translocation to protect cells from oxidative damage. Free Radic Biol Med 2020; 158:60-73. [PMID: 32679368 PMCID: PMC8195256 DOI: 10.1016/j.freeradbiomed.2020.06.027] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 06/09/2020] [Accepted: 06/17/2020] [Indexed: 02/07/2023]
Abstract
Apurinic/apyrimidinic endonuclease 1 (APE1) is an essential multifunctional protein in mammals that plays critical roles in DNA repair and redox signaling within the cell. Impaired APE1 function or dysregulation is associated with disease susceptibility and poor cancer prognosis. Orchestrated regulatory mechanisms are crucial to ensure its function in a specific subcellular location at specific time. Here, we report arginine methylation as a post-translational modification (PTM) that regulates APE1 translocation to mitochondria in HeLa and HEK-293 cells. Protein arginine methyl-transferase 1 (PRMT1) was shown to methylate APE1 in vitro. Site-directed mutagenesis identified R301 as the major methylation site. We confirmed that APE1 is methylated in cells and that the R301K mutation significantly reduces its methylation. Baseline mitochondrial APE1 levels were low under standard culture conditions, but they could be induced by oxidative agents. Methylation-deficient APE1 showed reduced mitochondrial translocation. Methylation affected the interaction of APE1 with Tom20, translocase of the outer mitochondrial membrane. Methylation-deficient APE1 resulted in increased mitochondrial DNA damage and increased cytochrome c release after stimuli. These data suggest that methylation of APE1 promotes its mitochondrial translocation and protects cells from oxidative damage. This work describes a novel PTM regulation model of APE1 subcellular distribution through arginine methylation.
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Affiliation(s)
- Yilan Zhang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Qi Zhang
- Department of Infectious Disease, Nanjing Liuhe District People's Hospital, Yangzhou University, Nanjing, 211500, China
| | - LuLu Li
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Dan Mu
- Department of Radiology, Affiliated Drum Tower Hospital, Nanjing University School of Medicine, Nanjing, 210008, China
| | - Ke Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Shusheng Ci
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China
| | - Lei Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA
| | - Li Zheng
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA
| | - Binghui Shen
- Department of Cancer Genetics and Epigenetics, City of Hope National Medical Center and Beckman Research Institute, Duarte, CA, 91010, USA.
| | - Zhigang Guo
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, Nanjing Normal University, 1 WenYuan Road, Nanjing, 210023, China.
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7
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Alkyladenine DNA glycosylase associates with transcription elongation to coordinate DNA repair with gene expression. Nat Commun 2019; 10:5460. [PMID: 31784530 PMCID: PMC6884549 DOI: 10.1038/s41467-019-13394-w] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Accepted: 11/05/2019] [Indexed: 12/17/2022] Open
Abstract
Base excision repair (BER) initiated by alkyladenine DNA glycosylase (AAG) is essential for removal of aberrantly methylated DNA bases. Genome instability and accumulation of aberrant bases accompany multiple diseases, including cancer and neurological disorders. While BER is well studied on naked DNA, it remains unclear how BER efficiently operates on chromatin. Here, we show that AAG binds to chromatin and forms complex with RNA polymerase (pol) II. This occurs through direct interaction with Elongator and results in transcriptional co-regulation. Importantly, at co-regulated genes, aberrantly methylated bases accumulate towards the 3′end in regions enriched for BER enzymes AAG and APE1, Elongator and active RNA pol II. Active transcription and functional Elongator are further crucial to ensure efficient BER, by promoting AAG and APE1 chromatin recruitment. Our findings provide insights into genome stability maintenance in actively transcribing chromatin and reveal roles of aberrantly methylated bases in regulation of gene expression. How genome stability is maintained at regions of active transcription is currently not entirely clear. Here, the authors reveal an association between base excision repair factors and transcription elongation to modulate DNA repair.
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8
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Fang Y, Zou P. Genome-Wide Mapping of Oxidative DNA Damage via Engineering of 8-Oxoguanine DNA Glycosylase. Biochemistry 2019; 59:85-89. [PMID: 31618020 DOI: 10.1021/acs.biochem.9b00782] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The occurrence of 8-oxo-7,8-dihydroguanine (OG) in the genome, as one of the major DNA oxidative damages, has been implicated in an array of biological processes, ranging from mutagenesis to transcriptional regulation. Genome-wide mapping of oxidative damages could shed light on the underlying cellular mechanism. In the present study, we engineered the hOGG1 enzyme, a primary 8-oxoguanine DNA glycosylase, into a guanine oxidation-profiling tool. Our method, called enTRAP-seq, successfully identified more than 1400 guanine oxidation sites in the mouse embryonic fibroblast genome. These OG peaks were enriched in open chromatin regions and regulatory elements, including promoters, 5' untranslated regions, and CpG islands. Collectively, we present a simple and generalizable approach for the genome-wide profiling of DNA damages with high sensitivity and specificity.
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Affiliation(s)
- Yuxin Fang
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Peking University , Beijing 100871 , China
| | - Peng Zou
- College of Chemistry and Molecular Engineering, Synthetic and Functional Biomolecules Center, Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education , Peking University , Beijing 100871 , China.,Peking-Tsinghua Center for Life Sciences , Peking University , Beijing 100871 , China.,PKU-IDG/McGovern Institute for Brain Research , Peking University , Beijing 100871 , China
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9
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Konopka A, Atkin JD. The Emerging Role of DNA Damage in the Pathogenesis of the C9orf72 Repeat Expansion in Amyotrophic Lateral Sclerosis. Int J Mol Sci 2018; 19:ijms19103137. [PMID: 30322030 PMCID: PMC6213462 DOI: 10.3390/ijms19103137] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/09/2018] [Accepted: 10/09/2018] [Indexed: 02/07/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a fatal, rapidly progressing neurodegenerative disease affecting motor neurons, and frontotemporal dementia (FTD) is a behavioural disorder resulting in early-onset dementia. Hexanucleotide (G4C2) repeat expansions in the gene encoding chromosome 9 open reading frame 72 (C9orf72) are the major cause of familial forms of both ALS (~40%) and FTD (~20%) worldwide. The C9orf72 repeat expansion is known to form abnormal nuclei acid structures, such as hairpins, G-quadruplexes, and R-loops, which are increasingly associated with human diseases involving microsatellite repeats. These configurations form during normal cellular processes, but if they persist they also damage DNA, and hence are a serious threat to genome integrity. It is unclear how the repeat expansion in C9orf72 causes ALS, but recent evidence implicates DNA damage in neurodegeneration. This may arise from abnormal nucleic acid structures, the greatly expanded C9orf72 RNA, or by repeat-associated non-ATG (RAN) translation, which generates toxic dipeptide repeat proteins. In this review, we detail recent advances implicating DNA damage in C9orf72-ALS. Furthermore, we also discuss increasing evidence that targeting these aberrant C9orf72 confirmations may have therapeutic value for ALS, thus revealing new avenues for drug discovery for this disorder.
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Affiliation(s)
- Anna Konopka
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
| | - Julie D Atkin
- Centre for MND Research, Department of Biomedical Sciences, Faculty of Medicine & Health Sciences, Macquarie University, Sydney, NSW 2109, Australia.
- La Trobe Institute for Molecular Science, Melbourne, VIC 3086, Australia.
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10
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Wu J, McKeague M, Sturla SJ. Nucleotide-Resolution Genome-Wide Mapping of Oxidative DNA Damage by Click-Code-Seq. J Am Chem Soc 2018; 140:9783-9787. [PMID: 29944356 DOI: 10.1021/jacs.8b03715] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Single-nucleotide-resolution sequencing of DNA damage is required to decipher the complex causal link between the identity and location of DNA adducts and their biological impact. However, the low abundance and inability to specifically amplify DNA damage hinders single-nucleotide mapping of adducts within whole genomes. Despite the high biological relevance of guanine oxidation and seminal recent advances in sequencing bulky adducts, single-nucleotide-resolution whole genome mapping of oxidative damage is not yet realized. We coupled the specificity of repair enzymes with the efficiency of a click DNA ligation reaction to insert a biocompatible locator code, enabling high-throughput, nucleotide-resolution sequencing of oxidative DNA damage in a genome. We uncovered thousands of oxidation sites with distinct patterns related to transcription, chromatin architecture, and chemical oxidation potential. Click-code-seq overcomes barriers to DNA damage sequencing and provides a new approach for generating comprehensive, sequence-specific information about chemical modification patterns in whole genomes.
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Affiliation(s)
- Junzhou Wu
- Department of Health Sciences and Technology , ETH Zürich , Schmelzbergstrasse 9 , 8092 Zürich , Switzerland
| | - Maureen McKeague
- Department of Health Sciences and Technology , ETH Zürich , Schmelzbergstrasse 9 , 8092 Zürich , Switzerland
| | - Shana J Sturla
- Department of Health Sciences and Technology , ETH Zürich , Schmelzbergstrasse 9 , 8092 Zürich , Switzerland
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van Gastel J, Boddaert J, Jushaj A, Premont RT, Luttrell LM, Janssens J, Martin B, Maudsley S. GIT2-A keystone in ageing and age-related disease. Ageing Res Rev 2018; 43:46-63. [PMID: 29452267 DOI: 10.1016/j.arr.2018.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/15/2022]
Abstract
Since its discovery, G protein-coupled receptor kinase-interacting protein 2, GIT2, and its family member, GIT1, have received considerable interest concerning their potential key roles in regulating multiple inter-connected physiological and pathophysiological processes. GIT2 was first identified as a multifunctional protein that is recruited to G protein-coupled receptors (GPCRs) during the process of receptor internalization. Recent findings have demonstrated that perhaps one of the most important effects of GIT2 in physiology concerns its role in controlling multiple aspects of the complex ageing process. Ageing can be considered the most prevalent pathophysiological condition in humans, affecting all tissue systems and acting as a driving force for many common and intractable disorders. The ageing process involves a complex interplay among various deleterious activities that profoundly disrupt the body's ability to cope with damage, thus increasing susceptibility to pathophysiologies such as neurodegeneration, central obesity, osteoporosis, type 2 diabetes mellitus and atherosclerosis. The biological systems that control ageing appear to function as a series of interconnected complex networks. The inter-communication among multiple lower-complexity signaling systems within the global ageing networks is likely coordinated internally by keystones or hubs, which regulate responses to dynamic molecular events through protein-protein interactions with multiple distinct partners. Multiple lines of research have suggested that GIT2 may act as one of these network coordinators in the ageing process. Identifying and targeting keystones, such as GIT2, is thus an important approach in our understanding of, and eventual ability to, medically ameliorate or interdict age-related progressive cellular and tissue damage.
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12
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Constitutive MAP-kinase activation suppresses germline apoptosis in NTH-1 DNA glycosylase deficient C. elegans. DNA Repair (Amst) 2017; 61:46-55. [PMID: 29202295 DOI: 10.1016/j.dnarep.2017.11.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 11/24/2017] [Accepted: 11/28/2017] [Indexed: 12/22/2022]
Abstract
Oxidation of DNA bases, an inevitable consequence of oxidative stress, requires the base excision repair (BER) pathway for repair. Caenorhabditis elegans is a well-established model to study phenotypic consequences and cellular responses to oxidative stress. To better understand how BER affects phenotypes associated with oxidative stress, we characterised the C. elegans nth-1 mutant, which lack the only DNA glycosylase dedicated to repair of oxidative DNA base damage, the NTH-1 DNA glycosylase. We show that nth-1 mutants have mitochondrial dysfunction characterised by lower mitochondrial DNA copy number, reduced mitochondrial membrane potential, and increased steady-state levels of reactive oxygen species. Consistently, nth-1 mutants express markers of chronic oxidative stress with high basal phosphorylation of MAP-kinases (MAPK) but further activation of MAPK in response to the superoxide generator paraquat is attenuated. Surprisingly, nth-1 mutants also failed to induce apoptosis in response to paraquat. The ability to induce apoptosis in response to paraquat was regained when basal MAPK activation was restored to wild type levels. In conclusion, the failure of nth-1 mutants to induce apoptosis in response to paraquat is not a direct effect of the DNA repair deficiency but an indirect consequence of the compensatory cellular stress response that includes MAPK activation.
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13
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The Role of DNA Polymerase β in Neural Genome Stability. J Neurosci 2017; 37:11069-11071. [PMID: 29142120 DOI: 10.1523/jneurosci.2380-17.2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/02/2017] [Accepted: 10/09/2017] [Indexed: 11/21/2022] Open
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14
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Markkanen E. Not breathing is not an option: How to deal with oxidative DNA damage. DNA Repair (Amst) 2017; 59:82-105. [PMID: 28963982 DOI: 10.1016/j.dnarep.2017.09.007] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 09/20/2017] [Indexed: 02/07/2023]
Abstract
Oxidative DNA damage constitutes a major threat to genetic integrity, and has thus been implicated in the pathogenesis of a wide variety of diseases, including cancer and neurodegeneration. 7,8-dihydro-8oxo-deoxyGuanine (8-oxo-G) is one of the best characterised oxidative DNA lesions, and it can give rise to point mutations due to its miscoding potential that instructs most DNA polymerases (Pols) to preferentially insert Adenine (A) opposite 8-oxo-G instead of the correct Cytosine (C). If uncorrected, A:8-oxo-G mispairs can give rise to C:G→A:T transversion mutations. Cells have evolved a variety of pathways to mitigate the mutational potential of 8-oxo-G that include i) mechanisms to avoid incorporation of oxidized nucleotides into DNA through nucleotide pool sanitisation enzymes (by MTH1, MTH2, MTH3 and NUDT5), ii) base excision repair (BER) of 8-oxo-G in DNA (involving MUTYH, OGG1, Pol λ, and other components of the BER machinery), and iii) faithful bypass of 8-oxo-G lesions during replication (using a switch between replicative Pols and Pol λ). In the following, the fate of 8-oxo-G in mammalian cells is reviewed in detail. The differential origins of 8-oxo-G in DNA and its consequences for genetic stability will be covered. This will be followed by a thorough discussion of the different mechanisms in place to cope with 8-oxo-G with an emphasis on Pol λ-mediated correct bypass of 8-oxo-G during MUTYH-initiated BER as well as replication across 8-oxo-G. Furthermore, the multitude of mechanisms in place to regulate key proteins involved in 8-oxo-G repair will be reviewed. Novel functions of 8-oxo-G as an epigenetic-like regulator and insights into the repair of 8-oxo-G within the cellular context will be touched upon. Finally, a discussion will outline the relevance of 8-oxo-G and the proteins involved in dealing with 8-oxo-G to human diseases with a special emphasis on cancer.
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Affiliation(s)
- Enni Markkanen
- Institute of Veterinary Pharmacology and Toxicology, Vetsuisse Faculty, University of Zürich, Winterthurerstr. 260, 8057 Zürich, Switzerland.
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15
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Boiteux S, Coste F, Castaing B. Repair of 8-oxo-7,8-dihydroguanine in prokaryotic and eukaryotic cells: Properties and biological roles of the Fpg and OGG1 DNA N-glycosylases. Free Radic Biol Med 2017; 107:179-201. [PMID: 27903453 DOI: 10.1016/j.freeradbiomed.2016.11.042] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 11/22/2016] [Accepted: 11/25/2016] [Indexed: 01/23/2023]
Abstract
Oxidatively damaged DNA results from the attack of sugar and base moieties by reactive oxygen species (ROS), which are formed as byproducts of normal cell metabolism and during exposure to endogenous or exogenous chemical or physical agents. Guanine, having the lowest redox potential, is the DNA base the most susceptible to oxidation, yielding products such as 8-oxo-7,8-dihydroguanine (8-oxoG) and 2-6-diamino-4-hydroxy-5-formamidopyrimidine (FapyG). In DNA, 8-oxoG was shown to be mutagenic yielding GC to TA transversions upon incorporation of dAMP opposite this lesion by replicative DNA polymerases. In prokaryotic and eukaryotic cells, 8-oxoG is primarily repaired by the base excision repair pathway (BER) initiated by a DNA N-glycosylase, Fpg and OGG1, respectively. In Escherichia coli, Fpg cooperates with MutY and MutT to prevent 8-oxoG-induced mutations, the "GO-repair system". In Saccharomyces cerevisiae, OGG1 cooperates with nucleotide excision repair (NER), mismatch repair (MMR), post-replication repair (PRR) and DNA polymerase η to prevent mutagenesis. Human and mouse cells mobilize all these pathways using OGG1, MUTYH (MutY-homolog also known as MYH), MTH1 (MutT-homolog also known as NUDT1), NER, MMR, NEILs and DNA polymerases η and λ, to prevent 8-oxoG-induced mutations. In fact, mice deficient in both OGG1 and MUTYH develop cancer in different organs at adult age, which points to the critical impact of 8-oxoG repair on genetic stability in mammals. In this review, we will focus on Fpg and OGG1 proteins, their biochemical and structural properties as well as their biological roles. Other DNA N-glycosylases able to release 8-oxoG from damaged DNA in various organisms will be discussed. Finally, we will report on the role of OGG1 in human disease and the possible use of 8-oxoG DNA N-glycosylases as therapeutic targets.
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Affiliation(s)
- Serge Boiteux
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
| | - Franck Coste
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France
| | - Bertrand Castaing
- Centre de Biophysique Moléculaire, CNRS, UPR4301, rue Charles Sadron, 45072 Orléans, France.
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16
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DNA Damage and Repair in Schizophrenia and Autism: Implications for Cancer Comorbidity and Beyond. Int J Mol Sci 2016; 17:ijms17060856. [PMID: 27258260 PMCID: PMC4926390 DOI: 10.3390/ijms17060856] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/12/2016] [Accepted: 05/27/2016] [Indexed: 12/16/2022] Open
Abstract
Schizophrenia and autism spectrum disorder (ASD) are multi-factorial and multi-symptomatic psychiatric disorders, each affecting 0.5%-1% of the population worldwide. Both are characterized by impairments in cognitive functions, emotions and behaviour, and they undermine basic human processes of perception and judgment. Despite decades of extensive research, the aetiologies of schizophrenia and ASD are still poorly understood and remain a significant challenge to clinicians and scientists alike. Adding to this unsatisfactory situation, patients with schizophrenia or ASD often develop a variety of peripheral and systemic disturbances, one prominent example of which is cancer, which shows a direct (but sometimes inverse) comorbidity in people affected with schizophrenia and ASD. Cancer is a disease characterized by uncontrolled proliferation of cells, the molecular origin of which derives from mutations of a cell's DNA sequence. To counteract such mutations and repair damaged DNA, cells are equipped with intricate DNA repair pathways. Oxidative stress, oxidative DNA damage, and deficient repair of oxidative DNA lesions repair have been proposed to contribute to the development of schizophrenia and ASD. In this article, we summarize the current evidence of cancer comorbidity in these brain disorders and discuss the putative roles of oxidative stress, DNA damage and DNA repair in the aetiopathology of schizophrenia and ASD.
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17
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Maynard S, Fang EF, Scheibye-Knudsen M, Croteau DL, Bohr VA. DNA Damage, DNA Repair, Aging, and Neurodegeneration. Cold Spring Harb Perspect Med 2015; 5:cshperspect.a025130. [PMID: 26385091 DOI: 10.1101/cshperspect.a025130] [Citation(s) in RCA: 228] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Aging in mammals is accompanied by a progressive atrophy of tissues and organs, and stochastic damage accumulation to the macromolecules DNA, RNA, proteins, and lipids. The sequence of the human genome represents our genetic blueprint, and accumulating evidence suggests that loss of genomic maintenance may causally contribute to aging. Distinct evidence for a role of imperfect DNA repair in aging is that several premature aging syndromes have underlying genetic DNA repair defects. Accumulation of DNA damage may be particularly prevalent in the central nervous system owing to the low DNA repair capacity in postmitotic brain tissue. It is generally believed that the cumulative effects of the deleterious changes that occur in aging, mostly after the reproductive phase, contribute to species-specific rates of aging. In addition to nuclear DNA damage contributions to aging, there is also abundant evidence for a causative link between mitochondrial DNA damage and the major phenotypes associated with aging. Understanding the mechanistic basis for the association of DNA damage and DNA repair with aging and age-related diseases, such as neurodegeneration, would give insight into contravening age-related diseases and promoting a healthy life span.
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Affiliation(s)
- Scott Maynard
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, DK-2200 Copenhagen, Denmark
| | - Evandro Fei Fang
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Morten Scheibye-Knudsen
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Deborah L Croteau
- Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
| | - Vilhelm A Bohr
- Department of Cellular and Molecular Medicine, Center for Healthy Aging, University of Copenhagen, DK-2200 Copenhagen, Denmark Laboratory of Molecular Gerontology, National Institute on Aging, National Institutes of Health, Baltimore, Maryland 21224
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Markkanen E, Fischer R, Ledentcova M, Kessler BM, Dianov GL. Cells deficient in base-excision repair reveal cancer hallmarks originating from adjustments to genetic instability. Nucleic Acids Res 2015; 43:3667-79. [PMID: 25800737 PMCID: PMC4402536 DOI: 10.1093/nar/gkv222] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 03/04/2015] [Indexed: 12/27/2022] Open
Abstract
Genetic instability, provoked by exogenous mutagens, is well linked to initiation of cancer. However, even in unstressed cells, DNA undergoes a plethora of spontaneous alterations provoked by its inherent chemical instability and the intracellular milieu. Base excision repair (BER) is the major cellular pathway responsible for repair of these lesions, and as deficiency in BER activity results in DNA damage it has been proposed that it may trigger the development of sporadic cancers. Nevertheless, experimental evidence for this model remains inconsistent and elusive. Here, we performed a proteomic analysis of BER deficient human cells using stable isotope labelling with amino acids in cell culture (SILAC), and demonstrate that BER deficiency, which induces genetic instability, results in dramatic changes in gene expression, resembling changes found in many cancers. We observed profound alterations in tissue homeostasis, serine biosynthesis, and one-carbon- and amino acid metabolism, all of which have been identified as cancer cell ‘hallmarks’. For the first time, this study describes gene expression changes characteristic for cells deficient in repair of endogenous DNA lesions by BER. These expression changes resemble those observed in cancer cells, suggesting that genetically unstable BER deficient cells may be a source of pre-cancerous cells.
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Affiliation(s)
- Enni Markkanen
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom
| | - Roman Fischer
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Marina Ledentcova
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrenteva 10, 630090 Novosibirsk, Russia
| | - Benedikt M Kessler
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7FZ, United Kingdom
| | - Grigory L Dianov
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Roosevelt Drive, Oxford OX3 7DQ, United Kingdom Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Lavrenteva 10, 630090 Novosibirsk, Russia
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Kashevarova AA, Nazarenko LP, Skryabin NA, Salyukova OA, Chechetkina NN, Tolmacheva EN, Sazhenova EA, Magini P, Graziano C, Romeo G, Kučinskas V, Lebedev IN. Array CGH analysis of a cohort of Russian patients with intellectual disability. Gene 2014; 536:145-50. [PMID: 24291026 DOI: 10.1016/j.gene.2013.11.029] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 10/30/2013] [Accepted: 11/01/2013] [Indexed: 12/20/2022]
Abstract
The use of array comparative genomic hybridization (array CGH) as a diagnostic tool in molecular genetics has facilitated the identification of many new microdeletion/microduplication syndromes (MMSs). Furthermore, this method has allowed for the identification of copy number variations (CNVs) whose pathogenic role has yet to be uncovered. Here, we report on our application of array CGH for the identification of pathogenic CNVs in 79 Russian children with intellectual disability (ID). Twenty-six pathogenic or likely pathogenic changes in copy number were detected in 22 patients (28%): 8 CNVs corresponded to known MMSs, and 17 were not associated with previously described syndromes. In this report, we describe our findings and comment on genes potentially associated with ID that are located within the CNV regions.
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Key Words
- ABLIM3
- ACAD10
- ADHD
- AFAP1L1
- AGA
- ASTN1
- Array comparative genomic hybridization (array CGH)
- CASP3
- CGH
- CHERISH
- CNS
- CNTN6
- CNV
- Copy number variation (CNV)
- DDX10
- DEAD (Asp-Glu-Ala-Asp) box polypeptide 10
- DECIPHER
- EEG
- EU
- European Union
- FJX1
- GLRA3
- HAND2
- HFE
- ID
- IFN
- IL17B
- ING2
- IQ
- IRF1
- IRF2
- Intellectual disability
- LDLRAD3
- METTL4
- MMP14
- MMSs
- MRI
- NDC80
- NDC80 kinetochore complex component
- NEIL3
- NO
- OMIM
- PCR
- PL CNS
- PON1
- PON2
- PON3
- SBF
- SCGN
- SCRG1
- SET domain binding factor
- SLC1A2
- SLC5A7
- SLC7A7
- SMCHD1
- SUFU
- SWAP switching B-cell complex 70kDa subunit
- SWAP70
- Ski-related novel protein N
- SnoN
- TGFβ
- TNR
- TRIM44
- WAGR
- Wilms tumor, aniridia, genitourinary anomalies and mental retardation syndrome
- actin binding LIM protein family, member 3
- actin filament associated protein 1-like 1
- acyl-CoA dehydrogenase family, member 10
- aspartylglucosaminidase
- astrotactin 1
- attention-deficit hyperactivity disorder
- caspase 3, apoptosis-related cysteine peptidase
- central nervous system
- comparative genomic hybridization
- contactin 6
- copy number variation
- database of chromosomal imbalance and phenotype in humans using ensembl resources
- electroencephalogram
- four jointed box 1 (Drosophila)
- glycine receptor, alpha 3
- grant of European Community's Seventh Framework Programme
- heart and neural crest derivatives expressed 2
- hemochromatosis
- inhibitor of growth family, member 2
- intellectual disability
- intelligence quotient
- interferon
- interferon regulatory factor 1
- interferon regulatory factor 2
- interleukin 17B
- low density lipoprotein receptor class A domain containing 3
- magnetic resonance imaging
- matrix metallopeptidase 14 (membrane-inserted)
- methyltransferase like 4
- microdeletion/microduplication syndromes
- nei endonuclease VIII-like 3 (E. coli)
- nitrogen oxide
- online mendelian inheritance in man
- paraoxonase 1
- paraoxonase 2
- paraoxonase 3
- perinatal lesion of central nervous system
- polymerase chain reaction
- qPCR
- quantitative PCR
- secretagogin, EF-hand calcium binding protein
- solute carrier family 1 (glial high affinity glutamate transporter), member 2
- solute carrier family 5 (sodium/choline cotransporter), member 7
- solute carrier family 7 (amino acid transporter light chain, y+L system), member 7
- stimulator of chondrogenesis 1
- structural maintenance of chromosomes flexible hinge domain containing 1
- suppressor of fused homolog (Drosophila)
- tenascin R
- transforming growth factor beta
- tripartite motif containing 44
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Vaidutis Kučinskas
- Vilnius University, Department of Human and Medical Genetics, Vilnius, Lithuania
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Markkanen E, Dorn J, Hübscher U. MUTYH DNA glycosylase: the rationale for removing undamaged bases from the DNA. Front Genet 2013; 4:18. [PMID: 23450852 PMCID: PMC3584444 DOI: 10.3389/fgene.2013.00018] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 02/01/2013] [Indexed: 12/13/2022] Open
Abstract
Maintenance of genetic stability is crucial for all organisms in order to avoid the onset of deleterious diseases such as cancer. One of the many proveniences of DNA base damage in mammalian cells is oxidative stress, arising from a variety of endogenous and exogenous sources, generating highly mutagenic oxidative DNA lesions. One of the best characterized oxidative DNA lesion is 7,8-dihydro-8-oxoguanine (8-oxo-G), which can give rise to base substitution mutations (also known as point mutations). This mutagenicity is due to the miscoding potential of 8-oxo-G that instructs most DNA polymerases (pols) to preferentially insert an Adenine (A) opposite 8-oxo-G instead of the appropriate Cytosine (C). If left unrepaired, such A:8-oxo-G mispairs can give rise to CG→AT transversion mutations. A:8-oxo-G mispairs are proficiently recognized by the MutY glycosylase homologue (MUTYH). MUTYH can remove the mispaired A from an A:8-oxo-G, giving way to the canonical base-excision repair (BER) that ultimately restores undamaged Guanine (G). The importance of this MUTYH-initiated pathway is illustrated by the fact that biallelic mutations in the MUTYH gene are associated with a hereditary colorectal cancer syndrome termed MUTYH-associated polyposis (MAP). In this review, we will focus on MUTYH, from its discovery to the most recent data regarding its cellular roles and interaction partners. We discuss the involvement of the MUTYH protein in the A:8-oxo-G BER pathway acting together with pol λ, the pol that can faithfully incorporate C opposite 8-oxo-G and thus bypass this lesion in a correct manner. We also outline the current knowledge about the regulation of MUTYH itself and the A:8-oxo-G repair pathway by posttranslational modifications (PTM). Finally, to achieve a clearer overview of the literature, we will briefly touch on the rather confusing MUTYH nomenclature. In short, MUTYH is a unique DNA glycosylase that catalyzes the excision of an undamaged base from DNA.
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Affiliation(s)
- Enni Markkanen
- Institute for Veterinary Biochemistry and Molecular Biology, University of Zürich-Irchel Zürich, Switzerland
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