1
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Shadfar S, Parakh S, Jamali MS, Atkin JD. Redox dysregulation as a driver for DNA damage and its relationship to neurodegenerative diseases. Transl Neurodegener 2023; 12:18. [PMID: 37055865 PMCID: PMC10103468 DOI: 10.1186/s40035-023-00350-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 03/16/2023] [Indexed: 04/15/2023] Open
Abstract
Redox homeostasis refers to the balance between the production of reactive oxygen species (ROS) as well as reactive nitrogen species (RNS), and their elimination by antioxidants. It is linked to all important cellular activities and oxidative stress is a result of imbalance between pro-oxidants and antioxidant species. Oxidative stress perturbs many cellular activities, including processes that maintain the integrity of DNA. Nucleic acids are highly reactive and therefore particularly susceptible to damage. The DNA damage response detects and repairs these DNA lesions. Efficient DNA repair processes are therefore essential for maintaining cellular viability, but they decline considerably during aging. DNA damage and deficiencies in DNA repair are increasingly described in age-related neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis and Huntington's disease. Furthermore, oxidative stress has long been associated with these conditions. Moreover, both redox dysregulation and DNA damage increase significantly during aging, which is the biggest risk factor for neurodegenerative diseases. However, the links between redox dysfunction and DNA damage, and their joint contributions to pathophysiology in these conditions, are only just emerging. This review will discuss these associations and address the increasing evidence for redox dysregulation as an important and major source of DNA damage in neurodegenerative disorders. Understanding these connections may facilitate a better understanding of disease mechanisms, and ultimately lead to the design of better therapeutic strategies based on preventing both redox dysregulation and DNA damage.
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Affiliation(s)
- Sina Shadfar
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia.
| | - Sonam Parakh
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia
| | - Md Shafi Jamali
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia
| | - Julie D Atkin
- Centre for Motor Neuron Disease Research, Macquarie Medical School, Macquarie University, Sydney, NSW, 2109, Australia.
- La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Melbourne, VIC, 3086, Australia.
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2
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Pan X, Yun J, Coban Akdemir ZH, Jiang X, Wu E, Huang JH, Sahni N, Yi SS. AI-DrugNet: A network-based deep learning model for drug repurposing and combination therapy in neurological disorders. Comput Struct Biotechnol J 2023; 21:1533-1542. [PMID: 36879885 PMCID: PMC9984442 DOI: 10.1016/j.csbj.2023.02.004] [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: 07/04/2022] [Revised: 02/03/2023] [Accepted: 02/03/2023] [Indexed: 02/10/2023] Open
Abstract
Discovering effective therapies is difficult for neurological and developmental disorders in that disease progression is often associated with a complex and interactive mechanism. Over the past few decades, few drugs have been identified for treating Alzheimer's disease (AD), especially for impacting the causes of cell death in AD. Although drug repurposing is gaining more success in developing therapeutic efficacy for complex diseases such as common cancer, the complications behind AD require further study. Here, we developed a novel prediction framework based on deep learning to identify potential repurposed drug therapies for AD, and more importantly, our framework is broadly applicable and may generalize to identifying potential drug combinations in other diseases. Our prediction framework is as follows: we first built a drug-target pair (DTP) network based on multiple drug features and target features, as well as the associations between DTP nodes where drug-target pairs are the DTP nodes and the associations between DTP nodes are represented as the edges in the AD disease network; furthermore, we incorporated the drug-target feature from the DTP network and the relationship information between drug-drug, target-target, drug-target within and outside of drug-target pairs, representing each drug-combination as a quartet to generate corresponding integrated features; finally, we developed an AI-based Drug discovery Network (AI-DrugNet), which exhibits robust predictive performance. The implementation of our network model help identify potential repurposed and combination drug options that may serve to treat AD and other diseases.
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Affiliation(s)
- Xingxin Pan
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
| | - Jun Yun
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX 78712, USA
| | - Zeynep H. Coban Akdemir
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Xiaoqian Jiang
- School of Biomedical Informatics, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Erxi Wu
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Surgery, Texas A & M University Health Science Center, College of Medicine, Temple, TX 76508, USA
- Department of Pharmaceutical Sciences, Texas A & M University Health Science Center, College of Pharmacy, College Station, TX 77843, USA
| | - Jason H. Huang
- Neuroscience Institute and Department of Neurosurgery, Baylor Scott & White Health, Temple, TX 76502, USA
- Department of Surgery, Texas A & M University Health Science Center, College of Medicine, Temple, TX 76508, USA
| | - Nidhi Sahni
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
- Quantitative and Computational Biosciences Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - S. Stephen Yi
- Livestrong Cancer Institutes, Department of Oncology, Dell Medical School, The University of Texas at Austin, Austin, TX 78712, USA
- Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX 78712, USA
- Interdisciplinary Life Sciences Graduate Programs (ILSGP), College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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3
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Qin N, Geng A, Xue R. Activated or Impaired: An Overview of DNA Repair in Neurodegenerative Diseases. Aging Dis 2022; 13:987-1004. [PMID: 35855336 PMCID: PMC9286913 DOI: 10.14336/ad.2021.1212] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 12/08/2021] [Indexed: 11/06/2022] Open
Abstract
As the population ages, age-related neurodegenerative diseases have become a major challenge in health science. Currently, the pathology of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease, is still not fully understood. Remarkably, emerging evidence indicates a role of genomic DNA damage and repair in various neurodegenerative disorders. Here, we summarized the current understanding of the function of DNA damage repair, especially base excision repair and double strand break repair pathways, in a variety of neurodegenerative diseases. We concluded that exacerbation of DNA lesions is found in almost all types of neurodegenerative diseases, whereas the activities of different DNA repair pathways demonstrate distinct trends, depending on disease type and even brain region. Specifically, key enzymes involved in base excision repair are likely impaired in Alzheimer's disease and amyotrophic lateral sclerosis but activated in Parkinson's disease, while nonhomologous end joining is likely downregulated in most types of neurodegenerative diseases. Hence, impairment of nonhomologous end joining is likely a common etiology for most neurodegenerative diseases, while defects in base excision repair are likely involved in the pathology of Alzheimer's disease and amyotrophic lateral sclerosis but are Parkinson's disease, based on current findings. Although there are still discrepancies and further studies are required to completely elucidate the exact roles of DNA repair in neurodegeneration, the current studies summarized here provide crucial insights into the pathology of neurodegenerative diseases and may reveal novel drug targets for corresponding neurodegenerative diseases.
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Affiliation(s)
- Nan Qin
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Anke Geng
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
| | - Renhao Xue
- Shanghai Key Laboratory of Maternal Fetal Medicine, Clinical and Translational Research Center of Shanghai First Maternity & Infant Hospital, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Tongji University, Shanghai, China
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4
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Pujar M, Vastrad B, Kavatagimath S, Vastrad C, Kotturshetti S. Identification of candidate biomarkers and pathways associated with type 1 diabetes mellitus using bioinformatics analysis. Sci Rep 2022; 12:9157. [PMID: 35650387 PMCID: PMC9160069 DOI: 10.1038/s41598-022-13291-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 05/16/2022] [Indexed: 12/14/2022] Open
Abstract
Type 1 diabetes mellitus (T1DM) is a metabolic disorder for which the underlying molecular mechanisms remain largely unclear. This investigation aimed to elucidate essential candidate genes and pathways in T1DM by integrated bioinformatics analysis. In this study, differentially expressed genes (DEGs) were analyzed using DESeq2 of R package from GSE162689 of the Gene Expression Omnibus (GEO). Gene ontology (GO) enrichment analysis, REACTOME pathway enrichment analysis, and construction and analysis of protein–protein interaction (PPI) network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network, and validation of hub genes were performed. A total of 952 DEGs (477 up regulated and 475 down regulated genes) were identified in T1DM. GO and REACTOME enrichment result results showed that DEGs mainly enriched in multicellular organism development, detection of stimulus, diseases of signal transduction by growth factor receptors and second messengers, and olfactory signaling pathway. The top hub genes such as MYC, EGFR, LNX1, YBX1, HSP90AA1, ESR1, FN1, TK1, ANLN and SMAD9 were screened out as the critical genes among the DEGs from the PPI network, modules, miRNA-hub gene regulatory network and TF-hub gene regulatory network. Receiver operating characteristic curve (ROC) analysis confirmed that these genes were significantly associated with T1DM. In conclusion, the identified DEGs, particularly the hub genes, strengthen the understanding of the advancement and progression of T1DM, and certain genes might be used as candidate target molecules to diagnose, monitor and treat T1DM.
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Affiliation(s)
- Madhu Pujar
- Department of Pediatrics, J J M Medical College, Davangere, Karnataka, 577004, India
| | - Basavaraj Vastrad
- Department of Pharmaceutical Chemistry, K.L.E. College of Pharmacy, Gadag, Karnataka, 582101, India
| | - Satish Kavatagimath
- Department of Pharmacognosy, K.L.E. College of Pharmacy, Belagavi, Karnataka, 590010, India
| | - Chanabasayya Vastrad
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, Karnataka, 580001, India.
| | - Shivakumar Kotturshetti
- Biostatistics and Bioinformatics, Chanabasava Nilaya, Bharthinagar, Dharwad, Karnataka, 580001, India
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5
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Bin-Jumah MN, Nadeem MS, Gilani SJ, Al-Abbasi FA, Ullah I, Alzarea SI, Ghoneim MM, Alshehri S, Uddin A, Murtaza BN, Kazmi I. Genes and Longevity of Lifespan. Int J Mol Sci 2022; 23:1499. [PMID: 35163422 PMCID: PMC8836117 DOI: 10.3390/ijms23031499] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/04/2022] [Accepted: 01/26/2022] [Indexed: 12/12/2022] Open
Abstract
Aging is a complex process indicated by low energy levels, declined physiological activity, stress induced loss of homeostasis leading to the risk of diseases and mortality. Recent developments in medical sciences and an increased availability of nutritional requirements has significantly increased the average human lifespan worldwide. Several environmental and physiological factors contribute to the aging process. However, about 40% human life expectancy is inherited among generations, many lifespan associated genes, genetic mechanisms and pathways have been demonstrated during last decades. In the present review, we have evaluated many human genes and their non-human orthologs established for their role in the regulation of lifespan. The study has included more than fifty genes reported in the literature for their contributions to the longevity of life. Intact genomic DNA is essential for the life activities at the level of cell, tissue, and organ. Nucleic acids are vulnerable to oxidative stress, chemotherapies, and exposure to radiations. Efficient DNA repair mechanisms are essential for the maintenance of genomic integrity, damaged DNA is not replicated and transferred to next generations rather the presence of deleterious DNA initiates signaling cascades leading to the cell cycle arrest or apoptosis. DNA modifications, DNA methylation, histone methylation, histone acetylation and DNA damage can eventually lead towards apoptosis. The importance of calorie restriction therapy in the extension of lifespan has also been discussed. The role of pathways involved in the regulation of lifespan such as DAF-16/FOXO (forkhead box protein O1), TOR and JNK pathways has also been particularized. The study provides an updated account of genetic factors associated with the extended lifespan and their interactive contributory role with cellular pathways.
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Affiliation(s)
- May Nasser Bin-Jumah
- Biology Department, College of Science, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
- Environment and Biomaterial Unit, Health Sciences Research Center, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Sadaf Jamal Gilani
- Department of Basic Health Sciences, Princess Nourah Bint Abdulrahman University, Riyadh 11671, Saudi Arabia;
| | - Fahad A. Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Inam Ullah
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan;
| | - Sami I. Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Aziz Uddin
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra 21300, Pakistan;
| | - Bibi Nazia Murtaza
- Department of Zoology, Abbottabad University of Science and Technology (AUST), Abbottabad 22310, Pakistan;
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
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6
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Zheng Y, Zheng L, Yu J, Jiang M, Zhang S, Cai X, Zhu M. Genetic variations in DNA repair gene NEIL1 associated with radiation pneumonitis risk in lung cancer patients. Mol Genet Genomic Med 2021; 9:e1698. [PMID: 34105905 PMCID: PMC8372061 DOI: 10.1002/mgg3.1698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 01/26/2021] [Accepted: 04/13/2021] [Indexed: 11/17/2022] Open
Abstract
Background Radiation pneumonitis (RP) is a common side effect in lung cancer patients who received radiotherapy. Our previous study found genetic variations in DNA repair gene NEIL1 may be a predictor of RP in patients with esophageal cancer. So, we hypothesis genetic variations in NEIL1 gene could affect the risk of RP in lung cancer patients following radiotherapy. Methods Genetic variations rs4462560 G>C and rs7402844 C>G in NEIL1 gene were genotyped in 174 lung cancer patients received radio(chemo)therapy. Luciferase assay, real‐time PCR and Western blot were used to access the effect of the variants on NEIL1 in HELF and HEF cell lines which were transfected with plasmids containing rs4462560 G>C and rs7402844 C>G. Results Patients with rs4462560 CC genotype had a lower risk of RP grade ≥2 than GG genotype. Compared with the CC genotype, rs7402844 GG genotype was associated with an increased RP grade ≥2 risk. What is more, rs4462560 G decreased the relative luciferase activity of NEIL1 gene promoter compared with the negative control in vitro, while rs4462560 C can increase the relative luciferase activity. The mRNA and protein level of the NEIL1 gene in rs4462560 G were lower than rs4462560 C. Conclusions Genetic variants of NEIL1 are associated with RP risk through regulation of NEIL1 expression and serve as independent biomarkers for prediction of RP in patients treated with thoracic radiotherapy.
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Affiliation(s)
- Yuming Zheng
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leizhen Zheng
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jiahua Yu
- Department of Radiation Oncology, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Mawei Jiang
- Department of Radiation Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Songfang Zhang
- Department of Radiation Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xuwei Cai
- Department of Radiation Oncology, Shanghai Chest Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Meiling Zhu
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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7
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Bonora E, Chakrabarty S, Kellaris G, Tsutsumi M, Bianco F, Bergamini C, Ullah F, Isidori F, Liparulo I, Diquigiovanni C, Masin L, Rizzardi N, Cratere MG, Boschetti E, Papa V, Maresca A, Cenacchi G, Casadio R, Martelli P, Matera I, Ceccherini I, Fato R, Raiola G, Arrigo S, Signa S, Sementa AR, Severino M, Striano P, Fiorillo C, Goto T, Uchino S, Oyazato Y, Nakamura H, Mishra SK, Yeh YS, Kato T, Nozu K, Tanboon J, Morioka I, Nishino I, Toda T, Goto YI, Ohtake A, Kosaki K, Yamaguchi Y, Nonaka I, Iijima K, Mimaki M, Kurahashi H, Raams A, MacInnes A, Alders M, Engelen M, Linthorst G, de Koning T, den Dunnen W, Dijkstra G, van Spaendonck K, van Gent DC, Aronica EM, Picco P, Carelli V, Seri M, Katsanis N, Duijkers FAM, Taniguchi-Ikeda M, De Giorgio R. Biallelic variants in LIG3 cause a novel mitochondrial neurogastrointestinal encephalomyopathy. Brain 2021; 144:1451-1466. [PMID: 33855352 DOI: 10.1093/brain/awab056] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Revised: 11/13/2020] [Accepted: 12/09/2020] [Indexed: 12/11/2022] Open
Abstract
Abnormal gut motility is a feature of several mitochondrial encephalomyopathies, and mutations in genes such as TYMP and POLG, have been linked to these rare diseases. The human genome encodes three DNA ligases, of which only one, ligase III (LIG3), has a mitochondrial splice variant and is crucial for mitochondrial health. We investigated the effect of reduced LIG3 activity and resulting mitochondrial dysfunction in seven patients from three independent families, who showed the common occurrence of gut dysmotility and neurological manifestations reminiscent of mitochondrial neurogastrointestinal encephalomyopathy. DNA from these patients was subjected to whole exome sequencing. In all patients, compound heterozygous variants in a new disease gene, LIG3, were identified. All variants were predicted to have a damaging effect on the protein. The LIG3 gene encodes the only mitochondrial DNA (mtDNA) ligase and therefore plays a pivotal role in mtDNA repair and replication. In vitro assays in patient-derived cells showed a decrease in LIG3 protein levels and ligase activity. We demonstrated that the LIG3 gene defects affect mtDNA maintenance, leading to mtDNA depletion without the accumulation of multiple deletions as observed in other mitochondrial disorders. This mitochondrial dysfunction is likely to cause the phenotypes observed in these patients. The most prominent and consistent clinical signs were severe gut dysmotility and neurological abnormalities, including leukoencephalopathy, epilepsy, migraine, stroke-like episodes, and neurogenic bladder. A decrease in the number of myenteric neurons, and increased fibrosis and elastin levels were the most prominent changes in the gut. Cytochrome c oxidase (COX) deficient fibres in skeletal muscle were also observed. Disruption of lig3 in zebrafish reproduced the brain alterations and impaired gut transit in vivo. In conclusion, we identified variants in the LIG3 gene that result in a mitochondrial disease characterized by predominant gut dysmotility, encephalopathy, and neuromuscular abnormalities.
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Affiliation(s)
- Elena Bonora
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Sanjiban Chakrabarty
- Department of Molecular Genetics, Erasmus MC, Rotterdam, 3000 CA, The Netherlands
| | - Georgios Kellaris
- Center for Human Disease Modeling, Duke University, Durham, NC 27710, USA
| | - Makiko Tsutsumi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, 470-1192, Japan
| | - Francesca Bianco
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Christian Bergamini
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Farid Ullah
- Center for Human Disease Modeling, Duke University, Durham, NC 27710, USA
| | - Federica Isidori
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Irene Liparulo
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Chiara Diquigiovanni
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Luca Masin
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Nicola Rizzardi
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Mariapia Giuditta Cratere
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy.,Division of Genetics and Cell Biology, San Raffaele Scientific Institute, Milan, 20132, Italy
| | - Elisa Boschetti
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Valentina Papa
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, 40123, Italy
| | - Alessandra Maresca
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, 40139, Italy
| | - Giovanna Cenacchi
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, 40123, Italy
| | - Rita Casadio
- Biocomputing Group, Department of Biological, Geological, Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - Pierluigi Martelli
- Biocomputing Group, Department of Biological, Geological, Environmental Sciences, University of Bologna, Bologna, 40126, Italy
| | - Ivana Matera
- IRCCS Istituto Giannina Gaslini, Genova, 16128, Italy
| | | | - Romana Fato
- Department of Pharmacy and Biotechnology, University of Bologna, Bologna, 40126, Italy
| | - Giuseppe Raiola
- Department of Paediatrics, Pugliese-Ciaccio Hospital, Catanzaro, 88100, Italy
| | - Serena Arrigo
- IRCCS Istituto Giannina Gaslini, Genova, 16128, Italy
| | - Sara Signa
- IRCCS Istituto Giannina Gaslini, Genova, 16128, Italy
| | | | | | | | | | - Tsuyoshi Goto
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, 611-0011, Japan
| | - Shumpei Uchino
- Department of Pediatrics, Teikyo University School of Medicine, Tokyo, 173-8605, Japan.,Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yoshinobu Oyazato
- Department of Pediatrics, Kakogawa Central City Hospital, Kakogawa, Hyogo, 675-8611, Japan
| | - Hisayoshi Nakamura
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Sushil K Mishra
- Glycoscience Group, National University of Ireland, Galway, H91 CF50, Ireland
| | - Yu-Sheng Yeh
- Laboratory of Molecular Function of Food, Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Uji, 611-0011, Japan
| | - Takema Kato
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, 470-1192, Japan
| | - Kandai Nozu
- Department of Pediatrics, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan
| | - Jantima Tanboon
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Ichiro Morioka
- Department of Pediatrics and Child Health, Nihon University School of Medicine, Tokyo, 173-8610, Japan
| | - Ichizo Nishino
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yu-Ichi Goto
- Department of Mental Retardation and Birth Defect Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Akira Ohtake
- Department of Pediatrics & Clinical Genomics, Faculty of Medicine, Saitama Medical University, Saitama, 350-0495, Japan
| | - Kenjiro Kosaki
- Center for Medical Genetics, Keio University School of Medicine, Tokyo, 160-8582, Japan
| | - Yoshiki Yamaguchi
- Laboratory of Pharmaceutical Physical Chemistry, Tohoku Medical and Pharmaceutical University, Miyagi, 981-8558, Japan
| | - Ikuya Nonaka
- Department of Neuromuscular Research, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Tokyo, 187-8502, Japan
| | - Kazumoto Iijima
- Department of Pediatrics, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan
| | - Masakazu Mimaki
- Department of Pediatrics, Teikyo University School of Medicine, Tokyo, 173-8605, Japan
| | - Hiroki Kurahashi
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, 470-1192, Japan
| | - Anja Raams
- Department of Molecular Genetics, Erasmus MC, Rotterdam, 3000 CA, The Netherlands
| | - Alyson MacInnes
- Department of Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Mariel Alders
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Marc Engelen
- Department of Neurology, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Gabor Linthorst
- Department of Metabolic Diseases, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Tom de Koning
- Department of Metabolic Diseases, UMCG, Groningen, 9700 RB, The Netherlands
| | | | - Gerard Dijkstra
- Department of Gastroenterology, UMCG, Groningen, 9700 RB, The Netherlands
| | - Karin van Spaendonck
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Dik C van Gent
- Department of Molecular Genetics, Erasmus MC, Rotterdam, 3000 CA, The Netherlands
| | - Eleonora M Aronica
- Department of Pathology, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Paolo Picco
- IRCCS Istituto Giannina Gaslini, Genova, 16128, Italy
| | - Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, 40123, Italy.,IRCCS Istituto delle Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, 40139, Italy
| | - Marco Seri
- Department of Medical and Surgical Sciences, St. Orsola-Malpighi Hospital, University of Bologna, Bologna, 40138, Italy
| | - Nicholas Katsanis
- Center for Human Disease Modeling, Duke University, Durham, NC 27710, USA
| | - Floor A M Duijkers
- Department of Clinical Genetics, Amsterdam UMC, University of Amsterdam, Amsterdam, 1100 DD, The Netherlands
| | - Mariko Taniguchi-Ikeda
- Division of Molecular Genetics, Institute for Comprehensive Medical Science, Fujita Health University, Aichi, 470-1192, Japan.,Department of Pediatrics, Kobe University Graduate School of Medicine, Hyogo, 650-0017, Japan.,Department of Clinical Genetics, Fujita Health University Hospital, Aichi, 470-1192, Japan
| | - Roberto De Giorgio
- Department of Morphology, Surgery and Experimental Medicine, St. Anna Hospital, University of Ferrara, Ferrara, 44124, Italy
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Deshmukh AL, Porro A, Mohiuddin M, Lanni S, Panigrahi GB, Caron MC, Masson JY, Sartori AA, Pearson CE. FAN1, a DNA Repair Nuclease, as a Modifier of Repeat Expansion Disorders. J Huntingtons Dis 2021; 10:95-122. [PMID: 33579867 PMCID: PMC7990447 DOI: 10.3233/jhd-200448] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
FAN1 encodes a DNA repair nuclease. Genetic deficiencies, copy number variants, and single nucleotide variants of FAN1 have been linked to karyomegalic interstitial nephritis, 15q13.3 microdeletion/microduplication syndrome (autism, schizophrenia, and epilepsy), cancer, and most recently repeat expansion diseases. For seven CAG repeat expansion diseases (Huntington's disease (HD) and certain spinocerebellar ataxias), modification of age of onset is linked to variants of specific DNA repair proteins. FAN1 variants are the strongest modifiers. Non-coding disease-delaying FAN1 variants and coding disease-hastening variants (p.R507H and p.R377W) are known, where the former may lead to increased FAN1 levels and the latter have unknown effects upon FAN1 functions. Current thoughts are that ongoing repeat expansions in disease-vulnerable tissues, as individuals age, promote disease onset. Fan1 is required to suppress against high levels of ongoing somatic CAG and CGG repeat expansions in tissues of HD and FMR1 transgenic mice respectively, in addition to participating in DNA interstrand crosslink repair. FAN1 is also a modifier of autism, schizophrenia, and epilepsy. Coupled with the association of these diseases with repeat expansions, this suggests a common mechanism, by which FAN1 modifies repeat diseases. Yet how any of the FAN1 variants modify disease is unknown. Here, we review FAN1 variants, associated clinical effects, protein structure, and the enzyme's attributed functional roles. We highlight how variants may alter its activities in DNA damage response and/or repeat instability. A thorough awareness of the FAN1 gene and FAN1 protein functions will reveal if and how it may be targeted for clinical benefit.
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Affiliation(s)
- Amit L. Deshmukh
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Antonio Porro
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mohiuddin Mohiuddin
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Gagan B. Panigrahi
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Marie-Christine Caron
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | - Jean-Yves Masson
- Department of Molecular Biology, Medical Biochemistry and Pathology; Laval University Cancer Research Center, Québec City, Quebec, Canada
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Québec City, Quebec, Canada
| | | | - Christopher E. Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- University of Toronto, Program of Molecular Genetics, Toronto, Ontario, Canada
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9
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Sharafeldin N, Richman J, Bosworth A, Chen Y, Singh P, Patel SK, Wang X, Francisco L, Forman SJ, Wong FL, Bhatia S. Clinical and Genetic Risk Prediction of Cognitive Impairment After Blood or Marrow Transplantation for Hematologic Malignancy. J Clin Oncol 2020; 38:1312-1321. [PMID: 32083992 DOI: 10.1200/jco.19.01085] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
PURPOSE Using a candidate gene approach, we tested the hypothesis that individual single nucleotide polymorphisms (SNPs) and gene-level variants are associated with cognitive impairment in patients with hematologic malignancies treated with blood or marrow transplantation (BMT) and that inclusion of these SNPs improves risk prediction beyond that offered by clinical and demographic characteristics. PATIENTS AND METHODS In the discovery cohort, BMT recipients underwent a standardized battery of neuropsychological tests pre-BMT and at 6 months, 1 year, 2 years, and 3 years post-BMT. Associations between 68 candidate genes and cognitive impairment were assessed using generalized estimating equation models. Elastic-Net regression was used to build Base (sociodemographic), Clinical, and Combined (Base plus Clinical plus genetic) risk prediction models of post-BMT impairment. An independent nonoverlapping cohort from the BMT Survivor Study with self-report of learning/memory problems (as identified by their health care provider) was used for model replication. RESULTS The discovery cohort included 277 participants (58.5% males; 68.6% non-Hispanic whites; and 46.6% allogeneic BMT recipients). Adjusting for BMT type, age at BMT, sex, race/ethnicity, and cognitive reserve, SNPs in the blood-brain barrier, telomere homeostasis, and DNA repair genes were significantly associated with cognitive impairment. Compared with the Clinical Model, the Combined Model had higher predictive power in both the discovery cohort (mean area under the receiver operating characteristic curve [AUC], 0.89; 95% CI, 0.85 to 0.93 v 0.77; 95% CI, 0.71 to 0.83; P = 1.24 × 10-9) and the replication cohort (AUC, 0.71; 95% CI, 0.66 to 0.76 v 0.63; 95% CI, 0.57 to 0.68; P = .004). CONCLUSION Inclusion of candidate genetic variants enhanced the prediction of risk of post-BMT cognitive impairment beyond that offered by demographic/clinical characteristics and represents a step toward a personalized approach to managing patients at high risk for cognitive impairment after BMT.
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Affiliation(s)
- Noha Sharafeldin
- Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Joshua Richman
- Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | | | - Yanjun Chen
- Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Purnima Singh
- Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | | | - Xuexia Wang
- Department of Mathematics, University of North Texas, Denton, TX
| | - Liton Francisco
- Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
| | - Stephen J Forman
- Hematology and Hematopoietic Cell Transplantation, City of Hope, Duarte, CA
| | | | - Smita Bhatia
- Institute for Cancer Outcomes and Survivorship, School of Medicine, University of Alabama at Birmingham, Birmingham, AL
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10
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Czarny P, Bialek K, Ziolkowska S, Strycharz J, Sliwinski T. DNA damage and repair in neuropsychiatric disorders. What do we know and what are the future perspectives? Mutagenesis 2019; 35:79-106. [DOI: 10.1093/mutage/gez035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Accepted: 09/27/2019] [Indexed: 12/11/2022] Open
Abstract
AbstractOver the past two decades, extensive research has been done to elucidate the molecular etiology and pathophysiology of neuropsychiatric disorders. In majority of them, including Alzheimer’s disease (AD), Parkinson’s disease (PD), amyotrophic lateral sclerosis (ALS), bipolar disorder (BD), schizophrenia and major depressive disorder, increased oxidative and nitrosative stress was found. This stress is known to induce oxidative damage to biomolecules, including DNA. Accordingly, increased mitochondrial and nuclear DNA, as well as RNA damage, were observed in patients suffering from these diseases. However, recent findings indicate that the patients are characterised by impaired DNA repair pathways, which may suggest that these DNA lesions could be also a result of their insufficient repair. In the current systematic, critical review, we aim to sum up, using available literature, the knowledge about the involvement of nuclear and mitochondrial DNA damage and repair, as well as about damage to RNA in pathoetiology of neuropsychiatric disorders, i.e., AD, PD, ALS, BD, schizophrenia and major depressive disorder, as well as the usefulness of the discussed factors as being diagnostic markers and targets for new therapies. Moreover, we also underline the new directions to which future studies should head to elucidate these phenomena.
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Affiliation(s)
- Piotr Czarny
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Katarzyna Bialek
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Sylwia Ziolkowska
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Justyna Strycharz
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Tomasz Sliwinski
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
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11
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Dinçer Y, Akkaya Ç, Mutlu T, Yavuzer S, Erkol G, Bozluolcay M, Guven M. DNA repair gene OGG1 polymorphism and its relation with oxidative DNA damage in patients with Alzheimer’s disease. Neurosci Lett 2019; 709:134362. [DOI: 10.1016/j.neulet.2019.134362] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 06/19/2019] [Accepted: 07/01/2019] [Indexed: 12/26/2022]
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12
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Ertuzun T, Semerci A, Cakir ME, Ekmekcioglu A, Gok MO, Soltys DT, de Souza-Pinto NC, Sezerman U, Muftuoglu M. Investigation of base excision repair gene variants in late-onset Alzheimer's disease. PLoS One 2019; 14:e0221362. [PMID: 31415677 PMCID: PMC6695184 DOI: 10.1371/journal.pone.0221362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/05/2019] [Indexed: 12/03/2022] Open
Abstract
Base excision repair (BER) defects and concomitant oxidative DNA damage accumulation play a role in the etiology and progression of late-onset Alzheimer’s disease (LOAD). However, it is not known whether genetic variant(s) of specific BER genes contribute to reduced BER activity in LOAD patients and whether they are associated with risk, development and/or progression of LOAD. Therefore, we performed targeted next generation sequencing for three BER genes, uracil glycosylase (UNG), endonuclease VIII-like DNA glycosylase 1 (NEIL1) and polymerase β (POLβ) including promoter, exonic and intronic regions in peripheral blood samples and postmortem brain tissues (temporal cortex, TC and cerebellum, CE) from LOAD patients, high-pathology control and cognitively normal age-matched controls. In addition, the known LOAD risk factor, APOE was included in this study to test whether any BER gene variants associate with APOE variants, particularly APOE ε4. We show that UNG carry five significant variants (rs1610925, rs2268406, rs80001089, rs1018782 and rs1018783) in blood samples of Turkish LOAD patients compared to age-matched controls and one of them (UNG rs80001089) is also significant in TC from Brazilian LOAD patients (p<0.05). The significant variants present only in CE and TC from LOAD are UNG rs2569987 and POLβ rs1012381950, respectively. There is also significant epistatic relationship (p = 0.0410) between UNG rs80001089 and NEIL1 rs7182283 in TC from LOAD subjects. Our results suggest that significant BER gene variants may be associated with the risk of LOAD in non-APOE ε4 carriers. On the other hand, there are no significant UNG, NEIL1 and POLβ variants that could affect their protein level and function, suggesting that there may be other factors such as post-transcriptional or–translational modifications responsible for the reduced activities and protein levels of these genes in LOAD pathogenesis. Further studies with increased sample size are needed to confirm the relationship between BER variants and LOAD risk.
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Affiliation(s)
- Tugce Ertuzun
- Department of Molecular Biology and Genetics
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Asli Semerci
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Mehmet Emin Cakir
- Department of Neurology, Medeniyet University, Goztepe Training and Research Hospital, Istanbul, Turkey
| | - Aysegul Ekmekcioglu
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Mehmet Oguz Gok
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Daniela T. Soltys
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Nadja C. de Souza-Pinto
- Departmento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
| | - Ugur Sezerman
- Department of Biostatistics and Medical Informatics, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Meltem Muftuoglu
- Department of Molecular Biology and Genetics
- Department of Medical Biotechnology, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
- * E-mail:
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13
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AP endonuclease 1 (Apex1) influences brain development linking oxidative stress and DNA repair. Cell Death Dis 2019; 10:348. [PMID: 31024003 PMCID: PMC6484078 DOI: 10.1038/s41419-019-1578-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Revised: 03/27/2019] [Accepted: 04/04/2019] [Indexed: 12/13/2022]
Abstract
Brain and neurons are particularly sensitive to reactive oxygen species (ROS). Oxidative damage from ROS results in increased 8-oxoguanine in DNA followed by repair through the base excision repair (BER) pathway. We reported earlier that AP endonuclease 1 (Apex1) not only participates directly in BER but also regulates transcription factor Creb1. Here, we investigated how Apex1 affects brain to respond effectively to oxidative damage during zebrafish development. Loss of Apex1 resulted in increased ROS, 8-oxoguanine, and abasic sites as well as loss of Ogg1, which recognizes 8-oxoguanine and is required for its repair. Moreover, knock-down of Apex1 not only resulted in reduction of expression of several major proteins in the BER pathway (Polb and Ogg1), and it also resulted in maldistribution and loss of four key brain transcription factors (fezf2, otx2, egr2a, and pax2a), leading to abnormal brain development. These results were independent of p53 protein level. In contrast, exposure to exogenous H2O2 resulted in increased transcription and protein of Apex1 along with other BER components, as well as Creb1. Taken together, these results indicate that oxidative stress increased when the level of Apex1 was reduced, revealing a novel pathway of how Apex1 manages oxidative stress in developing brain.
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14
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Lin E, Kuo PH, Liu YL, Yang AC, Tsai SJ. Polymorphisms of the DNA repair gene EXO1 modulate cognitive aging in old adults in a Taiwanese population. DNA Repair (Amst) 2019; 78:1-6. [PMID: 30928815 DOI: 10.1016/j.dnarep.2019.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 12/15/2022]
Abstract
Evidence indicates that the age-related neuropathological mechanisms associated with DNA repair genes may contribute to cognitive aging and Alzheimer's disease. In this study, we hypothesize that single nucleotide polymorphisms (SNPs) within 155 DNA repair genes may be linked to cognitive aging independently and/or through complex interactions in an older Taiwanese population. A total of 3,730 Taiwanese subjects aged over 60 years from the Taiwan Biobank were analyzed. Mini-Mental State Examination (MMSE) was administered to all subjects, and MMSE scores were used to measure cognitive functions. Our data showed that out of 1,652 SNPs, the rs1776181 (P = 1.47 × 10-5), rs1776177 (P = 8.42 × 10-7), rs1635510 (P = 7.97 × 10-6), and rs2526698 (P = 7.06 × 10-6) SNPs in the EXO1 gene were associated with cognitive aging. The association with these SNP remained significant after performing Bonferroni correction. Additionally, we found that interactions between the EXO1 and RAD51C genes influenced cognitive aging (P = 0.002). Finally, we pinpointed the influence of interactions between EXO1 and physical activity (P < 0.001) as well as between DCLRE1C and physical activity (P < 0.001). Our study indicated that DNA repair genes may contribute to susceptibility in cognitive aging independently as well as through gene-gene and gene-physical interactions.
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Affiliation(s)
- Eugene Lin
- Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA; Department of Electrical & Computer Engineering, University of Washington, Seattle, WA, 98195, USA; Graduate Institute of Biomedical Sciences, China Medical University, Taichung, Taiwan.
| | - Po-Hsiu Kuo
- Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Li Liu
- Center for Neuropsychiatric Research, National Health Research Institutes, Miaoli County, Taiwan
| | - Albert C Yang
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan; Division of Interdisciplinary Medicine and Biotechnology, Beth Israel Deaconess Medical Center/Harvard Medical School, Boston, MA, 02215, USA; Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan
| | - Shih-Jen Tsai
- Department of Psychiatry, Taipei Veterans General Hospital, Taipei, Taiwan; Division of Psychiatry, National Yang-Ming University, Taipei, Taiwan; Institute of Brain Science, National Yang-Ming University, Taipei, Taiwan.
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15
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DNA Repair Protein OGG1 in Pulmonary Infection and Other Inflammatory Lung Diseases. OXIDATIVE STRESS IN LUNG DISEASES 2019. [PMCID: PMC7121726 DOI: 10.1007/978-981-13-8413-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
In the last decades, extensive research has uncovered functional roles and underlying mechanisms of DNA repair enzyme 8-oxoguanine DNA glycosylase (OGG1) in the pathogenesis of inflammatory response in infection and other diseases in the lung. OGG1 excises 8-oxo-7,8-dihydroguanine (8-oxo-dG) lesion on DNA that is often induced by generation of reactive oxygen species (ROS) and has been linked to mutations, cancer development, and tissue damage. Most, if not all, environmental toxic agents and mammalian cellular metabolites elicit the generation of ROS, either directly, indirectly, or both, which is among the first cellular responses. ROS in combination with other oxidative molecules/moieties are recognized as a major factor for killing invading pathogens but meanwhile can cause tissue damage. ROS potentially modify proteins, lipids, and DNA due to the strong molecular reactivity. While oxidative stress causes increased levels of all types of oxidatively modified DNA bases, accumulation of 8-oxo-dG in the DNA has been singled out to be a main culprit linking to various inflammatory disease processes. Oxidatively damaged DNA bases such as 8-oxo-dG are primarily repaired by the base excision repair (BER) mechanism, in which OGG1, as the lesion recognition enzyme, plays a fundamental role in fixing this DNA damage. In this chapter, we summarize the roles and potential mechanistic analyses of OGG1 in lung infection and other inflammatory diseases.
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16
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Werner syndrome (WRN) DNA helicase and base excision repair (BER) factors maintain endothelial homeostasis. DNA Repair (Amst) 2018; 73:17-27. [PMID: 30413344 DOI: 10.1016/j.dnarep.2018.10.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Revised: 09/26/2018] [Accepted: 10/18/2018] [Indexed: 11/21/2022]
Abstract
The accelerated ageing disease Werner Syndrome (WRN) is characterized by pronounced atherosclerosis. Here, we investigated the influence of WRN downregulation on the functionality of non-replicating human endothelial cells. RNAi-mediated downregulation of WRN reduces cell motility and enhances the expression of factors regulating adhesion, inflammation, hemostasis and vasomotor tone. Moreover, WRN influences endothelial barrier function and Ca2+-release, while cell adhesion, Dil-acLDL-uptake and the mRNA expression of NO-synthases (eNOS, iNOS) remained unaffected. Regarding motility, we propose that WRN affects Rac1/FAK/ß1-integrin-related mechanisms regulating cell polarity and directed motility. Since oxidative DNA base damage contributes to aging and atherosclerosis and WRN affects DNA repair, we investigated whether downregulation of base excision repair (BER) factors mimics the effects of WRN knock-down. Indeed, downregulation of particular WRN-interacting base excision repair (BER) proteins (APE1, NEIL1, PARP1) imitates the inhibitory effect of WRN on motility. Knock-down of OGG1, which does not interact with WRN, does not influence motility but increases the mRNA expression of E-selectin, ICAM, VCAM, CCL2 and VEGFR and stimulates adhesion. Thus, individual BER factors themselves differently impact endothelial cell functionality and homeostasis. Impairment of endothelial activities caused by genotoxic stressor (tBHQ) remained largely unaffected by WRN. Summarizing, both WRN, WRN-associated BER proteins and OGG1 promote the maintenance of endothelial cell homeostasis, thereby counteracting the development of ageing-related endothelial malfunction in non-proliferating endothelial cells.
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17
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The interplay between inflammation, oxidative stress, DNA damage, DNA repair and mitochondrial dysfunction in depression. Prog Neuropsychopharmacol Biol Psychiatry 2018; 80:309-321. [PMID: 28669580 DOI: 10.1016/j.pnpbp.2017.06.036] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/05/2017] [Accepted: 06/29/2017] [Indexed: 12/13/2022]
Abstract
A growing body of evidence suggests that inflammation, mitochondrial dysfunction and oxidant-antioxidant imbalance may play a significant role in the development and progression of depression. Elevated levels of reactive oxygen and nitrogen species - a result of oxidant-antioxidant imbalance - may lead to increased damage of biomolecules, including DNA. This was confirmed in depressed patients in a research study conducted by our team and other scientists. 8-oxoguanine - a marker of oxidative DNA damage - was found in the patients' lymphocytes, urine and serum. These results were confirmed using a comet assay on lymphocytes. Furthermore, it was shown that the patients' cells repaired peroxide-induced DNA damage less efficiently than controls' cells and that some single nucleotide polymorphisms (SNP) of the genes involved in oxidative DNA damage repair may modulate the risk of depression. Lastly, less efficient DNA damage repair observed in the patients can be, at least partly, attributed to the presence of specific SNP variants, as it was revealed through a genotype-phenotype analysis. In conclusion, the available literature shows that both oxidative stress and less efficient DNA damage repair may lead to increased DNA damage in depressed patients. A similar mechanism may result in mitochondrial dysfunction, which is observed in depression.
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18
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Rumsey WL, Bolognese B, Davis AB, Flamberg PL, Foley JP, Katchur SR, Kotzer CJ, Osborn RR, Podolin PL. Effects of airborne toxicants on pulmonary function and mitochondrial DNA damage in rodent lungs. Mutagenesis 2017; 32:343-353. [PMID: 27993944 DOI: 10.1093/mutage/gew063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Inhalation of airborne toxicants such as cigarette smoke and ozone is a shared health risk among the world's populations. The use of toxic herbicides like paraquat (PQ) is restricted by many countries, yet in the developing world PQ has demonstrable ill effects. The present study examined changes in pulmonary function, mitochondrial DNA (mtDNA) integrity and markers of DNA repair induced by acute or repeated exposure of PQ to rats. Similar to cigarette smoke and ozone, PQ promotes oxidative stress, and the impact of PQ on mtDNA was compared with that obtained with these agents. Tracheal instillation (i.t.) of PQ (0.01-0.075 mg/kg) dose dependently increased Penh (dyspnoea) by 48 h while body weight and temperature declined. Lung wet weight and the wet/dry weight ratio rose; for the latter, by as much as 52%. At low doses (0.02 and 0.03 mg/kg), PQ increased Penh by about 7.5-fold at 72 h. It quickly waned to near baseline levels. The lung wet/dry weight ratio remained elevated 7 days after administration coincident with marked inflammatory cell infiltrate. Repeated administration of PQ (1 per week for 8 weeks) resulted in a similar rise in Penh on the first instillation, but the magnitude of this response was markedly attenuated upon subsequent exposures. Pulmonary [lactate] and catalase activity, [8-oxodG] and histone fragmentation (cell death) were significantly increased. Repeated PQ instillation downregulated the expression of the mitochondrial-encoded genes, mtATP8, mtNd2 and mtcyB and nuclear ones for the DNA glycosylases, Ogg1, Neil1, Neil2 and Neil3. Ogg1 protein content decreased after acute and repeated PQ administration. mtDNA damage or changes in mtDNA copy number were evident in lungs of PQ-, cigarette smoke- and ozone-exposed animals. Taken together, these data indicate that loss of pulmonary function and inflammation are coupled to the loss of mtDNA integrity and DNA repair capability following exposure to airborne toxicants.
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Affiliation(s)
- William L Rumsey
- Respiratory Therapeutic Area, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO Box 1539, King of Prussia, PA 19406, USA
| | - Brian Bolognese
- Respiratory Therapeutic Area, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO Box 1539, King of Prussia, PA 19406, USA
| | - Alicia B Davis
- Respiratory Therapeutic Area, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO Box 1539, King of Prussia, PA 19406, USA
| | - Pearl L Flamberg
- Respiratory Therapeutic Area, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO Box 1539, King of Prussia, PA 19406, USA
| | - Joseph P Foley
- Respiratory Therapeutic Area, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO Box 1539, King of Prussia, PA 19406, USA
| | - Steven R Katchur
- Respiratory Therapeutic Area, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO Box 1539, King of Prussia, PA 19406, USA
| | - Charles J Kotzer
- Respiratory Therapeutic Area, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO Box 1539, King of Prussia, PA 19406, USA
| | - Ruth R Osborn
- Respiratory Therapeutic Area, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO Box 1539, King of Prussia, PA 19406, USA
| | - Patricia L Podolin
- Respiratory Therapeutic Area, GlaxoSmithKline Pharmaceuticals, 709 Swedeland Road, PO Box 1539, King of Prussia, PA 19406, USA
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19
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Karahalil B, Elkama A, Orhan G. Oxidative stress gene polymorphisms may have an impact in the development of ischemic stroke. J Gene Med 2017; 19. [PMID: 28198160 DOI: 10.1002/jgm.2947] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 02/09/2017] [Accepted: 02/10/2017] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Antioxidants are responsible for detoxification of harmful effects of reactive oxygen species. Genetic factors may influence antioxidant activity as a result of polymorphisms on antioxidant enzymes. These polymorphisms can be risk in ischemic stroke (IS) risk. IS is a disorder with genetic and environmental factors contributing to overall risk. Although a few studies have been conducted, there have been no reports on catalase (CAT C262T), manganese superoxide dismutase (MnSOD Ala16Val) and glutathione peroxidase 1 (GPX1 Pro198Leu) gene polymorphisms and IS risk. METHODS We aimed to perform a case-control study to increase the awareness of the impact of oxidative stress (OS) gene polymorphism in the development of IS. A restriction fragment length polymorphism-polymerase chain reaction was used to determine genotypes. The interactions between genes and smoking and possible risk factors were evaluated. RESULTS An approximately four-fold higher IS risk was found in patients with the Val allele compared to the Ala allele. Smoking was a risk factor in the development of IS for CAT TT and MnSOD Ala/Val genotypes; we found a 3.5- to 5.5-fold higher IS risk in CAT TT and MnSOD Ala/Val genotypes. Different logistic regression models were performed for possible risk factors (smoking, body mass index, low-density lipoprotein and diabetes mellitus). The IS risk increases statistically significant only with age by multiple logistic regression analysis. CAT gene polymorphisms in IS patients were not different from controls. CONCLUSIONS It is unlikely that CAT and GPX1 single nucleotide polymorphisms are risk factors for IS. The results of the present study show that smoking may be a risk factor for IS risk in patients with MnSOD mutant genotypes.
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Affiliation(s)
- Bensu Karahalil
- Faculty of Pharmacy, Department of Toxicology, Gazi University, Ankara, Turkey
| | - Aylin Elkama
- Faculty of Pharmacy, Department of Toxicology, Gazi University, Ankara, Turkey
| | - Gürdal Orhan
- Clinics of Neurology, Ankara Numune Hospital, Ankara, Turkey
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Sliwinska A, Kwiatkowski D, Czarny P, Toma M, Wigner P, Drzewoski J, Fabianowska-Majewska K, Szemraj J, Maes M, Galecki P, Sliwinski T. The levels of 7,8-dihydrodeoxyguanosine (8-oxoG) and 8-oxoguanine DNA glycosylase 1 (OGG1) - A potential diagnostic biomarkers of Alzheimer's disease. J Neurol Sci 2016; 368:155-9. [PMID: 27538622 DOI: 10.1016/j.jns.2016.07.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 06/02/2016] [Accepted: 07/07/2016] [Indexed: 11/17/2022]
Abstract
Evidence indicates that oxidative stress contributes to neuronal cell death in Alzheimer's disease (AD). Increased oxidative DNA damage l, as measured with 8-oxoguanine (8-oxoG), and reduced capacity of proteins responsible for removing of DNA damage, including 8-oxoguanine DNA glycosylase 1 (OGG1), were detected in brains of AD patients. In the present study we assessed peripheral blood biomarkers of oxidative DNA damage, i.e. 8- oxoG and OGG1, in AD diagnosis, by comparing their levels between the patients and the controls. Our study was performed on DNA and serum isolated from peripheral blood taken from 100 AD patients and 110 controls. For 8-oxoG ELISA was employed. The OGG1 level was determined using ELISA and Western blot technique. Levels of 8-oxoG were significantly higher in DNA of AD patients. Both ELISA and Western blot showed decreased levels of OGG1 in serum of AD patients. Our results show that oxidative DNA damage biomarkers detected in peripheral tissue could reflect the changes occurring in the brain of patients with AD. These results also suggest that peripheral blood samples may be useful to measure oxidative stress biomarkers in AD.
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Affiliation(s)
- Agnieszka Sliwinska
- Department of Internal Disease, Diabetology and Clinical Pharmacology, Medical University of Lodz, Lodz, Poland
| | | | - Piotr Czarny
- University of Lodz, Department of Molecular Genetics, Lodz, Poland; Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Monika Toma
- University of Lodz, Department of Molecular Genetics, Lodz, Poland
| | - Paulina Wigner
- University of Lodz, Department of Molecular Genetics, Lodz, Poland
| | - Jozef Drzewoski
- Department of Internal Disease, Diabetology and Clinical Pharmacology, Medical University of Lodz, Lodz, Poland
| | | | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Lodz, Lodz, Poland
| | - Michael Maes
- Deakin University IMPACT Strategic Research Centre, Deakin University, School of Medicine, Barwon Health, Geelong, Australia; Department of Psychiatry, Chulalongkorn University, Bangkok, Thailand; Health Sciences Graduate Program, Health Sciences Center, State University of Londrina, Brazil
| | - Piotr Galecki
- Department of Adult Psychiatry, Medical University of Lodz, Lodz, Poland
| | - Tomasz Sliwinski
- University of Lodz, Department of Molecular Genetics, Lodz, Poland.
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