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Hishikawa A, Nishimura ES, Yoshimoto N, Nakamichi R, Hama EY, Ito W, Maruki T, Nagashima K, Shimizu-Hirota R, Takaishi H, Itoh H, Hayashi K. Predicting exacerbation of renal function by DNA methylation clock and DNA damage of urinary shedding cells: a pilot study. Sci Rep 2024; 14:11530. [PMID: 38773208 PMCID: PMC11109093 DOI: 10.1038/s41598-024-62405-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 05/16/2024] [Indexed: 05/23/2024] Open
Abstract
Recent reports have shown the feasibility of measuring biological age from DNA methylation levels in blood cells from specific regions identified by machine learning, collectively known as the epigenetic clock or DNA methylation clock. While extensive research has explored the association of the DNA methylation clock with cardiovascular diseases, cancer, and Alzheimer's disease, its relationship with kidney diseases remains largely unexplored. In particular, it is unclear whether the DNA methylation clock could serve as a predictor of worsening kidney function. In this pilot study involving 20 subjects, we investigated the association between the DNA methylation clock and subsequent deterioration of renal function. Additionally, we noninvasively evaluated DNA damage in urinary shedding cells using a previously reported method to examine the correlation with the DNA methylation clock and worsening kidney function. Our findings revealed that patients with an accelerated DNA methylation clock exhibited increased DNA damage in urinary shedding cells, along with a higher rate of eGFR decline. Moreover, in cases of advanced CKD (G4-5), the DNA damage in urinary shedding cells was significantly increased, highlighting the interplay between elevated DNA damage and eGFR decline. This study suggests the potential role of the DNA methylation clock and urinary DNA damage as predictive markers for the progression of chronic kidney disease.
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Affiliation(s)
- Akihito Hishikawa
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan.
| | - Erina Sugita Nishimura
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Norifumi Yoshimoto
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Ran Nakamichi
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Eriko Yoshida Hama
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Wataru Ito
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Tomomi Maruki
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan
| | - Kengo Nagashima
- Biostatistics Unit, Clinical and Translational Research Center, Keio University School of Medicine, Tokyo, Japan
| | - Ryoko Shimizu-Hirota
- Center for Preventive Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hiromasa Takaishi
- Center for Preventive Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Hiroshi Itoh
- Center for Preventive Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Kaori Hayashi
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-Ku, Tokyo, 160-8582, Japan.
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2
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Yang S, Liu C, Jiang M, Liu X, Geng L, Zhang Y, Sun S, Wang K, Yin J, Ma S, Wang S, Belmonte JCI, Zhang W, Qu J, Liu GH. A single-nucleus transcriptomic atlas of primate liver aging uncovers the pro-senescence role of SREBP2 in hepatocytes. Protein Cell 2024; 15:98-120. [PMID: 37378670 PMCID: PMC10833472 DOI: 10.1093/procel/pwad039] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Aging increases the risk of liver diseases and systemic susceptibility to aging-related diseases. However, cell type-specific changes and the underlying mechanism of liver aging in higher vertebrates remain incompletely characterized. Here, we constructed the first single-nucleus transcriptomic landscape of primate liver aging, in which we resolved cell type-specific gene expression fluctuation in hepatocytes across three liver zonations and detected aberrant cell-cell interactions between hepatocytes and niche cells. Upon in-depth dissection of this rich dataset, we identified impaired lipid metabolism and upregulation of chronic inflammation-related genes prominently associated with declined liver functions during aging. In particular, hyperactivated sterol regulatory element-binding protein (SREBP) signaling was a hallmark of the aged liver, and consequently, forced activation of SREBP2 in human primary hepatocytes recapitulated in vivo aging phenotypes, manifesting as impaired detoxification and accelerated cellular senescence. This study expands our knowledge of primate liver aging and informs the development of diagnostics and therapeutic interventions for liver aging and associated diseases.
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Affiliation(s)
- Shanshan Yang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Xuanwu Hospital Capital Medical University, Beijing 100053, China
| | - Chengyu Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mengmeng Jiang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Xiaoqian Liu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Lingling Geng
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Yiyuan Zhang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Shuhui Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Kang Wang
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jian Yin
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuai Ma
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
| | - Si Wang
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | | | - Weiqi Zhang
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences and China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Jing Qu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
| | - Guang-Hui Liu
- Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders, Xuanwu Hospital Capital Medical University, Beijing 100053, China
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Aging Translational Medicine Center, International Center for Aging and Cancer, Beijing Municipal Geriatric Medical Research Center, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
- Xuanwu Hospital Capital Medical University, Beijing 100053, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Institute for Stem Cell and Regeneration, Chinese Academy of Sciences, Beijing 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing 100101, China
- Aging Biomarker Consortium, Beijing 100101, China
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3
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Xie K, Ehninger D. Ageing-associated phenotypes in mice. Mech Ageing Dev 2023; 214:111852. [PMID: 37454704 DOI: 10.1016/j.mad.2023.111852] [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: 04/21/2023] [Revised: 06/22/2023] [Accepted: 07/10/2023] [Indexed: 07/18/2023]
Abstract
Ageing is a continuous process in life featuring progressive damage accumulation that leads to physiological decline, functional deterioration and ultimately death of an organism. Based on the relatively close anatomical and physiological similarity to humans, the mouse has been proven as a valuable model organism in ageing research over the last decades. In this review, we survey methods and tools currently in use to assess ageing phenotypes in mice. We summarize a range of ageing-associated alterations detectable at two major levels of analysis: (1) physiology and pathophysiology and (2) molecular biomarkers. Age-sensitive phenotypes provided in this article may serve to inform future studies targeting various aspects of organismal ageing in mice. In addition, we discuss conceptual and technical challenges faced by previous ageing studies in mice and, where possible, provide recommendations on how to resolve some of these issues.
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Affiliation(s)
- Kan Xie
- Translational Biogerontology Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1/99, 53127 Bonn, Germany
| | - Dan Ehninger
- Translational Biogerontology Lab, German Center for Neurodegenerative Diseases (DZNE), Venusberg-Campus 1/99, 53127 Bonn, Germany.
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4
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Singh P, Gollapalli K, Mangiola S, Schranner D, Yusuf MA, Chamoli M, Shi SL, Bastos BL, Nair T, Riermeier A, Vayndorf EM, Wu JZ, Nilakhe A, Nguyen CQ, Muir M, Kiflezghi MG, Foulger A, Junker A, Devine J, Sharan K, Chinta SJ, Rajput S, Rane A, Baumert P, Schönfelder M, Iavarone F, Lorenzo GD, Kumari S, Gupta A, Sarkar R, Khyriem C, Chawla AS, Sharma A, Sarper N, Chattopadhyay N, Biswal BK, Settembre C, Nagarajan P, Targoff KL, Picard M, Gupta S, Velagapudi V, Papenfuss AT, Kaya A, Ferreira MG, Kennedy BK, Andersen JK, Lithgow GJ, Ali AM, Mukhopadhyay A, Palotie A, Kastenmüller G, Kaeberlein M, Wackerhage H, Pal B, Yadav VK. Taurine deficiency as a driver of aging. Science 2023; 380:eabn9257. [PMID: 37289866 PMCID: PMC10630957 DOI: 10.1126/science.abn9257] [Citation(s) in RCA: 64] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Accepted: 04/14/2023] [Indexed: 06/10/2023]
Abstract
Aging is associated with changes in circulating levels of various molecules, some of which remain undefined. We find that concentrations of circulating taurine decline with aging in mice, monkeys, and humans. A reversal of this decline through taurine supplementation increased the health span (the period of healthy living) and life span in mice and health span in monkeys. Mechanistically, taurine reduced cellular senescence, protected against telomerase deficiency, suppressed mitochondrial dysfunction, decreased DNA damage, and attenuated inflammaging. In humans, lower taurine concentrations correlated with several age-related diseases and taurine concentrations increased after acute endurance exercise. Thus, taurine deficiency may be a driver of aging because its reversal increases health span in worms, rodents, and primates and life span in worms and rodents. Clinical trials in humans seem warranted to test whether taurine deficiency might drive aging in humans.
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Affiliation(s)
- Parminder Singh
- Metabolic Research Laboratories, National Institute of Immunology; New Delhi, India
| | - Kishore Gollapalli
- Vagelos College of Physicians and Surgeons, Columbia University; New York, USA
| | - Stefano Mangiola
- Department of Medical Biology, University of Melbourne; Melbourne, Australia
- School of Cancer Medicine, La Trobe University; Bundoora, Australia
- Olivia Newton-John Cancer Research Institute; Heidelberg, Australia
| | - Daniela Schranner
- Exercise Biology Group, Technical University of Munich; Munich, Germany
- Institute of Computational Biology, Helmholtz Zentrum München; Neuherberg, Germany
| | - Mohd Aslam Yusuf
- Department of Bioengineering, Integral University; Lucknow, India
| | - Manish Chamoli
- Buck Institute of Age Research, 8001 Redwood Blvd; California, USA
| | - Sting L. Shi
- Vagelos College of Physicians and Surgeons, Columbia University; New York, USA
| | - Bruno Lopes Bastos
- Institute for Research on Cancer and Aging of Nice (IRCAN); Nice, France
| | - Tripti Nair
- Molecular Aging Laboratory, National Institute of Immunology; New Delhi, India
| | - Annett Riermeier
- Exercise Biology Group, Technical University of Munich; Munich, Germany
| | - Elena M. Vayndorf
- Department of Laboratory Medicine and Pathology, University of Washington; WA, USA
| | - Judy Z. Wu
- Department of Laboratory Medicine and Pathology, University of Washington; WA, USA
| | - Aishwarya Nilakhe
- Metabolic Research Laboratories, National Institute of Immunology; New Delhi, India
| | - Christina Q. Nguyen
- Department of Laboratory Medicine and Pathology, University of Washington; WA, USA
| | - Michael Muir
- Department of Laboratory Medicine and Pathology, University of Washington; WA, USA
| | - Michael G. Kiflezghi
- Department of Laboratory Medicine and Pathology, University of Washington; WA, USA
| | - Anna Foulger
- Buck Institute of Age Research, 8001 Redwood Blvd; California, USA
| | - Alex Junker
- Department of Neurology, Columbia University; New York, USA
| | - Jack Devine
- Department of Neurology, Columbia University; New York, USA
| | - Kunal Sharan
- Mouse Genetics Project, Wellcome Sanger Institute; Cambridge, UK
| | | | - Swati Rajput
- Division of Endocrinology, CSIR-Central Drug Research Institute; Lucknow, India
| | - Anand Rane
- Buck Institute of Age Research, 8001 Redwood Blvd; California, USA
| | - Philipp Baumert
- Exercise Biology Group, Technical University of Munich; Munich, Germany
| | | | | | | | - Swati Kumari
- Metabolic Research Laboratories, National Institute of Immunology; New Delhi, India
| | - Alka Gupta
- Metabolic Research Laboratories, National Institute of Immunology; New Delhi, India
| | - Rajesh Sarkar
- Metabolic Research Laboratories, National Institute of Immunology; New Delhi, India
| | - Costerwell Khyriem
- Harry Perkins Institute of Medical Research; Perth, Australia
- Curtin Medical School, Curtin University; Perth, Australia
| | - Amanpreet S. Chawla
- Immunobiology Laboratory, National Institute of Immunology; New Delhi, India
- MRC-Protein Phosphorylation and Ubiquitination Unit, University of Dundee; Dundee, UK
| | - Ankur Sharma
- Harry Perkins Institute of Medical Research; Perth, Australia
- Curtin Medical School, Curtin University; Perth, Australia
| | - Nazan Sarper
- Pediatrics and Pediatric Hematology, Kocaeli University Hospital; Kocaeli, Turkey
| | | | - Bichitra K. Biswal
- Metabolic Research Laboratories, National Institute of Immunology; New Delhi, India
| | - Carmine Settembre
- Telethon Institute of Genetics and Medicine (TIGEM); Pozzuoli, Italy
- Department of Clinical Medicine and Surgery, Federico II University; Naples, Italy
| | - Perumal Nagarajan
- Primate Research Facility, National Institute of Immunology; New Delhi, India
- Small Animal Research Facility, National Institute of Immunology; New Delhi, India
| | - Kimara L. Targoff
- Division of Cardiology, Department of Pediatrics, Columbia University; New York, USA
| | - Martin Picard
- Department of Neurology, Columbia University; New York, USA
| | - Sarika Gupta
- Metabolic Research Laboratories, National Institute of Immunology; New Delhi, India
| | - Vidya Velagapudi
- Institute for Molecular Medicine Finland FIMM, University of Helsinki; Helsinki, Finland
| | | | - Alaattin Kaya
- Department of Biology, Virginia Commonwealth University; Virginia, USA
| | | | - Brian K. Kennedy
- Healthy Longevity Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore; Singapore, Singapore
- Centre for Healthy Longevity, National University Health System; Singapore, Singapore
- Departments of Biochemistry and Physiology, Yong Loo Lin School of Medicine, National University of Singapore; Singapore, Singapore
| | | | | | - Abdullah Mahmood Ali
- Department of Medicine, Columbia University Irving Medical Center; New York, USA
| | - Arnab Mukhopadhyay
- Molecular Aging Laboratory, National Institute of Immunology; New Delhi, India
| | - Aarno Palotie
- Institute for Molecular Medicine Finland FIMM, University of Helsinki; Helsinki, Finland
- Broad Institute of Harvard and MIT; Cambridge, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital; Boston, USA
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München; Neuherberg, Germany
| | - Matt Kaeberlein
- Department of Laboratory Medicine and Pathology, University of Washington; WA, USA
| | | | - Bhupinder Pal
- Department of Medical Biology, University of Melbourne; Melbourne, Australia
- School of Cancer Medicine, La Trobe University; Bundoora, Australia
| | - Vijay K. Yadav
- Metabolic Research Laboratories, National Institute of Immunology; New Delhi, India
- Vagelos College of Physicians and Surgeons, Columbia University; New York, USA
- Mouse Genetics Project, Wellcome Sanger Institute; Cambridge, UK
- Department of Genetics and Development, Columbia University; New York, USA
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5
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Significance of podocyte DNA damage and glomerular DNA methylation in CKD patients with proteinuria. Hypertens Res 2023; 46:1000-1008. [PMID: 36646881 DOI: 10.1038/s41440-023-01169-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 12/06/2022] [Accepted: 12/12/2022] [Indexed: 01/18/2023]
Abstract
The number of chronic kidney disease (CKD) patients is increasing worldwide, and it is necessary to diagnose CKD patients in earlier stages to improve their prognosis. Previously, in a study using human samples, we reported that DNA methylation and DNA damage in podocytes are potential markers for kidney function decline in IgA nephropathy; however, these candidate markers have not been adequately investigated in other glomerular diseases. Here, we report that the association of podocyte DNA damage and DNA methylation with eGFR decline and proteinuria differs depending on the type of glomerular disease. Patients diagnosed with minor glomerular abnormality (MGA, n = 33), membranous nephropathy (MN, n = 9) or diabetic nephropathy (DN, n = 10) following kidney biopsy at Keio University Hospital from 2015 to 2017 were included. In MGA patients, both podocyte DNA damage and glomerular DNA methylation were associated with the severity of proteinuria. In DN patients, podocyte DNA double-strand breaks (DSBs) and glomerular DNA methylation were associated with an eGFR decline. When patients with urinary protein levels of more than 1 g/gCr were examined, fewer podocyte DNA DSBs were detected in MN patients than in MGA patients, and the level of glomerular DNA methylation was lower in MN patients than in MGA or DN patients. These results indicate that investigating podocyte DNA DSBs and DNA methylation changes may be useful for understanding the pathogenesis of CKD with proteinuria in humans. This study suggested the association of podocyte DNA damage and subsequent DNA methylation with proteinuria in minor glomerular abnormalities (MGA) patients and those with eGFR declines in diabetic nephropathy (DN) patients, respectively.
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6
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Integrating Network Pharmacology and Transcriptomic Strategies to Explore the Pharmacological Mechanism of Hydroxysafflor Yellow A in Delaying Liver Aging. Int J Mol Sci 2022; 23:ijms232214281. [PMID: 36430769 PMCID: PMC9697017 DOI: 10.3390/ijms232214281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/03/2022] [Accepted: 11/16/2022] [Indexed: 11/19/2022] Open
Abstract
Aging affects the structure and function of the liver. Hydroxysafflor yellow A (HSYA) effectively improves liver aging (LA) in mice, but the potential mechanisms require further exploration. In this study, an integrated approach combining network pharmacology and transcriptomics was used to elucidate the potential mechanisms of HSYA delay of LA. The targets of HSYA were predicted using the PharmMapper, SwissTargetPrediction, and CTD databases, and the targets of LA were collected from the GeneCards database. An ontology (GO) analysis and a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation of genes related to HSYA delay of LA were performed using the DAVID database, and Cytoscape software was used to construct an HSYA target pathway network. The BMKCloud platform was used to sequence mRNA from mouse liver tissue, screen differentially expressed genes (DEGs) that were altered by HSYA, and enrich their biological functions and signaling pathways through the OmicShare database. The results of the network pharmacology and transcriptomic analyses were combined. Then, quantitative real-time PCR (qRT-PCR) and Western blot experiments were used to further verify the prediction results. Finally, the interactions between HSYA and key targets were assessed by molecular docking. The results showed that 199 potentially targeted genes according to network pharmacology and 480 DEGs according to transcriptomics were involved in the effects of HSYA against LA. An integrated analysis revealed that four key targets, including HSP90AA1, ATP2A1, NOS1 and CRAT, as well as their three related pathways (the calcium signaling pathway, estrogen signaling pathway and cGMP-PKG signaling pathway), were closely related to the therapeutic effects of HSYA. A gene and protein expression analysis revealed that HSYA significantly inhibited the expressions of HSP90AA1, ATP2A1 and NOS1 in the liver tissue of aging mice. The molecular docking results showed that HSYA had high affinities with the HSP90AA1, ATP2A1 and NOS1 targets. Our data demonstrate that HSYA may delay LA in mice by inhibiting the expressions of HSP90AA1, ATP2A1 and NOS1 and regulating the calcium signaling pathway, the estrogen signaling pathway, and the cGMP-PKG signaling pathway.
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7
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Gureev AP, Andrianova NV, Pevzner IB, Zorova LD, Chernyshova EV, Sadovnikova IS, Chistyakov DV, Popkov VA, Semenovich DS, Babenko VA, Silachev DN, Zorov DB, Plotnikov EY, Popov VN. Dietary restriction modulates mitochondrial DNA damage and oxylipin profile in aged rats. FEBS J 2022; 289:5697-5713. [DOI: 10.1111/febs.16451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/16/2022] [Accepted: 04/01/2022] [Indexed: 11/28/2022]
Affiliation(s)
- Artem P. Gureev
- Department of Genetics, Cytology and Bioengineering Voronezh State University Voronezh Russia
- Laboratory of Metagenomics and Food Biotechnology Voronezh State University of Engineering Technology Voronezh Russia
| | - Nadezda V. Andrianova
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Irina B. Pevzner
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology Moscow Russia
| | - Ljubava D. Zorova
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology Moscow Russia
| | | | - Irina S. Sadovnikova
- Department of Genetics, Cytology and Bioengineering Voronezh State University Voronezh Russia
| | - Dmitry V. Chistyakov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Vasily A. Popkov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology Moscow Russia
| | - Dmitry S. Semenovich
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
| | - Valentina A. Babenko
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology Moscow Russia
| | - Denis N. Silachev
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology Moscow Russia
| | - Dmitry B. Zorov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology Moscow Russia
| | - Egor Y. Plotnikov
- Belozersky Institute of Physico‐Chemical Biology Lomonosov Moscow State University Moscow Russia
- Kulakov National Medical Research Center of Obstetrics, Gynecology, and Perinatology Moscow Russia
| | - Vasily N. Popov
- Department of Genetics, Cytology and Bioengineering Voronezh State University Voronezh Russia
- Laboratory of Metagenomics and Food Biotechnology Voronezh State University of Engineering Technology Voronezh Russia
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8
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Clarke TL, Mostoslavsky R. DNA repair as a shared hallmark in cancer and ageing. Mol Oncol 2022; 16:3352-3379. [PMID: 35834102 PMCID: PMC9490147 DOI: 10.1002/1878-0261.13285] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/23/2022] [Accepted: 07/08/2022] [Indexed: 11/30/2022] Open
Abstract
Increasing evidence demonstrates that DNA damage and genome instability play a crucial role in ageing. Mammalian cells have developed a wide range of complex and well‐orchestrated DNA repair pathways to respond to and resolve many different types of DNA lesions that occur from exogenous and endogenous sources. Defects in these repair pathways lead to accelerated or premature ageing syndromes and increase the likelihood of cancer development. Understanding the fundamental mechanisms of DNA repair will help develop novel strategies to treat ageing‐related diseases. Here, we revisit the processes involved in DNA damage repair and how these can contribute to diseases, including ageing and cancer. We also review recent mechanistic insights into DNA repair and discuss how these insights are being used to develop novel therapeutic strategies for treating human disease. We discuss the use of PARP inhibitors in the clinic for the treatment of breast and ovarian cancer and the challenges associated with acquired drug resistance. Finally, we discuss how DNA repair pathway‐targeted therapeutics are moving beyond PARP inhibition in the search for ever more innovative and efficacious cancer therapies.
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Affiliation(s)
- Thomas L Clarke
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
| | - Raul Mostoslavsky
- The Massachusetts General Hospital Cancer Center, Harvard Medical School, 02114, Boston, MA, USA.,The Broad Institute of Harvard and MIT, 02142, Cambridge, MA, USA
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9
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Altered DNA methylation in kidney disease: useful markers and therapeutic targets. Clin Exp Nephrol 2022; 26:309-315. [PMID: 35024974 PMCID: PMC8930790 DOI: 10.1007/s10157-022-02181-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Accepted: 01/04/2022] [Indexed: 01/19/2023]
Abstract
Recent studies have demonstrated the association of altered epigenomes with lifestyle-related diseases. Epigenetic regulation promotes biological plasticity in response to environmental changes, and such plasticity may cause a ‘memory effect’, a sustained effect of transient treatment or an insult in the course of lifestyle-related diseases. We investigated the significance of epigenetic changes in several genes required for renal integrity, including the nephrin gene in podocytes, and the sustained anti-proteinuric effect, focusing on the transcription factor Krüppel-like factor 4 (KLF4). We further reported the role of the DNA repair factor lysine-acetyl transferase 5 (KAT5), which acts coordinately with KLF4, in podocyte injury caused by a hyperglycemic state through the acceleration of DNA damage and epigenetic alteration. In contrast, KAT5 in proximal tubular cells prevents acute kidney injury via glomerular filtration regulation by an epigenetic mechanism as well as promotion of DNA repair, indicating the cell type-specific action and roles of DNA repair factors. This review summarizes epigenetic alterations in kidney diseases, especially DNA methylation, and their utility as markers and potential therapeutic targets. Focusing on transcription factors or DNA damage repair factors associated with epigenetic changes may be meaningful due to their cell-specific expression or action. We believe that a better understanding of epigenetic alterations in the kidney will lead to the development of a novel strategy for chronic kidney disease (CKD) treatment.
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10
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Sugita E, Hayashi K, Hishikawa A, Itoh H. Epigenetic Alterations in Podocytes in Diabetic Nephropathy. Front Pharmacol 2021; 12:759299. [PMID: 34630127 PMCID: PMC8497789 DOI: 10.3389/fphar.2021.759299] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 09/13/2021] [Indexed: 01/19/2023] Open
Abstract
Recently, epigenetic alterations have been shown to be involved in the pathogenesis of diabetes and its complications. Kidney podocytes, which are glomerular epithelial cells, are important cells that form a slit membrane—a barrier for proteinuria. Podocytes are terminally differentiated cells without cell division or replenishment abilities. Therefore, podocyte damage is suggested to be one of the key factors determining renal prognosis. Recent studies, including ours, suggest that epigenetic changes in podocytes are associated with chronic kidney disease, including diabetic nephropathy. Furthermore, the association between DNA damage repair and epigenetic changes in diabetic podocytes has been demonstrated. Detection of podocyte DNA damage and epigenetic changes using human samples, such as kidney biopsy and urine-derived cells, may be a promising strategy for estimating kidney damage and renal prognoses in patients with diabetes. Targeting epigenetic podocyte changes and associated DNA damage may become a novel therapeutic strategy for preventing progression to end-stage renal disease (ESRD) and provide a possible prognostic marker in diabetic nephropathy. This review summarizes recent advances regarding epigenetic changes, especially DNA methylation, in podocytes in diabetic nephropathy and addresses detection of these alterations in human samples. Additionally, we focused on DNA damage, which is increased under high-glucose conditions and associated with the generation of epigenetic changes in podocytes. Furthermore, epigenetic memory in diabetes is discussed. Understanding the role of epigenetic changes in podocytes in diabetic nephropathy may be of great importance considering the increasing diabetic nephropathy patient population in an aging society.
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Affiliation(s)
- Erina Sugita
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Kaori Hayashi
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Akihito Hishikawa
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
| | - Hiroshi Itoh
- Department of Internal Medicine, School of Medicine, Keio University, Tokyo, Japan
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11
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Gureev AP, Mashkina OS, Shabanova EA, Vitkalova IY, Sitnikov VV, Popov VN. Study of the amount of oxidative damage to mitochondrial and chloroplast DNA in clones of white poplar (Populus alba L.) during long-term in vitro cultivation for 26 years. PLANT MOLECULAR BIOLOGY 2021; 106:479-489. [PMID: 33970418 DOI: 10.1007/s11103-021-01157-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 05/03/2021] [Indexed: 06/12/2023]
Affiliation(s)
- Artem P Gureev
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018.
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia, 394036.
| | - Olga S Mashkina
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018
- Breeding and Biotechnology, All-Russian Research Institute of Forest Genetics, Voronezh, Russia, 394087
| | - Ekaterina A Shabanova
- Breeding and Biotechnology, All-Russian Research Institute of Forest Genetics, Voronezh, Russia, 394087
| | - Inna Yu Vitkalova
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia, 394036
| | - Vadim V Sitnikov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018
- Breeding and Biotechnology, All-Russian Research Institute of Forest Genetics, Voronezh, Russia, 394087
| | - Vasily N Popov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia, 394018
- Laboratory of Metagenomics and Food Biotechnology, Voronezh State University of Engineering Technologies, Voronezh, Russia, 394036
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12
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Wandt VK, Winkelbeiner N, Lossow K, Kopp JF, Schwarz M, Alker W, Nicolai MM, Simon L, Dietzel C, Hertel B, Pohl G, Ebert F, Schomburg L, Bornhorst J, Haase H, Kipp AP, Schwerdtle T. Ageing-associated effects of a long-term dietary modulation of four trace elements in mice. Redox Biol 2021; 46:102083. [PMID: 34371368 PMCID: PMC8358688 DOI: 10.1016/j.redox.2021.102083] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 07/24/2021] [Accepted: 07/25/2021] [Indexed: 01/11/2023] Open
Abstract
Trace elements (TEs) are essential for diverse processes maintaining body function and health status. The complex regulation of the TE homeostasis depends among others on age, sex, and nutritional status. If the TE homeostasis is disturbed, negative health consequences can result, e.g., caused by impaired redox homeostasis and genome stability maintenance. Based on age-related shifts in TEs which have been described in mice well-supplied with TEs, we aimed to understand effects of a long-term feeding with adequate or suboptimal amounts of four TEs in parallel. As an additional intervention, we studied mice which received an age-adapted diet with higher concentrations of selenium and zinc to counteract the age-related decline of both TEs. We conducted comprehensive analysis of diverse endpoints indicative for the TE and redox status, complemented by analysis of DNA (hydroxy)methylation and markers denoting genomic stability maintenance. TE concentrations showed age-specific alterations which were relatively stable and independent of their nutritional supply. In addition, hepatic DNA hydroxymethylation was significantly increased in the elderly mice and markers indicative for the redox status were modulated. The reduced nutritional supply with TEs inconsistently affected their status, with most severe effects regarding Fe deficiency. This may have contributed to the sex-specific differences observed in the alterations related to the redox status and DNA repair activity. Overall, our results highlight the complexity of factors impacting on the TE status and its physiological consequences. Alterations in TE supply, age, and sex proved to be important determinants that need to be taken into account when considering TE interventions for improving general health and supporting convalescence in the clinics. Trace element profiles differ by age and sex under moderately modulated TE supply. Maintenance of age-related trace element shifts through all feeding groups. Cu/Zn ratio and DNA hydroxymethylation emerge as appropriate murine ageing markers.
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Affiliation(s)
- Viktoria K Wandt
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany; TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany.
| | - Nicola Winkelbeiner
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany; TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany.
| | - Kristina Lossow
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany; Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Str. 24, 07743, Jena, Germany; German Institute of Human Nutrition, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.
| | - Johannes F Kopp
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany; TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany.
| | - Maria Schwarz
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany; Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Str. 24, 07743, Jena, Germany.
| | - Wiebke Alker
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany; Chair of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Merle M Nicolai
- Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany.
| | - Luise Simon
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany; TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany.
| | - Caroline Dietzel
- Chair of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Barbara Hertel
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.
| | - Gabriele Pohl
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany.
| | - Franziska Ebert
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany; TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany.
| | - Lutz Schomburg
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany; Institute for Experimental Endocrinology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt Universität zu Berlin, and Berlin Institute of Health, Augustenburger Platz 1, 13353, Berlin, Germany.
| | - Julia Bornhorst
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany; Food Chemistry, Faculty of Mathematics and Natural Sciences, University of Wuppertal, Gaußstr. 20, 42119, Wuppertal, Germany.
| | - Hajo Haase
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany; Chair of Food Chemistry and Toxicology, Technische Universität Berlin, Straße des 17. Juni 135, 10623, Berlin, Germany.
| | - Anna P Kipp
- TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany; Department of Molecular Nutritional Physiology, Institute of Nutritional Sciences, Friedrich Schiller University Jena, Dornburger Str. 24, 07743, Jena, Germany.
| | - Tanja Schwerdtle
- Department of Food Chemistry, Institute of Nutritional Science, University of Potsdam, Arthur-Scheunert-Allee 114-116, 14558, Nuthetal, Germany; TraceAge - DFG Research Unit on Interactions of Essential Trace Elements in Healthy and Diseased Elderly (FOR 2558), Berlin-Potsdam-Jena-Wuppertal, Germany; German Federal Institute for Risk Assessment (BfR), Max-Dohrn-Str. 8-10, 10589, Berlin, Germany.
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13
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Vijg J. From DNA damage to mutations: All roads lead to aging. Ageing Res Rev 2021; 68:101316. [PMID: 33711511 PMCID: PMC10018438 DOI: 10.1016/j.arr.2021.101316] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/20/2022]
Abstract
Damage to the repository of genetic information in cells has plagued life since its very beginning 3-4 billion years ago. Initially, in the absence of an ozone layer, especially damage from solar UV radiation must have been frequent, with other sources, most notably endogenous sources related to cell metabolism, gaining in importance over time. To cope with this high frequency of damage to the increasingly long DNA molecules that came to encode the growing complexity of cellular functions in cells, DNA repair evolved as one of the earliest genetic traits. Then as now, errors during the repair of DNA damage generated mutations, which provide the substrate for evolution by natural selection. With the emergence of multicellular organisms also the soma became a target of DNA damage and mutations. In somatic cells selection against the adverse effects of DNA damage is greatly diminished, especially in postmitotic cells after the age of first reproduction. Based on an abundance of evidence, DNA damage is now considered as the single most important driver of the degenerative processes that collectively cause aging. Here I will first briefly review the evidence for DNA damage as a cause of aging since the beginning of life. Then, after discussing the possible direct adverse effects of DNA damage and its cellular responses, I will provide an overview of the considerable progress that has recently been made in analyzing a major consequence of DNA damage in humans and other complex organisms: somatic mutations and the resulting genome mosaicism. Recent advances in studying somatic mutagenesis and genome mosaicism in different human and animal tissues will be discussed with a focus on the possible mechanisms through which loss of DNA sequence integrity could cause age-related functional decline and disease.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA; Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China.
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14
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Qiang M, Khalid F, Phan T, Ludwig C, Scharffetter-Kochanek K, Iben S. Cockayne Syndrome-Associated CSA and CSB Mutations Impair Ribosome Biogenesis, Ribosomal Protein Stability, and Global Protein Folding. Cells 2021; 10:cells10071616. [PMID: 34203326 PMCID: PMC8306422 DOI: 10.3390/cells10071616] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/11/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
Cockayne syndrome (CS) is a developmental disorder with symptoms that are typical for the aging body, including subcutaneous fat loss, alopecia, and cataracts. Here, we show that in the cells of CS patients, RNA polymerase I transcription and the processing of the pre-rRNA are disturbed, leading to an accumulation of the 18S-E intermediate. The mature 18S rRNA level is reduced, and isolated ribosomes lack specific ribosomal proteins of the small 40S subunit. Ribosomal proteins are susceptible to unfolding and the CS cell proteome is heat-sensitive, indicating misfolded proteins and an error-prone translation process in CS cells. Pharmaceutical chaperones restored impaired cellular proliferation. Therefore, we provide evidence for severe protein synthesis malfunction, which together with a loss of proteostasis constitutes the underlying pathophysiology in CS.
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Affiliation(s)
- Mingyue Qiang
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
| | - Fatima Khalid
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
| | - Tamara Phan
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
| | - Christina Ludwig
- Bavarian Center for Biomedical Mass Spectrometry, TUM, University of Munich, 85354 Freising, Germany;
| | - Karin Scharffetter-Kochanek
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
| | - Sebastian Iben
- Department of Dermatology and Allergic Diseases, Ulm University, Albert-Einstein Allee 23, 89081 Ulm, Germany; (M.Q.); (F.K.); (T.P.); (K.S.-K.)
- Correspondence:
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15
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Li X, Qin P, Cao L, Lou Y, Shi J, Zhao P, Wang C, Ma J, Xu S, Peng X, Chen H, Zhao D, Hu F, Zhao Y. Dose-response association of the ZJU index and fatty liver disease risk: A large cohort in China. J Gastroenterol Hepatol 2021; 36:1326-1333. [PMID: 33001484 DOI: 10.1111/jgh.15286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 09/09/2020] [Accepted: 09/19/2020] [Indexed: 02/06/2023]
Abstract
AIM The aim of this study is to investigate the sex-specific association between the ZJU index and risk of fatty liver disease in a large Chinese cohort. METHODS A total of 28 729 adults without fatty liver disease at baseline and who completed at least one follow-up of annual examinations between 2009 and 2016 were included in this study. The Cox proportional hazards model was used to estimate hazard ratios (HRs) and 95% confidence intervals (CI) for fatty liver disease risk associated with the ZJU index. RESULTS During a median follow-up of 3.01 years, 7373 developed fatty liver disease. There were significant associations between the ZJU index and fatty liver disease for women and men with increasing HRs as the quartiles increase across Q2-Q4, corresponding HRs (95% CIs) in M3 were 2.28 (1.98-2.64), 3.52 (3.07-4.04), and 4.87 (4.24-5.59) for women and 2.44 (2.17-2.75), 4.18 (3.73-4.68), and 6.23 (5.56-6.98) for men. The association between the ZJU index and fatty liver disease risk remained significant in all the subgroups except that of T2DM and abdominal obesity subgroups for men. However, the association became nonsignificant when comparing Q3 and Q2 of the ZJU index with reference in the subgroups of T2DM for men, and nonsignificant when comparing Q3 of the ZJU index with reference in the subgroups of participants with T2DM and abdominal obesity for women. CONCLUSION The ZJU index was significantly associated with the risk of fatty liver disease in Chinese population. It will be better to keep body mass index, alanine aminotransferase, aspartate aminotransferase, triglyceride, and fasting plasma glucose at a normal level for preventing fatty liver disease.
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Affiliation(s)
- Xue Li
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Pei Qin
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Liming Cao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Yanmei Lou
- Department of Health Management, Beijing Xiaotangshan Hospital, Beijing, China
| | - Jing Shi
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
| | - Ping Zhao
- Department of Health Management, Beijing Xiaotangshan Hospital, Beijing, China
| | - Changyi Wang
- Department of Non-communicable Disease Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Jianping Ma
- Department of Non-communicable Disease Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Shan Xu
- Department of Non-communicable Disease Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Xiaolin Peng
- Department of Non-communicable Disease Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Hongen Chen
- Department of Non-communicable Disease Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Dan Zhao
- Department of Non-communicable Disease Prevention and Control, Shenzhen Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Fulan Hu
- Department of Epidemiology and Health Statistics, School of Public Health, Shenzhen University Health Science Center, Shenzhen, China
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, China
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A Multi-Endpoint Approach to Base Excision Repair Incision Activity Augmented by PARylation and DNA Damage Levels in Mice: Impact of Sex and Age. Int J Mol Sci 2020; 21:ijms21186600. [PMID: 32917005 PMCID: PMC7555950 DOI: 10.3390/ijms21186600] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023] Open
Abstract
Investigation of processes that contribute to the maintenance of genomic stability is one crucial factor in the attempt to understand mechanisms that facilitate ageing. The DNA damage response (DDR) and DNA repair mechanisms are crucial to safeguard the integrity of DNA and to prevent accumulation of persistent DNA damage. Among them, base excision repair (BER) plays a decisive role. BER is the major repair pathway for small oxidative base modifications and apurinic/apyrimidinic (AP) sites. We established a highly sensitive non-radioactive assay to measure BER incision activity in murine liver samples. Incision activity can be assessed towards the three DNA lesions 8-oxo-2’-deoxyguanosine (8-oxodG), 5-hydroxy-2’-deoxyuracil (5-OHdU), and an AP site analogue. We applied the established assay to murine livers of adult and old mice of both sexes. Furthermore, poly(ADP-ribosyl)ation (PARylation) was assessed, which is an important determinant in DDR and BER. Additionally, DNA damage levels were measured to examine the overall damage levels. No impact of ageing on the investigated endpoints in liver tissue were found. However, animal sex seems to be a significant impact factor, as evident by sex-dependent alterations in all endpoints investigated. Moreover, our results revealed interrelationships between the investigated endpoints indicative for the synergetic mode of action of the cellular DNA integrity maintaining machinery.
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17
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White RR, Maslov AY, Lee M, Wilner SE, Levy M, Vijg J. FOXO3a acts to suppress DNA double-strand break-induced mutations. Aging Cell 2020; 19:e13184. [PMID: 32720744 PMCID: PMC7511859 DOI: 10.1111/acel.13184] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 04/24/2020] [Accepted: 06/06/2020] [Indexed: 11/27/2022] Open
Abstract
Genomic instability is one of the hallmarks of aging, and both DNA damage and mutations have been found to accumulate with age in different species. Certain gene families, such as sirtuins and the FoxO family of transcription factors, have been shown to play a role in lifespan extension. However, the mechanism(s) underlying the increased longevity associated with these genes remains largely unknown and may involve the regulation of responses to cellular stressors, such as DNA damage. Here, we report that FOXO3a reduces genomic instability in cultured mouse embryonic fibroblasts (MEFs) treated with agents that induce DNA double-strand breaks (DSBs), that is, clastogens. We show that DSB treatment of both primary human and mouse fibroblasts upregulates FOXO3a expression. FOXO3a ablation in MEFs harboring the mutational reporter gene lacZ resulted in an increase in genome rearrangements after bleomycin treatment; conversely, overexpression of human FOXO3a was found to suppress mutation accumulation in response to bleomycin. We also show that overexpression of FOXO3a in human primary fibroblasts decreases DSB-induced γH2AX foci. Knocking out FOXO3a in mES cells increased the frequency of homologous recombination and non-homologous end-joining events. These results provide the first direct evidence that FOXO3a plays a role in suppressing genome instability, possibly by suppressing genome rearrangements.
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Affiliation(s)
- Ryan R. White
- Department of GeneticsAlbert Einstein College of MedicineBronxNew YorkUSA
| | | | - Moonsook Lee
- Department of GeneticsAlbert Einstein College of MedicineBronxNew YorkUSA
| | - Samantha E. Wilner
- Department of BiochemistryAlbert Einstein College of MedicineBronxNew YorkUSA
- Present address:
Chemistry DepartmentUrsinus CollegeCollegevillePennsylvaniaUSA
| | - Matthew Levy
- Department of BiochemistryAlbert Einstein College of MedicineBronxNew YorkUSA
- Present address:
Vitrisa TherapeuticsDurhamNorth CarolinaUSA
| | - Jan Vijg
- Department of GeneticsAlbert Einstein College of MedicineBronxNew YorkUSA
- Center for Single‐Cell Omics in Aging and DiseaseSchool of Public HealthShanghai Jiao Tong University School of MedicineShanghaiChina
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18
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Hishikawa A, Hayashi K, Abe T, Kaneko M, Yokoi H, Azegami T, Nakamura M, Yoshimoto N, Kanda T, Sakamaki Y, Itoh H. Decreased KAT5 Expression Impairs DNA Repair and Induces Altered DNA Methylation in Kidney Podocytes. Cell Rep 2020; 26:1318-1332.e4. [PMID: 30699357 DOI: 10.1016/j.celrep.2019.01.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 11/18/2018] [Accepted: 12/28/2018] [Indexed: 01/19/2023] Open
Abstract
Altered DNA methylation plays an important role in the onset and progression of kidney disease. However, little is known about how the changes arise in disease states. Here, we report that KAT5-mediated DNA damage repair is essential for the maintenance of kidney podocytes and is associated with DNA methylation status. Podocyte-specific KAT5-knockout mice develop severe albuminuria with increased DNA double-strand breaks (DSBs), increased DNA methylation of the nephrin promoter region, and decreased nephrin expression. Podocyte KAT5 expression is decreased, whereas DNA DSBs and DNA methylation are increased in diabetic nephropathy; moreover, KAT5 restoration by gene transfer attenuates albuminuria. Furthermore, KAT5 decreases DNA DSBs and DNA methylation at the same nephrin promoter region, which indicates that KAT5-mediated DNA repair may be related to DNA methylation status. These results suggest a concept in which an environment of DNA damage repair, which occurs with decreased KAT5, may affect DNA methylation status.
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Affiliation(s)
- Akihito Hishikawa
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Kaori Hayashi
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan.
| | - Takaya Abe
- Animal Resource Development Unit and Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, Hyogo 650-0047, Japan
| | - Mari Kaneko
- Animal Resource Development Unit and Genetic Engineering Team, RIKEN Center for Life Science Technologies, 2-2-3 Minatojima Minami-machi, Chuou-ku, Kobe, Hyogo 650-0047, Japan
| | - Hideki Yokoi
- Department of Nephrology, Kyoto University Graduate School of Medicine, 54 Shogoin Kawahara-cho, Sakyo, Kyoto 606-8507, Japan
| | - Tatsuhiko Azegami
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Mari Nakamura
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Norifumi Yoshimoto
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Takeshi Kanda
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
| | - Yusuke Sakamaki
- Department of Internal Medicine, Tokyo Dental College Hospital, 5-11-13 Sugano, Ichikawa-shi, Chiba 272-8513, Japan
| | - Hiroshi Itoh
- Division of Nephrology, Endocrinology and Metabolism, Department of Internal Medicine, Keio University School of Medicine, 35 Shinanomachi, Shinjuku-ku, Tokyo 160-8582, Japan
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DNA damage and expression of DNA methylation modulators in urine-derived cells of patients with hypertension and diabetes. Sci Rep 2020; 10:3377. [PMID: 32099032 PMCID: PMC7042287 DOI: 10.1038/s41598-020-60420-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 02/12/2020] [Indexed: 12/20/2022] Open
Abstract
Diabetes and hypertension have become the primary causes of chronic kidney disease worldwide. However, there are no established markers for early diagnosis or predicting renal prognosis. Here, we investigated the expression profiles of DNA repair and DNA methylation factors in human urine-derived cells as a possible diagnostic or renal prognosis-predicting marker. A total of 75 subjects, aged 63.3 ± 1.9 years old, were included in this study. DNA and RNA were extracted from 50 mL of urine samples. We evaluated DNA double-strand breaks (DSBs) by the quantitative long distance-PCR method and performed real-time RT-PCR analysis to analyze the expression of renal cell-specific markers, DNA DSB repair factor KAT5, DNA methyltransferases DNMTs, and demethylation enzymes TETs. In patients with hypertension and diabetes, DNA DSBs of the nephrin gene increased with decreased urine KAT5/nephrin expression, consistent with our previous study (Cell Rep 2019). In patients with hypertension, DNA DSBs of the AQP1 gene were increased with elevated urine DNMTs/AQP1 and TETs/AQP1 expression. Moreover, urine DNMTs/AQP1 expression was significantly correlated with the annual eGFR decline rate after adjustment for age, baseline eGFR, the presence of diabetes and the amount of albuminuria, suggesting a possible role as a renal prognosis predictor.
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20
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Association of glomerular DNA damage and DNA methylation with one-year eGFR decline in IgA nephropathy. Sci Rep 2020; 10:237. [PMID: 31937846 PMCID: PMC6959244 DOI: 10.1038/s41598-019-57140-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 12/03/2019] [Indexed: 12/03/2022] Open
Abstract
Accumulation of DNA double-strand breaks (DSBs) is linked to aging and age-related diseases. We recently reported the possible association of DNA DSBs with altered DNA methylation in murine models of kidney disease. However, DSBs and DNA methylation in human kidneys was not adequately investigated. This study was a cross-sectional observational study to evaluate the glomerular DNA DSB marker γH2AX and phosphorylated Ataxia Telangiectasia Mutated (pATM), and the DNA methylation marker 5-methyl cytosine (5mC) by immunostaining, and investigated the association with pathological features and clinical parameters in 29 patients with IgA nephropathy. To evaluate podocyte DSBs, quantitative long-distance PCR of the nephrin gene using laser-microdissected glomerular samples and immunofluorescent double-staining with WT1 and γH2AX were performed. Glomerular γH2AX level was associated with glomerular DNA methylation level in IgA nephropathy. Podocytopathic features were associated with increased number of WT1(+)γH2AX(+) cells and reduced amount of PCR product of the nephrin gene, which indicate podocyte DNA DSBs. Glomerular γH2AX and 5mC levels were significantly associated with the slope of eGFR decline over one year in IgA nephropathy patients using multiple regression analysis adjusted for age, baseline eGFR, amount of proteinuria at biopsy and immunosuppressive therapy after biopsy. Glomerular γH2AX level was associated with DNA methylation level, both of which may be a good predictor of renal outcome in IgA nephropathy.
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Sargsyan A, Simonyan A, Hovhannisyan G, Arakelyan M, Aroutiounian R. Application of the comet assay, micronucleus test and global DNA methylation analysis in Darevskia lizards as a sentinel organism for genotoxic monitoring of soil pollution. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2019; 842:117-124. [DOI: 10.1016/j.mrgentox.2018.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 10/20/2018] [Accepted: 10/22/2018] [Indexed: 12/20/2022]
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Quispe-Tintaya W, Lee M, Dong X, Weiser DA, Vijg J, Maslov AY. Bleomycin-induced genome structural variations in normal, non-tumor cells. Sci Rep 2018; 8:16523. [PMID: 30410071 PMCID: PMC6224559 DOI: 10.1038/s41598-018-34580-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2018] [Accepted: 10/16/2018] [Indexed: 01/22/2023] Open
Abstract
Many anticancer drugs are genotoxic agents inducing DNA breaks in actively proliferating cancer cells. However, these same drugs also induce mutations, mostly genome structural variations (GSVs). The detection of GSVs in normal cells and tissues is a major challenge due to the very low abundance of these mutations, which are essentially only detectable in clonal outgrowths, such as tumors. Previously we developed Structural Variant Search (SVS) – an NGS-based assay for the quantitative detection of somatic GSVs in normal cells. Using an improved version of SVS we now demonstrate that the same dose of the anti-cancer drug bleomycin induces about 5 times more somatic GSVs in quiescent primary human fibroblasts than in proliferating cells. GVS induction in non-dividing, normal cells was subsequently confirmed in vivo by demonstrating that a single dose of bleomycin leads to a significant increase of GSV frequency in mouse liver and heart, two postmitotic tissues. Our findings suggest that normal non-cycling differentiated cells may serve as a reservoir of iatrogenically induced mutations. These results provide more insight into the possible molecular mechanisms that underlie late-life morbidities in cancer survivors exposed to chemotherapy.
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Affiliation(s)
| | - Moonsook Lee
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Xiao Dong
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Daniel A Weiser
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
| | - Alexander Y Maslov
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA.
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Lack of Parkin Anticipates the Phenotype and Affects Mitochondrial Morphology and mtDNA Levels in a Mouse Model of Parkinson's Disease. J Neurosci 2017; 38:1042-1053. [PMID: 29222404 DOI: 10.1523/jneurosci.1384-17.2017] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 08/24/2017] [Accepted: 10/03/2017] [Indexed: 02/08/2023] Open
Abstract
PARK2 is the most common gene mutated in monogenic recessive familial cases of Parkinson's disease (PD). Pathogenic mutations cause a loss of function of the encoded protein Parkin. ParkinKO mice, however, poorly represent human PD symptoms as they only exhibit mild motor phenotypes, minor dopamine metabolism abnormalities, and no signs of dopaminergic neurodegeneration. Parkin has been shown to participate in mitochondrial turnover, by targeting damaged mitochondria with low membrane potential to mitophagy. We studied the role of Parkin on mitochondrial quality control in vivo by knocking out Parkin in the PD-mito-PstI mouse (males), where the mitochondrial DNA (mtDNA) undergoes double-strand breaks only in dopaminergic neurons. The lack of Parkin promoted earlier onset of dopaminergic neurodegeneration and motor defects in the PD-mito-PstI mice, but it did not worsen the pathology. The lack of Parkin affected mitochondrial morphology in dopaminergic axons and was associated with an increase in mtDNA levels (mutant and wild type). Unexpectedly, it did not cause a parallel increase in mitochondrial mass or mitophagy. Our results suggest that Parkin affects mtDNA levels in a mitophagy-independent manner.SIGNIFICANCE STATEMENT Parkinson's disease is characterized by progressive motor symptoms due to the selective loss of dopaminergic neurons in the substantia nigra. Loss-of-function mutations of Parkin cause some monogenic forms of Parkinson's disease, possibly through its role in mitochondrial turnover and quality control. To study whether Parkin has a role in vivo in the context of mitochondrial damage, we knocked out Parkin in a mouse model in which the mitochondrial DNA is damaged in dopaminergic neurons. We found that the loss of Parkin did not exacerbate the parkinsonian pathology already present in the mice, but it was associated with an increase in mtDNA levels (mutant and wild-type) without altering mitochondrial mass. These results shed new light on the function of Parkin in vivo.
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Cabral M, Cheng X, Singh S, Ivessa AS. Absence of Non-histone Protein Complexes at Natural Chromosomal Pause Sites Results in Reduced Replication Pausing in Aging Yeast Cells. Cell Rep 2017; 17:1747-1754. [PMID: 27829146 DOI: 10.1016/j.celrep.2016.10.050] [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: 05/24/2016] [Revised: 09/08/2016] [Accepted: 10/14/2016] [Indexed: 11/26/2022] Open
Abstract
There is substantial evidence that genomic instability increases during aging. Replication pausing (and stalling) at difficult-to-replicate chromosomal sites may induce genomic instability. Interestingly, in aging yeast cells, we observed reduced replication pausing at various natural replication pause sites (RPSs) in ribosomal DNA (rDNA) and non-rDNA locations (e.g., silent replication origins and tRNA genes). The reduced pausing occurs independent of the DNA helicase Rrm3p, which facilitates replication past these non-histone protein-complex-bound RPSs, and is independent of the deacetylase Sir2p. Conditions of caloric restriction (CR), which extend life span, also cause reduced replication pausing at the 5S rDNA and at tRNA genes. In aged and CR cells, the RPSs are less occupied by their specific non-histone protein complexes (e.g., the preinitiation complex TFIIIC), likely because members of these complexes have primarily cytosolic localization. These conditions may lead to reduced replication pausing and may lower replication stress at these sites during aging.
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Affiliation(s)
- Marleny Cabral
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Xin Cheng
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Sukhwinder Singh
- Pathology and Laboratory Medicine/Flow Cytometry and Immunology Core Laboratory, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA
| | - Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA.
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25
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Zhong HH, Hu SJ, Yu B, Jiang SS, Zhang J, Luo D, Yang MW, Su WY, Shao YL, Deng HL, Hong FF, Yang SL. Apoptosis in the aging liver. Oncotarget 2017; 8:102640-102652. [PMID: 29254277 PMCID: PMC5731987 DOI: 10.18632/oncotarget.21123] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/15/2017] [Indexed: 12/11/2022] Open
Abstract
Various changes in the liver during aging can reduce hepatic function and promote liver injury. Aging is associated with high morbidity and a poor prognosis in patients with various liver diseases, including nonalcoholic fatty liver disease, hepatitis C and liver cancer, as well as with surgeries such as partial hepatectomy and liver transplantation. In addition, apoptosis increases with liver aging. Because apoptosis is involved in regeneration, fibrosis and cancer prevention during liver aging, and restoration of the appropriate level of apoptosis can alleviate the adverse effects of liver aging, it is important to understand the mechanisms underlying this process. Herein, we elaborate on the causes of apoptosis during liver aging, with a focus on oxidative stress, genomic instability, lipotoxicity, endoplasmic reticulum stress, dysregulation of nutrient sensing, and liver stem/progenitor cell activity.
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Affiliation(s)
- Hua-Hua Zhong
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Shao-Jie Hu
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Bo Yu
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Sha-Sha Jiang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Jin Zhang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Dan Luo
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Mei-Wen Yang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Wan-Ying Su
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Ya-Lan Shao
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Hao-Lin Deng
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
| | - Fen-Fang Hong
- Department of Experimental Teaching Center, Nanchang University, Nanchang 330031, China
| | - Shu-Long Yang
- Department of Physiology, College of Medicine, Nanchang University, Nanchang 330006, China
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26
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Ivessa AS. Aging: Fewer Obstacles to DNA Replication? Trends Cancer 2017; 3:387-390. [PMID: 28718415 DOI: 10.1016/j.trecan.2017.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 03/30/2017] [Accepted: 04/10/2017] [Indexed: 10/19/2022]
Abstract
Many cancers are initiated by loss-of-heterozygosity (LOH) events that lead to the replacement of single, functional tumor suppressor genes by the mutant alleles. The underlying mechanisms, of why LOH rates increase with age, are not well understood. We discuss the possible involvement of difficult-to-replicate (fragile) chromosomal sites in this process.
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Affiliation(s)
- Andreas S Ivessa
- Department of Cell Biology and Molecular Medicine, Rutgers New Jersey Medical School, Rutgers Biomedical and Health Sciences, 185 South Orange Avenue, Newark, NJ 07101-1709, USA.
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27
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Matsuyama S, Palmer J, Bates A, Poventud-Fuentes I, Wong K, Ngo J, Matsuyama M. Bax-induced apoptosis shortens the life span of DNA repair defect Ku70-knockout mice by inducing emphysema. Exp Biol Med (Maywood) 2017; 241:1265-71. [PMID: 27302174 DOI: 10.1177/1535370216654587] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Cells with DNA damage undergo apoptosis or cellular senescence if the damage cannot be repaired. Recent studies highlight that cellular senescence plays a major role in aging. However, age-associated diseases, including emphysema and neurodegenerative disorders, are caused by apoptosis of lung alveolar epithelial cells and neurons, respectively. Therefore, enhanced apoptosis also promotes aging and shortens the life span depending on the cell type. Recently, we reported that ku70(-) (/) (-)bax(-) (/) (-) and ku70(-) (/) (-)bax(+/) (-) mice showed significantly extended life span in comparison with ku70(-) (/) (-)bax(+/+) mice. Ku70 is essential for non-homologous end joining pathway for DNA double strand break repair, and Bax plays an important role in apoptosis. Our study suggests that Bax-induced apoptosis has a significant impact on shortening the life span of ku70(-) (/) (-) mice, which are defective in one of DNA repair pathways. The lung alveolar space gradually enlarges during aging, both in mouse and human, and this age-dependent change results in the decrease of respiration capacity during aging that can lead to emphysema in more severe cases. We found that emphysema occurred in ku70(-) (/) (-) mice at the age of three-months old, and that Bax deficiency was able to suppress it. These results suggest that Bax-mediated apoptosis induces emphysema in ku70(-) (/) (-) mice. We also found that the number of cells, including bronchiolar epithelial cells and type 2 alveolar epithelial cells, shows a higher DNA double strand break damage response in ku70 KO mouse lung than in wild type. Recent studies suggest that non-homologous end joining activity decreases with increased age in mouse and rat model. Together, we hypothesize that the decline of Ku70-dependent DNA repair activity in lung alveolar epithelial cells is one of the causes of age-dependent decline of lung function resulting from excess Bax-mediated apoptosis of lung alveolar epithelial cells (and their progenitor cells).
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Affiliation(s)
- Shigemi Matsuyama
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4915, USA
| | - James Palmer
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4915, USA
| | - Adam Bates
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4915, USA
| | | | - Kelvin Wong
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4915, USA
| | - Justine Ngo
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4915, USA
| | - Mieko Matsuyama
- School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4915, USA
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28
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Gureev AP, Shaforostova EA, Starkov AA, Popov VN. Simplified qPCR method for detecting excessive mtDNA damage induced by exogenous factors. Toxicology 2017; 382:67-74. [PMID: 28286206 DOI: 10.1016/j.tox.2017.03.010] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 03/06/2017] [Accepted: 03/07/2017] [Indexed: 02/08/2023]
Abstract
Damage to mitochondrial DNA (mtDNA) is a meaningful biomarker for evaluating genotoxicity of drugs and environmental toxins. Existing PCR methods utilize long mtDNA fragments (∼8-10kb), which complicates detecting exact sites of mtDNA damage. To identify the mtDNA regions most susceptible to damage, we have developed and validated a set of primers to amplify ∼2kb long fragments, while covering over 95% of mouse mtDNA. We have modified the detection method by greatly increasing the enrichment of mtDNA, which allows us solving the problem of non-specific primer annealing to nuclear DNA. To validate our approach, we have determined the most damage-susceptible mtDNA regions in mice treated in vivo and in vitro with rotenone and H2O2. The GTGR-sequence-enriched mtDNA segments located in the D-loop region were found to be especially susceptible to damage. Further, we demonstrate that H2O2-induced mtDNA damage facilitates the relaxation of mtDNA supercoiled conformation, making the sequences with minimal damage more accessible to DNA polymerase, which, in turn, results in a decrease in threshold cycle value. Overall, our modified PCR method is simpler and more selective to the specific sites of damage in mtDNA.
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Affiliation(s)
- Artem P Gureev
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
| | - Ekaterina A Shaforostova
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
| | - Anatoly A Starkov
- Brain and Mind Research Institute, Weill Medical College of Cornell University, New York, NY, USA.
| | - Vasily N Popov
- Department of Genetics, Cytology and Bioengineering, Voronezh State University, Voronezh, Russia
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29
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Milholland B, Suh Y, Vijg J. Mutation and catastrophe in the aging genome. Exp Gerontol 2017; 94:34-40. [PMID: 28263867 DOI: 10.1016/j.exger.2017.02.073] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 02/22/2017] [Accepted: 02/24/2017] [Indexed: 02/06/2023]
Abstract
In the 1960s, Leslie Orgel proposed what is now known as the error catastrophe theory of aging, arguing that errors in protein translation that reduce the fidelity of the protein-translating enzymes would lead to a feedback loop of increasingly inaccurate protein synthesis, terminating in the death of the organism. This mechanism of aging would be consistent with the exponential increase of mortality observed in humans, but the error catastrophe theory of aging has been generally disregarded by researchers due to a lack of evidence for an age-related increase in protein errors. Another theory of aging, proposed at roughly the same time, is Leo Szilard's two-hit model of somatic mutation accumulation, which assumed a linear increase in mutations over time but explained the nonlinear pattern of human mortality through a mechanism of genetic and cellular redundancy which kept mortality low until the redundancy was exhausted, at which point mortality rapidly rose. Here, we synthesize the two theories, along with the latest advances in genomics research. We propose a new catastrophe theory of aging, this time with somatic mutations as the primary agent of the feedback loop. Similar to protein errors affecting translation itself, somatic mutations in genes involved in DNA replication and repair would lead to a feedback loop of exponentially increasing mutation load. The difference from protein errors is that somatic mutations would mainly affect gene regulatory regions rather than the much smaller part of the genome encoding protein-coding information. Although the self-stimulating accumulation of somatic mutations is not mutually exclusive with the Szilard-based loss of redundancy, we present evidence that suggests that the accumulated mutations themselves could be numerous enough to cause mortality. Finally, we acknowledge the limits of our current knowledge and propose a course of research practices that will help to confirm or refute our model and advance the field of aging research as a whole.
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Affiliation(s)
- Brandon Milholland
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States.
| | - Yousin Suh
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States; Department of Ophthalmology & Visual Sciences, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States; Department of Medicine, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States; Department of Ophthalmology & Visual Sciences, Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY 10461, United States.
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30
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Shiloh Y, Lederman HM. Ataxia-telangiectasia (A-T): An emerging dimension of premature ageing. Ageing Res Rev 2017; 33:76-88. [PMID: 27181190 DOI: 10.1016/j.arr.2016.05.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 12/28/2022]
Abstract
A-T is a prototype genome instability syndrome and a multifaceted disease. A-T leads to neurodegeneration - primarily cerebellar atrophy, immunodeficiency, oculocutaneous telangiectasia (dilated blood vessels), vestigial thymus and gonads, endocrine abnormalities, cancer predisposition and varying sensitivity to DNA damaging agents, particularly those that induce DNA double-strand breaks. With the recent increase in life expectancy of A-T patients, the premature ageing component of this disease is gaining greater awareness. The complex A-T phenotype reflects the ever growing number of functions assigned to the protein encoded by the responsible gene - the homeostatic protein kinase, ATM. The quest to thoroughly understand the complex A-T phenotype may reveal yet elusive ATM functions.
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31
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Barzilai A, Schumacher B, Shiloh Y. Genome instability: Linking ageing and brain degeneration. Mech Ageing Dev 2017; 161:4-18. [DOI: 10.1016/j.mad.2016.03.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 03/23/2016] [Accepted: 03/26/2016] [Indexed: 02/06/2023]
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32
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Amelioration of premature aging in mtDNA mutator mouse by exercise: the interplay of oxidative stress, PGC-1α, p53, and DNA damage. A hypothesis. Curr Opin Genet Dev 2016; 38:127-132. [PMID: 27497229 DOI: 10.1016/j.gde.2016.06.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 05/25/2016] [Accepted: 06/21/2016] [Indexed: 11/23/2022]
Abstract
The mtDNA mutator mouse lacks the proofreading capacity of the sole mtDNA polymerase, leading to accumulation of somatic mtDNA mutations, and a profound premature aging phenotype including elevated oxidative stress and apoptosis, and reduced mitochondrial function. We have previously reported that endurance exercise alleviates the aging phenotype in the mutator mice, reduces oxidative stress, and enhances mitochondrial biogenesis. Here we summarize our findings, with the emphasis on the central role of p53 in these adaptations. We demonstrate that mtDNA in sedentary and exercised PolG mice carry similar amounts of mutations in muscle, but in addition to that sedentary mice have more non-mutational damage, which is mitigated by exercise. It follows therefore that the profound alleviation of the mtDNA mutator phenotype in muscle by exercise may not require a reduction in mtDNA mutational load, but rather a decrease of mtDNA damage and/or oxidative stress. We further hypothesize that the observed 'alleviation without a reduction of mutational load' implies that the oxidative stress in PolG muscle is maintained, at least in part, by the 'malicious cycle', a hypothetical positive feedback potentially driven by the 'transcriptional mutagenesis', that is the conversion of chemically modified nucleotides into mutant RNA bases by the mitochondrial RNA polymerase.
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33
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Ribezzo F, Shiloh Y, Schumacher B. Systemic DNA damage responses in aging and diseases. Semin Cancer Biol 2016; 37-38:26-35. [PMID: 26773346 PMCID: PMC4886830 DOI: 10.1016/j.semcancer.2015.12.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Revised: 12/28/2015] [Accepted: 12/31/2015] [Indexed: 01/09/2023]
Abstract
The genome is constantly attacked by a variety of genotoxic insults. The causal role for DNA damage in aging and cancer is exemplified by genetic defects in DNA repair that underlie a broad spectrum of acute and chronic human disorders that are characterized by developmental abnormalities, premature aging, and cancer predisposition. The disease symptoms are typically tissue-specific with uncertain genotype-phenotype correlation. The cellular DNA damage response (DDR) has been extensively investigated ever since yeast geneticists discovered DNA damage checkpoint mechanisms, several decades ago. In recent years, it has become apparent that not only cell-autonomous but also systemic DNA damage responses determine the outcome of genome instability in organisms. Understanding the mechanisms of non-cell-autonomous DNA damage responses will provide important new insights into the role of genome instability in human aging and a host of diseases including cancer and might better explain the complex phenotypes caused by genome instability.
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Affiliation(s)
- Flavia Ribezzo
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD) Research Center, Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany
| | - Yosef Shiloh
- The David and Inez Myers Laboratory for Genetic Research, Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Björn Schumacher
- Institute for Genome Stability in Ageing and Disease, Cologne Cluster of Excellence in Cellular Stress Responses in Aging-associated Diseases (CECAD) Research Center, Center for Molecular Medicine (CMMC), University of Cologne, Cologne, Germany.
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Jarman SN, Polanowski AM, Faux CE, Robbins J, De Paoli-Iseppi R, Bravington M, Deagle BE. Molecular biomarkers for chronological age in animal ecology. Mol Ecol 2016; 24:4826-47. [PMID: 26308242 DOI: 10.1111/mec.13357] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 08/08/2015] [Accepted: 08/21/2015] [Indexed: 01/07/2023]
Abstract
The chronological age of an individual animal predicts many of its biological characteristics, and these in turn influence population-level ecological processes. Animal age information can therefore be valuable in ecological research, but many species have no external features that allow age to be reliably determined. Molecular age biomarkers provide a potential solution to this problem. Research in this area of molecular ecology has so far focused on a limited range of age biomarkers. The most commonly tested molecular age biomarker is change in average telomere length, which predicts age well in a small number of species and tissues, but performs poorly in many other situations. Epigenetic regulation of gene expression has recently been shown to cause age-related modifications to DNA and to cause changes in abundance of several RNA types throughout animal lifespans. Age biomarkers based on these epigenetic changes, and other new DNA-based assays, have already been applied to model organisms, humans and a limited number of wild animals. There is clear potential to apply these marker types more widely in ecological studies. For many species, these new approaches will produce age estimates where this was previously impractical. They will also enable age information to be gathered in cross-sectional studies and expand the range of demographic characteristics that can be quantified with molecular methods. We describe the range of molecular age biomarkers that have been investigated to date and suggest approaches for developing the newer marker types as age assays in nonmodel animal species.
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Affiliation(s)
- Simon N Jarman
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia
| | - Andrea M Polanowski
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia
| | - Cassandra E Faux
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia
| | - Jooke Robbins
- Center for Coastal Studies, 5 Holway Avenue, Provincetown, MA, 02657, USA
| | - Ricardo De Paoli-Iseppi
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia.,Institute of Marine and Antarctic Studies, University of Tasmania, Castray Esplanade, Hobart, Tas., 7000, Australia
| | - Mark Bravington
- Marine Laboratory, Commonwealth Scientific and Industrial Research Organisation, Castray Esplanade, Hobart, Tas., 7000, Australia
| | - Bruce E Deagle
- Australian Antarctic Division, 203 Channel Highway, Kingston, Tas., 7050, Australia
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35
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Van Houten B, Hunter SE, Meyer JN. Mitochondrial DNA damage induced autophagy, cell death, and disease. Front Biosci (Landmark Ed) 2016; 21:42-54. [PMID: 26709760 DOI: 10.2741/4375] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Mammalian mitochondria contain multiple small genomes. While these organelles have efficient base excision removal of oxidative DNA lesions and alkylation damage, many DNA repair systems that work on nuclear DNA damage are not active in mitochondria. What is the fate of DNA damage in the mitochondria that cannot be repaired or that overwhelms the repair system? Some forms of mitochondrial DNA damage can apparently trigger mitochondrial DNA destruction, either via direct degradation or through specific forms of autophagy, such as mitophagy. However, accumulation of certain types of mitochondrial damage, in the absence of DNA ligase III (Lig3) or exonuclease G (EXOG), can directly trigger cell death. This review examines the cellular effects of persistent damage to mitochondrial genomes and discusses the very different cell fates that occur in response to different kinds of damage.
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Affiliation(s)
- Bennett Van Houten
- Department of Pharmacology Chemical Biology, University of Pittsburgh, 15213-1863,
| | - Senyene E Hunter
- School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27516
| | - Joel N Meyer
- Nicholas School of the Environment, Duke University, Durham, NC 27708-0328
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36
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Porto ML, Rodrigues BP, Menezes TN, Ceschim SL, Casarini DE, Gava AL, Pereira TMC, Vasquez EC, Campagnaro BP, Meyrelles SS. Reactive oxygen species contribute to dysfunction of bone marrow hematopoietic stem cells in aged C57BL/6 J mice. J Biomed Sci 2015; 22:97. [PMID: 26498041 PMCID: PMC4619579 DOI: 10.1186/s12929-015-0201-8] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/01/2015] [Indexed: 12/19/2022] Open
Abstract
Background Stem cells of intensely regenerative tissues are susceptible to cellular damage. Although the response to this process in hematopoietic stem cells (HSCs) is crucial, the mechanisms by which hematopoietic homeostasis is sustained are not completely understood. Aging increases reactive oxygen species (ROS) levels and inflammation, which contribute to increased proliferation, senescence and/or apoptosis, leading to self-renewal premature exhaustion. In this study, we assessed ROS production, DNA damage, apoptosis, senescence and plasticity in young, middle and aged (2-, 12- and 24-month-old, respectively) C57BL/6 J mice. Results Aged HSCs showed an increase in intracellular superoxide anion (1.4-fold), hydrogen peroxide (2-fold), nitric oxide (1.6-fold), peroxynitrite/hidroxil (2.6-fold) compared with young cells. We found that mitochondria and NADPHox were the major sources of ROS production in the three groups studied, whereas CYP450 contributed in middle and aged, and xanthine oxidase only in aged HSCs. In addition, we observed DNA damage and apoptosis in the middle (4.2- and 2-fold, respectively) and aged (6- and 4-fold, respectively) mice; aged mice also exhibited a significantly shorter telomere length (−1.8-fold) and a lower expression of plasticity markers. Conclusion These data suggest that aging impairs the functionality of HSCs and that these age-associated alterations may affect the efficacy of aged HSC recovery and transplantation.
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Affiliation(s)
- Marcella L Porto
- Laboratory of Translational Physiology, Health Sciences Center, Federal University of Espirito Santo, Vitoria, Brazil.
| | - Bianca P Rodrigues
- Laboratory of Translational Physiology, Health Sciences Center, Federal University of Espirito Santo, Vitoria, Brazil.
| | - Thiago N Menezes
- Laboratory of Translational Physiology, Health Sciences Center, Federal University of Espirito Santo, Vitoria, Brazil.
| | - Sara L Ceschim
- Pharmaceutical Sciences Graduate Program, Vila Velha University, Vila Velha, ES, Brazil.
| | - Dulce E Casarini
- Nephrology Division, Department of Medicine, Federal University of Sao Paulo, Sao Paulo, SP, Brazil.
| | - Agata L Gava
- Division of Nephrology, McMaster University, Hamilton, ON, Canada.
| | - Thiago Melo C Pereira
- Laboratory of Translational Physiology, Health Sciences Center, Federal University of Espirito Santo, Vitoria, Brazil. .,Federal Institute of Education, Science and Technology, Vila Velha, ES, Brazil.
| | - Elisardo C Vasquez
- Laboratory of Translational Physiology, Health Sciences Center, Federal University of Espirito Santo, Vitoria, Brazil. .,Pharmaceutical Sciences Graduate Program, Vila Velha University, Vila Velha, ES, Brazil.
| | - Bianca P Campagnaro
- Pharmaceutical Sciences Graduate Program, Vila Velha University, Vila Velha, ES, Brazil.
| | - Silvana S Meyrelles
- Laboratory of Translational Physiology, Health Sciences Center, Federal University of Espirito Santo, Vitoria, Brazil.
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37
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Zhang R, Chen HZ, Liu DP. The Four Layers of Aging. Cell Syst 2015; 1:180-6. [PMID: 27135911 DOI: 10.1016/j.cels.2015.09.002] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Revised: 07/06/2015] [Accepted: 09/04/2015] [Indexed: 02/06/2023]
Abstract
Instead of considering aging in terms of discrete hallmarks, we suggest that it operates in four layers, each at a different biological scale. Malfunctions within each layer-and connections between them-produce the aged phenotype and its associated susceptibility to disease.
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Affiliation(s)
- Ran Zhang
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P.R. China
| | - Hou-Zao Chen
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P.R. China.
| | - De-Pei Liu
- State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100005, P.R. China.
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38
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Velegzhaninov I, Mezenceva V, Shostal O, Baranova A, Moskalev A. Age dynamics of DNA damage and CpG methylation in the peripheral blood leukocytes of mice. Mutat Res 2015; 775:38-42. [PMID: 25867117 DOI: 10.1016/j.mrfmmm.2015.03.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 03/10/2015] [Accepted: 03/20/2015] [Indexed: 06/04/2023]
Abstract
Certain types of DNA damage are known to accumulate with age. Here we present the quantitative data describing the extent of the spontaneous DNA damage in 144 SHK mice of various ages. In each animal, we assessed double strand breaks, single strand breaks and alkali-labile sites, as well as amounts of oxidized purines, oxidized pyrimidines and misincorporated uracils. In addition, overall levels of genome DNA methylation were evaluated. The amounts of oxidized pyrimidines were correlated with age in males only, while the amounts of double strand breaks (DSB) in DNA samples were correlated with age in females only (R=0.26; p<0.035). No age-related accumulation of single-strand breaks (SSB) was observed. The hypomethylation of DNA was significant in aging females, but not in aging males. Various types of DNA damage were correlated to each other. In attempt to develop more stable indicator of age-dependent alterations in DNA, the DNA Damage Level Differential (DDLD) indices was developed for comet assaying of peripheral blood leukocytes. As expected, DDLD index was shown to be better correlated with age than any single quantitative measure reflecting certain type of DNA damage. A variability of effectiveness of various kinds of DNA repair in individual animals was larger than expected. This conclusion may have a substantial impact on subsequent studies of the mutagens and other kinds of environmental stressors in animal populations. Nor DDLD neither individual quantitative measures of DNA damage were capable of prediction post-sampling survival time.
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Affiliation(s)
- Ilya Velegzhaninov
- Institute of Biology, Komi Science Center of RAS, 28 Kommunisticheskaya st., Syktyvkar 167982, Russia.
| | - Vera Mezenceva
- Institute of Biology, Komi Science Center of RAS, 28 Kommunisticheskaya st., Syktyvkar 167982, Russia.
| | - Olga Shostal
- Institute of Biology, Komi Science Center of RAS, 28 Kommunisticheskaya st., Syktyvkar 167982, Russia.
| | - Ancha Baranova
- Moscow Institute of Physics and Technology, 9 Instituitsky per., Dolgoprudny, Moscow Region 141700, Russia; School of Systems Biology, George Mason University (GMU), 4400 University drive, Fairfax, VA 22030, USA; Research Centre for Medical Genetics (RCMG) of RAMS, 1 Moskvorechie str, Moscow, Russia.
| | - Alexey Moskalev
- Institute of Biology, Komi Science Center of RAS, 28 Kommunisticheskaya st., Syktyvkar 167982, Russia; Syktyvkar State University, 55 Oktyabrsky ave., Syktyvkar 167001, Russia; Moscow Institute of Physics and Technology, 9 Instituitsky per., Dolgoprudny, Moscow Region 141700, Russia; School of Systems Biology, George Mason University (GMU), 4400 University drive, Fairfax, VA 22030, USA; The Vavilov Institute of General Genetics, 3 Gubkina street, Moscow, Russia.
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39
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Sampath H. Oxidative DNA damage in disease--insights gained from base excision repair glycosylase-deficient mouse models. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2014; 55:689-703. [PMID: 25044514 DOI: 10.1002/em.21886] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 06/24/2014] [Indexed: 05/10/2023]
Abstract
Cellular components, including nucleic acids, are subject to oxidative damage. If left unrepaired, this damage can lead to multiple adverse cellular outcomes, including increased mutagenesis and cell death. The major pathway for repair of oxidative base lesions is the base excision repair pathway, catalyzed by DNA glycosylases with overlapping but distinct substrate specificities. To understand the role of these glycosylases in the initiation and progression of disease, several transgenic mouse models have been generated to carry a targeted deletion or overexpression of one or more glycosylases. This review summarizes some of the major findings from transgenic animal models of altered DNA glycosylase expression, especially as they relate to pathologies ranging from metabolic disease and cancer to inflammation and neuronal health.
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Affiliation(s)
- Harini Sampath
- Oregon Institute of Occupational Health Sciences, Oregon Health & Science University, Portland, Oregon
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40
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Meira LB, Calvo JA, Shah D, Klapacz J, Moroski-Erkul CA, Bronson RT, Samson LD. Repair of endogenous DNA base lesions modulate lifespan in mice. DNA Repair (Amst) 2014; 21:78-86. [PMID: 24994062 PMCID: PMC4125484 DOI: 10.1016/j.dnarep.2014.05.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 04/30/2014] [Accepted: 05/20/2014] [Indexed: 12/21/2022]
Abstract
The accumulation of DNA damage is thought to contribute to the physiological decay associated with the aging process. Here, we report the results of a large-scale study examining longevity in various mouse models defective in the repair of DNA alkylation damage, or defective in the DNA damage response. We find that the repair of spontaneous DNA damage by alkyladenine DNA glycosylase (Aag/Mpg)-initiated base excision repair and O(6)-methylguanine DNA methyltransferase (Mgmt)-mediated direct reversal contributes to maximum life span in the laboratory mouse. We also uncovered important genetic interactions between Aag, which excises a wide variety of damaged DNA bases, and the DNA damage sensor and signaling protein, Atm. We show that Atm plays a role in mediating survival in the face of both spontaneous and induced DNA damage, and that Aag deficiency not only promotes overall survival, but also alters the tumor spectrum in Atm(-/-) mice. Further, the reversal of spontaneous alkylation damage by Mgmt interacts with the DNA mismatch repair pathway to modulate survival and tumor spectrum. Since these aging studies were performed without treatment with DNA damaging agents, our results indicate that the DNA damage that is generated endogenously accumulates with age, and that DNA alkylation repair proteins play a role in influencing longevity.
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Affiliation(s)
- Lisiane B Meira
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Jennifer A Calvo
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Dharini Shah
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Joanna Klapacz
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Catherine A Moroski-Erkul
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Roderick T Bronson
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Rodent Histopathology Core, Harvard Medical School, 126 Goldenson Building, Boston, MA 02115, United States
| | - Leona D Samson
- Biological Engineering Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Biology Department, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States; Rodent Histopathology Core, Harvard Medical School, 126 Goldenson Building, Boston, MA 02115, United States.
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41
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DNA repair abnormalities leading to ataxia: shared neurological phenotypes and risk factors. Neurogenetics 2014; 15:217-28. [PMID: 25038946 DOI: 10.1007/s10048-014-0415-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 07/11/2014] [Indexed: 02/06/2023]
Abstract
Since identification of mutations in the ATM gene leading to ataxia-telangiectasia, enormous efforts have been devoted to discovering the roles this protein plays in DNA repair as well as other cellular functions. Even before the identification of ATM mutations, it was clear that other diseases with different genomic loci had very similar neurological symptoms. There has been significant progress in understanding why cancer and immunodeficiency occur in ataxia-telangiectasia even though many details remain to be determined, but the field is no closer to determining why the nervous system requires ATM and other DNA repair genes. Even though rodent disease models have similar DNA repair abnormalities as the human diseases, they have no consistent, robust neuropathological phenotype making it difficult to understand the neurological underpinnings of disease. Therefore, it may be useful to reassess the neurological and neuropathological characteristics of ataxia-telangiectasia in human patients to look for potential commonalities in DNA repair diseases that result in ataxia. In doing so, it is clear that ataxia-telangiectasia and similar diseases share neurological features other than merely ataxia, such as length-dependent motor and sensory neuropathies, and that the neuroanatomical localization for these symptoms is understood. Cells affected in ataxia-telangiectasia and similar diseases are some of the largest single nucleated cells in the body. In addition, a subset of these diseases also has extrapyramidal movements and oculomotor apraxia. These neurological and neuropathological similarities may indicate a common DNA repair related pathogenesis with very large cell size as a critical risk factor.
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42
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Melis JPM, Jonker MJ, Vijg J, Hoeijmakers JHJ, Breit TM, van Steeg H. Aging on a different scale--chronological versus pathology-related aging. Aging (Albany NY) 2014; 5:782-8. [PMID: 24131799 PMCID: PMC3838780 DOI: 10.18632/aging.100606] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
In the next decades the elderly population will increase dramatically, demanding appropriate solutions in health care and aging research focusing on healthy aging to prevent high burdens and costs in health care. For this, research targeting tissue-specific and individual aging is paramount to make the necessary progression in aging research. In a recently published study we have attempted to make a step interpreting aging data on chronological as well as pathological scale. For this, we sampled five major tissues at regular time intervals during the entire C57BL/6J murine lifespan from a controlled in vivo aging study, measured the whole transcriptome and incorporated temporal as well as physical health aspects into the analyses. In total, we used 18 different age-related pathological parameters and transcriptomic profiles of liver, kidney, spleen, lung and brain and created a database that can now be used for a broad systems biology approach. In our study, we focused on the dynamics of biological processes during chronological aging and the comparison between chronological and pathology-related aging.
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Affiliation(s)
- Joost P M Melis
- National Institute for Public Health and the Environment (RIVM), Center for Health Protection, Bilthoven, the Netherlands
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43
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Aghili L, Foo J, DeGregori J, De S. Patterns of somatically acquired amplifications and deletions in apparently normal tissues of ovarian cancer patients. Cell Rep 2014; 7:1310-9. [PMID: 24794429 DOI: 10.1016/j.celrep.2014.03.071] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 02/06/2014] [Accepted: 03/28/2014] [Indexed: 12/20/2022] Open
Abstract
Little is understood about the occurrence of somatic genomic alterations in normal tissues and their significance in the context of disease. Here, we identified potential somatic copy number alterations (pSCNAs) in apparently normal ovarian tissue and peripheral blood of 423 ovarian cancer patients. There were, on average, two to four pSCNAs per sample detectable at a tissue-level resolution, although some individuals had orders of magnitude more. Accordingly, we estimated the lower bound of the rate of pSCNAs per cell division. Older individuals and BRCA mutation carriers had more pSCNAs than others. pSCNAs significantly overlapped with Alu and G-quadruplexes, and the affected genes were enriched for signaling and regulation. Some of the amplification/deletion hotspots in pan-cancer genomes were hot spots of pSCNAs in normal tissues as well, suggesting that those regions might be inherently unstable. Prevalence of pSCNA in peripheral blood predicted survival, implying that mutations in normal tissues might have consequences for cancer patients.
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Affiliation(s)
- Leila Aghili
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Jasmine Foo
- School of Mathematics, University of Minnesota, Minneapolis, MN 55455, USA
| | - James DeGregori
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO 80045, USA
| | - Subhajyoti De
- Department of Medicine, University of Colorado School of Medicine, Aurora, CO 80045, USA; Molecular Oncology Program, University of Colorado Cancer Center, Aurora, CO 80045, USA; Department of Biostatistics and Informatics, Colorado School of Public Health, Aurora, CO 80045, USA.
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44
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Tigges J, Krutmann J, Fritsche E, Haendeler J, Schaal H, Fischer JW, Kalfalah F, Reinke H, Reifenberger G, Stühler K, Ventura N, Gundermann S, Boukamp P, Boege F. The hallmarks of fibroblast ageing. Mech Ageing Dev 2014; 138:26-44. [PMID: 24686308 DOI: 10.1016/j.mad.2014.03.004] [Citation(s) in RCA: 156] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2013] [Revised: 03/11/2014] [Accepted: 03/18/2014] [Indexed: 12/26/2022]
Abstract
Ageing is influenced by the intrinsic disposition delineating what is maximally possible and extrinsic factors determining how that frame is individually exploited. Intrinsic and extrinsic ageing processes act on the dermis, a post-mitotic skin compartment mainly consisting of extracellular matrix and fibroblasts. Dermal fibroblasts are long-lived cells constantly undergoing damage accumulation and (mal-)adaptation, thus constituting a powerful indicator system for human ageing. Here, we use the systematic of ubiquitous hallmarks of ageing (Lopez-Otin et al., 2013, Cell 153) to categorise the available knowledge regarding dermal fibroblast ageing. We discriminate processes inducible in culture from phenomena apparent in skin biopsies or primary cells from old donors, coming to the following conclusions: (i) Fibroblasts aged in culture exhibit most of the established, ubiquitous hallmarks of ageing. (ii) Not all of these hallmarks have been detected or investigated in fibroblasts aged in situ (in the skin). (iii) Dermal fibroblasts aged in vitro and in vivo exhibit additional features currently not considered ubiquitous hallmarks of ageing. (iv) The ageing process of dermal fibroblasts in their physiological tissue environment has only been partially elucidated, although these cells have been a preferred model of cell ageing in vitro for decades.
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Affiliation(s)
- Julia Tigges
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Jean Krutmann
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Ellen Fritsche
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany
| | - Judith Haendeler
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany; Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Heiner Schaal
- Center for Microbiology and Virology, Institute of Virology, Heinrich-Heine-University, Med. Faculty, D-40225 Düsseldorf, Germany
| | - Jens W Fischer
- Institute for Pharmacology and Clinical Pharmacology, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Faiza Kalfalah
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Hans Reinke
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany; Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | - Kai Stühler
- Institute for Molecular Medicine, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany; Molecular Proteomics Laboratory, Centre for Biological and Medical Research (BMFZ), Heinrich-Heine-University, Düsseldorf, Germany
| | - Natascia Ventura
- Leibniz Research Institute for Environmental Medicine (IUF), Düsseldorf, Germany; Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany
| | | | - Petra Boukamp
- German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Fritz Boege
- Institute of Clinical Chemistry and Laboratory Diagnostics, Heinrich-Heine-University, Med. Faculty, Düsseldorf, Germany.
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Abstract
Genomes are inherently unstable because of the need for DNA sequence variation as a substrate for evolution through natural selection. However, most multicellular organisms have postmitotic tissues, with limited opportunity for selective removal of cells harboring persistent damage and deleterious mutations, which can therefore contribute to functional decline, disease, and death. Key in this process is the role of genome maintenance, the network of protein products that repair DNA damage and signal DNA damage response pathways. Genome maintenance is beneficial early in life by swiftly eliminating DNA damage or damaged cells, facilitating rapid cell proliferation. However, at later ages accumulation of unrepaired damage and mutations, as well as ongoing cell depletion, promotes cancer, atrophy, and other deleterious effects associated with aging. As such, genome maintenance and its phenotypic sequelae provide yet another example of antagonistic pleiotropy in aging and longevity.
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Affiliation(s)
- Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, New York, NY, USA
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