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Salameh Y, Bejaoui Y, El Hajj N. DNA Methylation Biomarkers in Aging and Age-Related Diseases. Front Genet 2020; 11:171. [PMID: 32211026 PMCID: PMC7076122 DOI: 10.3389/fgene.2020.00171] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Recent research efforts provided compelling evidence of genome-wide DNA methylation alterations in aging and age-related disease. It is currently well established that DNA methylation biomarkers can determine biological age of any tissue across the entire human lifespan, even during development. There is growing evidence suggesting epigenetic age acceleration to be strongly linked to common diseases or occurring in response to various environmental factors. DNA methylation based clocks are proposed as biomarkers of early disease risk as well as predictors of life expectancy and mortality. In this review, we will summarize key advances in epigenetic clocks and their potential application in precision health. We will also provide an overview of progresses in epigenetic biomarker discovery in Alzheimer's, type 2 diabetes, and cardiovascular disease. Furthermore, we will highlight the importance of prospective study designs to identify and confirm epigenetic biomarkers of disease.
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Affiliation(s)
| | | | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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102
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Lowe R, Danson AF, Rakyan VK, Yildizoglu S, Saldmann F, Viltard M, Friedlander G, Faulkes CG. DNA methylation clocks as a predictor for ageing and age estimation in naked mole-rats, Heterocephalus glaber. Aging (Albany NY) 2020; 12:4394-4406. [PMID: 32126024 PMCID: PMC7093186 DOI: 10.18632/aging.102892] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 02/25/2020] [Indexed: 01/07/2023]
Abstract
The naked mole-rat, Heterocephalus glaber (NMR), the longest-lived rodent, is of significance and interest in the study of biomarkers for ageing. Recent breakthroughs in this field have revealed ‘epigenetic clocks’ that are based on the temporal accumulation of DNA methylation at specific genomic sites. Here, we validate the hypothesis of an epigenetic clock in NMRs based on changes in methylation of targeted CpG sites. We initially analysed 51 CpGs in NMR livers spanning an age range of 39-1,144 weeks and found 23 to be significantly associated with age (p<0.05). We then built a predictor of age using these sites. To test the accuracy of this model, we analysed an additional set of liver samples, and were successfully able to predict their age with a root mean squared error of 166 weeks. We also profiled skin samples with the same age range, finding a striking correlation between their predicted age versus their actual age (R=0.93), but which was lower when compared to the liver, suggesting that skin ages slower than the liver in NMRs. Our model will enable the prediction of age in wild-caught and captive NMRs of unknown age, and will be invaluable for further mechanistic studies of mammalian ageing.
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Affiliation(s)
- Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Amy F Danson
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Centre for Genomic Health, Queen Mary University of London, London, UK
| | - Selin Yildizoglu
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Frédéric Saldmann
- Fondation pour la Recherche en Physiologie, Brussels, Belgium.,Service de Physiologie et Explorations Fonctionnelles, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Melanie Viltard
- Fondation pour la Recherche en Physiologie, Brussels, Belgium
| | - Gérard Friedlander
- Service de Physiologie et Explorations Fonctionnelles, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, Paris, France.,Université Paris Descartes, Faculté de Médecine, Paris, France.,INSERM UMR_S1151 CNRS UMR8253 Institut Necker-Enfants Malades (INEM), Paris, France
| | - Chris G Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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103
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Huang G, Liu L, Wang H, Gou M, Gong P, Tian C, Deng W, Yang J, Zhou TT, Xu GL, Liu L. Tet1 Deficiency Leads to Premature Reproductive Aging by Reducing Spermatogonia Stem Cells and Germ Cell Differentiation. iScience 2020; 23:100908. [PMID: 32114381 PMCID: PMC7049665 DOI: 10.1016/j.isci.2020.100908] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/08/2019] [Accepted: 02/07/2020] [Indexed: 12/17/2022] Open
Abstract
Ten-eleven translocation (Tet) enzymes are involved in DNA demethylation, important in regulating embryo development, stem cell pluripotency and tumorigenesis. Alterations of DNA methylation with age have been shown in various somatic cell types. We investigated whether Tet1 and Tet2 regulate aging. We showed that Tet1-deficient mice undergo a progressive reduction of spermatogonia stem cells and spermatogenesis and thus accelerated infertility with age. Tet1 deficiency decreases 5hmC levels in spermatogonia and downregulates a subset of genes important for cell cycle, germ cell differentiation, meiosis and reproduction, such as Ccna1 and Spo11, resulting in premature reproductive aging. Moreover, Tet1 and 5hmC both regulate signaling pathways key for stem cell development, including Wnt and PI3K-Akt, autophagy and stress response genes. In contrast, effect of Tet2 deficiency on male reproductive aging is minor. Hence, Tet1 maintains spermatogonia stem cells with age, revealing an important role of Tet1 in regulating stem cell aging. Tet1 regulates stem cell aging and differentiation Tet1 plays an important role in maintaining spermatogonial stem cells Loss of Tet1 results in exhaustion of spermatogonia and premature reproductive aging Effect of Tet2 deficiency on reproductive aging in males is minor
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Affiliation(s)
- Guian Huang
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Linlin Liu
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Huasong Wang
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Mo Gou
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Peng Gong
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Chenglei Tian
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Wei Deng
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Jiao Yang
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China
| | - Tian-Tian Zhou
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, Shanghai 200031, China.
| | - Lin Liu
- Department of Cell Biology and Genetics, College of Life Sciences, Nankai University, Tianjin 300071, China; State Key Laboratory of Medicinal Chemical Biology, Nankai University, Tianjin 300071, China.
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104
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Bell CG, Lowe R, Adams PD, Baccarelli AA, Beck S, Bell JT, Christensen BC, Gladyshev VN, Heijmans BT, Horvath S, Ideker T, Issa JPJ, Kelsey KT, Marioni RE, Reik W, Relton CL, Schalkwyk LC, Teschendorff AE, Wagner W, Zhang K, Rakyan VK. DNA methylation aging clocks: challenges and recommendations. Genome Biol 2019; 20:249. [PMID: 31767039 PMCID: PMC6876109 DOI: 10.1186/s13059-019-1824-y] [Citation(s) in RCA: 437] [Impact Index Per Article: 87.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 09/16/2019] [Indexed: 12/15/2022] Open
Abstract
Epigenetic clocks comprise a set of CpG sites whose DNA methylation levels measure subject age. These clocks are acknowledged as a highly accurate molecular correlate of chronological age in humans and other vertebrates. Also, extensive research is aimed at their potential to quantify biological aging rates and test longevity or rejuvenating interventions. Here, we discuss key challenges to understand clock mechanisms and biomarker utility. This requires dissecting the drivers and regulators of age-related changes in single-cell, tissue- and disease-specific models, as well as exploring other epigenomic marks, longitudinal and diverse population studies, and non-human models. We also highlight important ethical issues in forensic age determination and predicting the trajectory of biological aging in an individual.
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Affiliation(s)
- Christopher G Bell
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Robert Lowe
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
| | - Peter D Adams
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.
- Beatson Institute for Cancer Research and University of Glasgow, Glasgow, UK.
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA.
| | - Stephan Beck
- Medical Genomics, Paul O'Gorman Building, UCL Cancer Institute, University College London, London, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
- Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, NH, USA.
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Leiden, the Netherlands.
| | - Steve Horvath
- Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, CA, USA.
- Department of Biostatistics, School of Public Health, University of California-Los Angeles, Los Angeles, CA, USA.
| | - Trey Ideker
- San Diego Center for Systems Biology, University of California-San Diego, San Diego, CA, USA.
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research, Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA.
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, RI, USA.
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA.
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK.
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK.
- The Wellcome Trust Sanger Institute, Cambridge, UK.
| | - Caroline L Relton
- Medical Research Council Integrative Epidemiology Unit (MRC IEU), School of Social and Community Medicine, University of Bristol, Bristol, UK.
| | | | - Andrew E Teschendorff
- CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue Yang Road, Shanghai, 200031, China.
- UCL Cancer Institute, Paul O'Gorman Building, University College London, 72 Huntley Street, London, WC1E 6BT, UK.
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany.
| | - Kang Zhang
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau.
| | - Vardhman K Rakyan
- The Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK.
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105
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Yu YE, Xing Z, Do C, Pao A, Lee EJ, Krinsky-McHale S, Silverman W, Schupf N, Tycko B. Genetic and epigenetic pathways in Down syndrome: Insights to the brain and immune system from humans and mouse models. PROGRESS IN BRAIN RESEARCH 2019; 251:1-28. [PMID: 32057305 PMCID: PMC7286740 DOI: 10.1016/bs.pbr.2019.09.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The presence of an extra copy of human chromosome 21 (Hsa21) leads to a constellation of phenotypic manifestations in Down syndrome (DS), including prominent effects on the brain and immune system. Intensive efforts to unravel the molecular mechanisms underlying these phenotypes may help developing effective therapies, both in DS and in the general population. Here we review recent progress in genetic and epigenetic analysis of trisomy 21 (Ts21). New mouse models of DS based on syntenic conservation of segments of the mouse and human chromosomes are starting to clarify the contributions of chromosomal subregions and orthologous genes to specific phenotypes in DS. The expression of genes on Hsa21 is regulated by epigenetic mechanisms, and with recent findings of highly recurrent gene-specific changes in DNA methylation patterns in brain and immune system cells with Ts21, the epigenomics of DS has become an active research area. Here we highlight the value of combining human studies with mouse models for defining DS critical genes and understanding the trans-acting effects of a simple chromosomal aneuploidy on genome-wide epigenetic patterning. These genetic and epigenetic studies are starting to uncover fundamental biological mechanisms, leading to insights that may soon become therapeutically relevant.
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Affiliation(s)
- Y Eugene Yu
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States; Genetics, Genomics and Bioinformatics Program, State University of New York at Buffalo, Buffalo, NY, United States.
| | - Zhuo Xing
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Catherine Do
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Annie Pao
- The Children's Guild Foundation Down Syndrome Research Program, Genetics and Genomics Program and Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, United States
| | - Eun Joon Lee
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States
| | - Sharon Krinsky-McHale
- New York State Institute for Basic Research in Developmental Disabilities, Staten Island, NY, United States
| | - Wayne Silverman
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, United States; Department of Pediatrics, University of California at Irvine, Irvine, CA, United States
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, United States
| | - Benjamin Tycko
- Department of Biomedical Research, Division of Genetics & Epigenetics, Hackensack-Meridian Health Center for Discovery and Innovation and Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ, United States.
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106
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Hadad N, Masser DR, Blanco-Berdugo L, Stanford DR, Freeman WM. Early-life DNA methylation profiles are indicative of age-related transcriptome changes. Epigenetics Chromatin 2019; 12:58. [PMID: 31594536 PMCID: PMC6781367 DOI: 10.1186/s13072-019-0306-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 09/14/2019] [Indexed: 12/15/2022] Open
Abstract
Background Alterations to cellular and molecular programs with brain aging result in cognitive impairment and susceptibility to neurodegenerative disease. Changes in DNA methylation patterns, an epigenetic modification required for various CNS functions are observed with brain aging and can be prevented by anti-aging interventions, but the relationship of altered methylation to gene expression is poorly understood. Results Paired analysis of the hippocampal methylome and transcriptome with aging of male and female mice demonstrates that age-related differences in methylation and gene expression are anti-correlated within gene bodies and enhancers. Altered promoter methylation with aging was found to be generally un-related to altered gene expression. A more striking relationship was found between methylation levels at young age and differential gene expression with aging. Highly methylated gene bodies and promoters in early life were associated with age-related increases in gene expression even in the absence of significant methylation changes with aging. As well, low levels of methylation in early life were correlated to decreased expression with aging. This relationship was also observed in genes altered in two mouse Alzheimer’s models. Conclusion DNA methylation patterns established in youth, in combination with other epigenetic marks, were able to accurately predict changes in transcript trajectories with aging. These findings are consistent with the developmental origins of disease hypothesis and indicate that epigenetic variability in early life may explain differences in aging trajectories and age-related disease.
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Affiliation(s)
- Niran Hadad
- Oklahoma Center for Neuroscience, Oklahoma City, OK, USA.,Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.,The Jackson Laboratory, Bar Harbor, ME, 04609, USA
| | - Dustin R Masser
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.,Department of Physiology, Oklahoma City, OK, USA
| | | | - David R Stanford
- Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA.,Department of Physiology, Oklahoma City, OK, USA.,Oklahoma Nathan Shock Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - Willard M Freeman
- Oklahoma Center for Neuroscience, Oklahoma City, OK, USA. .,Reynolds Oklahoma Center on Aging, SLY-BRC 1370, 975 NE 10th St, Oklahoma City, OK, 73104, USA. .,Department of Physiology, Oklahoma City, OK, USA. .,Oklahoma Nathan Shock Center, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA. .,Oklahoma City VA Medical Center, Oklahoma City, OK, 73104, USA.
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107
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Martin-Herranz DE, Aref-Eshghi E, Bonder MJ, Stubbs TM, Choufani S, Weksberg R, Stegle O, Sadikovic B, Reik W, Thornton JM. Screening for genes that accelerate the epigenetic aging clock in humans reveals a role for the H3K36 methyltransferase NSD1. Genome Biol 2019; 20:146. [PMID: 31409373 PMCID: PMC6693144 DOI: 10.1186/s13059-019-1753-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/03/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Epigenetic clocks are mathematical models that predict the biological age of an individual using DNA methylation data and have emerged in the last few years as the most accurate biomarkers of the aging process. However, little is known about the molecular mechanisms that control the rate of such clocks. Here, we have examined the human epigenetic clock in patients with a variety of developmental disorders, harboring mutations in proteins of the epigenetic machinery. RESULTS Using the Horvath epigenetic clock, we perform an unbiased screen for epigenetic age acceleration in the blood of these patients. We demonstrate that loss-of-function mutations in the H3K36 histone methyltransferase NSD1, which cause Sotos syndrome, substantially accelerate epigenetic aging. Furthermore, we show that the normal aging process and Sotos syndrome share methylation changes and the genomic context in which they occur. Finally, we found that the Horvath clock CpG sites are characterized by a higher Shannon methylation entropy when compared with the rest of the genome, which is dramatically decreased in Sotos syndrome patients. CONCLUSIONS These results suggest that the H3K36 methylation machinery is a key component of the epigenetic maintenance system in humans, which controls the rate of epigenetic aging, and this role seems to be conserved in model organisms. Our observations provide novel insights into the mechanisms behind the epigenetic aging clock and we expect will shed light on the different processes that erode the human epigenetic landscape during aging.
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Affiliation(s)
- Daniel E. Martin-Herranz
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Chronomics Ltd., Cambridge, UK
| | - Erfan Aref-Eshghi
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Canada
| | - Marc Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
| | | | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Canada
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bekim Sadikovic
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
- Molecular Genetics Laboratory, Molecular Diagnostics Division, London Health Sciences Centre, London, Canada
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, UK
- Centre for Trophoblast Research, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Janet M. Thornton
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
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108
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The Impact of Caloric Restriction on the Epigenetic Signatures of Aging. Int J Mol Sci 2019; 20:ijms20082022. [PMID: 31022953 PMCID: PMC6515465 DOI: 10.3390/ijms20082022] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
Aging is characterized by an extensive remodeling of epigenetic patterns, which has been implicated in the physiopathology of age-related diseases. Nutrition plays a significant role in modulating the epigenome, and a growing amount of data indicate that dietary changes can modify the epigenetic marks associated with aging. In this review, we will assess the current advances in the relationship between caloric restriction, a proven anti-aging intervention, and epigenetic signatures of aging. We will specifically discuss the impact of caloric restriction on epigenetic regulation and how some of the favorable effects of caloric restriction on lifespan and healthspan could be mediated by epigenetic modifications.
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109
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Singh PP, Demmitt BA, Nath RD, Brunet A. The Genetics of Aging: A Vertebrate Perspective. Cell 2019; 177:200-220. [PMID: 30901541 PMCID: PMC7592626 DOI: 10.1016/j.cell.2019.02.038] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 02/07/2023]
Abstract
Aging negatively impacts vitality and health. Many genetic pathways that regulate aging were discovered in invertebrates. However, the genetics of aging is more complex in vertebrates because of their specialized systems. This Review discusses advances in the genetic regulation of aging in vertebrates from work in mice, humans, and organisms with exceptional lifespans. We highlight challenges for the future, including sex-dependent differences in lifespan and the interplay between genes and environment. We also discuss how the identification of reliable biomarkers of age and development of new vertebrate models can be leveraged for personalized interventions to counter aging and age-related diseases.
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Affiliation(s)
- Param Priya Singh
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | | | - Ravi D Nath
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Anne Brunet
- Department of Genetics, Stanford University, Stanford, CA 94305, USA; Glenn Laboratories for the Biology of Aging, Stanford, CA 94305, USA.
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110
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Ashapkin VV, Kutueva LI, Vanyushin BF. Epigenetic Clock: Just a Convenient Marker or an Active Driver of Aging? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1178:175-206. [PMID: 31493228 DOI: 10.1007/978-3-030-25650-0_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A global DNA hypomethylation and local changes in the methylation levels of specific DNA loci occur during aging in mammals. Global hypomethylation mainly affects highly methylated repeat sequences, such as transposable elements; it is an essentially stochastic process usually referred to as "epigenetic drift." Specific changes in DNA methylation affect various genome sequences and could be either hypomethylation or hypermethylation, but the prevailing tendencies are hypermethylation of promoter sequences associated with CpG islands and hypomethylation of CpG poor genes. Methylation levels of multiple CpG sites display a strong correlation to age common between individuals of the same species. Collectively, methylation of such CpG sites could be used as "epigenetic clocks" to predict biological age. Furthermore, the discrepancy between epigenetic and chronological ages could be predictive of all-cause mortality and multiple age-associated diseases. Random changes in DNA methylation (epigenetic drift) could also affect the aging phenotype, causing accidental changes in gene expression and increasing the transcriptional noise between cells of the same tissue. Both effects could become detrimental to tissue functioning and cause a gradual decline in organ function during aging. Strong evidence shows that epigenetic systems contribute to lifespan control in various organisms. Similar to other cell systems, the epigenome is prone to gradual degradation due to the genome damage, stressful agents and other aging factors. However, unlike mutations and many other hallmarks of aging, age-related epigenetic changes could be fully or partially reversed to a "young" state.
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Affiliation(s)
- Vasily V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Lyudmila I Kutueva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Boris F Vanyushin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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