51
|
Voisin S, Harvey NR, Haupt LM, Griffiths LR, Ashton KJ, Coffey VG, Doering TM, Thompson JLM, Benedict C, Cedernaes J, Lindholm ME, Craig JM, Rowlands DS, Sharples AP, Horvath S, Eynon N. An epigenetic clock for human skeletal muscle. J Cachexia Sarcopenia Muscle 2020; 11:887-898. [PMID: 32067420 PMCID: PMC7432573 DOI: 10.1002/jcsm.12556] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/15/2020] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Ageing is associated with DNA methylation changes in all human tissues, and epigenetic markers can estimate chronological age based on DNA methylation patterns across tissues. However, the construction of the original pan-tissue epigenetic clock did not include skeletal muscle samples and hence exhibited a strong deviation between DNA methylation and chronological age in this tissue. METHODS To address this, we developed a more accurate, muscle-specific epigenetic clock based on the genome-wide DNA methylation data of 682 skeletal muscle samples from 12 independent datasets (18-89 years old, 22% women, 99% Caucasian), all generated with Illumina HumanMethylation (HM) arrays (HM27, HM450, or HMEPIC). We also took advantage of the large number of samples to conduct an epigenome-wide association study of age-associated DNA methylation patterns in skeletal muscle. RESULTS The newly developed clock uses 200 cytosine-phosphate-guanine dinucleotides to estimate chronological age in skeletal muscle, 16 of which are in common with the 353 cytosine-phosphate-guanine dinucleotides of the pan-tissue clock. The muscle clock outperformed the pan-tissue clock, with a median error of only 4.6 years across datasets (vs. 13.1 years for the pan-tissue clock, P < 0.0001) and an average correlation of ρ = 0.62 between actual and predicted age across datasets (vs. ρ = 0.51 for the pan-tissue clock). Lastly, we identified 180 differentially methylated regions with age in skeletal muscle at a false discovery rate < 0.005. However, gene set enrichment analysis did not reveal any enrichment for gene ontologies. CONCLUSIONS We have developed a muscle-specific epigenetic clock that predicts age with better accuracy than the pan-tissue clock. We implemented the muscle clock in an r package called Muscle Epigenetic Age Test available on Bioconductor to estimate epigenetic age in skeletal muscle samples. This clock may prove valuable in assessing the impact of environmental factors, such as exercise and diet, on muscle-specific biological ageing processes.
Collapse
Affiliation(s)
- Sarah Voisin
- Institute for Health and Sport, Victoria University, Melbourne, Australia
| | - Nicholas R Harvey
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia.,Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Kevin J Ashton
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia
| | - Vernon G Coffey
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia
| | - Thomas M Doering
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia.,School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, Australia
| | | | - Christian Benedict
- Sleep Research Laboratory, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | | | - Malene E Lindholm
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jeffrey M Craig
- Centre for Molecular and Medical Research, Deakin University, Geelong, Australia.,Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - David S Rowlands
- School of Sport, Exercise and Nutrition, Massey University, Wellington, New Zealand
| | - Adam P Sharples
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway.,Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - Steve Horvath
- Department of Human Genetics and Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nir Eynon
- Institute for Health and Sport, Victoria University, Melbourne, Australia
| |
Collapse
|
52
|
Bergsma T, Rogaeva E. DNA Methylation Clocks and Their Predictive Capacity for Aging Phenotypes and Healthspan. Neurosci Insights 2020; 15:2633105520942221. [PMID: 32743556 PMCID: PMC7376380 DOI: 10.1177/2633105520942221] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
The number of age predictors based on DNA methylation (DNAm) profile is rising
due to their potential in predicting healthspan and application in age-related
illnesses, such as neurodegenerative diseases. The cumulative assessment of DNAm
levels at age-related CpGs (DNAm clock) may reflect biological aging. Such DNAm
clocks have been developed using various training models and could mirror
different aspects of disease/aging mechanisms. Hence, evaluating several DNAm
clocks together may be the most effective strategy in capturing the complexity
of the aging process. However, various confounders may influence the outcome of
these age predictors, including genetic and environmental factors, as well as
technical differences in the selected DNAm arrays. These factors should be taken
into consideration when interpreting DNAm clock predictions. In the current
review, we discuss 15 reported DNAm clocks with consideration for their utility
in investigating neurodegenerative diseases and suggest research directions
towards developing a more optimal measure for biological aging.
Collapse
Affiliation(s)
- Tessa Bergsma
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
| |
Collapse
|
53
|
Lessel D, Kubisch C. Hereditary Syndromes with Signs of Premature Aging. Dtsch Arztebl Int 2020; 116:489-496. [PMID: 31452499 DOI: 10.3238/arztebl.2019.0489] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 11/19/2018] [Accepted: 05/13/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND Segmental progeroid syndromes (SPS) are rare hereditary diseases in which the affected individuals show signs of premature aging in more than one organ or type of tissue. We review the clinical and genetic features of some of these syndromes and discuss the extent to which their study affords a complementary opportunity to study aging processes in general. METHODS This review is based on publications retrieved by a selective search in PubMed. RESULTS Segmental progeroid syndromes are a clinically and genetically heterogeneous group of hereditary diseases. They can be categorized, for example, by the age of onset of manifestations (congenital vs. infantile vs. juvenile/adult forms). They are diagnosed on clinical grounds supplemented by genetic testing on the basis of next-generation sequencing, which is of central importance in view of the marked heterogeneity and complexity of their overlapping clinical features. The elucidation of the genetic and molecular causes of these diseases can lead to causally directed treatment, as shown by the initial clinical trials in Hutchinson- Gilford progeria syndrome. The molecular features of SPS are identical in many ways to those of "physiological" aging. Thus, studying the molecular mechanisms of SPS may be helpful for the development of molecularly defined treatment approaches for age-associated diseases in general. CONCLUSION Segmental progeroid syndromes are a complex group of diseases with overlapping clinical features. Current research efforts focus on the elucidation of the molecular mechanisms of these diseases, most of which are very rare. This should enable the development of treatments that might be applicable to general processes of aging as well.
Collapse
Affiliation(s)
- Davor Lessel
- Institute of Human Genetics, University Medical Center Hamburg-Eppendorf, Hamburg; Martin Zeitz Center for Rare Diseases, University Medical Center Hamburg-Eppendorf, Hamburg
| | | |
Collapse
|
54
|
Charlier CF, Martins RAP. Protective Mechanisms Against DNA Replication Stress in the Nervous System. Genes (Basel) 2020; 11:E730. [PMID: 32630049 DOI: 10.3390/genes11070730] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023] Open
Abstract
The precise replication of DNA and the successful segregation of chromosomes are essential for the faithful transmission of genetic information during the cell cycle. Alterations in the dynamics of genome replication, also referred to as DNA replication stress, may lead to DNA damage and, consequently, mutations and chromosomal rearrangements. Extensive research has revealed that DNA replication stress drives genome instability during tumorigenesis. Over decades, genetic studies of inherited syndromes have established a connection between the mutations in genes required for proper DNA repair/DNA damage responses and neurological diseases. It is becoming clear that both the prevention and the responses to replication stress are particularly important for nervous system development and function. The accurate regulation of cell proliferation is key for the expansion of progenitor pools during central nervous system (CNS) development, adult neurogenesis, and regeneration. Moreover, DNA replication stress in glial cells regulates CNS tumorigenesis and plays a role in neurodegenerative diseases such as ataxia telangiectasia (A-T). Here, we review how replication stress generation and replication stress response (RSR) contribute to the CNS development, homeostasis, and disease. Both cell-autonomous mechanisms, as well as the evidence of RSR-mediated alterations of the cellular microenvironment in the nervous system, were discussed.
Collapse
|
55
|
Kwiatkowska KM, Bacalini MG, Sala C, Kaziyama H, de Andrade DC, Terlizzi R, Giannini G, Cevoli S, Pierangeli G, Cortelli P, Garagnani P, Pirazzini C. Analysis of Epigenetic Age Predictors in Pain-Related Conditions. Front Public Health 2020; 8:172. [PMID: 32582603 PMCID: PMC7296181 DOI: 10.3389/fpubh.2020.00172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/20/2020] [Indexed: 01/31/2023] Open
Abstract
Chronic pain prevalence is high worldwide and increases at older ages. Signs of premature aging have been associated with chronic pain, but few studies have investigated aging biomarkers in pain-related conditions. A set of DNA methylation (DNAm)-based estimates of age, called “epigenetic clocks,” has been proposed as biological measures of age-related adverse processes, morbidity, and mortality. The aim of this study is to assess if different pain-related phenotypes show alterations in DNAm age. In our analysis, we considered three cohorts for which whole-blood DNAm data were available: heat pain sensitivity (HPS), including 20 monozygotic twin pairs discordant for heat pain temperature threshold; fibromyalgia (FM), including 24 cases and 20 controls; and headache, including 22 chronic migraine and medication overuse headache patients (MOH), 18 episodic migraineurs (EM), and 13 healthy subjects. We used the Horvath's epigenetic age calculator to obtain DNAm-based estimates of epigenetic age, telomere length, levels of 7 proteins in plasma, number of smoked packs of cigarettes per year, and blood cell counts. We did not find differences in epigenetic age acceleration, calculated using five different epigenetic clocks, between subjects discordant for pain-related phenotypes. Twins with high HPS had increased CD8+ T cell counts (nominal p = 0.028). HPS thresholds were negatively associated with estimated levels of GDF15 (nominal p = 0.008). FM patients showed decreased naive CD4+ T cell counts compared with controls (nominal p = 0.015). The severity of FM manifestations expressed through various evaluation tests was associated with decreased levels of leptin, shorter length of telomeres, and reduced CD8+ T and natural killer cell counts (nominal p < 0.05), while the duration of painful symptoms was positively associated with telomere length (nominal p = 0.034). No differences in DNAm-based estimates were detected for MOH or EM compared with controls. In summary, our study suggests that HPS, FM, and MOH/EM do not show signs of epigenetic age acceleration in whole blood, while HPS and FM are associated with DNAm-based estimates of immunological parameters, plasma proteins, and telomere length. Future studies should extend these observations in larger cohorts.
Collapse
Affiliation(s)
| | | | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Helena Kaziyama
- Department of Neurology, Pain Center, LIM 62, University of São Paulo, São Paulo, Brazil
| | - Daniel Ciampi de Andrade
- Department of Neurology, Pain Center, LIM 62, University of São Paulo, São Paulo, Brazil.,Pain Center, Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
| | | | - Giulia Giannini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Sabina Cevoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Giulia Pierangeli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Pietro Cortelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Applied Biomedical Research Center (CRBA), Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy.,Unit of Bologna, CNR Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| |
Collapse
|
56
|
Matsuyama M, WuWong DJ, Horvath S, Matsuyama S. Epigenetic clock analysis of human fibroblasts in vitro: effects of hypoxia, donor age, and expression of hTERT and SV40 largeT. Aging (Albany NY) 2019; 11:3012-22. [PMID: 31113906 DOI: 10.18632/aging.101955] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022]
Abstract
Aging is associated with a genome-wide change of DNA methylation (DNAm). "DNAm age" is defined as the predicted chronological age by the age estimator based on DNAm. The estimator is called the epigenetic clock. The molecular mechanism underlining the epigenetic clock is still unknown. Here, we evaluated the effects of hypoxia and two immortalization factors, hTERT and SV40-LargeT (LT), on the DNAm age of human fibroblasts in vitro. We detected the cell division-associated progression of DNAm age after >10 population doublings. Moreover, the progression of DNAm age was slower under hypoxia (1% oxygen) compared to normoxia (21% oxygen), suggesting that oxygen levels determine the speed of the epigenetic aging. We show that the speed of cell division-associated DNAm age progression depends on the chronological age of the cell donor. hTERT expression did not arrest cell division-associated progression of DNAm age in most cells. SV40LT expression produced inconsistent effects, including rejuvenation of DNAm age. Our results show that a) oxygen and the targets of SV40LT (e.g. p53) modulate epigenetic aging rates and b) the chronological age of donor cells determines the speed of mitosis-associated DNAm age progression in daughter cells.
Collapse
|
57
|
Köhler F, Bormann F, Raddatz G, Gutekunst J, Corless S, Musch T, Lonsdorf AS, Erhardt S, Lyko F, Rodríguez-Paredes M. Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford progeria syndrome. Genome Med 2020; 12:46. [PMID: 32450911 PMCID: PMC7249329 DOI: 10.1186/s13073-020-00749-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/12/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Hutchinson-Gilford progeria syndrome (HGPS) is a progeroid disease characterized by the early onset of age-related phenotypes including arthritis, loss of body fat and hair, and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein lamin A (termed progerin) and have previously been shown to exhibit prominent histone modification changes. METHODS Here, we analyze the possibility that epigenetic deregulation of lamina-associated domains (LADs) is involved in the molecular pathology of HGPS. To do so, we studied chromatin accessibility (Assay for Transposase-accessible Chromatin (ATAC)-see/-seq), DNA methylation profiles (Infinium MethylationEPIC BeadChips), and transcriptomes (RNA-seq) of nine primary HGPS fibroblast cell lines and six additional controls, two parental and four age-matched healthy fibroblast cell lines. RESULTS Our ATAC-see/-seq data demonstrate that primary dermal fibroblasts from HGPS patients exhibit chromatin accessibility changes that are enriched in LADs. Infinium MethylationEPIC BeadChip profiling further reveals that DNA methylation alterations observed in HGPS fibroblasts are similarly enriched in LADs and different from those occurring during healthy aging and Werner syndrome (WS), another premature aging disease. Moreover, HGPS patients can be stratified into two different subgroups according to their DNA methylation profiles. Finally, we show that the epigenetic deregulation of LADs is associated with HGPS-specific gene expression changes. CONCLUSIONS Taken together, our results strongly implicate epigenetic deregulation of LADs as an important and previously unrecognized feature of HGPS, which contributes to disease-specific gene expression. Therefore, they not only add a new layer to the study of epigenetic changes in the progeroid syndrome, but also advance our understanding of the disease's pathology at the cellular level.
Collapse
Affiliation(s)
- Florian Köhler
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Felix Bormann
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Günter Raddatz
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Julian Gutekunst
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Samuel Corless
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
- DKFZ-ZMBH-Alliance, 69120, Heidelberg, Germany
- CellNetworks Excellence Cluster, Heidelberg University, 69120, Heidelberg, Germany
| | - Tanja Musch
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Anke S Lonsdorf
- Department of Dermatology, University Hospital, Ruprecht-Karls University of Heidelberg, Heidelberg, Germany
| | - Sylvia Erhardt
- Center for Molecular Biology of Heidelberg University (ZMBH), Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
- DKFZ-ZMBH-Alliance, 69120, Heidelberg, Germany
- CellNetworks Excellence Cluster, Heidelberg University, 69120, Heidelberg, Germany
| | - Frank Lyko
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany
| | - Manuel Rodríguez-Paredes
- Division of Epigenetics, DKFZ-ZMBH Alliance, German Cancer Research Center, Heidelberg, Germany.
| |
Collapse
|
58
|
Lu AT, Quach A, Wilson JG, Reiner AP, Aviv A, Raj K, Hou L, Baccarelli AA, Li Y, Stewart JD, Whitsel EA, Assimes TL, Ferrucci L, Horvath S. DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging (Albany NY) 2020; 11:303-327. [PMID: 30669119 PMCID: PMC6366976 DOI: 10.18632/aging.101684] [Citation(s) in RCA: 892] [Impact Index Per Article: 223.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/22/1969] [Indexed: 12/16/2022]
Abstract
It was unknown whether plasma protein levels can be estimated based on DNA methylation (DNAm) levels, and if so, how the resulting surrogates can be consolidated into a powerful predictor of lifespan. We present here, seven DNAm-based estimators of plasma proteins including those of plasminogen activator inhibitor 1 (PAI-1) and growth differentiation factor 15. The resulting predictor of lifespan, DNAm GrimAge (in units of years), is a composite biomarker based on the seven DNAm surrogates and a DNAm-based estimator of smoking pack-years. Adjusting DNAm GrimAge for chronological age generated novel measure of epigenetic age acceleration, AgeAccelGrim.Using large scale validation data from thousands of individuals, we demonstrate that DNAm GrimAge stands out among existing epigenetic clocks in terms of its predictive ability for time-to-death (Cox regression P=2.0E-75), time-to-coronary heart disease (Cox P=6.2E-24), time-to-cancer (P= 1.3E-12), its strong relationship with computed tomography data for fatty liver/excess visceral fat, and age-at-menopause (P=1.6E-12). AgeAccelGrim is strongly associated with a host of age-related conditions including comorbidity count (P=3.45E-17). Similarly, age-adjusted DNAm PAI-1 levels are associated with lifespan (P=5.4E-28), comorbidity count (P= 7.3E-56) and type 2 diabetes (P=2.0E-26). These DNAm-based biomarkers show the expected relationship with lifestyle factors including healthy diet and educational attainment.Overall, these epigenetic biomarkers are expected to find many applications including human anti-aging studies.
Collapse
Affiliation(s)
- Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Austin Quach
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Abraham Aviv
- Center of Development and Aging, New Jersey Medical School, Rutgers State University of New Jersey, Newark, NJ 07103, USA
| | - Kenneth Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, United Kingdom
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrea A Baccarelli
- Laboratory of Environmental Epigenetics, Departments of Environmental Health Sciences Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Yun Li
- Departments of Genetics, Biostatistics, Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - James D Stewart
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Themistocles L Assimes
- Department of Medicine (Division of Cardiovascular Medicine), Stanford University School of Medicine, Stanford, CA 94305, USA.,VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, USA, Baltimore, MD 21224, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
59
|
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.
Collapse
Affiliation(s)
| | | | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
| |
Collapse
|
60
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
61
|
Chen L, Wagner CL, Dong Y, Wang X, Shary JR, Huang Y, Hollis BW, Zhu H. Effects of Maternal Vitamin D3 Supplementation on Offspring Epigenetic Clock of Gestational Age at Birth: A Post-hoc Analysis of a Randomized Controlled Trial. Epigenetics 2020; 15:830-840. [PMID: 32089064 DOI: 10.1080/15592294.2020.1734148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Vitamin D could be beneficial for healthy ageing in humans. We previously found that vitamin D supplementation may slow down epigenetic ageing in young African American adults. We tested new epigenetic clocks developed for neonates among a multiethnic population, and tested the hypothesis that maternal vitamin D supplementation would slow down the epigenetic gestational age acceleration (GAA) in newborn babies. Ninety-two pregnant women (aged 29.6 ± 4.8 y; 21% African Americans, 28% Hispanics) were randomized to receive 4000 IU/day vitamin D3 or placebo, plus prenatal vitamins containing 400 IU vitamin D3 during pregnancy in a randomized controlled trial (RCT). Cord blood genome-wide methylation analysis was performed on the Illumina Infinium MethylationEPIC Beadchip. DNA methylation gestational age was calculated based on two calculations developed by Knight and Bohlin. DNA methylation gestational ages calculated by Knight's clock and Bohlin' clock were highly correlated with the gestational age in the placebo group (correlation coefficients = 0.88, p s< 0.001, respectively). GAA was associated with higher birth weight (p = 0.039). In the entire cohort, vitamin D3 supplementation was not associated with GAA (p > 0.05). However, vitamin D3 supplementation decreased GAA by both Knight's clock (β = -0.89, p = 0.047) and Bohlin's clock (β = -0.71, p = 0.005) in the African American participants. Maternal vitamin D3 supplementation may slow down the epigenetic gestational ageing process in African American neonates. Long-term follow-up studies are warranted to determine the role of epigenetic age acceleration in the growth and development of offspring.
Collapse
Affiliation(s)
- Li Chen
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
| | - Carol L Wagner
- Department of Pediatrics, Medical University of South Carolina ,SC, USA
| | - Yanbin Dong
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
| | - Xiaoling Wang
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
| | - Judith R Shary
- Department of Pediatrics, Medical University of South Carolina ,SC, USA
| | - Ying Huang
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
| | - Bruce W Hollis
- Department of Pediatrics, Medical University of South Carolina ,SC, USA
| | - Haidong Zhu
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
| |
Collapse
|
62
|
Bressler J, Marioni RE, Walker RM, Xia R, Gottesman RF, Windham BG, Grove ML, Guan W, Pankow JS, Evans KL, Mcintosh AM, Deary IJ, Mosley TH, Boerwinkle E, Fornage M. Epigenetic Age Acceleration and Cognitive Function in African American Adults in Midlife: The Atherosclerosis Risk in Communities Study. J Gerontol A Biol Sci Med Sci 2020; 75:473-480. [PMID: 31630168 PMCID: PMC7328191 DOI: 10.1093/gerona/glz245] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Indexed: 12/12/2022] Open
Abstract
Methylation levels measured at defined sites across the genome have recently been shown to be correlated with an individual's chronological age. Age acceleration, or the difference between age estimated from DNA methylation status and chronological age, has been proposed as a novel biomarker of aging. In this study, the cross-sectional association between two different measures of age acceleration and cognitive function was investigated using whole blood samples from 2,157 African American participants 47-70 years of age in the population-based Atherosclerosis Risk in Communities (ARIC) Study. Cognition was evaluated using three domain-specific tests. A significant inverse association between a 1-year increase in age acceleration calculated using a blood-based age predictor and scores on the Word Fluency Test was found using a general linear model adjusted for chronological age, gender, and years of education (β = -0.140 words; p = .001) and after adding other potential confounding variables (β = -0.104 words, p = .023). The results were replicated in 1,670 European participants in the Generation Scotland: Scottish Family Health Study (fully adjusted model: β = -0.199 words; p = .034). A significant association was also identified in a trans-ethnic meta-analysis across cohorts that included an additional 708 European American ARIC study participants (fully adjusted model: β = -0.110 words, p = .003). There were no associations found using an estimate of age acceleration derived from multiple tissues. These findings provide evidence that age acceleration is a correlate of performance on a test of verbal fluency in middle-aged adults.
Collapse
Affiliation(s)
- Jan Bressler
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, UK
| | - Rui Xia
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston
| | - Rebecca F Gottesman
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, Maryland
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland
| | - B Gwen Windham
- Division of Geriatrics, Department of Medicine, University of Mississippi Medical Center, Jackson
| | - Megan L Grove
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston
| | - Weihua Guan
- Division of Biostatistics, School of Public Health
| | - James S Pankow
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, UK
| | - Andrew M Mcintosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, UK
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, UK
- Department of Psychology, University of Edinburgh, UK
| | - Thomas H Mosley
- Division of Geriatrics, Department of Medicine, University of Mississippi Medical Center, Jackson
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston
| |
Collapse
|
63
|
Ferrucci L, Gonzalez‐Freire M, Fabbri E, Simonsick E, Tanaka T, Moore Z, Salimi S, Sierra F, de Cabo R. Measuring biological aging in humans: A quest. Aging Cell 2020; 19:e13080. [PMID: 31833194 PMCID: PMC6996955 DOI: 10.1111/acel.13080] [Citation(s) in RCA: 298] [Impact Index Per Article: 74.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/22/2019] [Accepted: 10/27/2019] [Indexed: 12/16/2022] Open
Abstract
The global population of individuals over the age of 65 is growing at an unprecedented rate and is expected to reach 1.6 billion by 2050. Most older individuals are affected by multiple chronic diseases, leading to complex drug treatments and increased risk of physical and cognitive disability. Improving or preserving the health and quality of life of these individuals is challenging due to a lack of well-established clinical guidelines. Physicians are often forced to engage in cycles of "trial and error" that are centered on palliative treatment of symptoms rather than the root cause, often resulting in dubious outcomes. Recently, geroscience challenged this view, proposing that the underlying biological mechanisms of aging are central to the global increase in susceptibility to disease and disability that occurs with aging. In fact, strong correlations have recently been revealed between health dimensions and phenotypes that are typical of aging, especially with autophagy, mitochondrial function, cellular senescence, and DNA methylation. Current research focuses on measuring the pace of aging to identify individuals who are "aging faster" to test and develop interventions that could prevent or delay the progression of multimorbidity and disability with aging. Understanding how the underlying biological mechanisms of aging connect to and impact longitudinal changes in health trajectories offers a unique opportunity to identify resilience mechanisms, their dynamic changes, and their impact on stress responses. Harnessing how to evoke and control resilience mechanisms in individuals with successful aging could lead to writing a new chapter in human medicine.
Collapse
Affiliation(s)
- Luigi Ferrucci
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Marta Gonzalez‐Freire
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Elisa Fabbri
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
- Department of Medical and Surgical SciencesUniversity of BolognaBolognaItaly
| | - Eleanor Simonsick
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Toshiko Tanaka
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Zenobia Moore
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Shabnam Salimi
- Department of Epidemiology and Public HealthUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Felipe Sierra
- Division of Aging BiologyNational Institute on AgingNIHBethesdaMDUSA
| | - Rafael de Cabo
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| |
Collapse
|
64
|
Gensous N, Garagnani P, Santoro A, Giuliani C, Ostan R, Fabbri C, Milazzo M, Gentilini D, di Blasio AM, Pietruszka B, Madej D, Bialecka-Debek A, Brzozowska A, Franceschi C, Bacalini MG. One-year Mediterranean diet promotes epigenetic rejuvenation with country- and sex-specific effects: a pilot study from the NU-AGE project. GeroScience 2020; 42:687-701. [PMID: 31981007 DOI: 10.1007/s11357-019-00149-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Mediterranean diet has been proposed to promote healthy aging, but its effects on aging biomarkers have been poorly investigated. We evaluated the impact of a 1-year Mediterranean-like diet in a pilot study including 120 elderly healthy subjects from the NU-AGE study (60 Italians, 60 Poles) by measuring the changes in their epigenetic age, assessed by Horvath's clock. We observed a trend towards epigenetic rejuvenation of participants after nutritional intervention. The effect was statistically significant in the group of Polish females and in subjects who were epigenetically older at baseline. A genome-wide association study of epigenetic age changes after the intervention did not return significant (adjusted p value < 0.05) loci. However, we identified small-effect alleles (nominal p value < 10-4), mapping in genes enriched in pathways related to energy metabolism, regulation of cell cycle, and of immune functions. Together, these findings suggest that Mediterranean diet can promote epigenetic rejuvenation but with country-, sex-, and individual-specific effects, thus highlighting the need for a personalized approach to nutritional interventions.
Collapse
|
65
|
Abstract
The study of epigenetics has its roots in the study of organism change over time and response to environmental change, although over the past several decades the definition has been formalized to include heritable alterations in gene expression that are not a result of alterations in underlying DNA sequence. In this chapter, we discuss first the history and milestones in the 100+ years of epigenetic study, including early discoveries of DNA methylation, histone posttranslational modification, and noncoding RNA. We then discuss how epigenetics has changed the way that we think of both health and disease, offering as examples studies examining the epigenetic contributions to aging, including the recent development of an epigenetic "clock", and explore how antiaging therapies may work through epigenetic modifications. We then discuss a nonpathogenic role for epigenetics in the clinic: epigenetic biomarkers. We conclude by offering two examples of modern state-of-the-art integrated multi-omics studies of epigenetics in disease pathogenesis, one which sought to capture shared mechanisms among multiple diseases, and another which used epigenetic big data to better understand the pathogenesis of a single tissue from one disease.
Collapse
|
66
|
Lewis SK, Nachun D, Martin MG, Horvath S, Coppola G, Jones DL. DNA Methylation Analysis Validates Organoids as a Viable Model for Studying Human Intestinal Aging. Cell Mol Gastroenterol Hepatol 2019; 9:527-541. [PMID: 31805439 PMCID: PMC7044532 DOI: 10.1016/j.jcmgh.2019.11.013] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/22/2019] [Accepted: 11/25/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND & AIMS The epithelia of the intestine and colon turn over rapidly and are maintained by adult stem cells at the base of crypts. Although the small intestine and colon have distinct, well-characterized physiological functions, it remains unclear if there are fundamental regional differences in stem cell behavior or region-dependent degenerative changes during aging. Mesenchyme-free organoids provide useful tools for investigating intestinal stem cell biology in vitro and have started to be used for investigating age-related changes in stem cell function. However, it is unknown whether organoids maintain hallmarks of age in the absence of an aging niche. We tested whether stem cell-enriched organoids preserved the DNA methylation-based aging profiles associated with the tissues and crypts from which they were derived. METHODS To address this, we used standard human methylation arrays and the human epigenetic clock as a biomarker of age to analyze in vitro-derived, 3-dimensional, stem cell-enriched intestinal organoids. RESULTS We found that human stem cell-enriched organoids maintained segmental differences in methylation patterns and that age, as measured by the epigenetic clock, also was maintained in vitro. Surprisingly, we found that stem cell-enriched organoids derived from the small intestine showed striking epigenetic age reduction relative to organoids derived from colon. CONCLUSIONS Our data validate the use of organoids as a model for studying human intestinal aging and introduce methods that can be used when modeling aging or age-onset diseases in vitro.
Collapse
Affiliation(s)
- Sophia K. Lewis
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California,Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California
| | - Daniel Nachun
- Department of Psychiatry and Semel Institute, University of California Los Angeles, Los Angeles, California
| | - Martin G. Martin
- Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California,Division of Gastroenterology and Nutrition, Department of Pediatrics, Mattel Children's Hospital and David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Steve Horvath
- Department of Human Genetics, Gonda Research Center, David Geffen School of Medicine, Los Angeles, California
| | - Giovanni Coppola
- Department of Psychiatry and Semel Institute, University of California Los Angeles, Los Angeles, California,Department of Neurology, University of California Los Angeles, Los Angeles, California
| | - D. Leanne Jones
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California,Eli and Edythe Broad Stem Cell Research Center, University of California Los Angeles, Los Angeles, California,Correspondence Address correspondence to: D. Leanne Jones, PhD, Department of Molecular, Cell, and Developmental Biology, Terasaki Life Sciences Building Room 5139, 610 Charles E. Young Drive South, University of California Los Angeles, Los Angeles, California 90095.
| |
Collapse
|
67
|
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: 410] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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.
| |
Collapse
|
68
|
Kabacik S, Horvath S, Cohen H, Raj K. Epigenetic ageing is distinct from senescence-mediated ageing and is not prevented by telomerase expression. Aging (Albany NY) 2019; 10:2800-2815. [PMID: 30332397 PMCID: PMC6224244 DOI: 10.18632/aging.101588] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/04/2018] [Indexed: 02/06/2023]
Abstract
The paramount role of senescent cells in ageing has prompted suggestions that re-expression of telomerase may prevent ageing; a proposition that is predicated on the assumption that senescent cells are the sole cause of ageing. Recently, several DNA methylation-based age estimators (epigenetic clocks) have been developed and they revealed that increased epigenetic age is associated with a host of age-related conditions, and is predictive of lifespan. Employing these clocks to measure epigenetic age in vitro, we interrogated the relationship between epigenetic ageing and telomerase activity. Although hTERT did not induce any perceptible change to the rate of epigenetic ageing, hTERT-expressing cells, which bypassed senescence, continued to age epigenetically. Employment of hTERT mutants revealed that neither telomere synthesis nor immortalisation is necessary for the continued increase in epigenetic age by these cells. Instead, the extension of their lifespan is sufficient to support continued epigenetic ageing of the cell. These characteristics, observed in cells from numerous donors and cell types, reveal epigenetic ageing to be distinct from replicative senescence. Hence, while re-activation of hTERT may stave off physical manifestation of ageing through avoidance of replicative senescence, it would have little impact on epigenetic ageing which continues in spite of telomerase activity.
Collapse
Affiliation(s)
- Sylwia Kabacik
- Cellular Biology Group, Radiation Effects Department, Centre for Radiation, Chemicals and Environmental Hazards (CRCE) Public Health England (PHE) Dicot, Chilton OX11 0RQ, Oxfordshire, United Kingdom
| | - Steve Horvath
- Departments of Human Genetics and Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Howard Cohen
- Elizabeth House Medical Practice, Warlingham, Surrey CR6 9LF, United Kingdom
| | - Kenneth Raj
- Cellular Biology Group, Radiation Effects Department, Centre for Radiation, Chemicals and Environmental Hazards (CRCE) Public Health England (PHE) Dicot, Chilton OX11 0RQ, Oxfordshire, United Kingdom
| |
Collapse
|
69
|
Thompson MJ, Chwiałkowska K, Rubbi L, Lusis AJ, Davis RC, Srivastava A, Korstanje R, Churchill GA, Horvath S, Pellegrini M. A multi-tissue full lifespan epigenetic clock for mice. Aging (Albany NY) 2019; 10:2832-2854. [PMID: 30348905 PMCID: PMC6224226 DOI: 10.18632/aging.101590] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/05/2018] [Indexed: 12/11/2022]
Abstract
Human DNA-methylation data have been used to develop highly accurate biomarkers of aging ("epigenetic clocks"). Recent studies demonstrate that similar epigenetic clocks for mice (Mus Musculus) can be slowed by gold standard anti-aging interventions such as calorie restriction and growth hormone receptor knock-outs. Using DNA methylation data from previous publications with data collected in house for a total 1189 samples spanning 193,651 CpG sites, we developed 4 novel epigenetic clocks by choosing different regression models (elastic net- versus ridge regression) and by considering different sets of CpGs (all CpGs vs highly conserved CpGs). We demonstrate that accurate age estimators can be built on the basis of highly conserved CpGs. However, the most accurate clock results from applying elastic net regression to all CpGs. While the anti-aging effect of calorie restriction could be detected with all types of epigenetic clocks, only ridge regression based clocks replicated the finding of slow epigenetic aging effects in dwarf mice. Overall, this study demonstrates that there are trade-offs when it comes to epigenetic clocks in mice. Highly accurate clocks might not be optimal for detecting the beneficial effects of anti-aging interventions.
Collapse
Affiliation(s)
- Michael J Thompson
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Karolina Chwiałkowska
- Centre for Bioinformatics and Data Analysis, Medical University of Bialystok, Bialystok, Poland
| | - Liudmilla Rubbi
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Aldons J Lusis
- Department of Microbiology, Immunology and Molecular Genetics, Department of Medicine, and Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Richard C Davis
- Department of Microbiology, Immunology and Molecular Genetics, Department of Medicine, and Department of Human Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | - Ron Korstanje
- The Jackson Laboratory, Bar Harbor, Maine 04609, USA
| | | | - Steve Horvath
- Department of Human Genetics and Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
70
|
Schmeer C, Kretz A, Wengerodt D, Stojiljkovic M, Witte OW. Dissecting Aging and Senescence-Current Concepts and Open Lessons. Cells 2019; 8:cells8111446. [PMID: 31731770 PMCID: PMC6912776 DOI: 10.3390/cells8111446] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 01/10/2023] Open
Abstract
In contrast to the programmed nature of development, it is still a matter of debate whether aging is an adaptive and regulated process, or merely a consequence arising from a stochastic accumulation of harmful events that culminate in a global state of reduced fitness, risk for disease acquisition, and death. Similarly unanswered are the questions of whether aging is reversible and can be turned into rejuvenation as well as how aging is distinguishable from and influenced by cellular senescence. With the discovery of beneficial aspects of cellular senescence and evidence of senescence being not limited to replicative cellular states, a redefinition of our comprehension of aging and senescence appears scientifically overdue. Here, we provide a factor-based comparison of current knowledge on aging and senescence, which we converge on four suggested concepts, thereby implementing the newly emerging cellular and molecular aspects of geroconversion and amitosenescence, and the signatures of a genetic state termed genosenium. We also address the possibility of an aging-associated secretory phenotype in analogy to the well-characterized senescence-associated secretory phenotype and delineate the impact of epigenetic regulation in aging and senescence. Future advances will elucidate the biological and molecular fingerprints intrinsic to either process.
Collapse
Affiliation(s)
- Christian Schmeer
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
- Correspondence:
| | - Alexandra Kretz
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Diane Wengerodt
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
| | - Milan Stojiljkovic
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Otto W. Witte
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| |
Collapse
|
71
|
Maierhofer A, Flunkert J, Oshima J, Martin GM, Poot M, Nanda I, Dittrich M, Müller T, Haaf T. Epigenetic signatures of Werner syndrome occur early in life and are distinct from normal epigenetic aging processes. Aging Cell 2019; 18:e12995. [PMID: 31259468 PMCID: PMC6718529 DOI: 10.1111/acel.12995] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 05/24/2019] [Accepted: 06/05/2019] [Indexed: 12/11/2022] Open
Abstract
Werner Syndrome (WS) is an adult-onset segmental progeroid syndrome. Bisulfite pyrosequencing of repetitive DNA families revealed comparable blood DNA methylation levels between classical (18 WRN-mutant) or atypical WS (3 LMNA-mutant and 3 POLD1-mutant) patients and age- and sex-matched controls. WS was not associated with either age-related accelerated global losses of ALU, LINE1, and α-satellite DNA methylations or gains of rDNA methylation. Single CpG methylation was analyzed with Infinium MethylationEPIC arrays. In a correspondence analysis, atypical WS samples clustered together with the controls and were clearly separated from classical WS, consistent with distinct epigenetic pathologies. In classical WS, we identified 659 differentially methylated regions (DMRs) comprising 3,656 CpG sites and 613 RefSeq genes. The top DMR was located in the HOXA4 promoter. Additional DMR genes included LMNA, POLD1, and 132 genes which have been reported to be differentially expressed in WRN-mutant/depleted cells. DMRs were enriched in genes with molecular functions linked to transcription factor activity and sequence-specific DNA binding to promoters transcribed by RNA polymerase II. We propose that transcriptional misregulation of downstream genes by the absence of WRN protein contributes to the variable premature aging phenotypes of WS. There were no CpG sites showing significant differences in DNA methylation changes with age between WS patients and controls. Genes with both WS- and age-related methylation changes exhibited a constant offset of methylation between WRN-mutant patients and controls across the entire analyzed age range. WS-specific epigenetic signatures occur early in life and do not simply reflect an acceleration of normal epigenetic aging processes.
Collapse
Affiliation(s)
- Anna Maierhofer
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Julia Flunkert
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Junko Oshima
- Department of Pathology University of Washington Seattle Washington USA
- Department of Clinical Cell Biology and Medicine, Graduate School of Medicine Chiba University Chiba Japan
| | - George M. Martin
- Department of Pathology University of Washington Seattle Washington USA
| | - Martin Poot
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Indrajit Nanda
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| | - Marcus Dittrich
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Tobias Müller
- Department of Bioinformatics Julius Maximilians University Würzburg Germany
| | - Thomas Haaf
- Institute of Human Genetics Julius Maximilians University Würzburg Germany
| |
Collapse
|
72
|
Horvath S, Oshima J, Martin GM, Lu AT, Quach A, Cohen H, Felton S, Matsuyama M, Lowe D, Kabacik S, Wilson JG, Reiner AP, Maierhofer A, Flunkert J, Aviv A, Hou L, Baccarelli AA, Li Y, Stewart JD, Whitsel EA, Ferrucci L, Matsuyama S, Raj K. Epigenetic clock for skin and blood cells applied to Hutchinson Gilford Progeria Syndrome and ex vivo studies. Aging (Albany NY) 2019; 10:1758-1775. [PMID: 30048243 PMCID: PMC6075434 DOI: 10.18632/aging.101508] [Citation(s) in RCA: 301] [Impact Index Per Article: 60.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 07/21/2018] [Indexed: 01/01/2023]
Abstract
DNA methylation (DNAm)-based biomarkers of aging have been developed for many tissues and organs. However, these biomarkers have sub-optimal accuracy in fibroblasts and other cell types used in ex vivo studies. To address this challenge, we developed a novel and highly robust DNAm age estimator (based on 391 CpGs) for human fibroblasts, keratinocytes, buccal cells, endothelial cells, lymphoblastoid cells, skin, blood, and saliva samples. High age correlations can also be observed in sorted neurons, glia, brain, liver, and even bone samples. Gestational age correlates with DNAm age in cord blood. When used on fibroblasts from Hutchinson Gilford Progeria Syndrome patients, this age estimator (referred to as the skin & blood clock) uncovered an epigenetic age acceleration with a magnitude that is below the sensitivity levels of other DNAm-based biomarkers. Furthermore, this highly sensitive age estimator accurately tracked the dynamic aging of cells cultured ex vivo and revealed that their proliferation is accompanied by a steady increase in epigenetic age. The skin & blood clock predicts lifespan and it relates to many age-related conditions. Overall, this biomarker is expected to become useful for forensic applications (e.g. blood or buccal swabs) and for a quantitative ex vivo human cell aging assay.
Collapse
Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Junko Oshima
- Department of Pathology, University of Washington, Seattle, WA 98195, USA.,Department of Clinical Cell Biology and Medicine, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - George M Martin
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Austin Quach
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Howard Cohen
- Elizabeth House, Warlingham, Surrey CR6 9LF, United Kingdom
| | - Sarah Felton
- Department of Dermatology, Oxford University Hospitals NHS Foundation Trust, Oxford OX3 7LJ, United Kingdom
| | - Mieko Matsuyama
- Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Donna Lowe
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, United Kingdom
| | - Sylwia Kabacik
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, United Kingdom
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Anna Maierhofer
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Julia Flunkert
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Abraham Aviv
- Center of Development and Aging, New Jersey Medical School, Rutgers State University of New Jersey, Newark, NJ 07103, USA
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrea A Baccarelli
- Laboratory of Environmental Epigenetics, Departments of Environmental Health Sciences and Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Yun Li
- Departments of Genetics, Biostatistics, Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - James D Stewart
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Shigemi Matsuyama
- Department of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Pathology and Pharmacology, Case Comprehensive Centre, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Kenneth Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, United Kingdom
| |
Collapse
|
73
|
Beydoun MA, Hossain S, Chitrala KN, Tajuddin SM, Beydoun HA, Evans MK, Zonderman AB. Association between epigenetic age acceleration and depressive symptoms in a prospective cohort study of urban-dwelling adults. J Affect Disord 2019; 257:64-73. [PMID: 31299406 PMCID: PMC6757325 DOI: 10.1016/j.jad.2019.06.032] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 06/07/2019] [Accepted: 06/29/2019] [Indexed: 01/07/2023]
Abstract
OBJECTIVE This study tests associations of DNA methylation-based (DNAm) measures of epigenetic age acceleration (EAA) with cross-sectional and longitudinal depressive symptoms in an urban sample of middle-aged adults. METHODS White and African-American adult participants in the Healthy Aging in Neighborhoods of Diversity across the Life Span study for whom DNA samples were analyzed (baseline age: 30-65 years) we included. We estimated three DNAm based EAA measures: (1) universal epigenetic age acceleration (AgeAccel); (2) intrinsic epigenetic age acceleration (IEAA); and (3) extrinsic epigenetic age acceleration (EEAA). Depressive symptoms were assessed using the 20-item Center for Epidemiological Studies-Depression scale total and sub-domain scores at baseline (2004-2009) and follow-up visits (2009-2013). Linear mixed-effects regression models were conducted, adjusting potentially confounding covariates, selection bias and multiple testing (N = 329 participants, ∼52% men, k = 1.9 observations/participant, mean follow-up time∼4.7 years). RESULTS None of the epigenetic age acceleration measures were associated with total depressive symptom scores at baseline or over time. IEAA - a measure of cellular epigenetic age acceleration irrespective of white blood cell composition - was cross-sectionally associated with decrement in "positive affect" in the total population (γ011± SE = -0.090 ± 0.030, P = 0.003, Cohen's D: -0.16) and among Whites (γ011 ± SE = -0.135 ± 0.048, P = 0.005, Cohen's D: -0.23), after correction for multiple testing. Baseline "positive affect" was similarly associated with AgeAccel. LIMITATIONS Limitations included small sample size, weak-moderate effects and measurement error. CONCLUSIONS IEAA and AgeAccel, two measures of EAA using Horvath algorithm, were linked to a reduced "positive affect", overall and among Whites. Future studies are needed to replicate our findings and test bi-directional relationships.
Collapse
Affiliation(s)
- May A. Beydoun
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD, United States,Corresponding author. (M.A. Beydoun)
| | - Sharmin Hossain
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD, United States
| | - Kumaraswamy Naidu Chitrala
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD, United States
| | - Salman M. Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD, United States
| | - Hind A. Beydoun
- Department of Research Programs, Fort Belvoir Community Hospital, Fort Belvoir, VA, United States
| | - Michele K. Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD, United States
| | - Alan B. Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIA/NIH/IRP, Baltimore, MD, United States
| |
Collapse
|
74
|
Abstract
Human longevity is a complex trait, and to disentangle its basis has a great theoretical and practical consequences for biomedicine. The genetics of human longevity is still poorly understood despite several investigations that used different strategies and protocols. Here, we argue that such rather disappointing harvest is largely because of the extraordinary complexity of the longevity phenotype in humans. The capability to reach the extreme decades of human lifespan seems to be the result of an intriguing mixture of gene-environment interactions. Accordingly, the genetics of human longevity is here described as a highly context-dependent phenomenon, within a new integrated, ecological, and evolutionary perspective, and is presented as a dynamic process, both historically and individually. The available literature has been scrutinized within this perspective, paying particular attention to factors (sex, individual biography, family, population ancestry, social structure, economic status, and education, among others) that have been relatively neglected. The strength and limitations of the most powerful and used tools, such as genome-wide association study and whole-genome sequencing, have been discussed, focusing on prominently emerged genes and regions, such as apolipoprotein E, Forkhead box O3, interleukin 6, insulin-like growth factor-1, chromosome 9p21, 5q33.3, and somatic mutations among others. The major results of this approach suggest that (1) the genetics of longevity is highly population specific; (2) small-effect alleles, pleiotropy, and the complex allele timing likely play a major role; (3) genetic risk factors are age specific and need to be integrated in the light of the geroscience perspective; (4) a close relationship between genetics of longevity and genetics of age-related diseases (especially cardiovascular diseases) do exist. Finally, the urgent need of a global approach to the largely unexplored interactions between the 3 genetics of human body, that is, nuclear, mitochondrial, and microbiomes, is stressed. We surmise that the comprehensive approach here presented will help in increasing the above-mentioned harvest.
Collapse
Affiliation(s)
- Cristina Giuliani
- From the Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology (C.G.), University of Bologna, Italy.,School of Anthropology and Museum Ethnography, University of Oxford, United Kingdom (C.G.).,Interdepartmental Centre 'L. Galvani' (CIG), University of Bologna, Italy (C.G.)
| | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES) (P.G.), University of Bologna, Italy.,Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden (P.G.)
| | | |
Collapse
|
75
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
76
|
Abstract
Survival predictors are of potential use for informing on biological age and targeting prevention of aging-related morbidity. We assessed associations of 2 novel methylomic survival indicators, a methylation-based mortality risk score (MRscore) and the epigenetic clock-derived age acceleration (AA), with a well-known survival predictor, frailty index (FI), and compared the 3 indicators in mortality prediction. In a large population-based cohort with 14-year follow-up, we found both MRscore and AA to be independently associated with FI, but the association was much stronger for MRscore than for AA. Although all 3 indicators were individually associated with all-cause mortality, robust associations only persisted for MRscore and FI when simultaneously including the 3 indicators in regression models, with hazard ratios (95% CI) of 1.91 (1.63–2.22), 1.37 (1.25–1.51), and 1.05 (0.90–1.22), respectively, per standard deviation increase of MRscore, FI, and AA. Prediction error curves, Harrell’s C-statistics, and time-dependent AUCs all showed higher predictive accuracy for MRscore than for FI and AA. These findings were validated in independent samples. Our study demonstrates the ability of the MRscore to strongly enhance survival prediction beyond established markers of biological age, such as FI and AA, and it thus bears potential of a surrogate endpoint for clinical research and intervention.
Collapse
Affiliation(s)
- Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany
| | - Kai-Uwe Saum
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany
| | - Ben Schöttker
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,Network Ageing Research, University of Heidelberg, Heidelberg 69115, Germany
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg D-69120, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg D-69120, Germany
| |
Collapse
|
77
|
Abstract
Identifying and validating molecular targets of interventions that extend the human health span and lifespan has been difficult, as most clinical biomarkers are not sufficiently representative of the fundamental mechanisms of ageing to serve as their indicators. In a recent breakthrough, biomarkers of ageing based on DNA methylation data have enabled accurate age estimates for any tissue across the entire life course. These 'epigenetic clocks' link developmental and maintenance processes to biological ageing, giving rise to a unified theory of life course. Epigenetic biomarkers may help to address long-standing questions in many fields, including the central question: why do we age?
Collapse
|
78
|
Jeffries AR, Maroofian R, Salter CG, Chioza BA, Cross HE, Patton MA, Dempster E, Temple IK, Mackay DJG, Rezwan FI, Aksglaede L, Baralle D, Dabir T, Hunter MF, Kamath A, Kumar A, Newbury-Ecob R, Selicorni A, Springer A, Van Maldergem L, Varghese V, Yachelevich N, Tatton-Brown K, Mill J, Crosby AH, Baple EL. Growth disrupting mutations in epigenetic regulatory molecules are associated with abnormalities of epigenetic aging. Genome Res 2019; 29:1057-1066. [PMID: 31160375 PMCID: PMC6633263 DOI: 10.1101/gr.243584.118] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 05/24/2019] [Indexed: 11/24/2022]
Abstract
Germline mutations in fundamental epigenetic regulatory molecules including DNA methyltransferase 3 alpha (DNMT3A) are commonly associated with growth disorders, whereas somatic mutations are often associated with malignancy. We profiled genome-wide DNA methylation patterns in DNMT3A c.2312G > A; p.(Arg771Gln) carriers in a large Amish sibship with Tatton-Brown–Rahman syndrome (TBRS), their mosaic father, and 15 TBRS patients with distinct pathogenic de novo DNMT3A variants. This defined widespread DNA hypomethylation at specific genomic sites enriched at locations annotated as genes involved in morphogenesis, development, differentiation, and malignancy predisposition pathways. TBRS patients also displayed highly accelerated DNA methylation aging. These findings were most marked in a carrier of the AML-associated driver mutation p.Arg882Cys. Our studies additionally defined phenotype-related accelerated and decelerated epigenetic aging in two histone methyltransferase disorders: NSD1 Sotos syndrome overgrowth disorder and KMT2D Kabuki syndrome growth impairment. Together, our findings provide fundamental new insights into aberrant epigenetic mechanisms, the role of epigenetic machinery maintenance, and determinants of biological aging in these growth disorders.
Collapse
Affiliation(s)
- Aaron R Jeffries
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - Reza Maroofian
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's University of London, London SW17 0RE, United Kingdom
| | - Claire G Salter
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom.,Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, United Kingdom
| | - Barry A Chioza
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - Harold E Cross
- Department of Ophthalmology and Vision Science, University of Arizona School of Medicine, Tucson, Arizona 85711, USA
| | - Michael A Patton
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom.,Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's University of London, London SW17 0RE, United Kingdom
| | - Emma Dempster
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - I Karen Temple
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, United Kingdom
| | - Deborah J G Mackay
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Faisal I Rezwan
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom
| | - Lise Aksglaede
- Department of Clinical Genetics, Copenhagen University Hospital, Blegdamsvej 3B, 2200 Copenhagen N, Denmark
| | - Diana Baralle
- Human Genetics and Genomic Medicine, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD, United Kingdom.,Wessex Clinical Genetics Service, Princess Anne Hospital, Southampton, SO16 5YA, United Kingdom
| | - Tabib Dabir
- Northern Ireland Regional Genetics Centre, Clinical Genetics Service, Belfast City Hospital, Belfast, BT9 7AB, United Kingdom
| | - Matthew F Hunter
- Monash Genetics, Monash Health, Clayton, Victoria, VIC 3168, Australia.,Department of Paediatrics, Monash University, Clayton, Victoria, VIC 3168, Australia
| | - Arveen Kamath
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, CF14 4XN, United Kingdom
| | - Ajith Kumar
- North East Thames Regional Genetics Service and Department of Clinical Genetics, Great Ormond Street Hospital, London, WC1N 3JH, United Kingdom
| | - Ruth Newbury-Ecob
- University Hospitals Bristol, Department of Clinical Genetics, St Michael's Hospital, Bristol, BS2 8EG, United Kingdom
| | | | - Amanda Springer
- Monash Genetics, Monash Health, Clayton, Victoria, VIC 3168, Australia.,Department of Paediatrics, Monash University, Clayton, Victoria, VIC 3168, Australia
| | - Lionel Van Maldergem
- Centre de génétique humaine and Clinical Investigation Center 1431 (INSERM), Université de Franche-Comté, 25000, Besançon, France
| | - Vinod Varghese
- Institute of Medical Genetics, University Hospital of Wales, Cardiff, CF14 4XN, United Kingdom
| | - Naomi Yachelevich
- Clinical Genetics Services, New York University Hospitals Center, New York University, New York, New York 10016, USA
| | - Katrina Tatton-Brown
- Genetics Research Centre, Molecular and Clinical Sciences Institute, St. George's University of London, London SW17 0RE, United Kingdom.,Division of Genetics and Epidemiology, Institute of Cancer Research, London SM2 5NG, United Kingdom.,South West Thames Regional Genetics Service, St. George's University Hospitals NHS Foundation Trust, London SW17 0QT, United Kingdom
| | - Jonathan Mill
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - Andrew H Crosby
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom
| | - Emma L Baple
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Wellcome Wolfson Centre, Royal Devon and Exeter NHS Foundation Trust, Exeter, EX2 5DW, United Kingdom.,Peninsula Clinical Genetics Service, Royal Devon and Exeter Hospital, Exeter, EX1 2ED, United Kingdom
| |
Collapse
|
79
|
Gensous N, Franceschi C, Santoro A, Milazzo M, Garagnani P, Bacalini MG. The Impact of Caloric Restriction on the Epigenetic Signatures of Aging. Int J Mol Sci. 2019;20. [PMID: 31022953 DOI: 10.3390/ijms20082022] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [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.
Collapse
|
80
|
Fransquet PD, Wrigglesworth J, Woods RL, Ernst ME, Ryan J. The epigenetic clock as a predictor of disease and mortality risk: a systematic review and meta-analysis. Clin Epigenetics 2019; 11:62. [PMID: 30975202 PMCID: PMC6458841 DOI: 10.1186/s13148-019-0656-7] [Citation(s) in RCA: 147] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Accepted: 03/25/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Ageing is one of the principal risk factors for many chronic diseases. However, there is considerable between-person variation in the rate of ageing and individual differences in their susceptibility to disease and death. Epigenetic mechanisms may play a role in human ageing, and DNA methylation age biomarkers may be good predictors of age-related diseases and mortality risk. The aims of this systematic review were to identify and synthesise the evidence for an association between peripherally measured DNA methylation age and longevity, age-related disease, and mortality risk. METHODS A systematic search was conducted in line with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Using relevant search terms, MEDLINE, Embase, Cochrane Central Register of Controlled Trials, and PsychINFO databases were searched to identify articles meeting the inclusion criteria. Studies were assessed for bias using Joanna Briggs Institute critical appraisal checklists. Data was extracted from studies measuring age acceleration as a predictor of age-related diseases, mortality or longevity, and the findings for similar outcomes compared. Using Review Manager 5.3 software, two meta-analyses (one per epigenetic clock) were conducted on studies measuring all-cause mortality. RESULTS Twenty-three relevant articles were identified, including a total of 41,607 participants. Four studies focused on ageing and longevity, 11 on age-related disease (cancer, cardiovascular disease, and dementia), and 11 on mortality. There was some, although inconsistent, evidence for an association between increased DNA methylation age and risk of disease. Meta-analyses indicated that each 5-year increase in DNA methylation age was associated an 8 to 15% increased risk of mortality. CONCLUSION Due to the small number of studies and heterogeneity in study design and outcomes, the association between DNA methylation age and age-related disease and longevity is inconclusive. Increased epigenetic age was associated with mortality risk, but positive publication bias needs to be considered. Further research is needed to determine the extent to which DNA methylation age can be used as a clinical biomarker.
Collapse
Affiliation(s)
- Peter D Fransquet
- Department of Epidemiology and Preventive Medicine, Monash University, ASPREE, Level 5, The Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia.,Disease Epigenetics, Murdoch Childrens Research Institute, The University of Melbourne, Parkville, Victoria, 3052, Australia
| | - Jo Wrigglesworth
- Department of Epidemiology and Preventive Medicine, Monash University, ASPREE, Level 5, The Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Robyn L Woods
- Department of Epidemiology and Preventive Medicine, Monash University, ASPREE, Level 5, The Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia
| | - Michael E Ernst
- Department of Pharmacy Practice and Science, College of Pharmacy, The University of Iowa, Iowa City, IA, USA.,Department of Family Medicine, Carver College of Medicine, The University of Iowa, Iowa City, IA, USA
| | - Joanne Ryan
- Department of Epidemiology and Preventive Medicine, Monash University, ASPREE, Level 5, The Alfred Centre, 99 Commercial Road, Melbourne, Victoria, 3004, Australia. .,Disease Epigenetics, Murdoch Childrens Research Institute, The University of Melbourne, Parkville, Victoria, 3052, Australia. .,INSERM, U1061, Neuropsychiatrie, Recherche Clinique et Epidémiologique, Neuropsychiatry: Research Epidemiological and Clinic, Université Montpellier, 34000, Montpellier, France.
| |
Collapse
|
81
|
Field AE, Robertson NA, Wang T, Havas A, Ideker T, Adams PD. DNA Methylation Clocks in Aging: Categories, Causes, and Consequences. Mol Cell 2018; 71:882-95. [PMID: 30241605 DOI: 10.1016/j.molcel.2018.08.008] [Citation(s) in RCA: 299] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 07/03/2018] [Accepted: 08/06/2018] [Indexed: 02/07/2023]
Abstract
Age-associated changes to the mammalian DNA methylome are well documented and thought to promote diseases of aging, such as cancer. Recent studies have identified collections of individual methylation sites whose aggregate methylation status measures chronological age, referred to as the DNA methylation clock. DNA methylation may also have value as a biomarker of healthy versus unhealthy aging and disease risk; in other words, a biological clock. Here we consider the relationship between the chronological and biological clocks, their underlying mechanisms, potential consequences, and their utility as biomarkers and as targets for intervention to promote healthy aging and longevity.
Collapse
|
82
|
Søraas A, Matsuyama M, de Lima M, Wald D, Buechner J, Gedde-Dahl T, Søraas CL, Chen B, Ferrucci L, Dahl JA, Horvath S, Matsuyama S. Epigenetic age is a cell-intrinsic property in transplanted human hematopoietic cells. Aging Cell 2019; 18:e12897. [PMID: 30712319 PMCID: PMC6413751 DOI: 10.1111/acel.12897] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/16/2018] [Accepted: 11/03/2018] [Indexed: 12/21/2022] Open
Abstract
The age of tissues and cells can be accurately estimated by DNA methylation analysis. The multitissue DNA methylation (DNAm) age predictor combines the DNAm levels of 353 CpG dinucleotides to arrive at an age estimate referred to as DNAm age. Recent studies based on short‐term observations showed that the DNAm age of reconstituted blood following allogeneic hematopoietic stem cell transplantation (HSCT) reflects the age of the donor. However, it is not known whether the DNAm age of donor blood remains independent of the recipient's age over the long term. Importantly, long‐term studies including child recipients have the potential to clearly reveal whether DNAm age is cell‐intrinsic or whether it is modulated by extracellular cues in vivo. Here, we address this question by analyzing blood methylation data from HSCT donor and recipient pairs who greatly differed in chronological age (age differences between 1 and 49 years). We found that the DNAm age of the reconstituted blood was not influenced by the recipient's age, even 17 years after HSCT, in individuals without relapse of their hematologic disorder. However, the DNAm age of recipients with relapse of leukemia was unstable. These data are consistent with our previous findings concerning the abnormal DNAm age of cancer cells, and it can potentially be exploited to monitor the health of HSCT recipients. Our data demonstrate that transplanted human hematopoietic stem cells have an intrinsic DNAm age that is unaffected by the environment in a recipient of a different age.
Collapse
Affiliation(s)
- Arne Søraas
- Department of Microbiology; Oslo University Hospital; Oslo Norway
| | - Mieko Matsuyama
- Division of Hematology/Oncology, Department of Medicine, School of Medicine; Case Western Reserve University; Cleveland Ohio
| | - Marcos de Lima
- Division of Hematology/Oncology, Department of Medicine, School of Medicine; Case Western Reserve University; Cleveland Ohio
- Stem Cell Transplant Program, University Hospitals of Cleveland; Case Western Reserve University; Cleveland Ohio
| | - David Wald
- Department of Pathology; Case Western Reserve University; Cleveland Ohio
| | - Jochen Buechner
- Department of Pediatric Hematology and Oncology; Oslo University Hospital; Oslo Norway
| | - Tobias Gedde-Dahl
- Department of Hematology; Oslo University Hospital; Oslo Norway
- Institute of Clinical Medicine; University of Oslo; Oslo Norway
| | | | - Brian Chen
- National Institute of Aging (NIA); National Institute of Health; Bethesda Maryland
| | - Luigi Ferrucci
- National Institute of Aging (NIA); National Institute of Health; Bethesda Maryland
| | - John Arne Dahl
- Department of Microbiology; Oslo University Hospital; Oslo Norway
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine; University of California, Los Angeles; Los Angeles California
- Department of Biostatistics, Fielding School of Public Health; University of California, Los Angeles; Los Angeles California
| | - Shigemi Matsuyama
- Division of Hematology/Oncology, Department of Medicine, School of Medicine; Case Western Reserve University; Cleveland Ohio
- Case Comprehensive Cancer Center; Case Western Reserve University; Cleveland Ohio
| |
Collapse
|
83
|
Hoshino A, Horvath S, Sridhar A, Chitsazan A, Reh TA. Synchrony and asynchrony between an epigenetic clock and developmental timing. Sci Rep 2019; 9:3770. [PMID: 30842553 DOI: 10.1038/s41598-019-39919-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/28/2019] [Indexed: 12/23/2022] Open
Abstract
Epigenetic changes have been used to estimate chronological age across the lifespan, and some studies suggest that epigenetic "aging" clocks may already operate in developing tissue. To better understand the relationship between developmental stage and epigenetic age, we utilized the highly regular sequence of development found in the mammalian neural retina and a well-established epigenetic aging clock based on DNA methylation. Our results demonstrate that the epigenetic age of fetal retina is highly correlated with chronological age. We further establish that epigenetic aging progresses normally in vitro, suggesting that epigenetic aging is a property of individual tissues. This correlation is also retained in stem cell-derived retinal organoids, but is accelerated in individuals with Down syndrome, a progeroid-like condition. Overall, our results suggest that epigenetic aging begins as early as a few weeks post-conception, in fetal tissues, and the mechanisms underlying the phenomenon of epigenetic aging might be studied in developing organs.
Collapse
|
84
|
Castagna A, Gareri P, Falvo F, Sestito S, Rocca M, Pensabene L, Concolino D, Coppolino G, Ruotolo G. Werner syndrome: a rare mutation. Aging Clin Exp Res 2019; 31:425-429. [PMID: 29876830 DOI: 10.1007/s40520-018-0982-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/30/2018] [Indexed: 10/14/2022]
Affiliation(s)
- Alberto Castagna
- Center for Cognitive Disorders and Dementia, DSS Catanzaro Lido, ASP Catanzaro, Viale Crotone, 88100, Catanzaro, Italy
| | - Pietro Gareri
- Center for Cognitive Disorders and Dementia, DSS Catanzaro Lido, ASP Catanzaro, Viale Crotone, 88100, Catanzaro, Italy.
| | - Francesca Falvo
- Department of Pediatrics, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Simona Sestito
- Department of Pediatrics, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Maurizio Rocca
- Center for Cognitive Disorders and Dementia, DSS Catanzaro Lido, ASP Catanzaro, Viale Crotone, 88100, Catanzaro, Italy
| | - Licia Pensabene
- Department of Pediatrics, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Daniela Concolino
- Department of Pediatrics, University Magna Graecia of Catanzaro, Catanzaro, Italy
| | - Giuseppe Coppolino
- Nephrology and Dialysis Unit, "Pugliese-Ciaccio" Hospital of Catanzaro, Catanzaro, Italy
| | - Giovanni Ruotolo
- SOC Geriatrics, Azienda Ospedaliera Pugliese-Ciaccio, Catanzaro, Italy
| |
Collapse
|
85
|
Olova N, Simpson DJ, Marioni RE, Chandra T. Partial reprogramming induces a steady decline in epigenetic age before loss of somatic identity. Aging Cell 2019; 18:e12877. [PMID: 30450724 PMCID: PMC6351826 DOI: 10.1111/acel.12877] [Citation(s) in RCA: 93] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 10/03/2018] [Accepted: 10/17/2018] [Indexed: 01/23/2023] Open
Abstract
Induced pluripotent stem cells (IPSCs), with their unlimited regenerative capacity, carry the promise for tissue replacement to counter age-related decline. However, attempts to realize in vivo iPSC have invariably resulted in the formation of teratomas. Partial reprogramming in prematurely aged mice has shown promising results in alleviating age-related symptoms without teratoma formation. Does partial reprogramming lead to rejuvenation (i.e., "younger" cells), rather than dedifferentiation, which bears the risk of cancer? Here, we analyse the dynamics of cellular age during human iPSC reprogramming and find that partial reprogramming leads to a reduction in the epigenetic age of cells. We also find that the loss of somatic gene expression and epigenetic age follows different kinetics, suggesting that they can be uncoupled and there could be a safe window where rejuvenation can be achieved with a minimized risk of cancer.
Collapse
Affiliation(s)
- Nelly Olova
- MRC Human Genetics Unit, MRC; Institute of Genetics and Molecular Medicine; University of Edinburgh; Edinburgh UK
| | - Daniel J. Simpson
- MRC Human Genetics Unit, MRC; Institute of Genetics and Molecular Medicine; University of Edinburgh; Edinburgh UK
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, Centre for Genomic and Experimental Medicine; Institute of Genetics and Molecular Medicine, University of Edinburgh; Edinburgh UK
| | - Tamir Chandra
- MRC Human Genetics Unit, MRC; Institute of Genetics and Molecular Medicine; University of Edinburgh; Edinburgh UK
| |
Collapse
|
86
|
Kane AE, Sinclair DA. Epigenetic changes during aging and their reprogramming potential. Crit Rev Biochem Mol Biol 2019; 54:61-83. [PMID: 30822165 PMCID: PMC6424622 DOI: 10.1080/10409238.2019.1570075] [Citation(s) in RCA: 137] [Impact Index Per Article: 27.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 01/09/2019] [Accepted: 01/11/2019] [Indexed: 02/07/2023]
Abstract
The aging process results in significant epigenetic changes at all levels of chromatin and DNA organization. These include reduced global heterochromatin, nucleosome remodeling and loss, changes in histone marks, global DNA hypomethylation with CpG island hypermethylation, and the relocalization of chromatin modifying factors. Exactly how and why these changes occur is not fully understood, but evidence that these epigenetic changes affect longevity and may cause aging, is growing. Excitingly, new studies show that age-related epigenetic changes can be reversed with interventions such as cyclic expression of the Yamanaka reprogramming factors. This review presents a summary of epigenetic changes that occur in aging, highlights studies indicating that epigenetic changes may contribute to the aging process and outlines the current state of research into interventions to reprogram age-related epigenetic changes.
Collapse
Affiliation(s)
- Alice E. Kane
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Charles Perkins Centre, The University of Sydney, Sydney, Australia
| | - David A. Sinclair
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Department of Pharmacology, The University of New South Wales, Sydney, Australia
| |
Collapse
|
87
|
Lautrup S, Caponio D, Cheung HH, Piccoli C, Stevnsner T, Chan WY, Fang EF. Studying Werner syndrome to elucidate mechanisms and therapeutics of human aging and age-related diseases. Biogerontology 2019; 20:255-69. [PMID: 30666569 DOI: 10.1007/s10522-019-09798-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 01/17/2019] [Indexed: 01/22/2023]
Abstract
Aging is a natural and unavoidable part of life. However, aging is also the primary driver of the dominant human diseases, such as cardiovascular disease, cancer, and neurodegenerative diseases, including Alzheimer's disease. Unraveling the sophisticated molecular mechanisms of the human aging process may provide novel strategies to extend 'healthy aging' and the cure of human aging-related diseases. Werner syndrome (WS), is a heritable human premature aging disease caused by mutations in the gene encoding the Werner (WRN) DNA helicase. As a classical premature aging disease, etiological exploration of WS can shed light on the mechanisms of normal human aging and facilitate the development of interventional strategies to improve healthspan. Here, we summarize the latest progress of the molecular understandings of WRN protein, highlight the advantages of using different WS model systems, including Caenorhabditis elegans, Drosophila melanogaster and induced pluripotent stem cell (iPSC) systems. Further studies on WS will propel drug development for WS patients, and possibly also for normal age-related diseases.
Collapse
|
88
|
Belsky DW, Harrati A. To the freezers! Stored biospecimens from human randomized trials are an important new direction for studies of biological aging. J Gerontol A Biol Sci Med Sci 2019; 74:89-90. [DOI: 10.1093/gerona/gly269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Daniel W Belsky
- Department of Epidemiology, Robert N Butler Aging Center, Columbia University, Mailman School of Public Health
| | - Amal Harrati
- Department of Medicine, Stanford University School of Medicine
| |
Collapse
|
89
|
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.
Collapse
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
| |
Collapse
|
90
|
Chen L, Dong Y, Bhagatwala J, Raed A, Huang Y, Zhu H. Effects of Vitamin D3 Supplementation on Epigenetic Aging in Overweight and Obese African Americans With Suboptimal Vitamin D Status: A Randomized Clinical Trial. J Gerontol A Biol Sci Med Sci 2019; 74:91-98. [PMID: 30256915 PMCID: PMC6612014 DOI: 10.1093/gerona/gly223] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Indexed: 01/21/2023] Open
Abstract
Background We have previously shown that vitamin D supplementation increases telomerase activity, suggesting an anti-aging effect. In this study, we aim to test the hypothesis that vitamin D supplementation would slow down epigenetic aging, a new marker of biological aging. Methods A randomized clinical trial was previously conducted among 70 overweight/obese African Americans with serum 25-hydroxyvitamin D [25(OH)D] < 50 nmol/L, who were randomly assigned into four groups of 600 IU/d, 2,000 IU/d, 4,000 IU/d of vitamin D3 supplements or placebo followed by 16-week interventions. Whole genome-wide DNA methylation analysis was conducted in 51 participants. DNA methylation ages were calculated according to the Horvath and the Hannum methods. Methylation-based age acceleration index (∆Age) is defined as the difference between DNA methylation age and chronological age in years. Mixed-effects models were used to evaluate the treatment effects. Results Fifty-one participants (aged 26.1 ± 9.3 years, 16% are male) were included in the study. After the adjustment of multi-covariates, vitamin D3 supplementation of 4,000 IU/d was associated with 1.85 years decrease in Horvath epigenetic aging compared with placebo (p value = .046), and 2,000 IU/d was associated with 1.90 years decrease in Hannum epigenetic aging (p value = .044). Serum 25(OH)D concentrations were significantly associated with decreased Horvath ∆Age only (p values = .002), regardless of treatments. Conclusions Our results suggest that vitamin D supplementation may slow down Horvath epigenetic aging. But the effect on Hannum epigenetic aging is not conclusive. Large-scale and longer duration clinical trials are needed to replicate the findings.
Collapse
Affiliation(s)
- Li Chen
- Georgia Prevention Institute, Department of Population Sciences
| | - Yanbin Dong
- Georgia Prevention Institute, Department of Population Sciences
| | - Jigar Bhagatwala
- Department of Medicine, Medical College of Georgia, Augusta University
| | - Anas Raed
- Department of Medicine, Medical College of Georgia, Augusta University
| | - Ying Huang
- Georgia Prevention Institute, Department of Population Sciences
| | - Haidong Zhu
- Georgia Prevention Institute, Department of Population Sciences
| |
Collapse
|
91
|
Abstract
Age predictors based on DNA methylation levels at a small set of CpG sites, DNAm clocks, have been developed for humans and extended to several other species. Three currently available versions of mouse DNAm clocks were either created for individual tissues or tuned toward young ages. Here, we constructed a robust multi-tissue age predictor based on 435 CpG sites, which covers the entire mouse lifespan and remains unbiased with respect to any particular age group. It can successfully detect the effects of certain lifespan-modulating interventions on DNAm age as well as the rejuvenation effect related to the transition from fibroblasts to iPSCs. We have carried out comparative analyses of available mouse DNAm clocks, which revealed their broad applicability, but also certain limitations to the use of tissue-specific and multi-tissue age predictors. Together, these tools should help address diverse questions in aging research.
Collapse
Affiliation(s)
- Margarita V Meer
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Dmitriy I Podolskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States.,Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| |
Collapse
|
92
|
Abstract
Recent research suggests that epigenetics, especially DNA methylation, plays a mechanistic role in aging. Epigenetic clocks, which measure changes in a few hundred specific CpG sites, can accurately predict chronological age in a variety of species, including humans. These clocks are currently the bestbiomarkers for predicting mortality in humans. Additionally, several studies have characterized the effects of aging across the methylome in a wide variety of tissues from humans and mice. A small fraction (~2%) of the CpG sites show age-related changes, either hypermethylation or hypomethylation with aging. Evaluation of non-CpG site methylation has only been examined in a few studies, with about ~0.5% of these sites showing achange with age. Therefore, while only a small fraction of cytosines in the genome show changes in DNA methylation with age, this represents 2 to 3 million cytosines in the genome. Importantly, the only study to compare the effect of aging on DNA methylation in male and female mice and humans found that N95% of the age-related changes in DNA methylation in the hippocampus were sexually divergent, i.e., the methylation did not differ between males and females atyoung age but age-related changes occurred in one sex but not the other. The age-related changes in DNA methylation tend to be enriched and under-represented in specific genomic contexts, with some commonalities between tissues and species that require further investigation. The strongest evidence that the age-related changes in DNA methylation play a role in aging comes from studies of anti-aging interventions (e.g., caloric restriction, dwarfism, and rapamycin treatment) in mice. These anti-aging interventions deaccelerate the epigenetic clocks and reverse/prevent 20 to 40% of the age-related changes in DNA methylation. It will be important in the future to demonstrate that at least some of the age-related changes in DNA methylation directly lead to alterations in the transcriptome of cells/tissues that could potentially contribute to aging.
Collapse
|
93
|
Hui CW, St-Pierre MK, Detuncq J, Aumailley L, Dubois MJ, Couture V, Skuk D, Marette A, Tremblay JP, Lebel M, Tremblay MÈ. Nonfunctional mutant Wrn protein leads to neurological deficits, neuronal stress, microglial alteration, and immune imbalance in a mouse model of Werner syndrome. Brain Behav Immun 2018; 73:450-469. [PMID: 29908963 DOI: 10.1016/j.bbi.2018.06.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 05/25/2018] [Accepted: 06/06/2018] [Indexed: 12/30/2022] Open
Abstract
Werner syndrome (WS) is a premature aging disorder caused by mutations in a RecQ-family DNA helicase, WRN. Mice lacking part of the helicase domain of the WRN orthologue exhibit many phenotypic features of WS, including metabolic abnormalities and a shorter lifespan. Yet, little is known about the impact of WRN mutations on the central nervous system in both humans and mouse models of WS. In the current study, we have performed a longitudinal behavioral assessment on mice bearing a Wrn helicase deletion. Behavioral tests demonstrated a loss of motor activity and coordination, reduction in perception, increase in repetitive behavior, and deficits in both spatial and social novelty memories in Wrn mutant mice compared to age-matched wild type mice. These neurological deficits were associated with biochemical and histological changes in the brain of aged Wrn mutant mice. Microglia, resident immune cells that regulate neuronal plasticity and function in the brain, were hyper-ramified in multiple regions involved with the behavioral deficits of Wrn mutant mice. Furthermore, western analyses indicated that Wrn mutant mice exhibited an increase of oxidative stress markers in the prefrontal cortex. Supporting these findings, electron microscopy studies revealed increased cellular aging and oxidative stress features, among microglia and neurons respectively, in the prefrontal cortex of aged Wrn mutant mice. In addition, multiplex immunoassay of serum identified significant changes in the expression levels of several pro- and anti-inflammatory cytokines. Taken together, these findings indicate that microglial dysfunction and neuronal oxidative stress, associated with peripheral immune system alterations, might be important driving forces leading to abnormal neurological symptoms in WS thus suggesting potential therapeutic targets for interventions.
Collapse
Affiliation(s)
- Chin Wai Hui
- Axe neurosciences, Centre de recherche du CHU de Québec, Centre Hospitalier de l'Université Laval (CHUL), 2705 Laurier Blvd., Québec City, Québec G1V 4G2, Canada
| | - Marie-Kim St-Pierre
- Axe neurosciences, Centre de recherche du CHU de Québec, Centre Hospitalier de l'Université Laval (CHUL), 2705 Laurier Blvd., Québec City, Québec G1V 4G2, Canada
| | - Jérôme Detuncq
- Axe neurosciences, Centre de recherche du CHU de Québec, Centre Hospitalier de l'Université Laval (CHUL), 2705 Laurier Blvd., Québec City, Québec G1V 4G2, Canada
| | - Lucie Aumailley
- Axe endocrinologie/néphrologie, Centre de recherche du CHU de Québec, Centre Hospitalier de l'Université Laval (CHUL), 2705 Laurier Blvd., Québec City, Québec G1V 4G2, Canada
| | - Marie-Julie Dubois
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, 2725 Chemin Sainte-Foy, Québec City, Québec G1V 4G5, Canada
| | - Vanessa Couture
- Axe neurosciences, Centre de recherche du CHU de Québec, Centre Hospitalier de l'Université Laval (CHUL), 2705 Laurier Blvd., Québec City, Québec G1V 4G2, Canada
| | - Daniel Skuk
- Axe neurosciences, Centre de recherche du CHU de Québec, Centre Hospitalier de l'Université Laval (CHUL), 2705 Laurier Blvd., Québec City, Québec G1V 4G2, Canada
| | - André Marette
- Institut Universitaire de Cardiologie et de Pneumologie de Québec, 2725 Chemin Sainte-Foy, Québec City, Québec G1V 4G5, Canada
| | - Jacques P Tremblay
- Axe neurosciences, Centre de recherche du CHU de Québec, Centre Hospitalier de l'Université Laval (CHUL), 2705 Laurier Blvd., Québec City, Québec G1V 4G2, Canada
| | - Michel Lebel
- Axe endocrinologie/néphrologie, Centre de recherche du CHU de Québec, Centre Hospitalier de l'Université Laval (CHUL), 2705 Laurier Blvd., Québec City, Québec G1V 4G2, Canada.
| | - Marie-Ève Tremblay
- Axe neurosciences, Centre de recherche du CHU de Québec, Centre Hospitalier de l'Université Laval (CHUL), 2705 Laurier Blvd., Québec City, Québec G1V 4G2, Canada.
| |
Collapse
|
94
|
Abstract
DNA methylation represents an annotation system for marking the genetic text, thus providing instruction as to how and when to read the information and control transcription. Unlike sequence information, which is inherited, methylation patterns are established in a programmed process that continues throughout development, thus setting up stable gene expression profiles. This DNA methylation paradigm is a key player in medicine. Some changes in methylation closely correlate with age providing a marker for biological ageing, and these same sites could also play a part in cancer. The genome continues to undergo programmed variation in methylation after birth in response to environmental inputs, serving as a memory device that could affect ageing and predisposition to various metabolic, autoimmune, and neurological diseases. Taking advantage of tissue-specific differences, methylation can be used to detect cell death and thereby monitor many common diseases with a simple cell-free circulating-DNA blood test.
Collapse
Affiliation(s)
- Yuval Dor
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel
| | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Hebrew University of Jerusalem, Faculty of Medicine, Jerusalem, Israel.
| |
Collapse
|
95
|
Ciccarone F, Tagliatesta S, Caiafa P, Zampieri M. DNA methylation dynamics in aging: how far are we from understanding the mechanisms? Mech Ageing Dev 2018; 174:3-17. [DOI: 10.1016/j.mad.2017.12.002] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 12/14/2017] [Accepted: 12/16/2017] [Indexed: 02/07/2023]
|
96
|
Nwanaji-Enwerem JC, Weisskopf MG, Baccarelli AA. Multi-tissue DNA methylation age: Molecular relationships and perspectives for advancing biomarker utility. Ageing Res Rev 2018; 45:15-23. [PMID: 29698722 PMCID: PMC6047923 DOI: 10.1016/j.arr.2018.04.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/29/2018] [Accepted: 04/18/2018] [Indexed: 12/31/2022]
Abstract
The multi-tissue DNA methylation estimator of chronological age (DNAm-age) has been associated with a wide range of exposures and health outcomes. Still, it is unclear how DNAm-age can have such broad relationships and how it can be best utilized as a biomarker. Understanding DNAm-age's molecular relationships is a promising approach to address this critical knowledge gap. In this review, we discuss the existing literature regarding DNAm-age's molecular relationships in six major categories: animal model systems, cancer processes, cellular aging processes, immune system processes, metabolic processes, and nucleic acid processes. We also present perspectives regarding the future of DNAm-age research, including the need to translate a greater number of ongoing research efforts to experimental and animal model systems.
Collapse
Affiliation(s)
- Jamaji C Nwanaji-Enwerem
- Department of Environmental Health, Harvard T.H. Chan School of Public Health and MD-PhD Program, Harvard Medical School, Boston, MA, USA.
| | - Marc G Weisskopf
- Department of Environmental Health and Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| |
Collapse
|
97
|
Flunkert J, Maierhofer A, Dittrich M, Müller T, Horvath S, Nanda I, Haaf T. Genetic and epigenetic changes in clonal descendants of irradiated human fibroblasts. Exp Cell Res 2018; 370:322-332. [PMID: 29964050 DOI: 10.1016/j.yexcr.2018.06.034] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Revised: 06/12/2018] [Accepted: 06/27/2018] [Indexed: 10/28/2022]
Abstract
To study delayed genetic and epigenetic radiation effects, which may trigger radiation-induced carcinogenesis, we have established single-cell clones from irradiated and non-irradiated primary human fibroblasts. Stable clones were endowed with the same karyotype in all analyzed metaphases after 20 population doublings (PDs), whereas unstable clones displayed mosaics of normal and abnormal karyotypes. To account for variation in radiation sensitivity, all experiments were performed with two different fibroblast strains. After a single X-ray dose of 2 Gy more than half of the irradiated clones exhibited radiation-induced genome instability (RIGI). Irradiated clones displayed an increased rate of loss of chromosome Y (LOY) and copy number variations (CNVs), compared to controls. CNV breakpoints clustered in specific chromosome regions, in particular 3p14.2 and 7q11.21, coinciding with common fragile sites. CNVs affecting the FHIT gene in FRA3B were observed in independent unstable clones and may drive RIGI. Bisulfite pyrosequencing of control clones and the respective primary culture revealed global hypomethylation of ALU, LINE-1, and alpha-satellite repeats as well as rDNA hypermethylation during in vitro ageing. Irradiated clones showed further reduced ALU and alpha-satellite methylation and increased rDNA methylation, compared to controls. Methylation arrays identified several hundred differentially methylated genes and several enriched pathways associated with in vitro ageing. Methylation changes in 259 genes and the MAP kinase signaling pathway were associated with delayed radiation effects (after 20 PDs). Collectively, our results suggest that both genetic (LOY and CNVs) and epigenetic changes occur in the progeny of exposed cells that were not damaged directly by irradiation, likely contributing to radiation-induced carcinogenesis. We did not observe epigenetic differences between stable and unstable irradiated clones. The fact that the DNA methylation (DNAm) age of clones derived from the same primary culture varied greatly suggests that DNAm age of a single cell (represented by a clone) can be quite different from the DNAm age of a tissue. We propose that DNAm age reflects the emergent property of a large number of individual cells whose respective DNAm ages can be highly variable.
Collapse
Affiliation(s)
- Julia Flunkert
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Anna Maierhofer
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany; Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Tobias Müller
- Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Indrajit Nanda
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany.
| |
Collapse
|
98
|
El Hajj N, Haertle L, Dittrich M, Denk S, Lehnen H, Hahn T, Schorsch M, Haaf T. DNA methylation signatures in cord blood of ICSI children. Hum Reprod 2018; 32:1761-1769. [PMID: 28575352 PMCID: PMC5850272 DOI: 10.1093/humrep/dex209] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/15/2017] [Indexed: 12/12/2022] Open
Abstract
STUDY QUESTION Does ICSI induce specific DNA methylation changes in the resulting offspring? SUMMARY ANSWER Although several thousand analyzed CpG sites (throughout the genome) displayed significant between-group methylation differences, both ICSI and spontaneously conceived children varied within the normal range of methylation variation. WHAT IS KNOWN ALREADY Children conceived by ART have increased risks for medical problems at birth and to the extent of present knowledge also in later life (i.e. impaired metabolic and cardiovascular functions). One plausible mechanism mediating these ART effects are epigenetic changes originating in the germ cells and/or early embryos and persisting during further development. STUDY DESIGN, SIZE, DURATION We compared the cord blood methylomes and candidate gene methylation patterns of newborns conceived through ICSI or spontaneously. PARTICIPANTS/MATERIALS, SETTING, METHODS Umbilical cord bloods were obtained from healthy newborn singletons conceived spontaneously (53 samples), through ICSI (89) or IVF (34). Bisulfite-converted DNA samples of 48 ICSI and 46 control pregnancies were used for genome-wide analyses with Illumina's 450K methylation arrays. Candidate genes from the methylation screen were analyzed in all three groups by bisulfite pyrosequencing. MAIN RESULTS AND THE ROLE OF CHANCE Altogether, 4730 (0.11%) of 428 227 analyzed CpG sites exhibited significant between-group methylation differences, but all with small (β < 10%) or very small (β < 1%) effect size. ICSI children showed a significantly decreased DNA methylation age at birth, lagging approximately half a week behind the controls. ART-susceptible CpGs were enriched in CpG islands with low methylation values (0-20%) and in imprinting control regions (ICRs). Eighteen promoter regions (six in microRNA and SNORD RNA genes), four CpG islands (three in genes including one long non-coding RNA), and two ICRs contained multiple significant sites. Three differentially methylated regions were studied in more detail by bisulfite pyrosequencing. ATG4C and SNORD114-9 could be validated in an independent ICSI group, following adjustment for maternal age and other confounding factors. ATG4C was also significant in the IVF group. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION The observed epigenetic effects are small and there are numerous potential confounding factors such as parental age and infertility. Although our study meets current standards for epigenetic screens, sample size is still two orders of magnitude below that of genome-wide association studies. WIDER IMPLICATIONS OF THE FINDINGS Our study suggests an impact of ICSI on the offspring's epigenome(s), which may contribute to phenotypic variation and disease susceptibility in ART children. Epigenetic regulation of gene expression by different classes of non-coding RNAs may be a key mechanism for developmental programming through ART. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by a research grant (no. 692185) from the European Union (ERA of ART). There are no competing interests.
Collapse
Affiliation(s)
- Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Larissa Haertle
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany.,Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Sarah Denk
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Harald Lehnen
- Department of Gynecology and Obstetrics, Municipal Clinics, Hubertusstrasse 100, 41239 Mönchengladbach, Germany
| | - Thomas Hahn
- Fertility Center, Mainzer Strasse 98-102, 65189 Wiesbaden, Germany
| | - Martin Schorsch
- Fertility Center, Mainzer Strasse 98-102, 65189 Wiesbaden, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| |
Collapse
|
99
|
Yamaga M, Takemoto M, Shoji M, Sakamoto K, Yamamoto M, Ishikawa T, Koshizaka M, Maezawa Y, Kobayashi K, Yokote K. Werner syndrome: a model for sarcopenia due to accelerated aging. Aging (Albany NY) 2018; 9:1738-1744. [PMID: 28738022 PMCID: PMC5559172 DOI: 10.18632/aging.101265] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/19/2017] [Indexed: 12/25/2022]
Abstract
Werner syndrome (WS) is a rare inheritable progeroid syndrome caused by a mutation in the WRN gene. Although WS has been described as a characteristic appearance of very slender extremities with a stocky trunk, few studies have investigated the loss of muscle mass, fat mass distribution (body composition), and mobility according to age and sex. Therefore, the aim of this study was to precisely describe the body composition in WS. Nine Japanese patients with WS (four males and five females; mean age 48±8.8 years) were recruited. Body composition was examined by dual-energy X-ray absorptiometry and computed tomography (CT). The hand grip strength and mobility were evaluated using the two-step test, stand-up test and 25-question geriatric locomotive function scale (GLFS). The mean skeletal muscle index (SMI) was 4.0±0.6 kg/m2. SMI of all patients met the criteria of sarcopenia, even though some patients were aged < 40 years. All patients also showed deceased mobility. In conclusion, these results indicate that all patients with WS, even those aged < 40 years, had already lost muscle mass to the level of sarcopenia. Continued research on sarcopenia in WS might facilitate the discovery of novel mechanisms and development of new treatment strategies for sarcopenia.
Collapse
Affiliation(s)
- Masaya Yamaga
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,Department of Medicine, Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, 260-8670, Japan
| | - Minoru Takemoto
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,School of Medicine, International University of Health and Welfare, Department of Diabetes, Metabolism and Endocrinology, Chiba, 286-8686, Japan
| | - Mayumi Shoji
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,Department of Medicine, Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, 260-8670, Japan
| | - Kenichi Sakamoto
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,Eastern Chiba Medical Center, Chiba, 283-8686, Japan
| | - Masashi Yamamoto
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,Department of Medicine, Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, 260-8670, Japan
| | - Takahiro Ishikawa
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,Department of Medicine, Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, 260-8670, Japan
| | - Masaya Koshizaka
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,Department of Medicine, Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, 260-8670, Japan
| | - Yoshiro Maezawa
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,Department of Medicine, Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, 260-8670, Japan
| | - Kazuki Kobayashi
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,Asahi General Hospital, 1326 I, Chiba, 289-2511, Japan
| | - Koutaro Yokote
- Department of Clinical Cell Biology and Medicine, Chiba University Graduate School of Medicine, Chiba, 260-8670, Japan.,Department of Medicine, Division of Diabetes, Metabolism and Endocrinology, Chiba University Hospital, Chiba, 260-8670, Japan
| |
Collapse
|
100
|
Levine ME, Lu AT, Quach A, Chen BH, Assimes TL, Bandinelli S, Hou L, Baccarelli AA, Stewart JD, Li Y, Whitsel EA, Wilson JG, Reiner AP, Aviv A, Lohman K, Liu Y, Ferrucci L, Horvath S. An epigenetic biomarker of aging for lifespan and healthspan. Aging (Albany NY) 2018; 10:573-591. [PMID: 29676998 PMCID: PMC5940111 DOI: 10.18632/aging.101414] [Citation(s) in RCA: 1238] [Impact Index Per Article: 206.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/08/2018] [Indexed: 04/08/2023]
Abstract
Identifying reliable biomarkers of aging is a major goal in geroscience. While the first generation of epigenetic biomarkers of aging were developed using chronological age as a surrogate for biological age, we hypothesized that incorporation of composite clinical measures of phenotypic age that capture differences in lifespan and healthspan may identify novel CpGs and facilitate the development of a more powerful epigenetic biomarker of aging. Using an innovative two-step process, we develop a new epigenetic biomarker of aging, DNAm PhenoAge, that strongly outperforms previous measures in regards to predictions for a variety of aging outcomes, including all-cause mortality, cancers, healthspan, physical functioning, and Alzheimer's disease. While this biomarker was developed using data from whole blood, it correlates strongly with age in every tissue and cell tested. Based on an in-depth transcriptional analysis in sorted cells, we find that increased epigenetic, relative to chronological age, is associated with increased activation of pro-inflammatory and interferon pathways, and decreased activation of transcriptional/translational machinery, DNA damage response, and mitochondrial signatures. Overall, this single epigenetic biomarker of aging is able to capture risks for an array of diverse outcomes across multiple tissues and cells, and provide insight into important pathways in aging.
Collapse
Affiliation(s)
- Morgan E. Levine
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Austin Quach
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Brian H. Chen
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, USA. Baltimore, MD 21224, USA
| | | | | | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrea A. Baccarelli
- Laboratory of Environmental Epigenetics, Departments of Environmental Health Sciences and Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - James D. Stewart
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Yun Li
- Department of Genetics, Department of Biostatistics, Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric A. Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Abraham Aviv
- Center of Human Development and Aging, New Jersey Medical School, Rutgers State University of New Jersey, Newark, NJ 07103, USA
| | - Kurt Lohman
- Center of Human Development and Aging, New Jersey Medical School, Rutgers State University of New Jersey, Newark, NJ 07103, USA
| | - Yongmei Liu
- Department of Epidemiology & Prevention, Division of Public Health Sciences, Wake Forrest School of Medicine, Winston-Salem, NC 27157, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, USA. Baltimore, MD 21224, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|