301
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Declerck K, Vanden Berghe W. Back to the future: Epigenetic clock plasticity towards healthy aging. Mech Ageing Dev 2018; 174:18-29. [PMID: 29337038 DOI: 10.1016/j.mad.2018.01.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/22/2022]
Abstract
Aging is the most important risk factor for major human lifestyle diseases, including cancer, neurological and cardiometabolic disorders. Due to the complex interplay between genetics, lifestyle and environmental factors, some individuals seem to age faster than others, whereas centenarians seem to have a slower aging process. Therefore, a biochemical biomarker reflecting the relative biological age would be helpful to predict an individual's health status and aging disease risk. Although it is already known for years that cumulative epigenetic changes occur upon aging, DNA methylation patterns were only recently used to construct an epigenetic clock predictor for biological age, which is a measure of how well your body functions compared to your chronological age. Moreover, the epigenetic DNA methylation clock signature is increasingly applied as a biomarker to estimate aging disease susceptibility and mortality risk. Finally, the epigenetic clock signature could be used as a lifestyle management tool to monitor healthy aging, to evaluate preventive interventions against chronic aging disorders and to extend healthy lifespan. Dissecting the mechanism of the epigenetic aging clock will yield valuable insights into the aging process and how it can be manipulated to improve health span.
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Affiliation(s)
- Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Belgium.
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302
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Gale CR, Marioni RE, Čukić I, Chastin SF, Dall PM, Dontje ML, Skelton DA, Deary IJ. The epigenetic clock and objectively measured sedentary and walking behavior in older adults: the Lothian Birth Cohort 1936. Clin Epigenetics 2018; 10:4. [PMID: 29321814 PMCID: PMC5759300 DOI: 10.1186/s13148-017-0438-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/21/2017] [Indexed: 01/24/2023] Open
Abstract
Background Estimates of biological age derived from DNA-methylation patterns-known as the epigenetic clock-are associated with mortality, physical and cognitive function, and frailty, but little is known about their relationship with sedentary behavior or physical activity. We investigated the cross-sectional relationship between two such estimates of biological age and objectively measured sedentary and walking behavior in older people. Methods Participants were 248 members of the Lothian Birth Cohort 1936. At age 79 years, sedentary behavior and physical activity were measured over 7 days using an activPAL activity monitor. Biological age was estimated using two measures of DNA methylation-based age acceleration-i.e., extrinsic and intrinsic epigenetic age acceleration. We used linear regression to assess the relationship between these two estimates of biological age and average daily time spent sedentary, number of sit-to-stand transitions, and step count. Results Of the six associations examined, only two were statistically significant in initial models adjusted for age and sex alone. Greater extrinsic age acceleration was associated with taking fewer steps (regression coefficient (95% CI) - 0.100 (- 0.008, - 0.001), and greater intrinsic age acceleration was associated with making more sit-to-stand transitions (regression coefficient (95% CI) 0.006 (0.0001, 0.012). When we controlled for multiple statistical testing, neither of these associations survived correction (both P ≥ 0.17). Conclusion In this cross-sectional study of 79-year-olds, we found no convincing evidence that biological age, as indexed by extrinsic or intrinsic epigenetic age acceleration, was associated with objectively measured sedentary or walking behavior.
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Affiliation(s)
- Catharine R. Gale
- Centre for Cognitive Ageing & Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
| | - Riccardo E. Marioni
- Centre for Cognitive Ageing & Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
| | - Iva Čukić
- Centre for Cognitive Ageing & Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - Sebastien F. Chastin
- Institute for Applied Health Research, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
- Department of Movement and Sports Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Philippa M. Dall
- Institute for Applied Health Research, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - Manon L. Dontje
- Institute for Applied Health Research, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
- School of Population and Global Health, University of Western Australia, Perth, Australia
| | - Dawn A. Skelton
- Institute for Applied Health Research, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
| | - Ian J. Deary
- Centre for Cognitive Ageing & Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
| | - on behalf of the Seniors USP Team
- Centre for Cognitive Ageing & Cognitive Epidemiology, Department of Psychology, University of Edinburgh, Edinburgh, UK
- MRC Lifecourse Epidemiology Unit, University of Southampton, Southampton, UK
- Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK
- Institute for Applied Health Research, School of Health and Life Sciences, Glasgow Caledonian University, Glasgow, UK
- Department of Movement and Sports Sciences, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- School of Population and Global Health, University of Western Australia, Perth, Australia
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303
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Gao X, Zhang Y, Breitling LP, Brenner H. Relationship of tobacco smoking and smoking-related DNA methylation with epigenetic age acceleration. Oncotarget 2018; 7:46878-46889. [PMID: 27276709 PMCID: PMC5216910 DOI: 10.18632/oncotarget.9795] [Citation(s) in RCA: 89] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 05/14/2016] [Indexed: 01/05/2023] Open
Abstract
Recent studies have identified biomarkers of chronological age based on DNA methylation levels. Since active smoking contributes to a wide spectrum of aging-related diseases in adults, this study intended to examine whether active smoking exposure could accelerate the DNA methylation age in forms of age acceleration (AA, residuals of the DNA methylation age estimate regressed on chronological age). We obtained the DNA methylation profiles in whole blood samples by Illumina Infinium Human Methylation450 Beadchip array in two independent subsamples of the ESTHER study and calculated their DNA methylation ages by two recently proposed algorithms. None of the self-reported smoking indicators (smoking status, cumulative exposure and smoking cessation time) or serum cotinine levels was significantly associated with AA. On the contrary, we successfully confirmed that 66 out of 150 smoking-related CpG sites were associated with AA, even after correction for multiple testing (FDR <0.05). We further built a smoking index (SI) based on these loci and demonstrated a monotonic dose-response relationship of this index with AA. In conclusion, DNA methylation-based biological indicators for current and past smoking exposure, but not self-reported smoking information or serum cotinine levels, were found to be related to DNA methylation defined AA. Further research should address potential mechanisms underlying the observed patterns, such as potential reflections of susceptibility to environmental hazards in both smoking related methylation changes and methylation defined AA.
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Affiliation(s)
- Xu Gao
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Lutz Philipp Breitling
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Pneumology and Respiratory Critical Care Medicine, Thoraxklinik, University of Heidelberg, Heidelberg, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany.,Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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304
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Debrabant B, Soerensen M, Christiansen L, Tan Q, McGue M, Christensen K, Hjelmborg J. DNA methylation age and perceived age in elderly Danish twins. Mech Ageing Dev 2018; 169:40-44. [PMID: 28965790 PMCID: PMC6190692 DOI: 10.1016/j.mad.2017.09.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 08/18/2017] [Accepted: 09/20/2017] [Indexed: 11/27/2022]
Abstract
Perceived age is an easily accessible biomarker of aging. Here, we studied its relation to DNA methylation age (DNAm age) as introduced in (Horvath, 2013) in 180 elderly Danish twins. We found perceived age and DNAm age to be associated with chronological age (P=0.04 resp. P=2.2e-10) when correcting for gender, but did not see an association between perceived age and DNAm age (P=0.44). Intrapair-analysis showed that the proportion of pairs where the twin with the highest perceived age also had the highest DNAm age was not different from 0.5 (P=1), and we did not see a trend when dividing pairs according to their difference in perceived age (P=0.36). Hence, intrapair analysis did not reveal links between perceived age and DNAm age. Moreover, none of the 353 CpGs underlying DNAm age was individually associated with perceived age after correction for multiple-testing (P>6e-4, FDR>0.21). Finally, when constructing an epigenetic signature based on these CpGs to predict perceived age, we only found a correlation of 0.18 (95%CI: -0.06 to 0.40) and a mean square error of 13.6 years2 between observed and predicted values in the test dataset, indicating poor predictive strength. Altogether, our results suggest that perceived age and DNAm age capture different aging aspects.
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Affiliation(s)
- Birgit Debrabant
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark.
| | - Mette Soerensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; The Danish Twin Registry and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Lene Christiansen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; The Danish Twin Registry and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; Unit of Human Genetics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Matt McGue
- Department of Psychology, University of Minnesota, Minneapolis, MN, USA; Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; The Danish Twin Registry and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Jacob Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Odense, Denmark; The Danish Twin Registry and the Danish Aging Research Center, Department of Public Health, University of Southern Denmark, Odense, Denmark
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305
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Epigenetics and Early Life Adversity: Current Evidence and Considerations for Epigenetic Studies in the Context of Child Maltreatment. THE BIOLOGY OF EARLY LIFE STRESS 2018. [DOI: 10.1007/978-3-319-72589-5_7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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306
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Abstract
In the face of shifting demographics and an increase in human longevity, it is important to examine carefully what is known about cognitive ageing, and to identify and promote possibly malleable lifestyle and health-related factors that might mitigate age-associated cognitive decline. The Lothian Birth Cohorts of 1921 (LBC1921, n = 550) and 1936 (LBC1936, n = 1091) are longitudinal studies of cognitive and brain ageing based in Scotland. Childhood IQ data are available for these participants, who were recruited in later life and then followed up regularly. This overview summarises some of the main LBC findings to date, illustrating the possible genetic and environmental contributions to cognitive function (level and change) and brain imaging biomarkers in later life. Key associations include genetic variation, health and fitness, psychosocial and lifestyle factors, and aspects of the brain's structure. It addresses some key methodological issues such as confounding by early-life intelligence and social factors and emphasises areas requiring further investigation. Overall, the findings that have emerged from the LBC studies highlight that there are multiple correlates of cognitive ability level in later life, many of which have small effects, that there are as yet few reliable predictors of cognitive change, and that not all of the correlates have independent additive associations. The concept of marginal gains, whereby there might be a cumulative effect of small incremental improvements across a wide range of lifestyle and health-related factors, may offer a useful way to think about and promote a multivariate recipe for healthy cognitive and brain ageing.
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Affiliation(s)
- J Corley
- Department of Psychology,The University of Edinburgh,Edinburgh,UK
| | - S R Cox
- Department of Psychology,The University of Edinburgh,Edinburgh,UK
| | - I J Deary
- Department of Psychology,The University of Edinburgh,Edinburgh,UK
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307
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Wolf EJ, Logue MW, Stoop TB, Schichman SA, Stone A, Sadeh N, Hayes JP, Miller MW. Accelerated DNA Methylation Age: Associations With Posttraumatic Stress Disorder and Mortality. Psychosom Med 2018; 80:42-48. [PMID: 29271864 PMCID: PMC5775924 DOI: 10.1097/psy.0000000000000506] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
OBJECTIVE Recently developed indices of cellular age based on DNA methylation (DNAm) data, referred to as DNAm age, are being used to study factors that influence the rate of aging and the health correlates of these metrics of the epigenetic clock. This study evaluated associations between trauma exposure, posttraumatic stress disorder (PTSD) symptoms, and accelerated versus decelerated DNAm age among military veterans. We also examined whether accelerated DNAm age predicted mortality over the course of a 6.5-year medical record review period. METHODS Three hundred thirty-nine genotype-confirmed white, non-Hispanic, middle-aged, trauma-exposed veterans underwent psychiatric assessment and genome-wide DNAm analysis. DNAm age was calculated using a previously validated algorithm. Medical records were available for a subset of 241 veterans and were reviewed approximately 6.5 years after DNA collection and PTSD assessment. RESULTS PTSD hyperarousal symptoms were associated with accelerated DNAm age (β = 0.20, p = .009) but trauma exposure and total PTSD severity were not. Accelerated DNAm age was also associated with 13% increased risk for all-cause mortality (hazard ratio = 1.13, 95% confidence interval = 1.01-1.26) during the medical record review period. CONCLUSIONS Findings of this study replicate the association between PTSD and accelerated DNAm age and suggest that this effect may be specific to the hyperarousal symptom cluster. Results point to the potential utility of DNAm age algorithms for identifying individuals who are aging at an accelerated rate and for determining the factors that influence this process.
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Affiliation(s)
- Erika J. Wolf
- National Center for PTSD, Behavioral Science Division, VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
| | - Mark W. Logue
- National Center for PTSD, Behavioral Science Division, VA Boston Healthcare System
- Biomedical Genetics, Boston University School of Medicine
- Department of Biostatistics, Boston University School of Public Health
| | | | - Steven A. Schichman
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System
| | - Annjanette Stone
- Pharmacogenomics Analysis Laboratory, Research Service, Central Arkansas Veterans Healthcare System
| | - Naomi Sadeh
- National Center for PTSD, Behavioral Science Division, VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
| | - Jasmeet P. Hayes
- National Center for PTSD, Behavioral Science Division, VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
| | - Mark W. Miller
- National Center for PTSD, Behavioral Science Division, VA Boston Healthcare System
- Department of Psychiatry, Boston University School of Medicine
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308
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Belsky DW, Huffman KM, Pieper CF, Shalev I, Kraus WE. Change in the Rate of Biological Aging in Response to Caloric Restriction: CALERIE Biobank Analysis. J Gerontol A Biol Sci Med Sci 2017; 73:4-10. [PMID: 28531269 DOI: 10.1093/gerona/glx096] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2017] [Indexed: 11/14/2022] Open
Abstract
Biological aging measures have been proposed as proxies for extension of healthy life span in trials of geroprotective therapies that aim to slow aging. Several methods to measure biological aging show promise but it is not known if these methods are sensitive to changes caused by geroprotective therapy. We conducted analysis of two proposed methods to quantify biological aging using data from a recently concluded trial of an established geroprotector, caloric restriction. We obtained data from the National Institute on Aging CALERIE randomized trial through its public-access biobank (https://calerie.duke.edu/). The CALERIE trial randomized N = 220 nonobese adults to 25% caloric restriction (n = 145; 11.7% caloric restriction was achieved, on average) or to maintain current diet (n = 75) for 2 years. We analyzed biomarker data collected at baseline, 12-, and 24-month follow-up assessments. We applied published biomarker algorithms to these data to calculate two biological age measures, Klemera-Doubal Method Biological Age and homeostatic dysregulation. Intent-to-treat analysis using mixed-effects growth models of within-person change over time tested if caloric restriction slowed increase in measures of biological aging across follow-up. Analyses of both measures indicated caloric restriction slowed biological aging. Weight loss did not account for the observed effects. Results suggest future directions for testing of geroprotective therapies in humans.
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Affiliation(s)
- Daniel W Belsky
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina.,Center for the Study of Aging and Human Development, Durham, North Carolina.,Center for Population Health Science, Duke University School of Medicine, Durham, North Carolina.,Social Science Research Institute, Duke University, Durham, North Carolina
| | - Kim M Huffman
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina.,Center for the Study of Aging and Human Development, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
| | - Carl F Pieper
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina.,Center for the Study of Aging and Human Development, Durham, North Carolina.,Department of Biostatistics, Duke University, Durham, North Carolina
| | - Idan Shalev
- Department of Biobehavioral Health, Pennsylvania State University, State College
| | - William E Kraus
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina.,Center for the Study of Aging and Human Development, Durham, North Carolina.,Duke Molecular Physiology Institute, Duke University, Durham, North Carolina
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309
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Karlsson Linnér R, Marioni RE, Rietveld CA, Simpkin AJ, Davies NM, Watanabe K, Armstrong NJ, Auro K, Baumbach C, Jan Bonder M, Buchwald J, Fiorito G, Ismail K, Iurato S, Joensuu A, Karell P, Kasela S, Lahti J, McRae AF, Mandaviya PR, Seppälä I, Wang Y, Baglietto L, Binder EB, Harris SE, Hodge AM, Horvath S, Hurme M, Johannesson M, Latvala A, Mather KA, Medland SE, Metspalu A, Milani L, Milne RL, Pattie A, Pedersen NL, Peters A, Polidoro S, Räikkönen K, Severi G, Starr JM, Stolk L, Waldenberger M, Eriksson JG, Esko T, Franke L, Gieger C, Giles GG, Hägg S, Jousilahti P, Kaprio J, Kähönen M, Lehtimäki T, Martin NG, van Meurs JBC, Ollikainen M, Perola M, Posthuma D, Raitakari OT, Sachdev PS, Taskesen E, Uitterlinden AG, Vineis P, Wijmenga C, Wright MJ, Relton C, Davey Smith G, Deary IJ, Koellinger PD, Benjamin DJ. An epigenome-wide association study meta-analysis of educational attainment. Mol Psychiatry 2017; 22:1680-1690. [PMID: 29086770 PMCID: PMC6372242 DOI: 10.1038/mp.2017.210] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 08/16/2017] [Accepted: 08/21/2017] [Indexed: 01/29/2023]
Abstract
The epigenome is associated with biological factors, such as disease status, and environmental factors, such as smoking, alcohol consumption and body mass index. Although there is a widespread perception that environmental influences on the epigenome are pervasive and profound, there has been little evidence to date in humans with respect to environmental factors that are biologically distal. Here we provide evidence on the associations between epigenetic modifications-in our case, CpG methylation-and educational attainment (EA), a biologically distal environmental factor that is arguably among the most important life-shaping experiences for individuals. Specifically, we report the results of an epigenome-wide association study meta-analysis of EA based on data from 27 cohort studies with a total of 10 767 individuals. We find nine CpG probes significantly associated with EA. However, robustness analyses show that all nine probes have previously been found to be associated with smoking. Only two associations remain when we perform a sensitivity analysis in the subset of never-smokers, and these two probes are known to be strongly associated with maternal smoking during pregnancy, and thus their association with EA could be due to correlation between EA and maternal smoking. Moreover, the effect sizes of the associations with EA are far smaller than the known associations with the biologically proximal environmental factors alcohol consumption, body mass index, smoking and maternal smoking during pregnancy. Follow-up analyses that combine the effects of many probes also point to small methylation associations with EA that are highly correlated with the combined effects of smoking. If our findings regarding EA can be generalized to other biologically distal environmental factors, then they cast doubt on the hypothesis that such factors have large effects on the epigenome.
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Affiliation(s)
- Richard Karlsson Linnér
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
- Institute for Behavior and Biology, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, the Netherlands
| | - Riccardo E Marioni
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Cornelius A Rietveld
- Institute for Behavior and Biology, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, the Netherlands
- Department of Applied Economics, Erasmus School of Economics, Erasmus University Rotterdam, Burgemeester Oudlaan 50, Rotterdam, 3062 PA, the Netherlands
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Andrew J Simpkin
- MRC Intergrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Barley House, Oakfield Grove, Bristol, BS28BN, United Kingdom
| | - Neil M Davies
- MRC Intergrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Barley House, Oakfield Grove, Bristol, BS28BN, United Kingdom
| | - Kyoko Watanabe
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
| | - Nicola J Armstrong
- Mathematics and Statistics, Murdoch University, 90 South St., Murdoch, 6150, WA, Australia
| | - Kirsi Auro
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- National Institute for Health and Welfare, Genomics and Biomarkers, PO Box 30, Helsinki, FI-00271, Finland
| | - Clemens Baumbach
- Research Unit of Molecular Epidemiology (AME), Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Munich, Germany, Neuherberg, 85764, Germany
| | - Marc Jan Bonder
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Jadwiga Buchwald
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Giovanni Fiorito
- Molecular and genetic epidemiology unit, Human Genetics Foundation Torino (HuGeF), Via Nizza 52, Turin, 10126, Italy
- Department of Medical Sciences, University of Torino, Corso Dogliotti 14
| | - Khadeeja Ismail
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Stella Iurato
- Department Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany, Kraepelinstr. 2-10, Munich, 80804, Germany
| | - Anni Joensuu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- National Institute for Health and Welfare, Genomics and Biomarkers, PO Box 30, Helsinki, FI-00271, Finland
| | - Pauliina Karell
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Silva Kasela
- Estonian Genome Center, University of Tartu, Riia 23B, Tartu, 51010, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010, Estonia
| | - Jari Lahti
- Institute of Behavioural Studies, Siltavuorenpenger 1A, University of Helsinki, Helsinki, FI-00014, Finland
- Collegium for Advanced Studies, University of Helsinki, Helsinki, FI-00014, Finland
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD
| | - Pooja R Mandaviya
- Department of Clinical Chemistry, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - Yunzhang Wang
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, Stockholm, 17177, Sweden
| | - Laura Baglietto
- Centre for Research in Epidemiology and Population Health, Inserm (Institut National de la Santé et de la Recherche Médicale), 114 rue Edouard Vaillant, Villejuif, 94805, France
| | - Elisabeth B Binder
- Department Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany, Kraepelinstr. 2-10, Munich, 80804, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, USA
| | - Sarah E Harris
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
- Medical Genetics Section, Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, EH4 2XU, United Kingdom
| | - Allison M Hodge
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, 3004, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Level 3, 207 Bouverie Street, Carlton, Melbourne, 3010, Victoria, Australia
| | - Steve Horvath
- Human Genetics and Biostatistics, University of California Los Angeles, 695 Charles E. Young Drive South, Box 708822, Los Angeles, CA 90095-7088, USA
| | - Mikko Hurme
- Department of Microbiology and Immunology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
- Gerontology Research Center, University of Tampere, Tampere 33014, Finland
- Fimlab Laboratories, Tampere 33520, Finland
| | - Magnus Johannesson
- Department of Economics, Stockholm School of Economics, Box 6501, Stockholm, 11383, Sweden
| | - Antti Latvala
- Department of Public Health, University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Karen A Mather
- Centre for Healthy Brain Ageing, Psychiatry, UNSW Australia, High St., Sydney, NSW 2052, Australia
| | - Sarah E Medland
- Psychiatric Genetics, QIMR Berghofer Medical Research Institute, 300 Herston Rd., Herston, QLD 4006, Australia
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Riia 23B, Tartu, 51010, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu, 51010, Estonia
| | - Lili Milani
- Estonian Genome Center, University of Tartu, Riia 23B, Tartu, 51010, Estonia
| | - Roger L Milne
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, 3004, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Level 3, 207 Bouverie Street, Carlton, Melbourne, 3010, Victoria, Australia
| | - Alison Pattie
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
| | - Nancy L Pedersen
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, Stockholm, 17177, Sweden
| | - Annette Peters
- Research Unit of Molecular Epidemiology (AME), Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Munich, Germany, Neuherberg, 85764, Germany
| | - Silvia Polidoro
- Molecular and genetic epidemiology unit, Human Genetics Foundation Torino (HuGeF), Via Nizza 52, Turin, 10126, Italy
| | - Katri Räikkönen
- Institute of Behavioural Studies, Siltavuorenpenger 1A, University of Helsinki, Helsinki, FI-00014, Finland
| | - Gianluca Severi
- Molecular and genetic epidemiology unit, Human Genetics Foundation Torino (HuGeF), Via Nizza 52, Turin, 10126, Italy
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, 3004, Victoria, Australia
- Centre for Research in Epidemiology and Population Health (CESP), Inserm (Institut National de la Santé et de la Recherche Médicale), 28 Rue Laennec, Lyon, 69373, France
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
- Alzheimer Scotland Dementia Research Centre, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
| | - Lisette Stolk
- Department of Clinical Chemistry, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
- Netherlands Consortium for Healthy Ageing, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology (AME), Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Munich, Germany, Neuherberg, 85764, Germany
| | | | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Tukholmankatu 8 B, Helsinki, FI-00014, Finland
- National Institute for Health and Welfare, P.O. Box 30, Helsinki, FI-00271, Finland
- Folkhälsan Research Center, Helsinki, Finland
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Riia 23B, Tartu, 51010, Estonia
- Program in Medical and Population Genetics, Broad Institute, 415 Main St., Cambridge, MA 02142, USA
| | - Lude Franke
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Christian Gieger
- Research Unit of Molecular Epidemiology (AME), Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstädter Landstr. 1, Munich, Germany, Neuherberg, 85764, Germany
| | - Graham G Giles
- Cancer Epidemiology Centre, Cancer Council Victoria, 615 St Kilda Road, Melbourne, 3004, Victoria, Australia
- Centre for Epidemiology and Biostatistics, School of Population and Global Health, The University of Melbourne, Level 3, 207 Bouverie Street, Carlton, Melbourne, 3010, Victoria, Australia
| | - Sara Hägg
- Medical Epidemiology and Biostatistics, Karolinska Institutet, Nobels väg 12A, Stockholm, 17177, Sweden
| | - Pekka Jousilahti
- National Institute for Health and Welfare, Genomics and Biomarkers, PO Box 30, Helsinki, FI-00271, Finland
| | - Jaakko Kaprio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- Department of Public Health, University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33521, Finland
- Department of Clinical Physiology, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland
- Department of Clinical Chemistry, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33014, Finland
| | - Nicholas G Martin
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, 300 Herston Rd, Herston, QLD 4006, Australia
| | - Joyce B C van Meurs
- Department of Internal Medicine, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
- Netherlands Consortium for Healthy Ageing, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
| | - Miina Ollikainen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- Department of Public Health, University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Tukholmankatu 8, 2B, Helsinki, FI-00014, Finland
- National Institute for Health and Welfare, Genomics and Biomarkers, PO Box 30, Helsinki, FI-00271, Finland
| | - Danielle Posthuma
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20521, Finland
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20014, Finland
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, Psychiatry, UNSW Australia, High St., Sydney, NSW 2052, Australia
- Neuropsychiatric Institute, Prince of Wales Hospital, Barker St. Randwick
| | - Erdogan Taskesen
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
- VU University Medical Center (VUMC), Alzheimer Center, Department of Neurology, Amsterdam, the Netherlands
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
- Netherlands Consortium for Healthy Ageing, Erasmus University Medical Center, Wytemaweg 80, Rotterdam, 3015 CN, The Netherlands
| | - Paolo Vineis
- Molecular and genetic epidemiology unit, Human Genetics Foundation Torino (HuGeF), Via Nizza 52, Turin, 10126, Italy
- MRC/PHE Centre for Environment and Health, School of Public Health, Imperial College London, St Mary’s Campus, Norfolk Place, London, W2 1PG, United Kingdom
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Margaret J Wright
- Queensland Brain Institute and Centre for Advanced Imaging, The University of Queensland, Brisbane, QLD, Australia
| | - Caroline Relton
- MRC Intergrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Barley House, Oakfield Grove, Bristol, BS28BN, United Kingdom
| | - George Davey Smith
- MRC Intergrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Barley House, Oakfield Grove, Bristol, BS28BN, United Kingdom
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
- Department of Psychology, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, United Kingdom
| | - Philipp D Koellinger
- Department of Complex Trait Genetics, Vrije Universiteit Amsterdam, Center for Neurogenomics and Cognitive Research, De Boelelaan 1085, Amsterdam, 1081HV, the Netherlands
- Institute for Behavior and Biology, Erasmus University Rotterdam, P.O. Box 1738, 3000 DR, Rotterdam, the Netherlands
| | - Daniel J Benjamin
- Center for Economic and Social Research, University of Southern California, Los Angeles, CA 90089-3332, USA
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310
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Jylhävä J, Kananen L, Raitanen J, Marttila S, Nevalainen T, Hervonen A, Jylhä M, Hurme M. Methylomic predictors demonstrate the role of NF-κB in old-age mortality and are unrelated to the aging-associated epigenetic drift. Oncotarget 2017; 7:19228-41. [PMID: 27015559 PMCID: PMC4991378 DOI: 10.18632/oncotarget.8278] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Accepted: 03/10/2016] [Indexed: 01/24/2023] Open
Abstract
Changes in the DNA methylation (DNAm) landscape have been implicated in aging and cellular senescence. To unravel the role of specific DNAm patterns in late-life survival, we performed genome-wide methylation profiling in nonagenarians (n=111) and determined the performance of the methylomic predictors and conventional risk markers in a longitudinal setting. The survival model containing only the methylomic markers was superior in terms of predictive accuracy compared with the model containing only the conventional predictors or the model containing conventional predictors combined with the methylomic markers. At the 2.55-year follow-up, we identified 19 mortality-associated (false-discovery rate <0.5) CpG sites that mapped to genes functionally clustering around the nuclear factor kappa B (NF-κB) complex. Interestingly, none of the mortality-associated CpG sites overlapped with the established aging-associated DNAm sites. Our results are in line with previous findings on the role of NF-κB in controlling animal life spans and demonstrate the role of this complex in human longevity.
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Affiliation(s)
- Juulia Jylhävä
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland
| | - Laura Kananen
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland
| | - Jani Raitanen
- School of Health Sciences, University of Tampere, Tampere, Finland.,UKK Institute for Health Promotion Research, Tampere, Finland
| | - Saara Marttila
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland
| | - Tapio Nevalainen
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland
| | - Antti Hervonen
- Gerontology Research Center, University of Tampere, Tampere, Finland.,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Marja Jylhä
- Gerontology Research Center, University of Tampere, Tampere, Finland.,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Mikko Hurme
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, University of Tampere, Tampere, Finland.,Fimlab Laboratories, Tampere, Finland
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311
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Hastings WJ, Shalev I, Belsky DW. Translating Measures of Biological Aging to Test Effectiveness of Geroprotective Interventions: What Can We Learn from Research on Telomeres? Front Genet 2017; 8:164. [PMID: 29213278 PMCID: PMC5702647 DOI: 10.3389/fgene.2017.00164] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 10/16/2017] [Indexed: 11/13/2022] Open
Abstract
Intervention studies in animals suggest molecular changes underlying age-related disease and disability can be slowed or reversed. To speed translation of these so-called "geroprotective" therapies to prevent age-related disease and disability in humans, biomarkers are needed that can track changes in the rate of human aging over the course of intervention trials. Algorithm methods that measure biological processes of aging from combinations of DNA methylation marks or clinical biomarkers show promise. To identify next steps for establishing utility of these algorithm-based measures of biological aging for geroprotector trials, we considered the history a candidate biomarker of aging that has received substantial research attention, telomere length. Although telomere length possesses compelling biology to recommend it as a biomarker of aging, mixed research findings have impeded clinical and epidemiologic translation. Strengths of telomeres that should be established for algorithm biomarkers of aging are correlation with chronological age across the lifespan, prediction of disease, disability, and early death, and responsiveness to risk and protective exposures. Key challenges in telomere research that algorithm biomarkers of aging must address are measurement precision and reliability, establishing links between longitudinal rates of change across repeated measurements and aging outcomes, and clarity over whether the biomarker is a causal mechanism of aging. These strengths and challenges suggest a research agenda to advance translation of algorithm-based aging biomarkers: establish validity in young-adult and midlife individuals; test responsiveness to exposures that shorten or extend healthy lifespan; and conduct repeated-measures longitudinal studies to test differential rates of change.
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Affiliation(s)
- Waylon J Hastings
- Department of Biobehavioral Health, Pennsylvania State University, State College, PA, United States
| | - Idan Shalev
- Department of Biobehavioral Health, Pennsylvania State University, State College, PA, United States
| | - Daniel W Belsky
- Department of Population Health Sciences, Duke University School of Medicine, Durham, NC, United States.,Center for the Study of Aging and Human Development, Duke University, Durham, NC, United States
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312
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Grant CD, Jafari N, Hou L, Li Y, Stewart JD, Zhang G, Lamichhane A, Manson JE, Baccarelli AA, Whitsel EA, Conneely KN. A longitudinal study of DNA methylation as a potential mediator of age-related diabetes risk. GeroScience 2017; 39:475-489. [PMID: 29159506 DOI: 10.1007/s11357-017-0001-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2017] [Accepted: 11/02/2017] [Indexed: 01/22/2023] Open
Abstract
DNA methylation (DNAm) has been found to show robust and widespread age-related changes across the genome. DNAm profiles from whole blood can be used to predict human aging rates with great accuracy. We sought to test whether DNAm-based predictions of age are related to phenotypes associated with type 2 diabetes (T2D), with the goal of identifying risk factors potentially mediated by DNAm. Our participants were 43 women enrolled in the Women's Health Initiative. We obtained methylation data via the Illumina 450K Methylation array on whole blood samples from participants at three timepoints, covering on average 16 years per participant. We employed the method and software of Horvath, which uses DNAm at 353 CpGs to form a DNAm-based estimate of chronological age. We then calculated the epigenetic age acceleration, or Δage, at each timepoint. We fit linear mixed models to characterize how Δage contributed to a longitudinal model of aging and diabetes-related phenotypes and risk factors. For most participants, Δage remained constant, indicating that age acceleration is generally stable over time. We found that Δage associated with body mass index (p = 0.0012), waist circumference (p = 0.033), and fasting glucose (p = 0.0073), with the relationship with BMI maintaining significance after correction for multiple testing. Replication in a larger cohort of 157 WHI participants spanning 3 years was unsuccessful, possibly due to the shorter time frame covered. Our results suggest that DNAm has the potential to act as a mediator between aging and diabetes-related phenotypes, or alternatively, may serve as a biomarker of these phenotypes.
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Affiliation(s)
- Crystal D Grant
- Genetics and Molecular Biology Graduate Program, Emory University, Atlanta, GA, USA. .,Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA.
| | - Nadereh Jafari
- Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.,Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Yun Li
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.,Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.,Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - James D Stewart
- Carolina Population Center, University of North Carolina, Chapel Hill, NC, USA
| | - Guosheng Zhang
- Department of Genetics, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Archana Lamichhane
- Environmental Health Sciences, RTI International, Research Triangle Park, NC, USA.,Department of Nutrition, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - JoAnn E Manson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA.,Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA, USA
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313
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Ibrahim O, Sutherland HG, Haupt LM, Griffiths LR. An emerging role for epigenetic factors in relation to executive function. Brief Funct Genomics 2017; 17:170-180. [DOI: 10.1093/bfgp/elx032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
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314
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Leung JM, Fishbane N, Jones M, Morin A, Xu S, Liu JC, MacIsaac J, Milloy MJ, Hayashi K, Montaner J, Horvath S, Kobor M, Sin DD, Harrigan PR, Man SFP. Longitudinal study of surrogate aging measures during human immunodeficiency virus seroconversion. Aging (Albany NY) 2017; 9:687-705. [PMID: 28237978 PMCID: PMC5391226 DOI: 10.18632/aging.101184] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 02/20/2017] [Indexed: 12/13/2022]
Abstract
Persons living with human immunodeficiency virus (HIV) harbor an increased risk of age-related conditions. We measured changes in telomere length and DNA methylation in the peripheral blood of 31 intravenous drug users, who were followed longitudinally with blood samples pre-HIV (T1), immediately post-HIV (T2; 1.9±1 year from T1), and at a later follow-up time (T3; 2.2±1 year from T2). Absolute telomere length measurements were performed using polymerase chain reaction methods. Methylation profiles were obtained using the Illumina Human Methylation450 platform. Methylation aging was assessed using the Horvath method. Telomere length significantly decreased between T1 and T2 (227±46 at T1 vs. 201±48 kbp/genome at T2, p=0.045), while no differences were observed between T2 and T3 (201±48 at T2 vs. 186±27 kbp/genome at T3, p=0.244). Methylation aging as measured by the age acceleration residual increased over the time course of HIV infection (p=0.035). CpG sites corresponding to PCBP2 and CSRNP1 were differentially methylated between T1 and T2 at a q-value <0.05. Telomere shortening and methylation changes can therefore be observed in the short-term period immediately following HIV seroconversion. Further studies to confirm these results in larger sample sizes and to compare these results to non-HIV and non-injection drug users are warranted.
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Affiliation(s)
- Janice M Leung
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada.,Division of Respiratory Medicine, Department of Medicine, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada.,BC Centre for Excellence in HIV/AIDS, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada
| | - Nick Fishbane
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada
| | - Meaghan Jones
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - Alexander Morin
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - Stella Xu
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada
| | - Joseph Cy Liu
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada
| | - Julie MacIsaac
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - M-J Milloy
- BC Centre for Excellence in HIV/AIDS, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada
| | - Kanna Hayashi
- BC Centre for Excellence in HIV/AIDS, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada.,Department of Medicine, University of British Columbia, Vancouver, V6Z 1Y6, Canada
| | - Julio Montaner
- BC Centre for Excellence in HIV/AIDS, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada
| | - Steve Horvath
- Departments of Human Genetics and Biostatistics, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Michael Kobor
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada.,Division of Respiratory Medicine, Department of Medicine, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada
| | - P Richard Harrigan
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, V5Z 4H4, Canada
| | - S F Paul Man
- Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada.,Division of Respiratory Medicine, Department of Medicine, St. Paul's Hospital, University of British Columbia, Vancouver, V6Z 1Y6, Canada
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315
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Soriano-Tárraga C, Giralt-Steinhauer E, Mola-Caminal M, Vivanco-Hidalgo RM, Ois A, Rodríguez-Campello A, Cuadrado-Godia E, Sayols-Baixeras S, Elosua R, Roquer J, Jiménez-Conde J. Ischemic stroke patients are biologically older than their chronological age. Aging (Albany NY) 2017; 8:2655-2666. [PMID: 27922817 PMCID: PMC5191861 DOI: 10.18632/aging.101028] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 08/16/2016] [Indexed: 12/24/2022]
Abstract
Ischemic stroke is associated with aging. It is possible to predict chronological age by measuring age-related changes in DNA methylation from multiple CpG sites across the genome, known as biological age. The difference between biological age and actual chronological age would indicate an individual's level of aging. Our aim was to determine the biological age of ischemic stroke patients and compare their aging with controls of the same chronological age. A total of 123 individuals, 41 controls and 82 patients with ischemic stroke were paired by chronological age, ranging from 39 to 82 years. Illumina HumanMethylation450 BeadChip array was used to measure DNA methylation in CpG sites in both groups, and biological age was estimated using methylation values of specific CpGs. Ischemic stroke patients were biologically an average 2.5 years older than healthy controls (p-value=0.010). Stratified by age tertiles, younger stroke patients (≤57 years old) were biologically older than controls (OR=1.19; 95%CI 1.00-1.41, p-value=0.046). The older groups showed no biological age differences between cases and controls, but were close to reaching the significance level. Ischemic stroke patients are biologically older than controls. Biological age should be considered as a potential new biomarker of stroke risk.
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Affiliation(s)
- Carolina Soriano-Tárraga
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Eva Giralt-Steinhauer
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Marina Mola-Caminal
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Rosa M Vivanco-Hidalgo
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Angel Ois
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Ana Rodríguez-Campello
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Elisa Cuadrado-Godia
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain
| | - Sergi Sayols-Baixeras
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain.,Universitat Pompeu Fabra, Barcelona, Spain
| | - Roberto Elosua
- Cardiovascular Epidemiology and Genetics Research Group, IMIM, Barcelona, Spain
| | - Jaume Roquer
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain.,Co-senior authorship
| | - Jordi Jiménez-Conde
- Department of Neurology, Hospital del Mar; Neurovascular Research Group, IMIM (Institut Hospital del Mar d'Investigacions Mèdiques); Universitat Autònoma de Barcelona/DCEXS-Universitat Pompeu Fabra, Barcelona, Spain.,Co-senior authorship
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316
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Abstract
Several articles describe highly accurate age estimation methods based on human DNA-methylation data. It is not yet known whether similar epigenetic aging clocks can be developed based on blood methylation data from canids. Using Reduced Representation Bisulfite Sequencing, we assessed blood DNA-methylation data from 46 domesticated dogs (Canis familiaris) and 62 wild gray wolves (C. lupus). By regressing chronological dog age on the resulting CpGs, we defined highly accurate multivariate age estimators for dogs (based on 41 CpGs), wolves (67 CpGs), and both combined (115 CpGs). Age related DNA methylation changes in canids implicate similar gene ontology categories as those observed in humans suggesting an evolutionarily conserved mechanism underlying age-related DNA methylation in mammals.
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317
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Simpkin AJ, Cooper R, Howe LD, Relton CL, Davey Smith G, Teschendorff A, Widschwendter M, Wong A, Kuh D, Hardy R. Are objective measures of physical capability related to accelerated epigenetic age? Findings from a British birth cohort. BMJ Open 2017; 7:e016708. [PMID: 29092899 PMCID: PMC5695310 DOI: 10.1136/bmjopen-2017-016708] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 06/08/2017] [Accepted: 07/13/2017] [Indexed: 01/07/2023] Open
Abstract
OBJECTIVES Our aim was to investigate the association of epigenetic age and physical capability in later life. Having a higher epigenetic than chronological age (known as age acceleration (AA)) has been found to be associated with an increased rate of mortality. Similarly, physical capability has been proposed as a marker of ageing due to its consistent associations with mortality. SETTING The MRC National Survey of Health and Development (NSHD) cohort study. PARTICIPANTS We used data from 790 women from the NSHD who had DNA methylation data available. DESIGN Epigenetic age was calculated using buccal cell (n=790) and matched blood tissue (n=152) from 790 female NSHD participants. We investigated the association of AA at age 53 with changes in physical capability in women from ages 53 to 60-64. Regression models of change in each measure of physical capability on AA were conducted. Secondary analysis focused on the relationship between AA and smoking, alcohol, body mass index (BMI) and socioeconomic position. OUTCOME MEASURES Three objective measures of physical capability were used: grip strength, standing balance time and chair rise speed. RESULTS Epigenetic age was lower than chronological age (mean 53.4) for both blood (50.3) and buccal cells (42.8). AA from blood was associated with a greater decrease in grip strength from ages 53 to 60-64 (0.42 kg decrease per year of AA, 95% CI 0.03, 0.82 kg; p=0.03, n=152), but no associations were observed with standing balance time or chair rise speed. Current smoking and lower BMI were associated with lower epigenetic age from buccal cells. CONCLUSIONS We found evidence that AA in blood is associated with a greater decrease in grip strength in British females aged between 53 and 60-64, but no association with standing balance time or chair rise speed was found.
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Affiliation(s)
- Andrew J Simpkin
- MRC Integrative Epidemiology Unit at the University of Bristol, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Insight Centre for Data Analytics, National University of Ireland, Galway, Galway, Ireland
| | - Rachel Cooper
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Laura D Howe
- MRC Integrative Epidemiology Unit at the University of Bristol, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit at the University of Bristol, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - George Davey Smith
- MRC Integrative Epidemiology Unit at the University of Bristol, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Andrew Teschendorff
- Department of Women's Cancer, University College London, London, UK
- CAS Key Lab of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
- Department of Statistical Cancer Genomics, UCL Cancer Institute, University College London, London, UK
| | | | - Andrew Wong
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Diana Kuh
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
| | - Rebecca Hardy
- MRC Unit for Lifelong Health and Ageing at UCL, London, UK
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318
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Chaix R, Alvarez-López MJ, Fagny M, Lemee L, Regnault B, Davidson RJ, Lutz A, Kaliman P. Epigenetic clock analysis in long-term meditators. Psychoneuroendocrinology 2017; 85:210-214. [PMID: 28889075 PMCID: PMC5863232 DOI: 10.1016/j.psyneuen.2017.08.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 08/12/2017] [Accepted: 08/12/2017] [Indexed: 10/19/2022]
Abstract
In this paper, we examined whether meditation practice influences the epigenetic clock, a strong and reproducible biomarker of biological aging, which is accelerated by cumulative lifetime stress and with age-related chronic diseases. Using the Illumina 450K array platform, we analyzed the DNA methylome from blood cells of long-term meditators and meditation-naïve controls to estimate their Intrinsic Epigenetic Age Acceleration (IEAA), using Horvath's calculator. IEAA was similar in both groups. However, controls showed a different IEAA trajectory with aging than meditators: older controls (age≥52) had significantly higher IEAAs compared with younger controls (age <52), while meditators were protected from this epigenetic aging effect. Notably, in the meditation group, we found a significant negative correlation between IEAA and the number of years of regular meditation practice. From our results, we hypothesize that the cumulative effects of a regular meditation practice may, in the long-term, help to slow the epigenetic clock and could represent a useful preventive strategy for age-related chronic diseases. Longitudinal randomized controlled trials in larger cohorts are warranted to confirm and further characterize these findings.
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Affiliation(s)
- Raphaëlle Chaix
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Univ Paris Diderot, Sorbonne Paris Cité, France.
| | - Maria Jesús Alvarez-López
- Unitat de Farmacologia, Facultat de Farmàcia, Institut de Biomedicina, Universitat de Barcelona (IBUB), Nucli Universitari de Pedralbes, Barcelone, 08028, Spain
| | - Maud Fagny
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Laure Lemee
- Plateforme de génotypage des eucaryotes, Biomics, CITECH, Institut Pasteur, 75015 Paris, France
| | - Béatrice Regnault
- Plateforme de génotypage des eucaryotes, Biomics, CITECH, Institut Pasteur, 75015 Paris, France
| | | | - Antoine Lutz
- Lyon Neuroscience Research Center, INSERM U1028, CNRS UMR5292, Lyon 1 University, 69500 Lyon, France
| | - Perla Kaliman
- Center for Mind and Brain, University of California Davis, Davis, CA 95618, USA.
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319
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Vidal-Bralo L, Lopez-Golan Y, Mera-Varela A, Rego-Perez I, Horvath S, Zhang Y, Del Real Á, Zhai G, Blanco FJ, Riancho JA, Gomez-Reino JJ, Gonzalez A. Specific premature epigenetic aging of cartilage in osteoarthritis. Aging (Albany NY) 2017; 8:2222-2231. [PMID: 27689435 PMCID: PMC5076459 DOI: 10.18632/aging.101053] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/14/2016] [Indexed: 12/18/2022]
Abstract
Osteoarthritis (OA) is a disease affecting multiple tissues of the joints in the elderly, but most notably articular cartilage. Premature biological aging has been described in this tissue and in blood cells, suggesting a systemic component of premature aging in the pathogenesis of OA. Here, we have explored epigenetic aging in OA at the local (cartilage and bone) and systemic (blood) levels. Two DNA methylation age-measures (DmAM) were used: the multi-tissue age estimator for cartilage and bone; and a blood-specific biomarker for blood. Differences in DmAM between OA patients and controls showed an accelerated aging of 3.7 years in articular cartilage (95% CI = 1.1 to 6.3, P = 0.008) of OA patients. By contrast, no difference in epigenetic aging was observed in bone (0.04 years; 95% CI = -1.8 to 1.9, P = 0.3) and in blood (-0.6 years; 95% CI = -1.5 to 0.3, P = 0.2) between OA patients and controls. Therefore, premature epigenetic aging according to DNA methylation changes was specific of OA cartilage, adding further evidence and insight on premature aging of cartilage as a component of OA pathogenesis that reflects damage and vulnerability.
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Affiliation(s)
- Laura Vidal-Bralo
- Laboratorio Investigacion 10 and Rheumatology Unit, Instituto Investigacion Sanitaria, Hospital Clinico Universitario de Santiago, Travesia Choupana, sn. 15706- Santiago de Compostela, Spain
| | - Yolanda Lopez-Golan
- Laboratorio Investigacion 10 and Rheumatology Unit, Instituto Investigacion Sanitaria, Hospital Clinico Universitario de Santiago, Travesia Choupana, sn. 15706- Santiago de Compostela, Spain
| | - Antonio Mera-Varela
- Laboratorio Investigacion 10 and Rheumatology Unit, Instituto Investigacion Sanitaria, Hospital Clinico Universitario de Santiago, Travesia Choupana, sn. 15706- Santiago de Compostela, Spain
| | - Ignacio Rego-Perez
- Grupo de Reumatología, Instituto de Investigación Biomédica de A Coruña. Complexo Hospitalario Universitario de A Coruña, Universidade da Coruña. As Xubias, sn. 15006- A Coruña, Spain
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Yuhua Zhang
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, A1B- St. John's, NL, Canada
| | - Álvaro Del Real
- Department of Internal Medicine, Hospital U. M. Valdecilla-IDIVAL, University of Cantabria, Cardenal Herrera Oria, 39011, Santander, Spain
| | - Guangju Zhai
- Discipline of Genetics, Faculty of Medicine, Memorial University of Newfoundland, A1B- St. John's, NL, Canada
| | - Francisco J Blanco
- Grupo de Reumatología, Instituto de Investigación Biomédica de A Coruña. Complexo Hospitalario Universitario de A Coruña, Universidade da Coruña. As Xubias, sn. 15006- A Coruña, Spain
| | - Jose A Riancho
- Department of Internal Medicine, Hospital U. M. Valdecilla-IDIVAL, University of Cantabria, Cardenal Herrera Oria, 39011, Santander, Spain
| | - Juan J Gomez-Reino
- Laboratorio Investigacion 10 and Rheumatology Unit, Instituto Investigacion Sanitaria, Hospital Clinico Universitario de Santiago, Travesia Choupana, sn. 15706- Santiago de Compostela, Spain
| | - Antonio Gonzalez
- Laboratorio Investigacion 10 and Rheumatology Unit, Instituto Investigacion Sanitaria, Hospital Clinico Universitario de Santiago, Travesia Choupana, sn. 15706- Santiago de Compostela, Spain
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320
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DNA methylation-based measures of biological age: meta-analysis predicting time to death. Aging (Albany NY) 2017; 8:1844-1865. [PMID: 27690265 PMCID: PMC5076441 DOI: 10.18632/aging.101020] [Citation(s) in RCA: 660] [Impact Index Per Article: 94.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/18/2016] [Indexed: 12/18/2022]
Abstract
Estimates of biological age based on DNA methylation patterns, often referred to as "epigenetic age", "DNAm age", have been shown to be robust biomarkers of age in humans. We previously demonstrated that independent of chronological age, epigenetic age assessed in blood predicted all-cause mortality in four human cohorts. Here, we expanded our original observation to 13 different cohorts for a total sample size of 13,089 individuals, including three racial/ethnic groups. In addition, we examined whether incorporating information on blood cell composition into the epigenetic age metrics improves their predictive power for mortality. All considered measures of epigenetic age acceleration were predictive of mortality (p≤8.2x10-9), independent of chronological age, even after adjusting for additional risk factors (p<5.4x10-4), and within the racial/ethnic groups that we examined (non-Hispanic whites, Hispanics, African Americans). Epigenetic age estimates that incorporated information on blood cell composition led to the smallest p-values for time to death (p=7.5x10-43). Overall, this study a) strengthens the evidence that epigenetic age predicts all-cause mortality above and beyond chronological age and traditional risk factors, and b) demonstrates that epigenetic age estimates that incorporate information on blood cell counts lead to highly significant associations with all-cause mortality.
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321
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Steinberg J, Shah KM, Gartland A, Zeggini E, Wilkinson JM. Effects of chronic cobalt and chromium exposure after metal-on-metal hip resurfacing: An epigenome-wide association pilot study. J Orthop Res 2017; 35:2323-2328. [PMID: 28098396 PMCID: PMC5655715 DOI: 10.1002/jor.23525] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 01/06/2017] [Indexed: 02/04/2023]
Abstract
Metal-on-metal (MOM) hip resurfacing has recently been a popular prosthesis choice for the treatment of symptomatic arthritis, but results in the release of cobalt and chromium ions into the circulation that can be associated with adverse clinical effects. The mechanism underlying these effects remains unclear. While chromosomal aneuploidy and translocations are associated with this exposure, the presence of subtle structural epigenetic modifications in patients with MOM joint replacements remains unexplored. Consequently, we analyzed whole blood DNA methylation in 34 OA patients with MOM hip resurfacing (MOM HR) compared to 34 OA patients with non-MOM total hip replacements (non-MOM THR), using the genome-wide Illumina HumanMethylation 450k BeadChip. No probes showed differential methylation significant at 5% false-discovery rate (FDR). We also tested association of probe methylation levels with blood chromium and cobalt levels directly; there were no significant associations at 5% FDR. Finally, we used the "epigenetic clock" to compare estimated to actual age at sample for all individuals. We found no significant difference between MOM HR and non-MOM THR, and no correlation of age acceleration with blood metal levels. Our results suggest the absence of large methylation differences systemically following metal exposure, however, larger sample sizes will be required to identify potential small effects. Any DNA methylation changes that may occur in the local periprosthetic tissues remain to be elucidated. © 2017 The Authors. Orthopaedic Research Society. Published by Wiley Periodicals, Inc. on behalf of Orthopaedic Research Society. J Orthop Res 35:2323-2328, 2017.
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Affiliation(s)
| | - Karan M. Shah
- Department of Oncology and Metabolism, The Mellanby Centre for Bone ResearchThe University of SheffieldSheffieldUK
| | - Alison Gartland
- Department of Oncology and Metabolism, The Mellanby Centre for Bone ResearchThe University of SheffieldSheffieldUK
| | | | - Jeremy Mark Wilkinson
- Department of Oncology and Metabolism, The Mellanby Centre for Bone ResearchThe University of SheffieldSheffieldUK
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322
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Eline Slagboom P, van den Berg N, Deelen J. Phenome and genome based studies into human ageing and longevity: An overview. Biochim Biophys Acta Mol Basis Dis 2017; 1864:2742-2751. [PMID: 28951210 DOI: 10.1016/j.bbadis.2017.09.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 09/11/2017] [Accepted: 09/15/2017] [Indexed: 12/13/2022]
Abstract
Human ageing is an extremely personal process leading across the life course of individuals to large population heterogeneity in the decline of functional capacity, health and lifespan. The extremes of this process are witnessed by the healthy vital 100-year-olds on one end and the 60-year-olds suffering from multiple morbid conditions on the other end of the spectrum. Molecular studies into the basis of this heterogeneity have focused on a range of endpoints and methodological approaches. The phenotype definitions most prominently investigated in these studies are either lifespan-related or biomarker based indices of the biological ageing rate of individuals and their tissues. Unlike for many complex, age-related diseases, consensus on the ultimate set of multi-biomarker ageing or lifespan-related phenotypes for genetic and genomic studies has not been reached yet. Comparable to animal models, hallmarks of age-related disease risk, healthy ageing and longevity include immune and metabolic pathways. Potentially novel genomic regions and pathways have been identified among many (epi)genomic studies into chronological age and studies into human lifespan regulation, with APOE and FOXO3A representing yet the most robust loci. Functional analysis of a handful of genes in cell-based and animal models is ongoing. The way forward in human ageing and longevity studies seems through improvements in the interpretation of the biology of the genome, in application of computational and systems biology, integration with animal models and by harmonization of repeated phenotypic and omics measures in longitudinal and intervention studies. This article is part of a Special Issue entitled: Model Systems of Aging - edited by "Houtkooper Riekelt".
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Affiliation(s)
- P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
| | - Niels van den Berg
- Department of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands.
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, Albinusdreef 2, 2333, ZA, Leiden, The Netherlands; Max Planck Institute for Biology of Ageing; Joseph-Stelzmann-Str. 9b, D-50931 Köln (Cologne), Germany.
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323
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Bacalini MG, Deelen J, Pirazzini C, De Cecco M, Giuliani C, Lanzarini C, Ravaioli F, Marasco E, van Heemst D, Suchiman HED, Slieker R, Giampieri E, Recchioni R, Marcheselli F, Salvioli S, Vitale G, Olivieri F, Spijkerman AMW, Dollé MET, Sedivy JM, Castellani G, Franceschi C, Slagboom PE, Garagnani P. Systemic Age-Associated DNA Hypermethylation of ELOVL2 Gene: In Vivo and In Vitro Evidences of a Cell Replication Process. J Gerontol A Biol Sci Med Sci 2017; 72:1015-1023. [PMID: 27672102 DOI: 10.1093/gerona/glw185] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 08/26/2016] [Indexed: 12/17/2022] Open
Abstract
Epigenetic remodeling is one of the major features of the aging process. We recently demonstrated that DNA methylation of ELOVL2 and FHL2 CpG islands is highly correlated with age in whole blood. Here we investigated several aspects of age-associated hypermethylation of ELOVL2 and FHL2. We showed that ELOVL2 methylation is significantly different in primary dermal fibroblast cultures from donors of different ages. Using epigenomic data from public resources, we demonstrated that most of the tissues show ELOVL2 and FHL2 hypermethylation with age. Interestingly, ELOVL2 hypermethylation was not found in tissues with very low replication rate. We demonstrated that ELOVL2 hypermethylation is associated with in vitro cell replication rather than with senescence. We confirmed intra-individual hypermethylation of ELOVL2 and FHL2 in longitudinally assessed participants from the Doetinchem Cohort Study. Finally we showed that, although the methylation of the two loci is not associated with longevity/mortality in the Leiden Longevity Study, ELOVL2 methylation is associated with cytomegalovirus status in nonagenarians, which could be informative of a higher number of replication events in a fraction of whole-blood cells. Collectively, these results indicate that ELOVL2 methylation is a marker of cell divisions occurring during human aging.
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Affiliation(s)
- Maria Giulia Bacalini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy.,Personal Genomics S.r.l., Verona, Italy
| | - Joris Deelen
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands.,Max Planck Institute for Biology of Ageing, Köln, Germany
| | - Chiara Pirazzini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | - Marco De Cecco
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, Rhode Island
| | | | - Catia Lanzarini
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | | | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine
| | - Diana van Heemst
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - H Eka D Suchiman
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - Roderick Slieker
- Department of Molecular Epidemiology, Leiden University Medical Center, The Netherlands
| | - Enrico Giampieri
- Department of Physics and Astronomy, University of Bologna, Italy
| | - Rina Recchioni
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Fiorella Marcheselli
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy
| | - Stefano Salvioli
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
| | - Giovanni Vitale
- Centro di Ricerche e Tecnologie Biomediche, Istituto Auxologico Italiano IRCCS, Cusano Milanino, Italy.,Department of Clinical Sciences and Community Health, University of Milan, Italy
| | - Fabiola Olivieri
- Center of Clinical Pathology and Innovative Therapy, INRCA-IRCCS National Institute, Ancona, Italy.,Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy
| | | | - Martijn E T Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - John M Sedivy
- Department of Molecular Biology, Cell Biology and Biochemistry, Center for Genomics and Proteomics, Brown University, Providence, Rhode Island
| | | | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine.,Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Ancona, Italy.,IRCCS Institute of Neurological Sciences, Bologna, Italy
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine.,Interdepartmental Center "L. Galvani," University of Bologna, Bologna, Italy
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324
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Davis EG, Humphreys KL, McEwen LM, Sacchet MD, Camacho MC, MacIsaac JL, Lin DTS, Kobor MS, Gotlib IH. Accelerated DNA methylation age in adolescent girls: associations with elevated diurnal cortisol and reduced hippocampal volume. Transl Psychiatry 2017; 7:e1223. [PMID: 28850111 PMCID: PMC5611751 DOI: 10.1038/tp.2017.188] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 06/06/2017] [Accepted: 07/04/2017] [Indexed: 12/21/2022] Open
Abstract
Numerous studies have linked exposure to stress to adverse health outcomes through the effects of cortisol, a product of the stress response system, on cellular aging processes. Accelerated DNA methylation age is a promising epigenetic marker associated with stress and disease risk that may constitute a link from stress response to changes in neural structures. Specifically, elevated glucocorticoid signaling likely contributes to accelerating DNA methylation age, which may signify a maladaptive stress-related cascade that leads to hippocampal atrophy. We examined the relations among diurnal cortisol levels, DNA methylation age and hippocampal volume in a longitudinal study of 46 adolescent girls. We computed area under the curve from two daily cortisol collection periods, and calculated DNA methylation age using previously established methods based on a set of CpG sites associated with chronological age. We computed a residual score by partialling out chronological age; higher discrepancies reflect relatively accelerated DNA methylation age. We assessed hippocampal volume via T1-weighted images and automated volumetric segmentation. We found that greater diurnal cortisol production was associated with accelerated DNA methylation age, which in turn was associated with reduced left hippocampal volume. Finally, accelerated DNA methylation age significantly mediated the association between diurnal cortisol and left hippocampal volume. Thus, accelerated DNA methylation age may be an epigenetic marker linking hypothalamic-pituitary-adrenal axis dysregulation with neural structure. If these findings are replicated, the current study provides a method for advancing our understanding of mechanisms by which glucocorticoid signaling is associated with cellular aging and brain development.
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Affiliation(s)
- E G Davis
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - K L Humphreys
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - L M McEwen
- Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - M D Sacchet
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - M C Camacho
- Department of Psychology, Stanford University, Stanford, CA, USA
| | - J L MacIsaac
- Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - D T S Lin
- Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - M S Kobor
- Department of Medical Genetics, BC Children’s Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - I H Gotlib
- Department of Psychology, Stanford University, Stanford, CA, USA
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325
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Forster VJ, McDonnell A, Theobald R, McKay JA. Effect of methotrexate/vitamin B 12 on DNA methylation as a potential factor in leukemia treatment-related neurotoxicity. Epigenomics 2017; 9:1205-1218. [PMID: 28809129 PMCID: PMC5638018 DOI: 10.2217/epi-2016-0165] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Methotrexate (MTX) is administered to treat childhood acute lymphoblastic leukemia (ALL). It acts by inhibiting dihydrofolate reductase which reduces methyltetrahydrofolate, a key component in one carbon metabolism, thus reducing cell proliferation. Further perturbations to one carbon metabolism, such as reduced vitamin B12 levels via the use of nitrous oxide for sedation during childhood ALL treatment, may increase neurotoxicity risk. With B12 as an enzymatic cofactor, methyltetrahydrofolate is essential to produce methionine, which is critical for DNA methylation. We investigated global and gene specific DNA methylation in neuronal cell lines in response to MTX treatment and vitamin B12 concentration individually, and in combination. Results: MTX treatment alone significantly increased LINE-1 methylation in SH-SY5Y (p = 0.040) and DAOY (p < 0.001), and increased FKBP5 methylation in MO3.13 cells (p = 0.009). Conclusion: We conclude that altered DNA methylation of brain/central nervous system cells could be one mechanism involved in MTX treatment-related neurotoxicities and neurocognitive late effects in ALL survivors.
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Affiliation(s)
- Victoria J Forster
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Alex McDonnell
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Rachel Theobald
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Jill A McKay
- Institute of Health & Society, Human Nutrition Research Centre, Newcastle University, Newcastle upon Tyne, UK
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326
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DNA methylation in ELOVL2 and C1orf132 correctly predicted chronological age of individuals from three disease groups. Int J Legal Med 2017; 132:1-11. [PMID: 28725932 PMCID: PMC5748441 DOI: 10.1007/s00414-017-1636-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 07/04/2017] [Indexed: 12/21/2022]
Abstract
Improving accuracy of the available predictive DNA methods is important for their wider use in routine forensic work. Information on age in the process of identification of an unknown individual may provide important hints that can speed up the process of investigation. DNA methylation markers have been demonstrated to provide accurate age estimation in forensics, but there is growing evidence that DNA methylation can be modified by various factors including diseases. We analyzed DNA methylation profile in five markers from five different genes (ELOVL2, C1orf132, KLF14, FHL2, and TRIM59) used for forensic age prediction in three groups of individuals with diagnosed medical conditions. The obtained results showed that the selected age-related CpG sites have unchanged age prediction capacity in the group of late onset Alzheimer’s disease patients. Aberrant hypermethylation and decreased prediction accuracy were found for TRIM59 and KLF14 markers in the group of early onset Alzheimer’s disease suggesting accelerated aging of patients. In the Graves’ disease patients, altered DNA methylation profile and modified age prediction accuracy were noted for TRIM59 and FHL2 with aberrant hypermethylation observed for the former and aberrant hypomethylation for the latter. Our work emphasizes high utility of the ELOVL2 and C1orf132 markers for prediction of chronological age in forensics by showing unchanged prediction accuracy in individuals affected by three diseases. The study also demonstrates that artificial neural networks could be a convenient alternative for the forensic predictive DNA analyses.
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327
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Nwanaji-Enwerem JC, Colicino E, Dai L, Cayir A, Sanchez-Guerra M, Laue HE, Nguyen VT, Di Q, Just AC, Hou L, Vokonas P, Coull BA, Weisskopf MG, Baccarelli AA, Schwartz JD. Impacts of the Mitochondrial Genome on the Relationship of Long-Term Ambient Fine Particle Exposure with Blood DNA Methylation Age. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:8185-8195. [PMID: 28636816 PMCID: PMC5555236 DOI: 10.1021/acs.est.7b02409] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The mitochondrial genome has long been implicated in age-related disease, but no studies have examined its role in the relationship of long-term fine particle (PM2.5) exposure and DNA methylation age (DNAm-age)-a novel measure of biological age. In this analysis based on 940 observations between 2000 and 2011 from 552 Normative Aging Study participants, we determined the roles of mitochondrial DNA haplogroup variation and mitochondrial genome abundance in the relationship of PM2.5 with DNAm-age. We used the GEOS-chem transport model to estimate address-specific, one-year PM2.5 levels for each participant. DNAm-age and mitochondrial DNA markers were measured from participant blood samples. Nine haplogroups (H, I, J, K, T, U, V, W, and X) were present in the population. In fully adjusted linear mixed-effects models, the association of PM2.5 with DNAm-age (in years) was significantly diminished in carriers of haplogroup V (Pinteraction = 0.01; β = 0.18, 95%CI: -0.41, 0.78) compared to noncarriers (β = 1.25, 95%CI: 0.58, 1.93). Mediation analysis estimated that decreases in mitochondrial DNA copy number, a measure of mitochondrial genome abundance, mediated 12% of the association of PM2.5 with DNAm-age. Our data suggests that the mitochondrial genome plays a role in DNAm-age relationships particularly in the context of long-term PM2.5 exposure.
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Affiliation(s)
- Jamaji C. Nwanaji-Enwerem
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
| | - Elena Colicino
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA, 10032
| | - Lingzhen Dai
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
| | - Akin Cayir
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
- Vocational Health College, Canakkale Onsekiz Mart University, Canakkale, Turkey, 17100
| | - Marco Sanchez-Guerra
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
- Department of Developmental Neurobiology, National Institute of Perinatology, Mexico City, Mexico, 11000
| | - Hannah E. Laue
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA, 10032
| | - Vy T. Nguyen
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
| | - Qian Di
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
| | - Allan C. Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA, 10029
| | - Lifang Hou
- Center for Population Epigenetics, Department of Preventive Medicine, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA, 60611
| | - Pantel Vokonas
- VA Normative Aging Study, Veterans Affairs Boston Healthcare System and the Department of Medicine, Boston University School of Medicine, Boston, MA, USA, 02118
| | - Brent A. Coull
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
| | - Marc G. Weisskopf
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
| | - Andrea A. Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA, 10032
| | - Joel D. Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA, 02115
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328
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Maintained memory in aging is associated with young epigenetic age. Neurobiol Aging 2017; 55:167-171. [DOI: 10.1016/j.neurobiolaging.2017.02.009] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/07/2017] [Accepted: 02/10/2017] [Indexed: 11/23/2022]
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329
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Verschoor CP, McEwen LM, Kohli V, Wolfson C, Bowdish DM, Raina P, Kobor MS, Balion C. The relation between DNA methylation patterns and serum cytokine levels in community-dwelling adults: a preliminary study. BMC Genet 2017. [PMID: 28637423 PMCID: PMC5480116 DOI: 10.1186/s12863-017-0525-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background The levels of circulating cytokines fluctuate with age, acute illness, and chronic disease, and are predictive of mortality; this is also true for patterns of DNA (CpG) methylation. Given that immune cells are particularly sensitive to changes in the concentration of cytokines in their microenvironment, we hypothesized that serum levels of TNF, IL-6, IL-8 and IL-10 would correlate with genome-wide alterations in the DNA methylation levels of blood leukocytes. To test this, we evaluated community-dwelling adults (n = 14; 48–78 years old) recruited to a pilot study for the Canadian Longitudinal Study on Aging (CLSA), examining DNA methylation patterns in peripheral blood mononuclear cells using the Illumina HumanMethylation 450 K BeadChip. Results We show that, apart from age, serum IL-10 levels exhibited the most substantial association to DNA methylation patterns, followed by TNF, IL-6 and IL-8. Furthermore, while the levels of these cytokines were higher in elderly adults, no associations with epigenetic accelerated aging, derived using the epigenetic clock, were observed. Conclusions As a preliminary study with a small sample size, the conclusions drawn from this work must be viewed with caution; however, our observations are encouraging and certainly warrant more suitably powered studies of this relationship. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0525-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chris P Verschoor
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main St. W, MIP309A, Hamilton, ON, Canada. .,McMaster Institute for Research on Aging, McMaster University, Hamilton, ON, Canada. .,Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada. .,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada.
| | - Lisa M McEwen
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
| | - Vikas Kohli
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main St. W, MIP309A, Hamilton, ON, Canada
| | - Christina Wolfson
- Canadian Longitudinal Study on Aging, Hamilton, ON, Canada.,Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - Dawn Me Bowdish
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main St. W, MIP309A, Hamilton, ON, Canada.,McMaster Institute for Research on Aging, McMaster University, Hamilton, ON, Canada.,Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
| | - Parminder Raina
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, ON, Canada.,McMaster Institute for Research on Aging, McMaster University, Hamilton, ON, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, Vancouver, BC, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
| | - Cynthia Balion
- Department of Pathology and Molecular Medicine, McMaster University, 1280 Main St. W, MIP309A, Hamilton, ON, Canada.,Canadian Longitudinal Study on Aging, Hamilton, ON, Canada
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330
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Affiliation(s)
- J. Ramón Tejedor
- Institute of Oncology of Asturias (IUOPA), HUCA; Universidad de Oviedo; Oviedo Spain
- Fundación para la Investigación Biosanitaria de Asturias (FINBA); Instituto de Investigación Sanitaria del Principado de Asturias (IISPA); Oviedo Asturias Spain
| | - Mario F. Fraga
- Nanomaterials and Nanotechnology Research Center (CINN-CSIC); Universidad de Oviedo; Principado de Asturias Spain
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331
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Kozlenkov A, Jaffe AE, Timashpolsky A, Apontes P, Rudchenko S, Barbu M, Byne W, Hurd YL, Horvath S, Dracheva S. DNA Methylation Profiling of Human Prefrontal Cortex Neurons in Heroin Users Shows Significant Difference between Genomic Contexts of Hyper- and Hypomethylation and a Younger Epigenetic Age. Genes (Basel) 2017; 8:genes8060152. [PMID: 28556790 PMCID: PMC5485516 DOI: 10.3390/genes8060152] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Revised: 04/21/2017] [Accepted: 05/25/2017] [Indexed: 12/30/2022] Open
Abstract
We employed Illumina 450 K Infinium microarrays to profile DNA methylation (DNAm) in neuronal nuclei separated by fluorescence-activated sorting from the postmortem orbitofrontal cortex (OFC) of heroin users who died from heroin overdose (N = 37), suicide completers (N = 22) with no evidence of heroin use and from control subjects who did not abuse illicit drugs and died of non-suicide causes (N = 28). We identified 1298 differentially methylated CpG sites (DMSs) between heroin users and controls, and 454 DMSs between suicide completers and controls (p < 0.001). DMSs and corresponding genes (DMGs) in heroin users showed significant differences in the preferential context of hyper and hypo DM. HyperDMSs were enriched in gene bodies and exons but depleted in promoters, whereas hypoDMSs were enriched in promoters and enhancers. In addition, hyperDMGs showed preference for genes expressed specifically by glutamatergic as opposed to GABAergic neurons and enrichment for axonogenesis- and synaptic-related gene ontology categories, whereas hypoDMGs were enriched for transcription factor activity- and gene expression regulation-related terms. Finally, we found that the DNAm-based “epigenetic age” of neurons from heroin users was younger than that in controls. Suicide-related results were more difficult to interpret. Collectively, these findings suggest that the observed DNAm differences could represent functionally significant marks of heroin-associated plasticity in the OFC.
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Affiliation(s)
- Alexey Kozlenkov
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Andrew E Jaffe
- Lieber Institute for Brain Development, Johns Hopkins Medical Campus, Baltimore, MD 21205, USA.
- Department of Biostatistics and Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
- Center for Computational Biology, Johns Hopkins University, Baltimore, MD, 21205, USA.
| | | | - Pasha Apontes
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
| | | | - Mihaela Barbu
- Hospital for Special Surgery, New York, NY 10021, USA.
| | - William Byne
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Yasmin L Hurd
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, 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, School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA.
| | - Stella Dracheva
- James J. Peters VA Medical Center, Bronx, NY 10468, USA.
- The Friedman Brain Institute and Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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332
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Genetic architecture of epigenetic and neuronal ageing rates in human brain regions. Nat Commun 2017; 8:15353. [PMID: 28516910 PMCID: PMC5454371 DOI: 10.1038/ncomms15353] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 03/23/2017] [Indexed: 12/21/2022] Open
Abstract
Identifying genes regulating the pace of epigenetic ageing represents a new frontier in genome-wide association studies (GWASs). Here using 1,796 brain samples from 1,163 individuals, we carry out a GWAS of two DNA methylation-based biomarkers of brain age: the epigenetic ageing rate and estimated proportion of neurons. Locus 17q11.2 is significantly associated (P=4.5 × 10−9) with the ageing rate across five brain regions and harbours a cis-expression quantitative trait locus for EFCAB5 (P=3.4 × 10−20). Locus 1p36.12 is significantly associated (P=2.2 × 10−8) with epigenetic ageing of the prefrontal cortex, independent of the proportion of neurons. Our GWAS of the proportion of neurons identified two genome-wide significant loci (10q26 and 12p13.31) and resulted in a gene set that overlaps significantly with sets found by GWAS of age-related macular degeneration (P=1.4 × 10−12), ulcerative colitis (P<1.0 × 10−20), type 2 diabetes (P=2.8 × 10−13), hip/waist circumference in men (P=1.1 × 10−9), schizophrenia (P=1.6 × 10−9), cognitive decline (P=5.3 × 10−4) and Parkinson's disease (P=8.6 × 10−3). Studies on the ‘epigenetic clock', a recently identified ageing biomarker, suggest that pathology might be linked to tissue-specific accelerated ageing. Here, the authors investigate ageing in the human brain and identify genetic loci associated with accelerated ageing in different brain regions.
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333
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Girchenko P, Lahti J, Czamara D, Knight AK, Jones MJ, Suarez A, Hämäläinen E, Kajantie E, Laivuori H, Villa PM, Reynolds RM, Kobor MS, Smith AK, Binder EB, Räikkönen K. Associations between maternal risk factors of adverse pregnancy and birth outcomes and the offspring epigenetic clock of gestational age at birth. Clin Epigenetics 2017; 9:49. [PMID: 28503212 PMCID: PMC5422977 DOI: 10.1186/s13148-017-0349-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Accepted: 04/28/2017] [Indexed: 12/15/2022] Open
Abstract
Background A recent study has shown that it is possible to accurately estimate gestational age (GA) at birth from the DNA methylation (DNAm) of fetal umbilical cord blood/newborn blood spots. This DNAm GA predictor may provide additional information relevant to developmental stage. In 814 mother-neonate pairs, we evaluated the associations between DNAm GA and a number of maternal and offspring characteristics. These characteristics reflect prenatal environmental adversity and are expected to influence newborn developmental stage. Results DNAm GA acceleration (GAA; i.e., older DNAm GA than chronological GA) of the offspring at birth was associated with maternal age of over 40 years at delivery, pre-eclampsia and fetal demise in a previous pregnancy, maternal pre-eclampsia and treatment with antenatal betamethasone in the index pregnancy, lower neonatal birth size, lower 1-min Apgar score, and female sex. DNAm GA deceleration (GAD; i.e., younger DNAm GA than chronological GA) of the offspring at birth was associated with insulin-treated gestational diabetes mellitus (GDM) in a previous pregnancy and Sjögren’s syndrome. These findings were more accentuated when the DNAm GA calculation was based on the raw difference between DNAm GA and GA than on the residual from the linear regression of DNAm GA on GA. Conclusions Our findings show that variations in the DNAm GA of the offspring at birth are associated with a number of maternal and offspring characteristics known to reflect exposure to prenatal environmental adversity. Future studies should be aimed at determining if this biological variation is predictive of developmental adversity. Electronic supplementary material The online version of this article (doi:10.1186/s13148-017-0349-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Polina Girchenko
- Institute of Behavioral Sciences, University of Helsinki, Helsinki, 00014 Finland
| | - Jari Lahti
- Institute of Behavioral Sciences, University of Helsinki, Helsinki, 00014 Finland.,Helsinki Collegium of Advanced Studies, University of Helsinki, Helsinki, 00014 Finland
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Department of Psychiatry and Behavioral Sciences, Max-Planck Institute of Psychiatry, Munich, 80804 Germany
| | - Anna K Knight
- Genetics and Molecular Biology Program, Emory University, Atlanta, 30322 GA USA
| | - Meaghan J Jones
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital and University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Anna Suarez
- Institute of Behavioral Sciences, University of Helsinki, Helsinki, 00014 Finland
| | - Esa Hämäläinen
- HUSLAB and Department of Clinical Chemistry, Helsinki University Hospital, Helsinki, 00029 Finland
| | - Eero Kajantie
- National Institute for Health and Welfare, Helsinki and Oulu, Helsinki, 00271 Finland.,Children's Hospital, Helsinki University Central Hospital and University of Helsinki, Helsinki, 00029 Finland
| | - Hannele Laivuori
- Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital Helsinki, Helsinki, 00029 Finland.,Medical and Clinical Genetics and Institute for Molecular Medicine Finland, University of Helsinki and Helsinki University Hospital, Helsinki, 00014 Finland
| | - Pia M Villa
- Obstetrics and Gynaecology, University of Helsinki and Helsinki University Hospital Helsinki, Helsinki, 00029 Finland
| | - Rebecca M Reynolds
- BHF Centre for Cardiovascular Science, Queen's Medical Research Institute, University of Edinburgh, Edinburgh, EH16 4TJ UK
| | - Michael S Kobor
- Centre for Molecular Medicine and Therapeutics, BC Children's Hospital and University of British Columbia, Vancouver, V6T 1Z4 Canada
| | - Alicia K Smith
- Genetics and Molecular Biology Program, Emory University, Atlanta, 30322 GA USA.,Department of Gynecology and Obstetrics, School of Medicine, Emory University, Atlanta, 30322 GA USA.,Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, Atlanta, GA USA
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Department of Psychiatry and Behavioral Sciences, Max-Planck Institute of Psychiatry, Munich, 80804 Germany.,Department of Psychiatry and Behavioral Sciences, School of Medicine, Emory University, Atlanta, 30322 GA USA
| | - Katri Räikkönen
- Institute of Behavioral Sciences, University of Helsinki, Helsinki, 00014 Finland
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334
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Armstrong NJ, Mather KA, Thalamuthu A, Wright MJ, Trollor JN, Ames D, Brodaty H, Schofield PR, Sachdev PS, Kwok JB. Aging, exceptional longevity and comparisons of the Hannum and Horvath epigenetic clocks. Epigenomics 2017; 9:689-700. [PMID: 28470125 DOI: 10.2217/epi-2016-0179] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
AIM To examine the relationships between two epigenetic clocks, aging and exceptional longevity. MATERIALS & METHODS Participants were from three adult cohorts with blood DNA methylation data (Illumina 450 K, n = 275, 34-103 years). Epigenetic age (DNAmage) and age acceleration measures were calculated using the Hannum and Horvath epigenetic clocks. RESULTS Across all cohorts, DNAmage was correlated with chronological age. In the long-lived cohort (Sydney Centenarian Study; 95+, n = 23), DNAmage was lower than chronological age for both clocks. Mean Sydney Centenarian Study Hannum age acceleration was negative, while the converse was observed for the Horvath model. CONCLUSION Long-lived individuals have a young epigenetic age compared with their chronological age.
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Affiliation(s)
- Nicola J Armstrong
- Centre for Healthy Brain Aging, School of Psychiatry, UNSW Australia, Sydney, Australia.,Department of Mathematics & Statistics, Murdoch University, Perth, Australia
| | - Karen A Mather
- Centre for Healthy Brain Aging, School of Psychiatry, UNSW Australia, Sydney, Australia
| | - Anbupalam Thalamuthu
- Centre for Healthy Brain Aging, School of Psychiatry, UNSW Australia, Sydney, Australia
| | - Margaret J Wright
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Centre for Advanced Imaging, University of Queensland, Brisbane, Australia
| | - Julian N Trollor
- Centre for Healthy Brain Aging, School of Psychiatry, UNSW Australia, Sydney, Australia.,Department of Developmental Disability Neuropsychiatry, UNSW Australia, Sydney, Australia
| | - David Ames
- Academic Unit for Psychiatry of Old Age, University of Melbourne, Melbourne, Australia.,National Aging Research Institute, Melbourne, Australia
| | - Henry Brodaty
- Centre for Healthy Brain Aging, School of Psychiatry, UNSW Australia, Sydney, Australia.,Dementia Collaborative Research Centre - Assessment & Better Care, UNSW Australia, Sydney, Australia
| | - Peter R Schofield
- Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, UNSW Australia, Sydney, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Aging, School of Psychiatry, UNSW Australia, Sydney, Australia.,Neuropsychiatric Institute, Prince of Wales Hospital, Randwick, Australia
| | - John B Kwok
- Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, UNSW Australia, Sydney, Australia.,Brain and Mind Centre - University of Sydney, Camperdown, Australia
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335
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Demanelis K, Virani S, Colacino JA, Basu N, Nishijo M, Ruangyuttikarn W, Swaddiwudhipong W, Nambunmee K, Rozek LS. Cadmium exposure and age-associated DNA methylation changes in non-smoking women from northern Thailand. ENVIRONMENTAL EPIGENETICS 2017; 3:dvx006. [PMID: 29492308 PMCID: PMC5804546 DOI: 10.1093/eep/dvx006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Revised: 05/08/2017] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
DNA methylation changes with age, and may serve as a biomarker of aging. Cadmium (Cd) modifies cellular processes that promote aging and disrupts methylation globally. Whether Cd modifies aging processes by influencing establishment of age-associated methylation marks is currently unknown. In this pilot study, we characterized methylation profiles in > 450 000 CpG sites in 40 non-smoking women (age 40-80) differentially exposed to environmental Cd from Thailand. Based on specific gravity adjusted urinary Cd, we classified them as high (HE) and low (LE) exposed and age-matched within 5 years. Urinary Cd was defined as below 2 µg/l in the LE group. We predicted epigenetic age (DNAm-age) using two published methods by Horvath and Hannum and examined the difference between epigenetic age and chronologic age (Δage). We assessed differences by Cd exposure using linear mixed models adjusted for estimated white blood cell proportions, BMI, and urinary creatinine. We identified 213 age-associated CpG sites in our population (P < 10-4). Counterintuitively, the mean Δage was smaller in HE vs. LE (Hannum: 3.6 vs. 7.6 years, P = 0.0093; Horvath: 2.4 vs. 4.5 years, P = 0.1308). The Cd exposed group was associated with changes in methylation (P < 0.05) at 12, 8, and 20 age-associated sites identified in our population, Hannum, and Horvath. From the results of this pilot study, elevated Cd exposure is associated with methylation changes at age-associated sites and smaller differences between DNAm-age and chronologic age, in contrast to expected age-accelerating effects. Cd may modify epigenetic aging, and biomarkers of aging warrant further investigation when examining Cd and its relationship with chronic disease and mortality.
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Affiliation(s)
- Kathryn Demanelis
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48104, USA
| | - Shama Virani
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48104, USA
| | - Justin A. Colacino
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48104, USA
| | - Niladri Basu
- Faculty of Agricultural and Environmental Sciences, McGill University, Montreal, QC, H9X3V9, Canada
| | - Muneko Nishijo
- Department of Public Health, Kanazawa Medical University Hospital, Uchinada, 920-0293, Ishikawa, Japan
| | - Werawan Ruangyuttikarn
- Department of Forensic Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Witaya Swaddiwudhipong
- Department of Community and Social Science, Mae Sot General Hospital, Mae Sot District, Tak Province 63110, Thailand
| | - Kowit Nambunmee
- School of Health Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Laura S. Rozek
- Department of Environmental Health Sciences, University of Michigan, Ann Arbor, MI 48104, USA
- Correspondence address. Department of Environmental Health Sciences, Office of Global Public Health, University of Michigan School of Public Health, 1415 Washington Heights, Ann Arbor, MI 48109-2200, USA. Tel: 734-615-9816; E-mail:
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336
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Nwanaji-Enwerem JC, Dai L, Colicino E, Oulhote Y, Di Q, Kloog I, Just AC, Hou L, Vokonas P, Baccarelli AA, Weisskopf MG, Schwartz JD. Associations between long-term exposure to PM 2.5 component species and blood DNA methylation age in the elderly: The VA normative aging study. ENVIRONMENT INTERNATIONAL 2017; 102:57-65. [PMID: 28284819 PMCID: PMC5396466 DOI: 10.1016/j.envint.2016.12.024] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 12/30/2016] [Accepted: 12/31/2016] [Indexed: 05/17/2023]
Abstract
BACKGROUND Long-term PM2.5 exposure and aging have been implicated in multiple shared diseases; studying their relationship is a promising strategy to further understand the adverse impact of PM2.5 on human health. OBJECTIVE We assessed the relationship of major PM2.5 component species (ammonium, elemental carbon, organic carbon, nitrate, and sulfate) with Horvath and Hannum DNA methylation (DNAm) age, two DNA methylation-based predictors of chronological age. METHODS This analysis included 552 participants from the Normative Aging Study with multiple visits between 2000 and 2011 (n=940 visits). We estimated 1-year PM2.5 species levels at participants' addresses using the GEOS-chem transport model. Blood DNAm-age was calculated using CpG sites on the Illumina HumanMethylation450 BeadChip. We fit linear mixed-effects models, controlling for PM2.5 mass and lifestyle/environmental factors as fixed effects, with the adaptive LASSO penalty to identify PM2.5 species associated with DNAm-age. RESULTS Sulfate and ammonium were selected by the LASSO in the Horvath DNAm-age models. In a fully-adjusted multiple-species model, interquartile range increases in both 1-year sulfate (95%CI: 0.28, 0.74, P<0.0001) and ammonium (95%CI: 0.02, 0.70, P=0.04) levels were associated with at least a 0.36-year increase in Horvath DNAm-age. No PM2.5 species were selected by the LASSO in the Hannum DNAm-age models. Our findings persisted in sensitivity analyses including only visits with 1-year PM2.5 levels within US EPA national ambient air quality standards. CONCLUSION Our results demonstrate that sulfate and ammonium were most associated with Horvath DNAm-age and suggest that DNAm-age measures differ in their sensitivity to ambient particle exposures and potentially disease.
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Affiliation(s)
| | - Lingzhen Dai
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Elena Colicino
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Youssef Oulhote
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Qian Di
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Itai Kloog
- Department of Geography and Environmental Development, Ben-Gurion University of the Negev, Beer Sheva, Israel
| | - Allan C Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Lifang Hou
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Pantel Vokonas
- VA Normative Aging Study, Veterans Affairs Boston Healthcare System, The Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Columbia Mailman School of Public Health, New York, NY, USA
| | - Marc G Weisskopf
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Joel D Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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McEwen LM, Morin AM, Edgar RD, MacIsaac JL, Jones MJ, Dow WH, Rosero-Bixby L, Kobor MS, Rehkopf DH. Differential DNA methylation and lymphocyte proportions in a Costa Rican high longevity region. Epigenetics Chromatin 2017; 10:21. [PMID: 28465725 PMCID: PMC5408416 DOI: 10.1186/s13072-017-0128-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 04/13/2017] [Indexed: 01/01/2023] Open
Abstract
Background The Nicoya Peninsula in Costa Rica has one of the highest old-age life expectancies in the world, but the underlying biological mechanisms of this longevity are not well understood. As DNA methylation is hypothesized to be a component of biological aging, we focused on this malleable epigenetic mark to determine its association with current residence in Nicoya versus elsewhere in Costa Rica. Examining a population’s unique DNA methylation pattern allows us to differentiate hallmarks of longevity from individual stochastic variation. These differences may be characteristic of a combination of social, biological, and environmental contexts. Methods In a cross-sectional subsample of the Costa Rican Longevity and Healthy Aging Study, we compared whole blood DNA methylation profiles of residents from Nicoya (n = 48) and non-Nicoya (other Costa Rican regions, n = 47) using the Infinium HumanMethylation450 microarray. Results We observed a number of differences that may be markers of delayed aging, such as bioinformatically derived differential CD8+ T cell proportions. Additionally, both site- and region-specific analyses revealed DNA methylation patterns unique to Nicoyans. We also observed lower overall variability in DNA methylation in the Nicoyan population, another hallmark of younger biological age. Conclusions Nicoyans represent an interesting group of individuals who may possess unique immune cell proportions as well as distinct differences in their epigenome, at the level of DNA methylation. Electronic supplementary material The online version of this article (doi:10.1186/s13072-017-0128-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lisa M McEwen
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Alexander M Morin
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Rachel D Edgar
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - Meaghan J Jones
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - William H Dow
- School of Public Health, University of California, Berkeley, Berkeley, CA USA
| | - Luis Rosero-Bixby
- Centro Centroamericano de Población, Universidad de Costa Rica, San José, Costa Rica
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, BC Children's Hospital Research Institute, University of British Columbia, 950 West 28th Ave, Vancouver, Canada
| | - David H Rehkopf
- Division of General Medical Disciplines, Department of Medicine, School of Medicine, Stanford University, 1070 Arastradero Road, Suite 300, Palo Alto, CA 94304 USA
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338
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Stubbs TM, Bonder MJ, Stark AK, Krueger F, von Meyenn F, Stegle O, Reik W. Multi-tissue DNA methylation age predictor in mouse. Genome Biol 2017; 18:68. [PMID: 28399939 PMCID: PMC5389178 DOI: 10.1186/s13059-017-1203-5] [Citation(s) in RCA: 235] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Accepted: 03/29/2017] [Indexed: 12/18/2022] Open
Abstract
Background DNA methylation changes at a discrete set of sites in the human genome are predictive of chronological and biological age. However, it is not known whether these changes are causative or a consequence of an underlying ageing process. It has also not been shown whether this epigenetic clock is unique to humans or conserved in the more experimentally tractable mouse. Results We have generated a comprehensive set of genome-scale base-resolution methylation maps from multiple mouse tissues spanning a wide range of ages. Many CpG sites show significant tissue-independent correlations with age which allowed us to develop a multi-tissue predictor of age in the mouse. Our model, which estimates age based on DNA methylation at 329 unique CpG sites, has a median absolute error of 3.33 weeks and has similar properties to the recently described human epigenetic clock. Using publicly available datasets, we find that the mouse clock is accurate enough to measure effects on biological age, including in the context of interventions. While females and males show no significant differences in predicted DNA methylation age, ovariectomy results in significant age acceleration in females. Furthermore, we identify significant differences in age-acceleration dependent on the lipid content of the diet. Conclusions Here we identify and characterise an epigenetic predictor of age in mice, the mouse epigenetic clock. This clock will be instrumental for understanding the biology of ageing and will allow modulation of its ticking rate and resetting the clock in vivo to study the impact on biological age. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1203-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas M Stubbs
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK
| | - Marc Jan Bonder
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK
| | | | - Felix Krueger
- Bioinformatics Group, The Babraham Institute, Cambridge, CB22 3AT, UK
| | | | | | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, CB10 1SD, UK.
| | - Wolf Reik
- Epigenetics Programme, The Babraham Institute, Cambridge, CB22 3AT, UK. .,Centre for Trophoblast Research, University of Cambridge, Cambridge, CB2 3EG, UK. .,Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
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339
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Epigenetic Age Acceleration Assessed with Human White-Matter Images. J Neurosci 2017; 37:4735-4743. [PMID: 28385874 DOI: 10.1523/jneurosci.0177-17.2017] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/15/2017] [Accepted: 03/28/2017] [Indexed: 12/31/2022] Open
Abstract
The accurate estimation of age using methylation data has proved a useful and heritable biomarker, with acceleration in epigenetic age predicting a number of age-related phenotypes. Measures of white matter integrity in the brain are also heritable and highly sensitive to both normal and pathological aging processes across adulthood. We consider the phenotypic and genetic interrelationships between epigenetic age acceleration and white matter integrity in humans. Our goal was to investigate processes that underlie interindividual variability in age-related changes in the brain. Using blood taken from a Mexican-American extended pedigree sample (n = 628; age = 23.28-93.11 years), epigenetic age was estimated using the method developed by Horvath (2013). For n = 376 individuals, diffusion tensor imaging scans were also available. The interrelationship between epigenetic age acceleration and global white matter integrity was investigated with variance decomposition methods. To test for neuroanatomical specificity, 16 specific tracts were additionally considered. We observed negative phenotypic correlations between epigenetic age acceleration and global white matter tract integrity (ρpheno = -0.119, p = 0.028), with evidence of shared genetic (ρgene = -0.463, p = 0.013) but not environmental influences. Negative phenotypic and genetic correlations with age acceleration were also seen for a number of specific white matter tracts, along with additional negative phenotypic correlations between granulocyte abundance and white matter integrity. These findings (i.e., increased acceleration in epigenetic age in peripheral blood correlates with reduced white matter integrity in the brain and shares common genetic influences) provide a window into the neurobiology of aging processes within the brain and a potential biomarker of normal and pathological brain aging.SIGNIFICANCE STATEMENT Epigenetic measures can be used to predict age with a high degree of accuracy and so capture acceleration in biological age, relative to chronological age. The white matter tracts within the brain are also highly sensitive to aging processes. We show that increased biological aging (measured using epigenetic data from blood samples) is correlated with reduced integrity of white matter tracts within the human brain (measured using diffusion tensor imaging) with data from a large sample of Mexican-American families. Given the family design of the sample, we are also able to demonstrate that epigenetic aging and white matter tract integrity also share common genetic influences. Therefore, epigenetic age may be a potential, and accessible, biomarker of brain aging.
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Durso DF, Bacalini MG, Sala C, Pirazzini C, Marasco E, Bonafé M, do Valle ÍF, Gentilini D, Castellani G, Faria AMC, Franceschi C, Garagnani P, Nardini C. Acceleration of leukocytes' epigenetic age as an early tumor and sex-specific marker of breast and colorectal cancer. Oncotarget 2017; 8:23237-23245. [PMID: 28423572 PMCID: PMC5410300 DOI: 10.18632/oncotarget.15573] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 02/12/2017] [Indexed: 01/12/2023] Open
Abstract
Changes in blood epigenetic age have been associated with several pathological conditions and have recently been described to anticipate cancer development. In this work, we analyze a publicly available leukocytes methylation dataset to evaluate the relation between DNA methylation age and the prospective development of specific types of cancer. We calculated DNA methylation age acceleration using five state-of-the-art estimators (three multi-site: Horvath, Hannum, Weidner; and two CpG specific: ELOV2 and FHL2) in a cohort including 845 subjects from the EPIC-Italy project and we compared 424 samples that remained cancer-free over the approximately ten years of follow-up with 235 and 166 subjects who developed breast and colorectal cancer, respectively. We show that the epigenetic age estimated from blood DNA methylation data is statistically significantly associated to future breast and male colorectal cancer development. These results are corroborated by survival analysis that shows significant association between age acceleration and cancer incidence suggesting that the chance of developing age-related diseases may be predicted by circulating epigenetic markers, with a dependence upon tumor type, sex and age estimator. These are encouraging results towards the non-invasive and perspective usage of epigenetic biomarkers.
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Affiliation(s)
- Danielle Fernandes Durso
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- National Counsel of Technological and Scientific Development (CNPq), Ministry of Science Technology and Innovation (MCTI), Brasilia, Brazil
| | | | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | - Massimiliano Bonafé
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
| | | | - Davide Gentilini
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | - Gastone Castellani
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Ana Maria Caetano Faria
- Biochemistry and Immunology Department, Biological Sciences Institute, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | | | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, Alma Mater Studiorum-University of Bologna, Bologna, Italy
- Applied Biomedical Research Center, S. Orsola-Malpighi Polyclinic, Bologna, Italy
- Interdepartmental Center “L. Galvani”, University of Bologna, Bologna, Italy
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, Stockholm, Sweden
| | - Christine Nardini
- Personal Genomics S.r.l., Verona, Italy
- CNR IAC “Mauro Picone”, Rome, Italy
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341
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Ambatipudi S, Horvath S, Perrier F, Cuenin C, Hernandez-Vargas H, Le Calvez-Kelm F, Durand G, Byrnes G, Ferrari P, Bouaoun L, Sklias A, Chajes V, Overvad K, Severi G, Baglietto L, Clavel-Chapelon F, Kaaks R, Barrdahl M, Boeing H, Trichopoulou A, Lagiou P, Naska A, Masala G, Agnoli C, Polidoro S, Tumino R, Panico S, Dollé M, Peeters PHM, Onland-Moret NC, Sandanger TM, Nøst TH, Weiderpass E, Quirós JR, Agudo A, Rodriguez-Barranco M, Huerta Castaño JM, Barricarte A, Fernández AM, Travis RC, Vineis P, Muller DC, Riboli E, Gunter M, Romieu I, Herceg Z. DNA methylome analysis identifies accelerated epigenetic ageing associated with postmenopausal breast cancer susceptibility. Eur J Cancer 2017; 75:299-307. [PMID: 28259012 PMCID: PMC5512160 DOI: 10.1016/j.ejca.2017.01.014] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 12/16/2016] [Accepted: 01/20/2017] [Indexed: 01/12/2023]
Abstract
AIM OF THE STUDY A vast majority of human malignancies are associated with ageing, and age is a strong predictor of cancer risk. Recently, DNA methylation-based marker of ageing, known as 'epigenetic clock', has been linked with cancer risk factors. This study aimed to evaluate whether the epigenetic clock is associated with breast cancer risk susceptibility and to identify potential epigenetics-based biomarkers for risk stratification. METHODS Here, we profiled DNA methylation changes in a nested case-control study embedded in the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort (n = 960) using the Illumina HumanMethylation 450K BeadChip arrays and used the Horvath age estimation method to calculate epigenetic age for these samples. Intrinsic epigenetic age acceleration (IEAA) was estimated as the residuals by regressing epigenetic age on chronological age. RESULTS We observed an association between IEAA and breast cancer risk (OR, 1.04; 95% CI, 1.007-1.076, P = 0.016). One unit increase in IEAA was associated with a 4% increased odds of developing breast cancer (OR, 1.04; 95% CI, 1.007-1.076). Stratified analysis based on menopausal status revealed that IEAA was associated with development of postmenopausal breast cancers (OR, 1.07; 95% CI, 1.020-1.11, P = 0.003). In addition, methylome-wide analyses revealed that a higher mean DNA methylation at cytosine-phosphate-guanine (CpG) islands was associated with increased risk of breast cancer development (OR per 1 SD = 1.20; 95 %CI: 1.03-1.40, P = 0.02) whereas mean methylation levels at non-island CpGs were indistinguishable between cancer cases and controls. CONCLUSION Epigenetic age acceleration and CpG island methylation have a weak, but statistically significant, association with breast cancer susceptibility.
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Affiliation(s)
| | - Steve Horvath
- Human Genetics and Biostatistics, University of California Los Angeles, Los Angeles, CA 90095-7088, USA
| | - Flavie Perrier
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC), Lyon, France
| | | | | | - Geoffroy Durand
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Graham Byrnes
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Pietro Ferrari
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Liacine Bouaoun
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Athena Sklias
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Véronique Chajes
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Kim Overvad
- Section for Epidemiology, Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Gianluca Severi
- Inserm, Centre de Recherche en Epidémiologie et Santé des Populations (CESP, U1018), Université Paris-Saclay, Université Paris-Sud, UVSQ, Institut Gustave Roussy, Villejuif, France; Human Genetics Foundation (HuGeF), Torino, Italy; Cancer Epidemiology Centre, Cancer Council Victoria and Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourn, Australia
| | - Laura Baglietto
- Inserm, Centre de Recherche en Epidémiologie et Santé des Populations (CESP, U1018), Université Paris-Saclay, Université Paris-Sud, UVSQ, Institut Gustave Roussy, Villejuif, France; Cancer Epidemiology Centre, Cancer Council Victoria and Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, University of Melbourn, Australia
| | - Françoise Clavel-Chapelon
- Inserm, Centre de Recherche en Epidémiologie et Santé des Populations (CESP, U1018), Université Paris-Saclay, Université Paris-Sud, UVSQ, Institut Gustave Roussy, Villejuif, France
| | - Rudolf Kaaks
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Myrto Barrdahl
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Heiner Boeing
- Department of Epidemiology, German Institute of Human Nutrition Potsdam-Rehbrücke, Nuthetal, Germany
| | - Antonia Trichopoulou
- Hellenic Health Foundation, Athens, Greece; WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, University of Athens Medical School, Athens, Greece
| | - Pagona Lagiou
- Hellenic Health Foundation, Athens, Greece; WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, University of Athens Medical School, Athens, Greece; Department of Epidemiology, Harvard School of Public Health, Boston, USA
| | - Androniki Naska
- Hellenic Health Foundation, Athens, Greece; WHO Collaborating Center for Nutrition and Health, Unit of Nutritional Epidemiology and Nutrition in Public Health, Department of Hygiene, Epidemiology and Medical Statistics, University of Athens Medical School, Athens, Greece
| | - Giovanna Masala
- Molecular and Nutritional Epidemiology Unit, Cancer Research and Prevention Institute - ISPO, Florence, Italy
| | - Claudia Agnoli
- Epidemiology and Prevention Unit, Fondazione IRCCS Istituto Nazionale Tumori, Milano, Italy
| | | | - Rosario Tumino
- Cancer Registry and Histopathology Unit, "Civic M.P. Arezzo" Hospital, ASP Ragusa, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | - Martijn Dollé
- Centre for Health Protection, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Petra H M Peeters
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands; MRC-PHE Centre for Environment and Health, Dept of Epidemiology and Biostatistics, School of Public Health, Imperial College, London, UK
| | - N Charlotte Onland-Moret
- Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Torkjel M Sandanger
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, Norway
| | - Therese H Nøst
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, Norway
| | - Elisabete Weiderpass
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, Norway; Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden; Genetic Epidemiology Group, Folkhälsan Research Center, Helsinki, Finland
| | | | - Antonio Agudo
- Unit of Nutrition and Cancer, Cancer Epidemiology Research Program, Catalan Institute of Oncology-IDIBELL, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Miguel Rodriguez-Barranco
- Escuela Andaluza de Salud Pública, Instituto de Investigación Biosanitaria ibsn Granada, Hospitales Universitarios de Granada/Universidad de Granada, Granada, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | - José María Huerta Castaño
- Department of Epidemiology, Murcia Regional Health Council, IMIB-Arrixaca, Murcia, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | - Aurelio Barricarte
- Navarra Public Health Institute, Pamplona, Spain; Navarra Institute for Health Research (IdiSNA) Pamplona, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Spain
| | - Ander Matheu Fernández
- Cellular Oncology Group, Biodonostia Health Research Institute, Paseo Dr. Beguiristain s/n, San Sebastian, Spain; IKERBASQUE, Basque Foundation, Spain
| | - Ruth C Travis
- Cancer Epidemiology Unit, Nuffield Department of Population Health University of Oxford, Oxford UK
| | - Paolo Vineis
- School of Public Health, Imperial College London, London, UK
| | - David C Muller
- School of Public Health, Imperial College London, London, UK
| | - Elio Riboli
- School of Public Health, Imperial College London, London, UK
| | - Marc Gunter
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Isabelle Romieu
- International Agency for Research on Cancer (IARC), Lyon, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), Lyon, France.
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Abstract
The search for reliable indicators of biological age, rather than chronological age, has been ongoing for over three decades, and until recently, largely without success. Advances in the fields of molecular biology have increased the variety of potential candidate biomarkers that may be considered as biological age predictors. In this review, we summarize current state-of-the-art findings considering six potential types of biological age predictors: epigenetic clocks, telomere length, transcriptomic predictors, proteomic predictors, metabolomics-based predictors, and composite biomarker predictors. Promising developments consider multiple combinations of these various types of predictors, which may shed light on the aging process and provide further understanding of what contributes to healthy aging. Thus far, the most promising, new biological age predictor is the epigenetic clock; however its true value as a biomarker of aging requires longitudinal confirmation. Telomere length is the most well studied biological age predictor, but many new predictors are emerging. The epigenetic clock is currently the best biological age predictor, as it correlates well with age and predicts mortality. The various biological age predictors tend to reflect different aspects of the aging process.
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343
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The epigenetic landscape of age-related diseases: the geroscience perspective. Biogerontology 2017; 18:549-559. [PMID: 28352958 PMCID: PMC5514215 DOI: 10.1007/s10522-017-9695-7] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/14/2017] [Indexed: 12/11/2022]
Abstract
In this review, we summarize current knowledge regarding the epigenetics of age-related diseases, focusing on those studies that have described DNA methylation landscape in cardio-vascular diseases, musculoskeletal function and frailty. We stress the importance of adopting the conceptual framework of “geroscience”, which starts from the observation that advanced age is the major risk factor for several of these pathologies and aims at identifying the mechanistic links between aging and age-related diseases. DNA methylation undergoes a profound remodeling during aging, which includes global hypomethylation of the genome, hypermethylation at specific loci and an increase in inter-individual variation and in stochastic changes of DNA methylation values. These epigenetic modifications can be an important contributor to the development of age-related diseases, but our understanding on the complex relationship between the epigenetic signatures of aging and age-related disease is still poor. The most relevant results in this field come from the use of the so called “epigenetics clocks” in cohorts of subjects affected by age-related diseases. We report these studies in final section of this review.
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Machin M, Amaral AFS, Wielscher M, Rezwan FI, Imboden M, Jarvelin MR, Adcock IM, Probst-Hensch N, Holloway JW, Jarvis DL. Systematic review of lung function and COPD with peripheral blood DNA methylation in population based studies. BMC Pulm Med 2017; 17:54. [PMID: 28320365 PMCID: PMC5360084 DOI: 10.1186/s12890-017-0397-3] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 03/16/2017] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Epigenetic variations in peripheral blood have potential as biomarkers for disease. This systematic review assesses the association of lung function and chronic obstructive pulmonary disease (COPD) with DNA methylation profiles in peripheral blood from population-based studies. METHODS Online databases Medline, Embase, and Web of Science were searched. Google Scholar was searched to identify grey literature. After removing duplicate articles, 1155 articles were independently screened by two investigators. Peer reviewed reports on population-based studies that examined peripheral blood DNA methylation in participants with measured lung function (FEV1, FEV1/FVC ratio) or known COPD status were selected for full-text review. Six articles were suitable for inclusion. Information regarding study characteristics, designs, methodologies and conclusions was extracted. A narrative synthesis was performed based on published results. RESULTS Three of the six articles assessed the association of COPD with DNA methylation, and two of these also included associations with lung function. Overall, five reports examined the association of lung function with DNA methylation profiles. Five of the six articles reported 'significant' results. However, no consistent CpG sites were identified across studies for COPD status or lung function values. CONCLUSIONS DNA methylation patterns in peripheral blood from individuals with reduced lung function or COPD may be different to those in people with normal lung function. However, this systematic review did not find any consistent associations of lung function or COPD with differentially methylated CpG sites. Large studies with a longitudinal design to address reverse causality may prove a more fruitful area of research. TRIAL REGISTRATION PROSPERO 2016: CRD42016037352 .
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Affiliation(s)
| | - André F S Amaral
- Population Health and Occupational Disease, NHLI, Imperial College London, London, UK.
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.
| | - Matthias Wielscher
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Faisal I Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Medea Imboden
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Marjo-Riitta Jarvelin
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Ian M Adcock
- Airways Disease Section, NHLI, Imperial College London, London, UK
| | - Nicole Probst-Hensch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - John W Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | - Deborah L Jarvis
- Population Health and Occupational Disease, NHLI, Imperial College London, London, UK
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
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Conserved effect of aging on DNA methylation and association with EZH2 polycomb protein in mice and humans. Mech Ageing Dev 2017; 162:27-37. [PMID: 28249716 DOI: 10.1016/j.mad.2017.02.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 01/11/2017] [Accepted: 02/16/2017] [Indexed: 11/22/2022]
Abstract
In humans, DNA methylation at specific CpG sites can be used to estimate the 'epigenetic clock', a biomarker of aging and health. The mechanisms that regulate the aging epigenome and level of conservation are not entirely clear. We performed affinity-based enrichment with methyl-CpG binding domain protein followed by high-throughput sequencing (MBD-seq) to assay DNA methylation in mouse samples. Consistent with previous reports, aging is associated with increase in methylation at CpG islands that likely overlap regulatory regions of genes that have been implicated in cancers (e.g., C1ql3, Srd5a2 and Ptk7). The differentially methylated regions in mice have high sequence conservation in humans and the pattern of methylation is also largely conserved between the two species. Based on human ENCODE data, these sites are targeted by polycomb proteins, including EZH2. Chromatin immunoprecipitation confirmed that these regions interact with EZH2 in mice as well, and there may be reduction in EZH2 occupancy with age at C1ql3. This adds to the growing evidence that EZH2 is part of the protein machinery that shapes the aging epigenome. The conservation in both sequence and methylation patterns of the age-dependent CpGs indicate that the epigenetic clock is a fundamental feature of aging in mammals.
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346
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Raina A, Zhao X, Grove ML, Bressler J, Gottesman RF, Guan W, Pankow JS, Boerwinkle E, Mosley TH, Fornage M. Cerebral white matter hyperintensities on MRI and acceleration of epigenetic aging: the atherosclerosis risk in communities study. Clin Epigenetics 2017; 9:21. [PMID: 28289478 PMCID: PMC5310061 DOI: 10.1186/s13148-016-0302-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/12/2016] [Indexed: 02/03/2023] Open
Abstract
Background Cerebral white matter hyperintensities (WMH) on magnetic resonance imaging (MRI) are part of the spectrum of brain vascular injury accompanying aging and are associated with a substantial risk of stroke and dementia. We investigated the association of cerebral WMH burden on MRI with a DNA methylation-based biomarker of aging, termed DNA methylation age acceleration, which represents the deviation of the DNA methylation-predicted age from the chronologic age. Results In this cross-sectional observational study of 713 African-American participants of the Atherosclerosis Risk in Communities study, aged 51–73 years, estimates of predicted age were obtained based on two algorithms (Hannum et al. and Horvath) from DNA methylation measured using the Illumina HM450 array on genomic DNA extracted from blood. Age acceleration, calculated as the residual values from the regression of each of the predicted age measures onto the chronologic age, was significantly associated with WMH burden after accounting for chronologic age and sex, body mass index, systolic blood pressure, hypertension, diabetes, current smoking, and blood cell composition, and results were similar for either Hannum et al.- or Horvath-derived estimates (P = 0.016 and 0.026). An age acceleration increase by 1 year was associated with an increase of WMH burden by ~1 grade. To shed light on possible biological mechanisms underlying this association, we conducted a genome-wide association study of age acceleration and identified four loci harboring genes implicated in hemostasis, cell proliferation, protein degradation, and histone methylation. However, none of these loci were associated with WMH burden. Conclusions In this population-based study of middle-aged to older African-American adults, we report an association between accelerated epigenetic aging and increased WMH burden, independent of known risk factors, including chronologic age. Additional studies are needed to clarify whether DNA methylation age reflects biological mechanisms implicated in the aging of the cerebral white matter. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0302-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Abhay Raina
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, 1825 Pressler Street, 77030 Houston, TX USA
| | - Xiaoping Zhao
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, 1825 Pressler Street, 77030 Houston, TX USA
| | - Megan L Grove
- Division of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Jan Bressler
- Division of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Rebecca F Gottesman
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Weihua Guan
- Division of Biostatistics, School of Public Health, University of Minnesota, Minneapolis, MN USA
| | - James S Pankow
- Division of Epidemiology & Community Health, School of Public Health, University of Minnesota, Minneapolis, MN USA
| | - Eric Boerwinkle
- Division of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX USA
| | - Thomas H Mosley
- Division of Geriatrics, School of Medicine, University of Mississippi Medical Center, Jackson, MS USA
| | - Myriam Fornage
- Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, 1825 Pressler Street, 77030 Houston, TX USA.,Division of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX USA
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347
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Nevalainen T, Kananen L, Marttila S, Jylhävä J, Mononen N, Kähönen M, Raitakari OT, Hervonen A, Jylhä M, Lehtimäki T, Hurme M. Obesity accelerates epigenetic aging in middle-aged but not in elderly individuals. Clin Epigenetics 2017; 9:20. [PMID: 28289477 PMCID: PMC5310016 DOI: 10.1186/s13148-016-0301-7] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 12/09/2016] [Indexed: 11/17/2022] Open
Abstract
Background Human aging is associated with profound changes in one of the major epigenetic mechanisms, DNA methylation. Some of these changes occur in a clock-like fashion, i.e., correlating with the calendar age of an individual, thus providing a new aging biomarker. Some reports have identified factors associated with the acceleration of the epigenetic age. However, it is also important to analyze the temporal changes in the epigenetic age, i.e., the duration of the observed acceleration, and the effects of the possible therapeutic and lifestyle modifications. Methods To address this issue, we determined the epigenetic age for a cohort of 183 healthy individuals using blood samples derived from two time points that were 25 years apart (between 15–24 and 40–49 years of age). Additionally, we also determined the epigenetic ages of 119 individuals in a cohort consisting of 90-year-old participants (nonagenarians). These were determined by using the Horvath algorithm based on the methylation level of 353 CpG sites. The data are indicated as the deviation of the epigenetic age from the calendar age (calendar age minus epigenetic age = delta age, ΔAGE). As obesity is often associated with accelerating aging and degenerative phenotypes, the correlation of the body mass index (BMI) with the ΔAGE was analyzed in the following three age groups: young adults, middle-aged, and nonagenarian. Results The data showed that BMI is associated with decreased ΔAGE, i.e., increased epigenetic age, in middle-aged individuals. This effect is also seen during the 25-year period from early adulthood to middle age, in which an increase in the BMI is significantly associated with a decrease in the ΔAGE. We also analyzed the association between BMI and epigenetic age in young and elderly individuals, but these associations were not significant. Conclusion Taken together, the main finding on this report suggests that association between increased BMI and accelerated epigenetic aging in the blood cells of middle-aged individuals can be observed, and this effect is also detectable if the BMI has increased in adulthood. The fact that the association between BMI and epigenetic age can only be observed in the middle-aged group does not exclude the possibility that this association could be present throughout the human lifespan; it might just be masked by confounding factors in young adults and nonagenarian individuals. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0301-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Tapio Nevalainen
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, Tampere, Finland
| | - Laura Kananen
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, Tampere, Finland
| | - Saara Marttila
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, Tampere, Finland
| | - Juulia Jylhävä
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, School of Medicine, University of Tampere, Tampere, Finland.,Fimlab laboratories, Tampere, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and University of Tampere, School of Medicine, Tampere, Finland
| | - Olli T Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine and the Department of Clinical Physiology and Nuclear Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Antti Hervonen
- Gerontology Research Center, Tampere, Finland.,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Marja Jylhä
- Gerontology Research Center, Tampere, Finland.,School of Health Sciences, University of Tampere, Tampere, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, School of Medicine, University of Tampere, Tampere, Finland.,Fimlab laboratories, Tampere, Finland
| | - Mikko Hurme
- Department of Microbiology and Immunology, School of Medicine, University of Tampere, Tampere, Finland.,Gerontology Research Center, Tampere, Finland.,Fimlab laboratories, Tampere, Finland
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348
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Quach A, Levine ME, Tanaka T, Lu AT, Chen BH, Ferrucci L, Ritz B, Bandinelli S, Neuhouser ML, Beasley JM, Snetselaar L, Wallace RB, Tsao PS, Absher D, Assimes TL, Stewart JD, Li Y, Hou L, Baccarelli AA, Whitsel EA, Horvath S. Epigenetic clock analysis of diet, exercise, education, and lifestyle factors. Aging (Albany NY) 2017; 9:419-446. [PMID: 28198702 PMCID: PMC5361673 DOI: 10.18632/aging.101168] [Citation(s) in RCA: 446] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Accepted: 01/25/2017] [Indexed: 12/17/2022]
Abstract
Behavioral and lifestyle factors have been shown to relate to a number of health-related outcomes, yet there is a need for studies that examine their relationship to molecular aging rates. Toward this end, we use recent epigenetic biomarkers of age that have previously been shown to predict all-cause mortality, chronic conditions, and age-related functional decline. We analyze cross-sectional data from 4,173 postmenopausal female participants from the Women's Health Initiative, as well as 402 male and female participants from the Italian cohort study, Invecchiare nel Chianti.Extrinsic epigenetic age acceleration (EEAA) exhibits significant associations with fish intake (p=0.02), moderate alcohol consumption (p=0.01), education (p=3x10-5), BMI (p=0.01), and blood carotenoid levels (p=1x10-5)-an indicator of fruit and vegetable consumption, whereas intrinsic epigenetic age acceleration (IEAA) is associated with poultry intake (p=0.03) and BMI (p=0.05). Both EEAA and IEAA were also found to relate to indicators of metabolic syndrome, which appear to mediate their associations with BMI. Metformin-the first-line medication for the treatment of type 2 diabetes-does not delay epigenetic aging in this observational study. Finally, longitudinal data suggests that an increase in BMI is associated with increase in both EEAA and IEAA.Overall, the epigenetic age analysis of blood confirms the conventional wisdom regarding the benefits of eating a high plant diet with lean meats, moderate alcohol consumption, physical activity, and education, as well as the health risks of obesity and metabolic syndrome.
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Affiliation(s)
| | | | | | - Ake T. Lu
- 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
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, USA. Baltimore, MD 21224, USA
| | - Beate Ritz
- Department of Neurology, UCLA School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Department of Epidemiology, UCLA Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | | | - Marian L. Neuhouser
- Cancer Prevention Program, Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | | | - Linda Snetselaar
- Department of Epidemiology, University of Iowa, 145 N. Riverside Drive, Iowa City, IA 52242, USA
| | - Robert B. Wallace
- Department of Epidemiology, University of Iowa, 145 N. Riverside Drive, Iowa City, IA 52242, USA
| | - Philip S. Tsao
- Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
- VA Palo Alto Health Care System, Palo Alto CA 94304, USA
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, 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, School of Medicine, University of North Carolina, Chapel Hill, NC 27599, USA
- Department of Biostatistics, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University Chicago, IL 60611, USA
- Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University 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
| | - 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
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- Dept. of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
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349
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Zhang Y, Hapala J, Brenner H, Wagner W. Individual CpG sites that are associated with age and life expectancy become hypomethylated upon aging. Clin Epigenetics 2017; 9:9. [PMID: 28168006 PMCID: PMC5288846 DOI: 10.1186/s13148-017-0315-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/19/2017] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND There is a growing interest in simple molecular biomarkers for biological aging. Age-associated DNA methylation (DNAm) changes at specific CG dinucleotides can be combined into epigenetic age predictors to estimate chronological age-and the deviation of chronological and predicted age (∆age) seems to be associated with all-cause mortality. In this study, we have further validated this association and analyzed whether or not individual age-associated CG-dinucleotides (CpGs) are related to life expectancy. FINDINGS In the German ESTHER cohort, we used 864 DNAm profiles of blood samples as the discovery set and 1000 DNAm profiles as the validation set to predict chronological age with three previously reported age predictors-based on 99, 71, or 353 age-associated CpGs. Several of these individual CpGs were significantly associated with life expectancy, and for some of these CpGs, this was even reproducible in the independent datasets. Notably, those CpGs that revealed significant association with life expectancy were overall rather hypomethylated upon aging. CONCLUSION Individual age-associated CpGs may provide biomarkers for all-cause mortality-but confounding factors need to be critically taken into consideration, and alternative methods, which facilitate more quantitative measurements at individual CpGs, might be advantageous. Our data suggest that particularly specific CpGs that become hypomethylated upon aging are indicative of biological aging.
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Affiliation(s)
- Yan Zhang
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581/TP4, 69120 Heidelberg, Germany
| | - Jan Hapala
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, University Hospital of the RWTH Aachen, Pauwelsstrasse 20, 52074 Aachen, Germany.,Institute for Biomedical Engineering-Cell Biology, University Hospital of the RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581/TP4, 69120 Heidelberg, Germany.,Network Aging Research (NAR), University of Heidelberg, Bergheimer Strasse 20, 69120 Heidelberg, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, University Hospital of the RWTH Aachen, Pauwelsstrasse 20, 52074 Aachen, Germany.,Institute for Biomedical Engineering-Cell Biology, University Hospital of the RWTH Aachen, Pauwelsstrasse 30, 52074 Aachen, Germany
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350
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Bowers EC, McCullough SD. Linking the Epigenome with Exposure Effects and Susceptibility: The Epigenetic Seed and Soil Model. Toxicol Sci 2017; 155:302-314. [PMID: 28049737 PMCID: PMC5291212 DOI: 10.1093/toxsci/kfw215] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The epigenome is a dynamic mediator of gene expression that shapes the way that cells, tissues, and organisms respond to their environment. Initial studies in the emerging field of "toxicoepigenetics" have described either the impact of an environmental exposure on the epigenome or the association of epigenetic signatures with the onset or progression of disease; however, the majority of these pioneering studies examined the relationship between discrete epigenetic modifications and the effects of a single environmental factor. Although these data provide critical blocks with which we construct our understanding of the role of the epigenome in susceptibility and disease, they are akin to individual letters in a complex alphabet that is used to compose the language of the epigenome. Advancing the use of epigenetic data to gain a more comprehensive understanding of the mechanisms underlying exposure effects, identify susceptible populations, and inform the next generation risk assessment depends on our ability to integrate these data in a way that accounts for their cumulative impact on gene regulation. Here we will review current examples demonstrating associations between the epigenetic impacts of intrinsic factors, such as such as age, genetics, and sex, and environmental exposures shape the epigenome and susceptibility to exposure effects and disease. We will also demonstrate how the "epigenetic seed and soil" model can be used as a conceptual framework to explain how epigenetic states are shaped by the cumulative impacts of intrinsic and extrinsic factors and how these in turn determine how an individual responds to subsequent exposure to environmental stressors.
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Affiliation(s)
- Emma C Bowers
- Curriculum in Toxicology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Shaun D McCullough
- Environmental Public Health Division, National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711
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