101
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Franke K, Bublak P, Hoyer D, Billiet T, Gaser C, Witte OW, Schwab M. In vivo biomarkers of structural and functional brain development and aging in humans. Neurosci Biobehav Rev 2021; 117:142-164. [PMID: 33308708 DOI: 10.1016/j.neubiorev.2017.11.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 12/25/2022]
Abstract
Brain aging is a major determinant of aging. Along with the aging population, prevalence of neurodegenerative diseases is increasing, therewith placing economic and social burden on individuals and society. Individual rates of brain aging are shaped by genetics, epigenetics, and prenatal environmental. Biomarkers of biological brain aging are needed to predict individual trajectories of aging and the risk for age-associated neurological impairments for developing early preventive and interventional measures. We review current advances of in vivo biomarkers predicting individual brain age. Telomere length and epigenetic clock, two important biomarkers that are closely related to the mechanistic aging process, have only poor deterministic and predictive accuracy regarding individual brain aging due to their high intra- and interindividual variability. Phenotype-related biomarkers of global cognitive function and brain structure provide a much closer correlation to age at the individual level. During fetal and perinatal life, autonomic activity is a unique functional marker of brain development. The cognitive and structural biomarkers also boast high diagnostic specificity for determining individual risks for neurodegenerative diseases.
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Affiliation(s)
- K Franke
- Department of Neurology, Jena University Hospital, Jena, Germany.
| | - P Bublak
- Department of Neurology, Jena University Hospital, Jena, Germany
| | - D Hoyer
- Department of Neurology, Jena University Hospital, Jena, Germany
| | | | - C Gaser
- Department of Neurology, Jena University Hospital, Jena, Germany; Department of Psychiatry, Jena University Hospital, Jena, Germany
| | - O W Witte
- Department of Neurology, Jena University Hospital, Jena, Germany
| | - M Schwab
- Department of Neurology, Jena University Hospital, Jena, Germany
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102
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Kerepesi C, Zhang B, Lee SG, Trapp A, Gladyshev VN. Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging. SCIENCE ADVANCES 2021; 7:eabg6082. [PMID: 34172448 PMCID: PMC8232908 DOI: 10.1126/sciadv.abg6082] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 05/12/2021] [Indexed: 05/05/2023]
Abstract
The notion that the germ line does not age goes back to the 19th-century ideas of August Weismann. However, being metabolically active, the germ line accumulates damage and other changes over time, i.e., it ages. For new life to begin in the same young state, the germ line must be rejuvenated in the offspring. Here, we developed a multi-tissue epigenetic clock and applied it, together with other aging clocks, to track changes in biological age during mouse and human prenatal development. This analysis revealed a significant decrease in biological age, i.e., rejuvenation, during early stages of embryogenesis, followed by an increase in later stages. We further found that pluripotent stem cells do not age even after extensive passaging and that the examined epigenetic age dynamics is conserved across species. Overall, this study uncovers a natural rejuvenation event during embryogenesis and suggests that the minimal biological age (ground zero) marks the beginning of organismal aging.
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Affiliation(s)
- Csaba Kerepesi
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Bohan Zhang
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Alexandre Trapp
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA.
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103
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Maden SK, Thompson RF, Hansen KD, Nellore A. Human methylome variation across Infinium 450K data on the Gene Expression Omnibus. NAR Genom Bioinform 2021; 3:lqab025. [PMID: 33937763 PMCID: PMC8061458 DOI: 10.1093/nargab/lqab025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/11/2021] [Accepted: 04/19/2021] [Indexed: 12/16/2022] Open
Abstract
While DNA methylation (DNAm) is the most-studied epigenetic mark, few recent studies probe the breadth of publicly available DNAm array samples. We collectively analyzed 35 360 Illumina Infinium HumanMethylation450K DNAm array samples published on the Gene Expression Omnibus. We learned a controlled vocabulary of sample labels by applying regular expressions to metadata and used existing models to predict various sample properties including epigenetic age. We found approximately two-thirds of samples were from blood, one-quarter were from brain and one-third were from cancer patients. About 19% of samples failed at least one of Illumina's 17 prescribed quality assessments; signal distributions across samples suggest modifying manufacturer-recommended thresholds for failure would make these assessments more informative. We further analyzed DNAm variances in seven tissues (adipose, nasal, blood, brain, buccal, sperm and liver) and characterized specific probes distinguishing them. Finally, we compiled DNAm array data and metadata, including our learned and predicted sample labels, into database files accessible via the recountmethylation R/Bioconductor companion package. Its vignettes walk the user through some analyses contained in this paper.
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Affiliation(s)
- Sean K Maden
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Reid F Thompson
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
| | - Kasper D Hansen
- Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Abhinav Nellore
- Computational Biology Program, Oregon Health & Science University, Portland, OR 97239, USA
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104
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Nabais MF, Laws SM, Lin T, Vallerga CL, Armstrong NJ, Blair IP, Kwok JB, Mather KA, Mellick GD, Sachdev PS, Wallace L, Henders AK, Zwamborn RAJ, Hop PJ, Lunnon K, Pishva E, Roubroeks JAY, Soininen H, Tsolaki M, Mecocci P, Lovestone S, Kłoszewska I, Vellas B, Furlong S, Garton FC, Henderson RD, Mathers S, McCombe PA, Needham M, Ngo ST, Nicholson G, Pamphlett R, Rowe DB, Steyn FJ, Williams KL, Anderson TJ, Bentley SR, Dalrymple-Alford J, Fowder J, Gratten J, Halliday G, Hickie IB, Kennedy M, Lewis SJG, Montgomery GW, Pearson J, Pitcher TL, Silburn P, Zhang F, Visscher PM, Yang J, Stevenson AJ, Hillary RF, Marioni RE, Harris SE, Deary IJ, Jones AR, Shatunov A, Iacoangeli A, van Rheenen W, van den Berg LH, Shaw PJ, Shaw CE, Morrison KE, Al-Chalabi A, Veldink JH, Hannon E, Mill J, Wray NR, McRae AF. Meta-analysis of genome-wide DNA methylation identifies shared associations across neurodegenerative disorders. Genome Biol 2021; 22:90. [PMID: 33771206 PMCID: PMC8004462 DOI: 10.1186/s13059-021-02275-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Accepted: 01/20/2021] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND People with neurodegenerative disorders show diverse clinical syndromes, genetic heterogeneity, and distinct brain pathological changes, but studies report overlap between these features. DNA methylation (DNAm) provides a way to explore this overlap and heterogeneity as it is determined by the combined effects of genetic variation and the environment. In this study, we aim to identify shared blood DNAm differences between controls and people with Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. RESULTS We use a mixed-linear model method (MOMENT) that accounts for the effect of (un)known confounders, to test for the association of each DNAm site with each disorder. While only three probes are found to be genome-wide significant in each MOMENT association analysis of amyotrophic lateral sclerosis and Parkinson's disease (and none with Alzheimer's disease), a fixed-effects meta-analysis of the three disorders results in 12 genome-wide significant differentially methylated positions. Predicted immune cell-type proportions are disrupted across all neurodegenerative disorders. Protein inflammatory markers are correlated with profile sum-scores derived from disease-associated immune cell-type proportions in a healthy aging cohort. In contrast, they are not correlated with MOMENT DNAm-derived profile sum-scores, calculated using effect sizes of the 12 differentially methylated positions as weights. CONCLUSIONS We identify shared differentially methylated positions in whole blood between neurodegenerative disorders that point to shared pathogenic mechanisms. These shared differentially methylated positions may reflect causes or consequences of disease, but they are unlikely to reflect cell-type proportion differences.
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Grants
- U24 AG021886 NIA NIH HHS
- U01 AG016976 NIA NIH HHS
- Department of Health
- U01 AG024904 NIA NIH HHS
- 108890/Z/15/Z Wellcome Trust
- 503480 Medical Research Council
- TURNER/OCT15/972-797 Motor Neurone Disease Association
- U01 AG032984 NIA NIH HHS
- R01 HL105756 NHLBI NIH HHS
- 082604/2/07/Z Wellcome Trust
- R01 AG033193 NIA NIH HHS
- National Health and Medical Research Council
- Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge
- Medical Research Council (UK)
- Economic and Social Research Council
- National Institute for Health Research (NIHR)
- the European Community’s Health Seventh Framework Programme
- Horizon 2020 Programme
- MND Association and the Wellcome Trust.
- European Research Council (ERC)
- EU Joint Programme – Neurodegenerative Disease Research ()
- EU Joint Programme - Neurodegenerative Disease Research (JPND)
- Australian Research Council
- Mater Foundation
- ForeFront - NHMRC
- Australian National Health and Medical Research Council
- University of Otago Research Grant, together with financial support from the Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd
- National Health and Medical Research Council and the Dementia Collaborative Research Centres program (DCRC2), as well as funding from the Science and Industry Endowment Fund (SIEF) and the Cooperative Research Centre (CRC) for Mental Health – funded throug
- EU Joint Programme - Neurodegenerative Disease Research (JPND), co-funded through the Australian National Health and Medical Research (NHMRC) Council, Motor Neurone Disease Research Institute of Australia Ice Bucket Challenge,
- EU Joint Programme - Neurodegenerative Disease Research (JPND), United Kingdom Medical Research Council, Economic and Social Research Council, Motor Neuro Disease Association (GB), National Institute for Health Research (NIHR) Biomedical Research Centre at
- EU Joint Programme - Neurodegenerative Disease Research (JPND), European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program, PPP Allowance made available by Health~Holland, Top Sector Life Sciences & Health, Unit
- National Health and Medical Research Council, Australian Research Council, Mater Foundation,
- Australian National Health and Medical Research Council (
- University of Otago Research Grant, Jim and Mary Carney Charitable Trust
- Commonwealth Scientific Industrial and research Organization (CSIRO), Edith Cowan University (ECU), Mental Health Research institute (MHRI), National Ageing Research Institute (NARI), Austin Health, CogState Ltd., National Health and Medical Research Counc
- EFPIA companies and SMEs as part of InnoMed (Innovative Medicines in Europe), an Integrated Project funded by the European Union of the Sixth Framework program
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Affiliation(s)
- Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Simon M Laws
- School of Medical and Health Sciences, Edith Cowan University, 270 Joondalup Dr, Joondalup, WA, 6027, Australia
| | - Tian Lin
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Costanza L Vallerga
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Department of Internal Medicine, Erasmus MC, University Medical Center, 3015GD, Rotterdam, The Netherlands
| | | | - Ian P Blair
- Australian Centre for Precision Health, University of South Australia Cancer Research Institute, School of Health Sciences, University of South Australia, Adelaide, SA, 5001, Australia
| | - John B Kwok
- Brain and Mind Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Karen A Mather
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuroscience Research Australia Institute, Randwick, NSW, 2031, Australia
| | - George D Mellick
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Perminder S Sachdev
- Centre for Healthy Brain Ageing, School of Psychiatry, University of New South Wales, Sydney, NSW, 2031, Australia
- Neuropsychiatric Institute, The Prince of Wales Hospital, UNSW, Randwick, NSW, 2031, Australia
| | - Leanne Wallace
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Anjali K Henders
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Ramona A J Zwamborn
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Paul J Hop
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Katie Lunnon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Ehsan Pishva
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Janou A Y Roubroeks
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Hilkka Soininen
- Institute of Clinical Medicine, Neurology, University of Eastern Finland, Kuopio, Finland
| | - Magda Tsolaki
- 1st Department of Neurology, Memory and Dementia Unit, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Patrizia Mecocci
- Department of Medicine, Institute of Gerontology and Geriatrics, University of Perugia, Perugia, Italy
| | - Simon Lovestone
- Department of Psychiatry, Warneford Hospital, University of Oxford, Oxford, UK
| | | | - Bruno Vellas
- INSERM U 558, University of Toulouse, Toulouse, France
| | - Sarah Furlong
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Fleur C Garton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Robert D Henderson
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Susan Mathers
- Calvary Health Care Bethlehem, Parkdale, VIC, 3195, Australia
| | - Pamela A McCombe
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
| | - Merrilee Needham
- Fiona Stanley Hospital, Perth, WA, 6150, Australia
- Notre Dame University, Fremantle, WA, 6160, Australia
- Institute for Immunology and Infectious Diseases, Murdoch University, Perth, WA, 6150, Australia
| | - Shyuan T Ngo
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
- Centre for Clinical Research, The University of Queensland, Brisbane, QLD, 4019, Australia
- The Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Garth Nicholson
- ANZAC Research Institute, Concord Repatriation General Hospital, Sydney, NSW, 2139, Australia
| | - Roger Pamphlett
- Discipline of Pathology and Department of Neuropathology, Brain and Mind Centre, The University of Sydney, Sydney, NSW, 2050, Australia
| | - Dominic B Rowe
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Frederik J Steyn
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, 4029, Australia
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kelly L Williams
- Centre for Motor Neuron Disease Research, Macquarie University, Sydney, NSW, 2109, Australia
| | - Tim J Anderson
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Steven R Bentley
- Eskitis Institute for Drug Discovery, Griffith University, Brisbane, Australia
| | - John Dalrymple-Alford
- New Zealand Brain Research Institute, Christchurch, New Zealand
- School of Psychology, Speech and Hearing, University of Canterbury, Christchurch, New Zealand
| | - Javed Fowder
- Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, Australia
| | - Jacob Gratten
- Mater Research, Translational Research Institute, Brisbane, Australia
- Mater Research Institute, The University of Queensland, Brisbane, Australia
| | - Glenda Halliday
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Ian B Hickie
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Martin Kennedy
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Simon J G Lewis
- Brain and Mind Research Centre, Sydney Medical School, The University of Sydney, Sydney, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - John Pearson
- Department of Pathology, University of Otago, Christchurch, New Zealand
| | - Toni L Pitcher
- New Zealand Brain Research Institute, Christchurch, New Zealand
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Peter Silburn
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Futao Zhang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Peter M Visscher
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Jian Yang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts group, University of Edinburgh, 7 George Square, Edinburgh, EH8 9JZ, UK
| | - Ashley R Jones
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Aleksey Shatunov
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Alfredo Iacoangeli
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | - Wouter van Rheenen
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | | | - Cristopher E Shaw
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
| | | | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, King's College London, Institute of Psychiatry, Psychology and Neuroscience, London, SE5 9RX, UK
- King's College Hospital, London, SE5 9RS, UK
| | - Jan H Veldink
- Department of Neurology, University Medical Center Utrecht Brain Center, Utrecht University, Utrecht, The Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
- Institute of Psychiatry, Psychology & Neuroscience, King's College London, London, SE5 8AF, UK
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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105
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Shireby GL, Davies JP, Francis PT, Burrage J, Walker EM, Neilson GWA, Dahir A, Thomas AJ, Love S, Smith RG, Lunnon K, Kumari M, Schalkwyk LC, Morgan K, Brookes K, Hannon E, Mill J. Recalibrating the epigenetic clock: implications for assessing biological age in the human cortex. Brain 2021; 143:3763-3775. [PMID: 33300551 PMCID: PMC7805794 DOI: 10.1093/brain/awaa334] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/14/2022] Open
Abstract
Human DNA methylation data have been used to develop biomarkers of ageing, referred to as ‘epigenetic clocks’, which have been widely used to identify differences between chronological age and biological age in health and disease including neurodegeneration, dementia and other brain phenotypes. Existing DNA methylation clocks have been shown to be highly accurate in blood but are less precise when used in older samples or in tissue types not included in training the model, including brain. We aimed to develop a novel epigenetic clock that performs optimally in human cortex tissue and has the potential to identify phenotypes associated with biological ageing in the brain. We generated an extensive dataset of human cortex DNA methylation data spanning the life course (n = 1397, ages = 1 to 108 years). This dataset was split into ‘training’ and ‘testing’ samples (training: n = 1047; testing: n = 350). DNA methylation age estimators were derived using a transformed version of chronological age on DNA methylation at specific sites using elastic net regression, a supervised machine learning method. The cortical clock was subsequently validated in a novel independent human cortex dataset (n = 1221, ages = 41 to 104 years) and tested for specificity in a large whole blood dataset (n = 1175, ages = 28 to 98 years). We identified a set of 347 DNA methylation sites that, in combination, optimally predict age in the human cortex. The sum of DNA methylation levels at these sites weighted by their regression coefficients provide the cortical DNA methylation clock age estimate. The novel clock dramatically outperformed previously reported clocks in additional cortical datasets. Our findings suggest that previous associations between predicted DNA methylation age and neurodegenerative phenotypes might represent false positives resulting from clocks not robustly calibrated to the tissue being tested and for phenotypes that become manifest in older ages. The age distribution and tissue type of samples included in training datasets need to be considered when building and applying epigenetic clock algorithms to human epidemiological or disease cohorts.
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Affiliation(s)
- Gemma L Shireby
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan P Davies
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Paul T Francis
- University of Exeter Medical School, University of Exeter, Exeter, UK.,Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Joe Burrage
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma M Walker
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Grant W A Neilson
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Aisha Dahir
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Alan J Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Seth Love
- Dementia Research Group, Institute of Clinical Neurosciences, School of Clinical Sciences, University of Bristol, Bristol, UK
| | - Rebecca G Smith
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Katie Lunnon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Meena Kumari
- Institute for Social and Economic Research, University of Essex, Colchester, UK
| | | | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Keeley Brookes
- School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Eilis Hannon
- University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, Exeter, UK
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106
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Pirazzini C, Azevedo T, Baldelli L, Bartoletti-Stella A, Calandra-Buonaura G, Dal Molin A, Dimitri GM, Doykov I, Gómez-Garre P, Hägg S, Hällqvist J, Halsband C, Heywood W, Jesús S, Jylhävä J, Kwiatkowska KM, Labrador-Espinosa MA, Licari C, Maturo MG, Mengozzi G, Meoni G, Milazzo M, Periñán-Tocino MT, Ravaioli F, Sala C, Sambati L, Schade S, Schreglmann S, Spasov S, Tenori L, Williams D, Xumerle L, Zago E, Bhatia KP, Capellari S, Cortelli P, Garagnani P, Houlden H, Liò P, Luchinat C, Delledonne M, Mills K, Mir P, Mollenhauer B, Nardini C, Pedersen NL, Provini F, Strom S, Trenkwalder C, Turano P, Bacalini MG, Franceschi C. A geroscience approach for Parkinson's disease: Conceptual framework and design of PROPAG-AGEING project. Mech Ageing Dev 2021; 194:111426. [PMID: 33385396 DOI: 10.1016/j.mad.2020.111426] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/07/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022]
Abstract
Advanced age is the major risk factor for idiopathic Parkinson's disease (PD), but to date the biological relationship between PD and ageing remains elusive. Here we describe the rationale and the design of the H2020 funded project "PROPAG-AGEING", whose aim is to characterize the contribution of the ageing process to PD development. We summarize current evidences that support the existence of a continuum between ageing and PD and justify the use of a Geroscience approach to study PD. We focus in particular on the role of inflammaging, the chronic, low-grade inflammation characteristic of elderly physiology, which can propagate and transmit both locally and systemically. We then describe PROPAG-AGEING design, which is based on the multi-omic characterization of peripheral samples from clinically characterized drug-naïve and advanced PD, PD discordant twins, healthy controls and "super-controls", i.e. centenarians, who never showed clinical signs of motor disability, and their offspring. Omic results are then validated in a large number of samples, including in vitro models of dopaminergic neurons and healthy siblings of PD patients, who are at higher risk of developing PD, with the final aim of identifying the molecular perturbations that can deviate the trajectories of healthy ageing towards PD development.
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Affiliation(s)
- Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Tiago Azevedo
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Luca Baldelli
- Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | | | - Giovanna Calandra-Buonaura
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | | | - Giovanna Maria Dimitri
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Ivan Doykov
- Centre for Inborn Errors of Metabolism, UCL Institute of Child Health, London, United Kingdom
| | - Pilar Gómez-Garre
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Jenny Hällqvist
- Centre for Inborn Errors of Metabolism, UCL Institute of Child Health, London, United Kingdom
| | - Claire Halsband
- Department of Clinical Neurophysiology, University Medical Center Göttingen, Göttingen, Germany; Department of Gerontopsychiatry, Rhein-Mosel-Fachklinik, Andernach, Germany
| | - Wendy Heywood
- Centre for Inborn Errors of Metabolism, UCL Institute of Child Health, London, United Kingdom; NIHR Great Ormond Street Biomedical Research Centre, Great Ormond Street Hospital and UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Silvia Jesús
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Juulia Jylhävä
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | - Miguel A Labrador-Espinosa
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Cristina Licari
- CERM, University of Florence, Sesto Fiorentino, Florence, Italy
| | - Maria Giovanna Maturo
- Department of Biotechnological and Applied Clinical Sciences, University of L'Aquila, L'Aquila, Italy
| | - Giacomo Mengozzi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | | | - Maddalena Milazzo
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Maria Teresa Periñán-Tocino
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Francesco Ravaioli
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Luisa Sambati
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | - Sebastian Schade
- Department of Clinical Neurophysiology, University Medical Center Göttingen, Göttingen, Germany
| | - Sebastian Schreglmann
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Simeon Spasov
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Leonardo Tenori
- Consorzio Interuniversitario Risonanze Magnetiche di Metalloproteine (CIRMMP), Florence, Italy
| | - Dylan Williams
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | | | | | - Kailash P Bhatia
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, United Kingdom
| | - Sabina Capellari
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | - Pietro Cortelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic, and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, United Kingdom
| | - Pietro Liò
- Department of Computer Science and Technology, University of Cambridge, Cambridge, United Kingdom
| | - Claudio Luchinat
- CERM, University of Florence, Sesto Fiorentino, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Italy
| | | | - Kevin Mills
- Centre for Inborn Errors of Metabolism, UCL Institute of Child Health, London, United Kingdom; NIHR Great Ormond Street Biomedical Research Centre, Great Ormond Street Hospital and UCL Great Ormond Street Institute of Child Health, London, United Kingdom
| | - Pablo Mir
- Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Unidad de Trastornos del Movimiento, Servicio de Neurología y NeurofisiologíaClínica, Instituto de Biomedicina de Sevilla, Seville, Spain; Centro de Investigación Biomédicaen Red sobreEnfermedades Neurodegenerativas (CIBERNED), Spain
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, Kassel, Germany; Department of Neurology, University Medical Centre Goettingen, Goettingen, Germany
| | - Christine Nardini
- Istituto per le Applicazioni del Calcolo Mauro Picone, CNR, Roma, Italy
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Federica Provini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Department of Biomedical and NeuroMotor Sciences (DiBiNeM), University of Bologna, Italy
| | - Stephen Strom
- Department of Laboratory Medicine, Karolinska Institute and Karolinska Universitetssjukhuset, 171 76, Stockholm, Sweden
| | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, Kassel, Germany; Department of Neurosurgery, University Medical Center Göttingen, Germany
| | - Paola Turano
- CERM, University of Florence, Sesto Fiorentino, Florence, Italy; Department of Chemistry "Ugo Schiff", University of Florence, Italy
| | | | - Claudio Franceschi
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy; Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
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Chiavellini P, Canatelli-Mallat M, Lehmann M, Gallardo MD, Herenu CB, Cordeiro JL, Clement J, Goya RG. Aging and rejuvenation - a modular epigenome model. Aging (Albany NY) 2021; 13:4734-4746. [PMID: 33627519 PMCID: PMC7950254 DOI: 10.18632/aging.202712] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/08/2021] [Indexed: 12/21/2022]
Abstract
The view of aging has evolved in parallel with the advances in biomedical sciences. Long considered as an irreversible process where interventions were only aimed at slowing down its progression, breakthrough discoveries like animal cloning and cell reprogramming have deeply changed our understanding of postnatal development, giving rise to the emerging view that the epigenome is the driver of aging. The idea was significantly strengthened by the converging discovery that DNA methylation (DNAm) at specific CpG sites could be used as a highly accurate biomarker of age defined by an algorithm known as the Horvath clock. It was at this point where epigenetic rejuvenation came into play as a strategy to reveal to what extent biological age can be set back by making the clock tick backwards. Initial evidence suggests that when the clock is forced to tick backwards in vivo, it is only able to drag the phenotype to a partially rejuvenated condition. In order to explain the results, a bimodular epigenome is proposed, where module A represents the DNAm clock component and module B the remainder of the epigenome. Epigenetic rejuvenation seems to hold the key to arresting or even reversing organismal aging.
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Affiliation(s)
- Priscila Chiavellini
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Martina Canatelli-Mallat
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Marianne Lehmann
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Maria D. Gallardo
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
| | - Claudia B. Herenu
- Institute for Experimental Pharmacology (IFEC), School of Chemical Sciences, National University of Cordoba, Cordoba, Argentina
| | | | | | - Rodolfo G. Goya
- Institute for Biochemical Research (INIBIOLP) - Histology B and Pathology B, School of Medicine, National University of La Plata, La Plata, Argentina
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108
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Nasamran CA, Sachan ANS, Mott J, Kuras YI, Scherzer CR, Study HB, Ricciardelli E, Jepsen K, Edland SD, Fisch KM, Desplats P. Differential blood DNA methylation across Lewy body dementias. ALZHEIMER'S & DEMENTIA (AMSTERDAM, NETHERLANDS) 2021; 13:e12156. [PMID: 33665346 PMCID: PMC7896631 DOI: 10.1002/dad2.12156] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 12/29/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD) are characterized by cognitive alterations, visual hallucinations, and motor impairment. Diagnosis is based on type and timing of clinical manifestations; however, determination of clinical subtypes is challenging. The utility of blood DNA methylation as a biomarker for Lewy body disorders (LBD) is mostly unexplored. METHODS We performed a cross-sectional analysis of blood methylation in 42 DLB and 50 PDD cases applying linear models to compare groups and logistic least absolute shrinkage and selection operator regression to explore the discriminant power of methylation signals. RESULTS DLB blood shows differential methylation compared to PDD. Some methylation changes associate with core features of LBD. Sets of probes show high predictive value to discriminate between variants. DISCUSSION Our study is the first to explore LBD blood methylation. Despite overlapping clinical presentation, we detected differential epigenetic signatures that, if confirmed in independent cohorts, could be developed into useful biomarkers.
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Affiliation(s)
- Chanond A. Nasamran
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Anubhav Nikunj Singh Sachan
- Division of Biostatistics, Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Jennifer Mott
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Yuliya I. Kuras
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | - Clemens R. Scherzer
- Center for Advanced Parkinson Research and Precision Neurology Program, Harvard Medical SchoolBrigham & Women's HospitalBostonMassachusettsUSA
| | | | - Eugenia Ricciardelli
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kristen Jepsen
- Genomics CenterInstitute for Genomics MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Steven D. Edland
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Family Medicine and Public HealthUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Kathleen M. Fisch
- Center for Computational Biology & BioinformaticsDepartment of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
| | - Paula Desplats
- Department of Neurosciences, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
- Department of Pathology, School of MedicineUniversity of California San DiegoLa JollaCaliforniaUSA
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109
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Vaccarino V, Huang M, Wang Z, Hui Q, Shah AJ, Goldberg J, Smith N, Kaseer B, Murrah N, Levantsevych OM, Shallenberger L, Driggers E, Bremner JD, Sun YV. Epigenetic Age Acceleration and Cognitive Decline: A Twin Study. J Gerontol A Biol Sci Med Sci 2021; 76:1854-1863. [PMID: 33606025 PMCID: PMC8436988 DOI: 10.1093/gerona/glab047] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Little is known about the role of DNA methylation (DNAm) epigenetic age acceleration in cognitive decline. Using a twin study design, we examined whether DNAm age acceleration is related to cognitive decline measured longitudinally in persons without a clinical diagnosis of dementia. METHODS We studied 266 paired male twins (133 pairs) with a mean age of 56 years at baseline. Of these, 114 paired twins returned for a follow-up after an average of 11.5 years. We obtained 6 indices of DNAm age acceleration based on epigenome-wide data from peripheral blood lymphocytes. At both baseline and follow-up, we administered a battery of cognitive measures and constructed 2 composite scores, one for executive function and one for memory function. We fitted multivariable mixed regression models to examine the association of DNAm age acceleration markers with cognitive function within pairs. RESULTS In cross-sectional analyses at baseline, there was no association between DNAm age acceleration and cognitive function scores. In longitudinal analyses, however, comparing twins within pairs, each additional year of age acceleration using the Horvath's method was associated with a 3% decline (95% CI, 1%-5%) in the composite executive function score and a 2.5% decline (95% CI, 0.01%-4.9%) in the memory function score. These results did not attenuate after adjusting for education and other risk factors. CONCLUSIONS Middle-aged men who had older DNAm age relative to their brothers of the same demographic age showed a faster rate of cognitive decline in the subsequent 11.5 years. These results point to the role of epigenetic modifications in cognitive aging.
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Affiliation(s)
- Viola Vaccarino
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US.,Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, US
| | - Minxuan Huang
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US
| | - Zeyuan Wang
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US
| | - Qin Hui
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US
| | - Amit J Shah
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US.,Department of Medicine, Division of Cardiology, Emory University School of Medicine, Atlanta, Georgia, US.,Atlanta Veterans Affairs Health Care System, Decatur, Georgia, US
| | - Jack Goldberg
- Vietnam Era Twin Registry, Seattle Epidemiologic Research and Information Center, US Department of Veterans Affairs, Seattle, Washington, US
| | - Nicholas Smith
- Vietnam Era Twin Registry, Seattle Epidemiologic Research and Information Center, US Department of Veterans Affairs, Seattle, Washington, US
| | - Belal Kaseer
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US
| | - Nancy Murrah
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US
| | - Oleksiy M Levantsevych
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US
| | - Lucy Shallenberger
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US
| | - Emily Driggers
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US
| | - J Douglas Bremner
- Atlanta Veterans Affairs Health Care System, Decatur, Georgia, US.,Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, Georgia, US
| | - Yan V Sun
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, Georgia, US.,Atlanta Veterans Affairs Health Care System, Decatur, Georgia, US.,Department of Biomedical Informatics, Emory University School of Medicine, Atlanta, Georgia, US
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Dada O, Adanty C, Dai N, Jeremian R, Alli S, Gerretsen P, Graff A, Strauss J, De Luca V. Biological aging in schizophrenia and psychosis severity: DNA methylation analysis. Psychiatry Res 2021; 296:113646. [PMID: 33444986 DOI: 10.1016/j.psychres.2020.113646] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 12/10/2020] [Indexed: 01/08/2023]
Abstract
The physiological changes associated with normal aging are known to occur earlier in individuals with schizophrenia (SCZ). One of the phenomena linked with normal aging is the change in patterns of epigenetic modifications. We recruited 138 individuals with SCZ spectrum disorders and extracted DNA from white blood cells. The combinations of pre-selected DNA methylation sites were utilized to estimate the 'methylation age' (DNAm age) and evaluate evidence of epigenetic age acceleration. We investigated the correlation between the epigenetic age acceleration measures and psychosis severity; furthermore, we estimated blood cell counts based on DNA methylation levels. The extrinsic epigenetic age acceleration showed a significant correlation with the Brief Psychiatric Rating Scale (BPRS) disorganization subscale(r=0.222, p=0.039).Both Horvath age acceleration and Hannum age acceleration showed a significant correlation (r=0.221, p=0.029; r=0.242, p=0.017 respectively) with the Symptom Checklist 90 (SCL-90) psychotic domain. Overall, this study shows some evidence of epigenetic age acceleration associated with psychosis severity using two different algorithms for DNAm age analysis.
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Affiliation(s)
- Oluwagbenga Dada
- CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Christopher Adanty
- CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Nasia Dai
- CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Richie Jeremian
- CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Sauliha Alli
- CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Philip Gerretsen
- CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Ariel Graff
- CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - John Strauss
- CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada
| | - Vincenzo De Luca
- CAMH, Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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111
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Okazaki S, Otsuka I, Shinko Y, Horai T, Hirata T, Yamaki N, Sora I, Hishimoto A. Epigenetic Clock Analysis in Children With Fetal Alcohol Spectrum Disorder. Alcohol Clin Exp Res 2021; 45:329-337. [PMID: 33296097 DOI: 10.1111/acer.14532] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 11/24/2020] [Indexed: 12/20/2022]
Abstract
BACKGROUND Fetal alcohol spectrum disorder (FASD) is characterized by severe clinical impairment, considerable social burden, and high mortality and morbidity, which are due to various malformations, sepsis, and cancer. As >50% of deaths from FASD occur during the first year of life, we hypothesized that there is the acceleration of biological aging in FASD. Several recent studies have established genome-wide DNA methylation (DNAm) profiles as "epigenetic clocks" that can estimate biological aging, and FASD has been associated with differential DNAm patterns. Therefore, we tested this hypothesis using epigenetic clocks. METHODS We investigated 5 DNAm-based measures of epigenetic age (HorvathAge, HannumAge, SkinBloodAge, PhenoAge, and GrimAge) and telomere length (DNAmTL) using 4 independent publicly available DNAm datasets; 2 datasets were derived from buccal epithelium, and the other 2 datasets were derived from peripheral blood. RESULTS Compared with controls, children with FASD exhibited an acceleration of GrimAge in 1 buccal and 2 blood datasets. No significant difference was found in other DNAm ages and DNAmTL. Meta-analyses showed a significant acceleration of GrimAge in the blood samples but not in the buccal samples. CONCLUSIONS This study provides novel evidence regarding accelerated epigenetic aging in children with FASD.
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Affiliation(s)
- Satoshi Okazaki
- From, Department of Psychiatry, (SO, IO, YS, THo, THi, NY, IS, AH), Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ikuo Otsuka
- From, Department of Psychiatry, (SO, IO, YS, THo, THi, NY, IS, AH), Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yutaka Shinko
- From, Department of Psychiatry, (SO, IO, YS, THo, THi, NY, IS, AH), Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tadasu Horai
- From, Department of Psychiatry, (SO, IO, YS, THo, THi, NY, IS, AH), Kobe University Graduate School of Medicine, Kobe, Japan
| | - Takashi Hirata
- From, Department of Psychiatry, (SO, IO, YS, THo, THi, NY, IS, AH), Kobe University Graduate School of Medicine, Kobe, Japan
| | - Naruhisa Yamaki
- From, Department of Psychiatry, (SO, IO, YS, THo, THi, NY, IS, AH), Kobe University Graduate School of Medicine, Kobe, Japan
| | - Ichiro Sora
- From, Department of Psychiatry, (SO, IO, YS, THo, THi, NY, IS, AH), Kobe University Graduate School of Medicine, Kobe, Japan
| | - Akitoyo Hishimoto
- From, Department of Psychiatry, (SO, IO, YS, THo, THi, NY, IS, AH), Kobe University Graduate School of Medicine, Kobe, Japan.,Department of Psychiatry, (AH), Yokohama City University Graduate School of Medicine, Yokohama, Japan
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Ayodele T, Rogaeva E, Kurup JT, Beecham G, Reitz C. Early-Onset Alzheimer's Disease: What Is Missing in Research? Curr Neurol Neurosci Rep 2021; 21:4. [PMID: 33464407 PMCID: PMC7815616 DOI: 10.1007/s11910-020-01090-y] [Citation(s) in RCA: 83] [Impact Index Per Article: 27.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/18/2020] [Indexed: 12/14/2022]
Abstract
PURPOSE OF REVIEW Early-onset Alzheimer's disease (EOAD), defined as Alzheimer's disease (AD) occurring before age 65, is significantly less well studied than the late-onset form (LOAD) despite EOAD often presenting with a more aggressive disease progression. The aim of this review is to summarize the current understanding of the etiology of EOAD, their translation into clinical practice, and to suggest steps to be taken to move our understanding forward. RECENT FINDINGS EOAD cases make up 5-10% of AD cases but only 10-15% of these cases show known mutations in the APP, PSEN1, and PSEN2, which are linked to EOAD. New data suggests that these unexplained cases following a non-Mendelian pattern of inheritance is potentially caused by a mix of common and newly discovered rare variants. However, only a fraction of this genetic variation has been identified to date leaving the molecular mechanisms underlying this type of AD and their association with clinical, biomarker, and neuropathological changes unclear. While great advancements have been made in characterizing EOAD, much work is needed to disentangle the molecular mechanisms underlying this type of AD and to identify putative targets for more precise disease screening, diagnosis, prevention, and treatment.
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Affiliation(s)
- Temitope Ayodele
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA
- Department of Neurology, Columbia University, New York, NY, USA
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, 60 Leonard Avenue, Toronto, ON, M5T 0S8, Canada
| | - Jiji T Kurup
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA
| | - Gary Beecham
- The John P. Hussman Institute for Human Genomics, University of Miami, Miami, FL, USA
| | - Christiane Reitz
- The Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Columbia University, New York, NY, USA.
- The Gertrude H. Sergievsky Center, Columbia University, New York, NY, USA.
- Department of Neurology, Columbia University, New York, NY, USA.
- Department of Epidemiology, Sergievsky Center, Taub Institute for Research on the Aging Brain, Columbia University, 630 W 168th Street, New York, NY, 10032, USA.
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113
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Lau CHE, Robinson O. DNA methylation age as a biomarker for cancer. Int J Cancer 2021; 148:2652-2663. [PMID: 33394520 DOI: 10.1002/ijc.33451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
Cancer is well established as an age-associated disease, and there is substantial overlap in the molecular, cellular and physiological changes observed with both ageing and the progression of cancer. Age-specific declines in resilience mechanisms such as DNA repair or epigenetic maintenance may contribute to the development of cancer. These declines may be assessed through biomarkers that measure biological age and through the related concept of "age acceleration". Epigenetic clocks, assessed through DNA methylation levels, are among the most widely used biological age markers in cancer studies. In this review, we discuss the use of DNA methylation ageing measures to predict population cancer incidence, mortality and survival. Blood-based DNA methylation age estimators appear to be promising measures of increased cancer risk and mortality, although their reported effects are generally weak, thus its clinical relevance remains to be validated in large case-cohort and longitudinal studies. Future development of epigenetic and other biological age biomarkers will likely further elucidate the links between ageing and cancer.
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Affiliation(s)
- Chung-Ho E Lau
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
| | - Oliver Robinson
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
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114
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Irizar H, Kanchan K, Mathias RA, Bunyavanich S. Advancing Food Allergy Through Omics Sciences. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY. IN PRACTICE 2021; 9:119-129. [PMID: 32777389 PMCID: PMC7855623 DOI: 10.1016/j.jaip.2020.07.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023]
Abstract
Since the publication of the first draft of the human genome, there has been an explosion of new technologies with increasing power to interrogate the totality of biological molecules (eg, DNA, RNA, proteins, metabolites) and their modifications (eg, DNA methylation, histone modifications). These technologies, collectively called omics, have been widely applied in the last 2 decades to study biological systems to gain deeper insight into mechanisms driving the physiology and pathophysiology of human health and disease. Because of its complex, multifactorial nature, food allergy is especially well suited to be investigated using omics approaches. In this rostrum, we review how omic technologies have been applied to explore diverse aspects of food allergy, including adaptive and innate immune processes in food-allergic responses, the role of the microbiome in food allergy risk, metabolic changes in the gut and blood associated with food allergy, and the identification of biomarkers and potential therapeutic targets for the condition. We discuss the strengths and limitations of the studies performed thus far and the need to adopt systems biology approaches that integrate data from multiple omics to fully leverage the potential of these technologies to advance food allergy research and care.
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Affiliation(s)
- Haritz Irizar
- Division of Psychiatry, University College London, London, United Kingdom; Department of Genetics & Genomic Sciences and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY
| | - Kanika Kanchan
- Department of Medicine, Johns Hopkins University, Baltimore, Md
| | | | - Supinda Bunyavanich
- Department of Genetics & Genomic Sciences and Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY.
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115
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Wang C, Ni W, Yao Y, Just A, Heiss J, Wei Y, Gao X, Coull BA, Kosheleva A, Baccarelli AA, Peters A, Schwartz JD. DNA methylation-based biomarkers of age acceleration and all-cause death, myocardial infarction, stroke, and cancer in two cohorts: The NAS, and KORA F4. EBioMedicine 2020; 63:103151. [PMID: 33279859 PMCID: PMC7724153 DOI: 10.1016/j.ebiom.2020.103151] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/13/2020] [Accepted: 11/16/2020] [Indexed: 12/25/2022] Open
Abstract
Background DNA methylation (DNAm) may play a role in age-related outcomes. It is not yet known which DNAm-based biomarkers of age acceleration (BoAA) has the strongest association with age-related endpoints. Methods We collected the blood samples from two independent cohorts: the Normative Ageing Study, and the Cooperative Health Research in the Region of Augsburg cohort. We measured epigenome-wide DNAm level, and generated five DNAm BoAA at baseline. We used Cox proportional hazards model to analyze the relationships between BoAA and all-cause death. We applied the Fine and Gray competing risk model to estimate the risk of BoAA on myocardial infarction (MI), stroke, and cancer, accounting for death of other reasons as the competing risks. We used random-effects meta-analyses to pool the individual results, with adjustment for multiple testing. Findings The mean chronological ages in the two cohorts were 74, and 61, respectively. Baseline GrimAgeAccel, and DNAm-related mortality risk score (DNAmRS) both had strong associations with all-cause death, MI, and stroke, independent from chronological age. For example, a one standard deviation (SD) increment in GrimAgeAccel was significantly associated with increased risk of all-cause death [hazard ratio (HR): 2.01; 95% confidence interval (CI), 1.15, 3.50], higher risk of MI (HR: 1.44; 95% CI, 1.16, 1.79), and elevated risk of stroke (HR: 1.42; 95% CI, 1.06, 1.91). There were no associations between any BoAA and cancer. Interpretation From the public health perspective, GrimAgeAccel is the most useful tool for identifying at-risk elderly, and evaluating the efficacy of anti-aging interventions. Funding National Institute of Environmental Health Sciences of U.S., Harvard Chan-NIEHS Center for Environmental Health, German Federal Ministry of Education and Research, and the State of Bavaria in Germany.
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Affiliation(s)
- Cuicui Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, 401 Park Drive, West of Landmark Center, Boston, MA 02215, United States.
| | - Wenli Ni
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Yueli Yao
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Allan Just
- Department of Environmental Medicine, and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jonathan Heiss
- Department of Environmental Medicine, and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Yaguang Wei
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, 401 Park Drive, West of Landmark Center, Boston, MA 02215, United States
| | - Xu Gao
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Brent A Coull
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, 401 Park Drive, West of Landmark Center, Boston, MA 02215, United States; Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, United States
| | - Anna Kosheleva
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, 401 Park Drive, West of Landmark Center, Boston, MA 02215, United States
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany; Institute of Medical Information Science, Biometry, and Epidemiology, Ludwig Maximilians University, Munich, Germany
| | - Joel D Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, 401 Park Drive, West of Landmark Center, Boston, MA 02215, United States
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116
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Rivero-Segura NA, Bello-Chavolla OY, Barrera-Vázquez OS, Gutierrez-Robledo LM, Gomez-Verjan JC. Promising biomarkers of human aging: In search of a multi-omics panel to understand the aging process from a multidimensional perspective. Ageing Res Rev 2020; 64:101164. [PMID: 32977058 DOI: 10.1016/j.arr.2020.101164] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/14/2022]
Abstract
The aging process has been linked to the occurrence of chronic diseases and functional impairments, including cancer, sarcopenia, frailty, metabolic, cardiovascular, and neurodegenerative diseases. Nonetheless, aging is highly variable and heterogeneous and represents a challenge for its characterization. In this sense, intrinsic capacity (IC) stands as a novel perspective by the World Health Organization, which integrates the individual wellbeing, environment, and risk factors to understand aging. However, there is a lack of quantitative and qualitative attributes to define it objectively. Therefore, in this review we attempt to summarize the most relevant and promising biomarkers described in clinical studies at date over different molecular levels, including epigenomics, transcriptomics, proteomics, metabolomics, and the microbiome. To aid gerontologists, geriatricians, and biomedical researchers to understand the aging process through the IC. Aging biomarkers reflect the physiological state of individuals and the underlying mechanisms related to homeostatic changes throughout an individual lifespan; they demonstrated that aging could be measured independently of time (that may explain its heterogeneity) and to be helpful to predict age-related syndromes and mortality. In summary, we highlight the areas of opportunity and gaps of knowledge that must be addressed to fully integrate biomedical findings into clinically useful tools and interventions.
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Affiliation(s)
| | - O Y Bello-Chavolla
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico; Department of Physiology, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - O S Barrera-Vázquez
- Departamento de Famacología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | | | - J C Gomez-Verjan
- Dirección de Investigación, Instituto Nacional de Geriatría, Mexico.
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117
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Ryan J, Wrigglesworth J, Loong J, Fransquet PD, Woods RL. A Systematic Review and Meta-analysis of Environmental, Lifestyle, and Health Factors Associated With DNA Methylation Age. J Gerontol A Biol Sci Med Sci 2020; 75:481-494. [PMID: 31001624 DOI: 10.1093/gerona/glz099] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Indexed: 02/07/2023] Open
Abstract
DNA methylation (DNAm) algorithms of biological age provide a robust estimate of an individual's chronological age and can predict their risk of age-related disease and mortality. This study reviewed the evidence that environmental, lifestyle and health factors are associated with the Horvath and Hannum epigenetic clocks. A systematic search identified 61 studies. Chronological age was correlated with DNAm age in blood (median .83, range .13-.99). In a meta-analysis body mass index (BMI) was associated with increased DNAm age (Hannum β: 0.07, 95% CI 0.04 to 0.10; Horvath β: 0.06, 95% CI 0.02 to 0.10), but there was no association with smoking (Hannum β: 0.12, 95% CI -0.50 to 0.73; Horvath β:0.18, 95% CI -0.10 to 0.46). DNAm age was positively associated with frailty (three studies, n = 3,093), and education was negatively associated with the Hannum estimate of DNAm age specifically (four studies, n = 13,955). For most other exposures, findings were too inconsistent to draw conclusions. In conclusion, BMI was positively associated with biological aging measured using DNAm, with some evidence that frailty also increased aging. More research is needed to provide conclusive evidence regarding other exposures. This field of research has the potential to provide further insights into how to promote slower biological aging and ultimately prolong healthy life.
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Affiliation(s)
- Joanne Ryan
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia.,INSERM, Univ Montpellier, Neuropsychiatry, Epidemiological and Clinical Research, Montpellier, France
| | - Jo Wrigglesworth
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Jun Loong
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Peter D Fransquet
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Robyn L Woods
- School of Public Health and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
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118
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Prediction of Lung Function in Adolescence Using Epigenetic Aging: A Machine Learning Approach. Methods Protoc 2020; 3:mps3040077. [PMID: 33182250 PMCID: PMC7712054 DOI: 10.3390/mps3040077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 10/31/2020] [Accepted: 11/05/2020] [Indexed: 12/25/2022] Open
Abstract
Epigenetic aging has been found to be associated with a number of phenotypes and diseases. A few studies have investigated its effect on lung function in relatively older people. However, this effect has not been explored in the younger population. This study examines whether lung function in adolescence can be predicted with epigenetic age accelerations (AAs) using machine learning techniques. DNA methylation based AAs were estimated in 326 matched samples at two time points (at 10 years and 18 years) from the Isle of Wight Birth Cohort. Five machine learning regression models (linear, lasso, ridge, elastic net, and Bayesian ridge) were used to predict FEV1 (forced expiratory volume in one second) and FVC (forced vital capacity) at 18 years from feature selected predictor variables (based on mutual information) and AA changes between the two time points. The best models were ridge regression (R2 = 75.21% ± 7.42%; RMSE = 0.3768 ± 0.0653) and elastic net regression (R2 = 75.38% ± 6.98%; RMSE = 0.445 ± 0.069) for FEV1 and FVC, respectively. This study suggests that the application of machine learning in conjunction with tracking changes in AA over the life span can be beneficial to assess the lung health in adolescence.
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119
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Coninx E, Chew YC, Yang X, Guo W, Coolkens A, Baatout S, Moons L, Verslegers M, Quintens R. Hippocampal and cortical tissue-specific epigenetic clocks indicate an increased epigenetic age in a mouse model for Alzheimer's disease. Aging (Albany NY) 2020; 12:20817-20834. [PMID: 33082299 PMCID: PMC7655172 DOI: 10.18632/aging.104056] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 08/27/2020] [Indexed: 04/17/2023]
Abstract
Epigenetic clocks are based on age-associated changes in DNA methylation of CpG-sites, which can accurately measure chronological age in different species. Recently, several studies have indicated that the difference between chronological and epigenetic age, defined as the age acceleration, could reflect biological age indicating functional decline and age-associated diseases. In humans, an epigenetic clock associated Alzheimer's disease (AD) pathology with an acceleration of the epigenetic age. In this study, we developed and validated two mouse brain region-specific epigenetic clocks from the C57BL/6J hippocampus and cerebral cortex. Both clocks, which could successfully estimate chronological age, were further validated in a widely used mouse model for AD, the triple transgenic AD (3xTg-AD) mouse. We observed an epigenetic age acceleration indicating an increased biological age for the 3xTg-AD mice compared to non-pathological C57BL/6J mice, which was more pronounced in the cortex as compared to the hippocampus. Genomic region enrichment analysis revealed that age-dependent CpGs were enriched in genes related to developmental, aging-related, neuronal and neurodegenerative functions. Due to the limited access of human brain tissues, these epigenetic clocks specific for mouse cortex and hippocampus might be important in further unravelling the role of epigenetic mechanisms underlying AD pathology or brain aging in general.
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Affiliation(s)
- Emma Coninx
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Yap Ching Chew
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Xiaojing Yang
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Wei Guo
- Epigenetics Technologies, Zymo Research Corporation, Irvine, CA 92614, USA
| | - Amelie Coolkens
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Sarah Baatout
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Lieve Moons
- Neural Circuit Development and Regeneration Research Group, Department of Biology, KU Leuven, Leuven 3000, Belgium
| | - Mieke Verslegers
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
| | - Roel Quintens
- Radiobiology Unit, Institute for Environment, Health and Safety, Belgian Nuclear Research Centre (SCK CEN), Mol 2400, Belgium
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120
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Kuzmina NS, Luong TM, Rubanovich AV. Changes in DNA Methylation Induced by Dioxins and Dioxin-Like Compounds as Potential Predictor of Disease Risk. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420100063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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121
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Yan Q, Paul KC, Lu AT, Kusters C, Binder AM, Horvath S, Ritz B. Epigenetic mutation load is weakly correlated with epigenetic age acceleration. Aging (Albany NY) 2020; 12:17863-17894. [PMID: 32991324 PMCID: PMC7585066 DOI: 10.18632/aging.103950] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 08/08/2020] [Indexed: 01/24/2023]
Abstract
DNA methylation (DNAm) age estimators are widely used to study aging-related conditions. It is not yet known whether DNAm age is associated with the accumulation of stochastic epigenetic mutations (SEMs), which reflect dysfunctions of the epigenetic maintenance system. Here, we defined epigenetic mutation load (EML) as the total number of SEMs per individual. We assessed associations between EML and DNAm age acceleration estimators using biweight midcorrelations in four population-based studies (total n = 6,388). EML was not only positively associated with chronological age (meta r = 0.171), but also with four measures of epigenetic age acceleration: the Horvath pan tissue clock, intrinsic epigenetic age acceleration, the Hannum clock, and the GrimAge clock (meta-analysis correlation ranging from r = 0.109 to 0.179). We further conducted pathway enrichment analyses for each participant's SEMs. The enrichment result demonstrated the stochasticity of epigenetic mutations, meanwhile implicated several pathways: signaling, neurogenesis, neurotransmitter, glucocorticoid, and circadian rhythm pathways may contribute to faster DNAm age acceleration. Finally, investigating genomic-region specific EML, we found that EMLs located within regions of transcriptional repression (TSS1500, TSS200, and 1stExon) were associated with faster age acceleration. Overall, our findings suggest a role for the accumulation of epigenetic mutations in the aging process.
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Affiliation(s)
- Qi Yan
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Kimberly C. Paul
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Cynthia Kusters
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA
| | - Alexandra M. Binder
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA,Population Sciences in the Pacific Program (Cancer Epidemiology), University of Hawaii Cancer Center, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA 90095, USA,Department of Neurology, UCLA School of Medicine, Los Angeles, CA 90095, USA
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Galet B, Cheval H, Ravassard P. Patient-Derived Midbrain Organoids to Explore the Molecular Basis of Parkinson's Disease. Front Neurol 2020; 11:1005. [PMID: 33013664 PMCID: PMC7500100 DOI: 10.3389/fneur.2020.01005] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Induced pluripotent stem cell-derived organoids offer an unprecedented access to complex human tissues that recapitulate features of architecture, composition and function of in vivo organs. In the context of Parkinson's Disease (PD), human midbrain organoids (hMO) are of significant interest, as they generate dopaminergic neurons expressing markers of Substantia Nigra identity, which are the most vulnerable to degeneration. Combined with genome editing approaches, hMO may thus constitute a valuable tool to dissect the genetic makeup of PD by revealing the effects of risk variants on pathological mechanisms in a representative cellular environment. Furthermore, the flexibility of organoid co-culture approaches may also enable the study of neuroinflammatory and neurovascular processes, as well as interactions with other brain regions that are also affected over the course of the disease. We here review existing protocols to generate hMO, how they have been used so far to model PD, address challenges inherent to organoid cultures, and discuss applicable strategies to dissect the molecular pathophysiology of the disease. Taken together, the research suggests that this technology represents a promising alternative to 2D in vitro models, which could significantly improve our understanding of PD and help accelerate therapeutic developments.
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Affiliation(s)
- Benjamin Galet
- Molecular Pathophysiology of Parkinson's Disease Group, Paris Brain Institute (ICM), INSERM U, CNRS UMR 7225, Sorbonne University, Paris, France
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Proskovec AL, Rezich MT, O’Neill J, Morsey B, Wang T, Ideker T, Swindells S, Fox HS, Wilson TW. Association of Epigenetic Metrics of Biological Age With Cortical Thickness. JAMA Netw Open 2020; 3:e2015428. [PMID: 32926115 PMCID: PMC7490648 DOI: 10.1001/jamanetworkopen.2020.15428] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
IMPORTANCE Magnetic resonance imaging (MRI) studies of aging adults have shown substantial intersubject variability across various brain metrics, and some of this variability is likely attributable to chronological age being an imprecise measure of age-related change. Accurately quantifying one's biological age could allow better quantification of healthy and pathological changes in the aging brain. OBJECTIVE To investigate the association of DNA methylation (DNAm)-based biological age with cortical thickness and to assess whether biological age acceleration compared with chronological age captures unique variance in cortical thinning. DESIGN, SETTING, AND PARTICIPANTS This cross-sectional study used high-resolution structural brain MRI data collected from a sample of healthy aging adults who were participating in a larger ongoing neuroimaging study that began in May 2014. This population-based study accrued participants from the greater Omaha, Nebraska, metropolitan area. One hundred sixty healthy adults were contacted for the MRI component, 82 of whom participated in both DNAm and MRI study components. Data analysis was performed from March to June 2019. MAIN OUTCOMES AND MEASURES Vertexwise cortical thickness, DNAm-based biological age, and biological age acceleration compared with chronological age were measured. A pair of multivariable regression models were computed in which cortical thickness was regressed on DNAm-based biological age, controlling for sex in the first model and also controlling for chronological age in the second model. RESULTS Seventy-nine adult participants (38 women; mean [SD] age, 43.82 [14.50] years; age range, 22-72 years) were included in all final analyses. Advancing biological age was correlated with cortical thinning across frontal, superior temporal, inferior parietal, and medial occipital regions. In addition, biological age acceleration relative to chronological age was associated with cortical thinning in orbitofrontal, superior and inferior temporal, somatosensory, parahippocampal, and fusiform regions. Specifically, for every 1 year of biological age acceleration, cortical thickness would be expected to decrease by 0.024 mm (95% CI, -0.04 to -0.01 mm) in the left orbitofrontal cortex (partial r, -0.34; P = .002), 0.014 mm (95% CI, -0.02 to -0.01 mm) in the left superior temporal gyrus (partial r, -0.36; P = .001), 0.015 mm (95% CI, -0.02 to -0.01 mm) in the left fusiform gyrus (partial r, -0.38; P = .001), 0.015 mm (95% CI, -0.02 to -0.01 mm) in the right fusiform gyrus (partial r, -0.43; P < .001), 0.019 mm (95% CI, -0.03 to -0.01 mm) in the right inferior temporal sulcus (partial r, -0.34; P = .002), and 0.011 mm (95% CI, -0.02 to -0.01 mm) in the right primary somatosensory cortex (partial r, -0.37; P = .001). CONCLUSIONS AND RELEVANCE To our knowledge, this is the first study to investigate vertexwise cortical thickness in relation to DNAm-based biological age, and the findings suggest that this metric of biological age may yield additional insight on healthy and pathological cortical aging compared with standard measures of chronological age alone.
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Affiliation(s)
- Amy L. Proskovec
- Center for Magnetoencephalography, University of Nebraska Medical Center, Omaha
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha
- Department of Psychology, University of Nebraska Omaha, Omaha
- Magnetoencephalography Center of Excellence, University of Texas Southwestern Medical Center, Dallas
| | - Michael T. Rezich
- Center for Magnetoencephalography, University of Nebraska Medical Center, Omaha
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha
| | - Jennifer O’Neill
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha
| | - Brenda Morsey
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha
| | - Tina Wang
- Department of Medicine, University of California San Diego, La Jolla
| | - Trey Ideker
- Department of Medicine, University of California San Diego, La Jolla
| | - Susan Swindells
- Department of Internal Medicine, Division of Infectious Diseases, University of Nebraska Medical Center, Omaha
| | - Howard S. Fox
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha
| | - Tony W. Wilson
- Center for Magnetoencephalography, University of Nebraska Medical Center, Omaha
- Department of Neurological Sciences, University of Nebraska Medical Center, Omaha
- Department of Psychology, University of Nebraska Omaha, Omaha
- Cognitive Neuroscience of Development & Aging Center, University of Nebraska Medical Center, Omaha
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Soriano-Tárraga C, Lazcano U, Jiménez-Conde J, Ois A, Cuadrado-Godia E, Giralt-Steinhauer E, Rodríguez-Campello A, Gomez-Gonzalez A, Avellaneda-Gómez C, Vivanco-Hidalgo RM, Roquer J. Biological age is a novel biomarker to predict stroke recurrence. J Neurol 2020; 268:285-292. [PMID: 32789606 DOI: 10.1007/s00415-020-10148-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Revised: 07/24/2020] [Accepted: 08/06/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND Stroke recurrence (SR) after an ischemic stroke is an important cause of death and disability. We conducted a hospital-based study to evaluate the role of biological age (b-Age: age-related DNA-methylation changes) as a risk factor for SR. METHODS We included 587 patients in the acute phase of stroke, assessed at one tertiary stroke center (Hospital del Mar: Barcelona, Spain). B-Age was estimated with 5 different methods based on DNA methylation, and Hannum's method was the one that better performed. We analyzed the relationships between b-Age, chronological age, sex, vascular risk factors, coronary and peripheral arterial disease, atrial fibrillation, initial neurological severity assessed by National Institutes of Health Stroke Scale (NIHSS), transient ischemic attack (TIA) in the 7 days preceding the index stroke, and symptomatic atherosclerosis. Stroke recurrence definition include: new symptoms that suggest a new ischemic event had occurred within 3 months after stroke onset and worsening by four points in the initial neurological severity (measured by National Institutes of Health Stroke Scale (NIHSS) score). RESULTS Logistic regression analysis associated b-Age with SR [p = 0.003; OR = 1.06 (95% CI: 1.02-1.09)], independently of chronological age [p = 0.022; OR = 0.96 (95% CI 0.94-1.00)], symptomatic atherosclerosis (stenosis > 50% in the symptomatic territory), transient ischemic attack (TIA) in the 7 days preceding the index stroke, and initial NIHSS. The b-Age of patients with SR was 2.7 years older than patients without SR. CONCLUSIONS Patients with SR were biologically older than those without SR. B-Age was independently associated with high risk of developing SR.
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Affiliation(s)
- Carol 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. .,Department of Psychiatry, Washington University School of Medicine, 660 S. Euclid Avenue, Saint-Louis, MO, 63110, USA. .,NeuroGenomics and Informatics, Washington University School of Medicine, 425 S. Euclid Avenue, Saint-Louis, MO, 63110, USA. .,Servicio de Neurología, Hospital del Mar, Passeig Maritim 25-29, 08003, Barcelona, Spain.
| | - Uxue Lazcano
- 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
| | - 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
| | - 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. .,Servicio de Neurología, Hospital del Mar, Passeig Maritim 25-29, 08003, 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
| | - 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
| | - 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
| | - Alejandra Gomez-Gonzalez
- 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
| | - Carla Avellaneda-Gómez
- 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
| | - 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
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Matsuyama M, Søraas A, Yu S, Kim K, Stavrou EX, Caimi PF, Wald D, deLima M, Dahl JA, Horvath S, Matsuyama S. Analysis of epigenetic aging in vivo and in vitro: Factors controlling the speed and direction. Exp Biol Med (Maywood) 2020; 245:1543-1551. [PMID: 32762265 DOI: 10.1177/1535370220947015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
IMPACT STATEMENT Aging is associated with DNA methylation (DNAm) changes. Recent advancement of the whole-genome DNAm analysis technology allowed scientists to develop DNAm-based age estimators. A majority of these estimators use DNAm data from a single tissue type such as blood. In 2013, a multi-tissue age estimator using DNAm pattern of 353 CpGs was developed by Steve Horvath. This estimator was named "epigenetic clock", and the improved version using DNAm pattern of 391 CpGs was developed in 2018. The estimated age by epigenetic clock is named DNAmAge. DNAmAge can be used as a biomarker of aging predicting the risk of age-associated diseases and mortality. Although the DNAm-based age estimators were developed, the mechanism of epigenetic aging is still enigmatic. The biological significance of epigenetic aging is not well understood, either. This minireview discusses the current understanding of the mechanism of epigenetic aging and the future direction of aging research.
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Affiliation(s)
- Mieko Matsuyama
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Arne Søraas
- Department of Microbiology, Oslo University Hospital, Case Comprehensive Cancer Center, Oslo 0372, Norway
| | - Sarah Yu
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Kyuhyeon Kim
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Evi X Stavrou
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - Paolo F Caimi
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - David Wald
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA.,Department of Microbiology, Oslo University Hospital, Case Comprehensive Cancer Center, Oslo 0372, Norway
| | - Marcos deLima
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
| | - John A Dahl
- Department of Microbiology, Oslo University Hospital, Case Comprehensive Cancer Center, Oslo 0372, Norway
| | - Steve Horvath
- Department of Pathology, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA.,Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Shigemi Matsuyama
- Division of Hematology and Oncology, Department of Medicine, School of Medicine, Case Western Reserve University and University Hospitals, Case Comprehensive Cancer Center, Cleveland, OH 44106, USA
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Morselli M, Farrell C, Rubbi L, Fehling HL, Henkhaus R, Pellegrini M. Targeted bisulfite sequencing for biomarker discovery. Methods 2020; 187:13-27. [PMID: 32755621 DOI: 10.1016/j.ymeth.2020.07.006] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/16/2020] [Accepted: 07/19/2020] [Indexed: 12/14/2022] Open
Abstract
Cytosine methylation is one of the best studied epigenetic modifications. In mammals, DNA methylation patterns vary among cells and is mainly found in the CpG context. DNA methylation is involved in important processes during development and differentiation and its dysregulation can lead to or is associated with diseases, such as cancer, loss-of-imprinting syndromes and neurological disorders. It has been also shown that DNA methylation at the cellular, tissue and organism level varies with age. To overcome the costs of Whole-Genome Bisulfite Sequencing, the gold standard method to detect 5-methylcytosines at a single base resolution, DNA methylation arrays have been developed and extensively used. This method allows one to assess the status of a fraction of the CpG sites present in the genome of an organism. In order to combine the relatively low cost of Methylation Arrays and digital signals of bisulfite sequencing, we developed a Targeted Bisulfite Sequencing method that can be applied to biomarker discovery for virtually any phenotype. Here we describe a comprehensive step-by-step protocol to build a DNA methylation-based epigenetic clock.
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Affiliation(s)
- Marco Morselli
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States; UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, United States; Institute for Quantitative and Computational Biosciences - The Collaboratory, University of California Los Angeles, Los Angeles, CA 90095, United States.
| | - Colin Farrell
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States.
| | - Liudmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States.
| | - Heather L Fehling
- Clinical Reference Laboratory, Inc., Lenexa, KS 66215, United States.
| | - Rebecca Henkhaus
- Clinical Reference Laboratory, Inc., Lenexa, KS 66215, United States.
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, United States; UCLA-DOE Institute for Genomics and Proteomics, University of California Los Angeles, Los Angeles, CA 90095, United States; Institute for Quantitative and Computational Biosciences - The Collaboratory, University of California Los Angeles, Los Angeles, CA 90095, United States.
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127
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Hillary RF, Stevenson AJ, McCartney DL, Campbell A, Walker RM, Howard DM, Ritchie CW, Horvath S, Hayward C, McIntosh AM, Porteous DJ, Deary IJ, Evans KL, Marioni RE. Epigenetic measures of ageing predict the prevalence and incidence of leading causes of death and disease burden. Clin Epigenetics 2020; 12:115. [PMID: 32736664 PMCID: PMC7394682 DOI: 10.1186/s13148-020-00905-6] [Citation(s) in RCA: 94] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/14/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Individuals of the same chronological age display different rates of biological ageing. A number of measures of biological age have been proposed which harness age-related changes in DNA methylation profiles. These measures include five 'epigenetic clocks' which provide an index of how much an individual's biological age differs from their chronological age at the time of measurement. The five clocks encompass methylation-based predictors of chronological age (HorvathAge, HannumAge), all-cause mortality (DNAm PhenoAge, DNAm GrimAge) and telomere length (DNAm Telomere Length). A sixth epigenetic measure of ageing differs from these clocks in that it acts as a speedometer providing a single time-point measurement of the pace of an individual's biological ageing. This measure of ageing is termed DunedinPoAm. In this study, we test the association between these six epigenetic measures of ageing and the prevalence and incidence of the leading causes of disease burden and mortality in high-income countries (n ≤ 9537, Generation Scotland: Scottish Family Health Study). RESULTS DNAm GrimAge predicted incidence of clinically diagnosed chronic obstructive pulmonary disease (COPD), type 2 diabetes and ischemic heart disease after 13 years of follow-up (hazard ratios = 2.22, 1.52 and 1.41, respectively). DunedinPoAm predicted the incidence of COPD and lung cancer (hazard ratios = 2.02 and 1.45, respectively). DNAm PhenoAge predicted incidence of type 2 diabetes (hazard ratio = 1.54). DNAm Telomere Length associated with the incidence of ischemic heart disease (hazard ratio = 0.80). DNAm GrimAge associated with all-cause mortality, the prevalence of COPD and spirometry measures at the study baseline. These associations were present after adjusting for possible confounding risk factors including alcohol consumption, body mass index, deprivation, education and tobacco smoking and surpassed stringent Bonferroni-corrected significance thresholds. CONCLUSIONS Our data suggest that epigenetic measures of ageing may have utility in clinical settings to complement gold-standard methods for disease assessment and management.
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Affiliation(s)
- Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Anna J Stevenson
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - David M Howard
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, SE5 8AF, UK.,Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Craig W Ritchie
- Edinburgh Dementia Prevention, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, 90095-7088, USA.,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, 90095-1772, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.,Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, EH16 4UX, UK
| | - David J Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Ian J Deary
- Lothian Birth Cohorts, University of Edinburgh, Edinburgh, EH8 9JZ, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU, UK.
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128
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Sato K, Mano T, Suzuki K, Toda T, Iwatsubo T, Iwata A. Attempt to Predict A/T/N-Based Alzheimer's Disease Cerebrospinal Fluid Biomarkers Using a Peripheral Blood DNA Methylation Clock. J Alzheimers Dis Rep 2020; 4:287-296. [PMID: 32904719 PMCID: PMC7458568 DOI: 10.3233/adr-200205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Background: Although aging is the strongest risk factor for the development of Alzheimer’s disease (AD), it remains uncertain if the blood DNA methylation clock, which reflects the effect of biological aging on DNA methylation (DNAme) status of blood cells, may be used as a surrogate biomarker for AD pathology in the central nervous system (CNS). Objective: We aimed to develop a practical model to predict for A/T/N-based AD biomarkers as the prediction targets using the aging acceleration of blood cells. Methods: We obtained data of North American ADNI study participants (n = 317) whose blood DNA methylation microarray (Illumina HumanMethylation EPIC Beadchips) and cerebrospinal fluid (CSF) AD biomarkers (Aβ, t-tau, and p-tau) were recorded simultaneously. Methylation clock was calculated to conduct machine learning, in order to predict binary statuses (+ or –) for A (corresponding to the lowered CSF Aβ), T (the elevated CSF p-tau), or N (the elevated CSF t-tau). The predictive performance of the models was evaluated by area under curve (AUC) in the test subset within ADNI. Results: Among the 317 included samples, 194 (61.2%) were A+, 247 (77.9%) were T+, and 104 (32.8%) were N+. The degree of blood aging acceleration showed weak positive correlation with the CSF Aβ levels, even after adjustment with APOE genotype and other covariates. However, the contribution of aging acceleration to improve the predictive performance of models was not significant for any of A+, T+, or N+. Conclusion: Our exploratory attempts could not demonstrate the substantial utility of the peripheral blood cells’ methylation clock as a predictor for A/T/N-based CSF biomarkers of AD, and further additional work should be conducted to determine whether the blood DNAme signatures including methylation clock have substantial utility in detecting underlying amyloid, tau or neurodegeneration pathology of AD.
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Affiliation(s)
- Kenichiro Sato
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Tatsuo Mano
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Kazushi Suzuki
- Unit for Early and Exploratory Clinical Development, The University of Tokyo Hospital, Tokyo, Japan
| | - Tatsushi Toda
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Takeshi Iwatsubo
- Department of Neuropathology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Atsushi Iwata
- Department of Neurology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan.,Department of Neurology, Tokyo Metropolitan Geriatric Medical Center Hospital, Tokyo, Japan
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129
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Zheng C, Berger NA, Li L, Xu R. Epigenetic age acceleration and clinical outcomes in gliomas. PLoS One 2020; 15:e0236045. [PMID: 32692766 PMCID: PMC7373289 DOI: 10.1371/journal.pone.0236045] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/27/2020] [Indexed: 12/03/2022] Open
Abstract
Epigenetic age acceleration-the difference between an individual's DNA methylation age and chronological age-is associated with many diseases including cancer. This study aims to evaluate epigenetic age acceleration as a prognostic biomarker for gliomas. DNA methylation data of gliomas patients (516 low-grade and intermediate-grade gliomas and 140 glioblastoma) were obtained from The Cancer Genome Atlas (TCGA) and patient epigenetic ages were computed using Horvath's age prediction model. We used multivariate linear regression to assess the association of epigenetic age acceleration with tumor molecular subtypes, including Codel, Classic-like, G-CIMP-high, G-CIMP-low, Mesenchymal-like and PA-like. Compared with Codel subtype, epigenetic ages in other molecular subtypes show deceleration after controlling age and race. Age deceleration for Classic-like, G-CIMP-high, G-CIMP-low, Mesenchymal-like and PA-like were 15.42 years (CI: 7.98-22.86, p = 5.38E-05), 25.00 years (CI: 20.79-29.22, p = 4.06E-28), 28.56 years (CI: 14.37-42.74, p = 8.75E-05), 45.34 years (CI: 38.80-51.88, p = 2.15E-36), and 53.58 years (CI: 44.90-62.26, p = 4.81E-30), respectively. Then, Cox proportional hazards regression was used to assess the association of epigenetic age acceleration with patient overall survival. Our results show epigenetic age acceleration is positively associated with patient overall survival (per 10-year age acceleration, HR = 0.89; 95%CI: 0.82-0.97; p = 9.04E-03) in multivariate analysis. When stratified by molecular subtypes, epigenetic age acceleration remains positively associated with patient survival after adjusting age and tumor grade. In conclusion, epigenetic age acceleration is significantly associated with molecular subtypes and patient overall survival in gliomas, indication that epigenetic age acceleration has potential as a quantitative prognostic biomarker for gliomas.
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Affiliation(s)
- Chunlei Zheng
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
| | - Nathan A. Berger
- Center for Science, Health, and Society, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States of America
| | - Li Li
- Department of Family Medicine, School of Medicine, University of Virginia, Charlottesville, VA, United States of America
| | - Rong Xu
- Center for Artificial Intelligence in Drug Discovery, School of Medicine, Case Western Reserve University, Cleveland, OH, United States of America
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH, United States of America
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130
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Bergsma T, Rogaeva E. DNA Methylation Clocks and Their Predictive Capacity for Aging Phenotypes and Healthspan. Neurosci Insights 2020; 15:2633105520942221. [PMID: 32743556 PMCID: PMC7376380 DOI: 10.1177/2633105520942221] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 06/23/2020] [Indexed: 12/12/2022] Open
Abstract
The number of age predictors based on DNA methylation (DNAm) profile is rising
due to their potential in predicting healthspan and application in age-related
illnesses, such as neurodegenerative diseases. The cumulative assessment of DNAm
levels at age-related CpGs (DNAm clock) may reflect biological aging. Such DNAm
clocks have been developed using various training models and could mirror
different aspects of disease/aging mechanisms. Hence, evaluating several DNAm
clocks together may be the most effective strategy in capturing the complexity
of the aging process. However, various confounders may influence the outcome of
these age predictors, including genetic and environmental factors, as well as
technical differences in the selected DNAm arrays. These factors should be taken
into consideration when interpreting DNAm clock predictions. In the current
review, we discuss 15 reported DNAm clocks with consideration for their utility
in investigating neurodegenerative diseases and suggest research directions
towards developing a more optimal measure for biological aging.
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Affiliation(s)
- Tessa Bergsma
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Faculty of Science and Engineering, University of Groningen, Groningen, The Netherlands
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada.,Division of Neurology, Department of Medicine, University of Toronto, Toronto, ON, Canada
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131
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Gao X, Colicino E, Shen J, Just AC, Nwanaji-Enwerem JC, Wang C, Coull B, Lin X, Vokonas P, Zheng Y, Hou L, Schwartz J, Baccarelli AA. Comparative validation of an epigenetic mortality risk score with three aging biomarkers for predicting mortality risks among older adult males. Int J Epidemiol 2020; 48:1958-1971. [PMID: 31038702 DOI: 10.1093/ije/dyz082] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/05/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND A 'mortality risk score' (MS) based on ten prominent mortality-related cytosine-phosphate-guanine (CpG) sites was previously associated with all-cause mortality, but has not been verified externally. We aimed to validate the association of MS with mortality and to compare MS with three aging biomarkers: telomere length (TL), DNA methylation age (DNAmAge) and phenotypic age (DNAmPhenoAge) to explore whether MS can serve as a reliable measure of biological aging and mortality. METHODS Among 534 males aged 55-85 years from the US Normative Aging Study, the MS, DNAmAge and DNAmPhenoAge were derived from blood DNA methylation profiles from the Illumina HumanMethylation450 BeadChip, and TL was measured by quantitative real-time polymerase chain reaction (qRT-PCR). RESULTS A total of 147 participants died during a median follow-up of 9.4 years. The MS showed strong associations with all-cause, cardiovascular disease (CVD) and cancer mortality. After controlling for all potential covariates, participants with high MS (>5 CpG sites with aberrant methylation) had almost 4-fold all-cause mortality (hazard ratio: 3.84, 95% confidence interval: 1.92-7.67) compared with participants with a low MS (0-1 CpG site with aberrant methylation). Similar patterns were observed with respect to CVD and cancer mortality. MS was associated with TL and DNAmPhenoAge acceleration but not with DNAmAge acceleration. Although the MS and DNAmPhenoAge acceleration were independently associated with all-cause mortality, the former exhibited a higher predictive accuracy of mortality than the latter. CONCLUSIONS MS has the potential to be a prominent predictor of mortality that could enhance survival prediction in clinical settings.
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Affiliation(s)
- Xu Gao
- Laboratory of Precision Environmental Health, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Elena Colicino
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jincheng Shen
- Department of Population Health Sciences, University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Allan C Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Cuicui Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Brent Coull
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xihong Lin
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Pantel Vokonas
- Veterans Affairs Normative Aging Study, Veterans Affairs Boston Healthcare System, Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Yinan Zheng
- Department of Preventive 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
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Andrea A Baccarelli
- Laboratory of Precision Environmental Health, Mailman School of Public Health, Columbia University, New York, NY, USA
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Koop BE, Reckert A, Becker J, Han Y, Wagner W, Ritz-Timme S. Epigenetic clocks may come out of rhythm-implications for the estimation of chronological age in forensic casework. Int J Legal Med 2020; 134:2215-2228. [PMID: 32661599 PMCID: PMC7578121 DOI: 10.1007/s00414-020-02375-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Accepted: 07/08/2020] [Indexed: 01/01/2023]
Abstract
There is a growing perception that DNA methylation may be influenced by exogenous and endogenous parameters. Knowledge of these factors is of great relevance for the interpretation of DNA-methylation data for the estimation of chronological age in forensic casework. We performed a literature review to identify parameters, which might be of relevance for the prediction of chronological age based on DNA methylation. The quality of age predictions might particularly be influenced by lifetime adversities (chronic stress, trauma/post-traumatic stress disorder (PTSD), violence, low socioeconomic status/education), cancer, obesity and related diseases, infectious diseases (especially HIV and Cytomegalovirus (CMV) infections), sex, ethnicity and exposure to toxins (alcohol, smoking, air pollution, pesticides). Such factors may alter the DNA methylation pattern and may explain the partly high deviations between epigenetic age and chronological age in single cases (despite of low mean absolute deviations) that can also be observed with “epigenetic clocks” comprising a high number of CpG sites. So far, only few publications dealing with forensic age estimation address these confounding factors. Future research should focus on the identification of further relevant confounding factors and the development of models that are “robust” against the influence of such biological factors by systematic investigations under targeted inclusion of diverse and defined cohorts.
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Affiliation(s)
- Barbara Elisabeth Koop
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany.
| | - Alexandra Reckert
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Julia Becker
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
| | - Yang Han
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany
| | - Wolfgang Wagner
- Helmholtz-Institute for Biomedical Engineering, Stem Cell Biology and Cellular Engineering, RWTH Aachen Faculty of Medicine, Aachen, Germany
| | - Stefanie Ritz-Timme
- Institute of Legal Medicine, University Hospital Düsseldorf, 40225, Düsseldorf, Germany
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Furlong MA, Paul KC, Yan Q, Chuang YH, Cockburn MG, Bronstein JM, Horvath S, Ritz B. An epigenome-wide association study of ambient pyrethroid pesticide exposures in California's central valley. Int J Hyg Environ Health 2020; 229:113569. [PMID: 32679516 DOI: 10.1016/j.ijheh.2020.113569] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 05/08/2020] [Accepted: 05/22/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Pyrethroid pesticide use is increasing worldwide, although the full extent of associated health effects is unknown. An epigenome-wide association study (EWAS) with exploratory pathway analysis may help identify potential pyrethroid-related health effects. METHODS We performed an exploratory EWAS of chronic ambient pyrethroid exposure using control participants' blood in the Parkinson's Environment and Genes Study in the Central Valley of California (N = 237). We estimated associations of living and working near agricultural pyrethroid pesticide applications in the past 5 years (binary) with site-specific differential methylation, and used a false discovery rate (FDR) cut off of 0.05 for significance. We controlled for age, sex, education, cell count, and an ancestral marker for Hispanic ethnicity. We normalized methylation values for Type I/II probe bias using Beta-Mixture Quantile (BMIQ) normalization, filtered out cross-reactive probes, and evaluated for remaining bias with Surrogate Variable Analysis (SVA). We also evaluated the effects of controlling for cell count and normalizing for Type I/II probe bias by comparing changes in effect estimates and p-values for the top hits across BMIQ and GenomeStudio normalization methods, and controlling for cell count. To facilitate broader interpretation, we annotated genes to the CpG sites and performed gene set overrepresentation analysis, using genes annotated to CpG sites that were associated with pyrethroids at a raw p < 0.05, and controlling for background representation of CpG sites on the chip. We did this for both a biological process context (Gene Ontology terms) using missMethyl, and a disease set context using WebGestalt. For these gene set overrepresentation analyses we also used an FDR cut off of 0.05 for significance of gene sets. RESULTS After controlling for cell count and applying BMIQ normalization, 4 CpG sites were differentially methylated in relation to pyrethroid exposures. When using GenomeStudio's Illumina normalization, 415 CpG sites were differentially methylated, including all four identified with the BMIQ method. In the gene set overrepresentation analyses, we identified 6 GO terms using BMIQ normalization, and 76 using Illumina normalization, including the 6 identified by BMIQ. For disease sets, we identified signals for Alzheimer's disease, leukemia and several other cancers, diabetes, birth defects, and other diseases, for both normalization methods. We identified minimal changes in effect estimates after controlling for cell count, and controlling for cell count generally weakened p-values. BMIQ normalization, however, resulted in different beta coefficients and weakened p-values. CONCLUSIONS Chronic ambient pyrethroid exposure is associated with differential methylation at CpG sites that annotate to a wide variety of disease states and biological mechanisms that align with prior research. However, this EWAS also implicates several novel diseases for future investigation, and highlights the relative importance of different background normalization methods in identifying associations.
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Affiliation(s)
- Melissa A Furlong
- Department of Community, Environment, and Policy, University of Arizona Mel and Enid Zuckerman College of Public Health, Tucson, AZ, USA.
| | - Kimberly C Paul
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Qi Yan
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Yu-Hsuan Chuang
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Myles G Cockburn
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, CA, USA
| | - Jeff M Bronstein
- Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, CA, USA; Department of Biostatistics, UCLA Fielding School of Public Health, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, UCLA Fielding School of Public Health, Los Angeles, CA, USA; Department of Neurology, David Geffen School of Medicine, Los Angeles, CA, USA
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Go RCP, Corley MJ, Ross GW, Petrovitch H, Masaki KH, Maunakea AK, He Q, Tiirikainen MI. Genome-wide epigenetic analyses in Japanese immigrant plantation workers with Parkinson's disease and exposure to organochlorines reveal possible involvement of glial genes and pathways involved in neurotoxicity. BMC Neurosci 2020; 21:31. [PMID: 32650713 PMCID: PMC7350633 DOI: 10.1186/s12868-020-00582-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 07/07/2020] [Indexed: 12/29/2022] Open
Abstract
Background Parkinson’s disease (PD) is a disease of the central nervous system that progressively affects the motor system. Epidemiological studies have provided evidence that exposure to agriculture-related occupations or agrichemicals elevate a person’s risk for PD. Here, we sought to examine the possible epigenetic changes associated with working on a plantation on Oahu, HI and/or exposure to organochlorines (OGC) in PD cases. Results We measured genome-wide DNA methylation using the Illumina Infinium HumanMethylation450K BeadChip array in matched peripheral blood and postmortem brain biospecimens in PD cases (n = 20) assessed for years of plantation work and presence of organochlorines in brain tissue. The comparison of 10+ to 0 years of plantation work exposure detected 7 and 123 differentially methylated loci (DML) in brain and blood DNA, respectively (p < 0.0001). The comparison of cases with 4+ to 0–2 detectable levels of OGCs, identified 8 and 18 DML in brain and blood DNA, respectively (p < 0.0001). Pathway analyses revealed links to key neurotoxic and neuropathologic pathways related to impaired immune and proinflammatory responses as well as impaired clearance of damaged proteins, as found in the predominantly glial cell population in these environmental exposure-related PD cases. Conclusions These results suggest that distinct DNA methylation biomarker profiles related to environmental exposures in PD cases with previous exposure can be found in both brain and blood.
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Affiliation(s)
- Rodney C P Go
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Kuakini Health Systems, 347 N Kuakini St, Honolulu, HI, 96817, USA.,Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, 1665 University Blvd, Birmingham, AL, 35294, USA
| | - Michael J Corley
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i at Manoa, 650 Ilalo St, Honolulu, HI, 96813, USA
| | - G Webster Ross
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Veterans Affairs Pacific Islands Health Care System, 459 Patterson Rd, Honolulu, HI, 96819, USA.,Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 650 Ilalo St, Honolulu, HI, 96817, USA
| | - Helen Petrovitch
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Veterans Affairs Pacific Islands Health Care System, 459 Patterson Rd, Honolulu, HI, 96819, USA.,Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 650 Ilalo St, Honolulu, HI, 96817, USA
| | - Kamal H Masaki
- Kuakini Health Systems, 347 N Kuakini St, Honolulu, HI, 96817, USA.,Department of Geriatric Medicine, John A. Burns School of Medicine, University of Hawaii at Manoa, 650 Ilalo St, Honolulu, HI, 96817, USA
| | - Alika K Maunakea
- Department of Native Hawaiian Health, John A. Burns School of Medicine, University of Hawai'i at Manoa, 650 Ilalo St, Honolulu, HI, 96813, USA
| | - Qimei He
- Pacific Health Research and Education Institute, 3375 Koapaka Street, Suite I-540, Honolulu, HI, 96819, USA.,Kuakini Health Systems, 347 N Kuakini St, Honolulu, HI, 96817, USA.,Veterans Affairs Pacific Islands Health Care System, 459 Patterson Rd, Honolulu, HI, 96819, USA
| | - Maarit I Tiirikainen
- University of Hawaii Cancer Center, University of Hawaii at Manoa, 701 Ilalo St, Honolulu, HI, 96813, USA.
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135
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Epigenetics in Lewy Body Diseases: Impact on Gene Expression, Utility as a Biomarker, and Possibilities for Therapy. Int J Mol Sci 2020; 21:ijms21134718. [PMID: 32630630 PMCID: PMC7369933 DOI: 10.3390/ijms21134718] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 06/29/2020] [Accepted: 06/30/2020] [Indexed: 02/07/2023] Open
Abstract
Lewy body disorders (LBD) include Parkinson's disease (PD) and dementia with Lewy bodies (DLB). They are synucleinopathies with a heterogeneous clinical manifestation. As a cause of neuropathological overlap with other neurodegenerative diseases, the establishment of a correct clinical diagnosis is still challenging, and clinical management may be difficult. The combination of genetic variation and epigenetic changes comprising gene expression-modulating DNA methylation and histone alterations modifies the phenotype, disease course, and susceptibility to disease. In this review, we summarize the results achieved in the deciphering of the LBD epigenome. To provide an appropriate context, first LBD genetics is briefly outlined. Afterwards, a detailed review of epigenetic modifications identified for LBD in human cells, postmortem, and peripheral tissues is provided. We also focus on the difficulty of identifying epigenome-related biomarker candidates and discuss the results obtained so far. Additionally, epigenetic changes as therapeutic targets, as well as different epigenome-based treatments, are revised. The number of studies focusing on PD is relatively limited and practically inexistent for DLB. There is a lack of replication studies, and some results are even contradictory, probably due to differences in sample collection and analytical techniques. In summary, we show the current achievements and directions for future research.
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136
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Amenyah SD, Ward M, Strain JJ, McNulty H, Hughes CF, Dollin C, Walsh CP, Lees-Murdock DJ. Nutritional Epigenomics and Age-Related Disease. Curr Dev Nutr 2020; 4:nzaa097. [PMID: 32666030 PMCID: PMC7335360 DOI: 10.1093/cdn/nzaa097] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 04/27/2020] [Accepted: 05/21/2020] [Indexed: 12/24/2022] Open
Abstract
Recent advances in epigenetic research have enabled the development of epigenetic clocks, which have greatly enhanced our ability to investigate molecular processes that contribute to aging and age-related disease. These biomarkers offer the potential to measure the effect of environmental exposures linked to dynamic changes in DNA methylation, including nutrients, as factors in age-related disease. They also offer a compelling insight into how imbalances in the supply of nutrients, particularly B-vitamins, or polymorphisms in regulatory enzymes involved in 1-carbon metabolism, the key pathway that supplies methyl groups for epigenetic reactions, may influence epigenetic age and interindividual disease susceptibility. Evidence from recent studies is critically reviewed, focusing on the significant contribution of the epigenetic clock to nutritional epigenomics and its impact on health outcomes and age-related disease. Further longitudinal studies and randomized nutritional interventions are required to advance the field.
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Affiliation(s)
- Sophia D Amenyah
- Genomic Medicine Research Group , School of Biomedical Sciences, Ulster University, Northern Ireland, United Kingdom. BT52 1SA
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom. BT52 1SA
| | - Mary Ward
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom. BT52 1SA
| | - J J Strain
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom. BT52 1SA
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom. BT52 1SA
| | - Catherine F Hughes
- Nutrition Innovation Centre for Food and Health (NICHE), School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom. BT52 1SA
| | - Caitlin Dollin
- Genomic Medicine Research Group , School of Biomedical Sciences, Ulster University, Northern Ireland, United Kingdom. BT52 1SA
| | - Colum P Walsh
- Genomic Medicine Research Group , School of Biomedical Sciences, Ulster University, Northern Ireland, United Kingdom. BT52 1SA
| | - Diane J Lees-Murdock
- Genomic Medicine Research Group , School of Biomedical Sciences, Ulster University, Northern Ireland, United Kingdom. BT52 1SA
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137
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Kwiatkowska KM, Bacalini MG, Sala C, Kaziyama H, de Andrade DC, Terlizzi R, Giannini G, Cevoli S, Pierangeli G, Cortelli P, Garagnani P, Pirazzini C. Analysis of Epigenetic Age Predictors in Pain-Related Conditions. Front Public Health 2020; 8:172. [PMID: 32582603 PMCID: PMC7296181 DOI: 10.3389/fpubh.2020.00172] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Accepted: 04/20/2020] [Indexed: 01/31/2023] Open
Abstract
Chronic pain prevalence is high worldwide and increases at older ages. Signs of premature aging have been associated with chronic pain, but few studies have investigated aging biomarkers in pain-related conditions. A set of DNA methylation (DNAm)-based estimates of age, called “epigenetic clocks,” has been proposed as biological measures of age-related adverse processes, morbidity, and mortality. The aim of this study is to assess if different pain-related phenotypes show alterations in DNAm age. In our analysis, we considered three cohorts for which whole-blood DNAm data were available: heat pain sensitivity (HPS), including 20 monozygotic twin pairs discordant for heat pain temperature threshold; fibromyalgia (FM), including 24 cases and 20 controls; and headache, including 22 chronic migraine and medication overuse headache patients (MOH), 18 episodic migraineurs (EM), and 13 healthy subjects. We used the Horvath's epigenetic age calculator to obtain DNAm-based estimates of epigenetic age, telomere length, levels of 7 proteins in plasma, number of smoked packs of cigarettes per year, and blood cell counts. We did not find differences in epigenetic age acceleration, calculated using five different epigenetic clocks, between subjects discordant for pain-related phenotypes. Twins with high HPS had increased CD8+ T cell counts (nominal p = 0.028). HPS thresholds were negatively associated with estimated levels of GDF15 (nominal p = 0.008). FM patients showed decreased naive CD4+ T cell counts compared with controls (nominal p = 0.015). The severity of FM manifestations expressed through various evaluation tests was associated with decreased levels of leptin, shorter length of telomeres, and reduced CD8+ T and natural killer cell counts (nominal p < 0.05), while the duration of painful symptoms was positively associated with telomere length (nominal p = 0.034). No differences in DNAm-based estimates were detected for MOH or EM compared with controls. In summary, our study suggests that HPS, FM, and MOH/EM do not show signs of epigenetic age acceleration in whole blood, while HPS and FM are associated with DNAm-based estimates of immunological parameters, plasma proteins, and telomere length. Future studies should extend these observations in larger cohorts.
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Affiliation(s)
| | | | - Claudia Sala
- Department of Physics and Astronomy, University of Bologna, Bologna, Italy
| | - Helena Kaziyama
- Department of Neurology, Pain Center, LIM 62, University of São Paulo, São Paulo, Brazil
| | - Daniel Ciampi de Andrade
- Department of Neurology, Pain Center, LIM 62, University of São Paulo, São Paulo, Brazil.,Pain Center, Instituto do Câncer do Estado de São Paulo, São Paulo, Brazil
| | | | - Giulia Giannini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Sabina Cevoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
| | - Giulia Pierangeli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Pietro Cortelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy.,Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, Bologna, Italy.,Department of Laboratory Medicine, Clinical Chemistry, Karolinska Institutet, Karolinska University Hospital, Stockholm, Sweden.,Applied Biomedical Research Center (CRBA), Policlinico S.Orsola-Malpighi Polyclinic, Bologna, Italy.,Unit of Bologna, CNR Institute of Molecular Genetics Luigi Luca Cavalli-Sforza, Bologna, Italy
| | - Chiara Pirazzini
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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138
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Wang C, Just A, Heiss J, Coull BA, Hou L, Zheng Y, Sparrow D, Vokonas PS, Baccarelli A, Schwartz J. Biomarkers of aging and lung function in the normative aging study. Aging (Albany NY) 2020; 12:11942-11966. [PMID: 32561690 PMCID: PMC7343502 DOI: 10.18632/aging.103363] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 05/20/2020] [Indexed: 12/17/2022]
Abstract
Elderly individuals who are never smokers but have the same height and chronological age can have substantial differences in lung function. The underlying biological mechanisms are unclear. To evaluate the associations of different biomarkers of aging (BoA) and lung function, we performed a repeated-measures analysis in the Normative Aging Study using linear mixed-effect models. We generated GrimAgeAccel, PhenoAgeAccel, extrinsic and intrinsic epigenetic age acceleration using a publically available online calculator. We calculated Zhang's DNAmRiskScore based on 10 CpGs. We measured telomere length (TL) and mitochondrial DNA copy number (mtDNA-CN) using quantitative real-time polymerase chain reaction. A pulmonary function test was performed measuring forced expiratory volume in 1 second / forced vital capacity (FEV1/FVC), FEV1, and maximum mid-expiratory flow (MMEF). Epigenetic-based BoA were associated with lower lung function. For example, a one-year increase in GrimAgeAccel was associated with a 13.64 mL [95% confidence interval (CI), 5.11 to 22.16] decline in FEV1; a 0.2 increase in Zhang's DNAmRiskScore was associated with a 0.009 L/s (0.005 to 0.013) reduction in MMEF. No association was found between TL/mtDNA-CN and lung function. Overall, this paper shows that epigenetics might be a potential mechanism underlying pulmonary dysfunction in the elderly.
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Affiliation(s)
- Cuicui Wang
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Allan Just
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jonathan Heiss
- Department of Environmental Medicine and Public Health, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Brent A Coull
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Lifang Hou
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Yinan Zheng
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - David Sparrow
- VA Normative Aging Study, VA Boston Healthcare System, Boston, MA 02130, USA.,Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Pantel S Vokonas
- VA Normative Aging Study, VA Boston Healthcare System, Boston, MA 02130, USA.,Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Andrea Baccarelli
- Department of Epidemiology and Environmental Health Sciences, Columbia University, New York, NY 10027, USA
| | - Joel Schwartz
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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139
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Epigenetic clock analysis of human fibroblasts in vitro: effects of hypoxia, donor age, and expression of hTERT and SV40 largeT. Aging (Albany NY) 2020; 11:3012-3022. [PMID: 31113906 PMCID: PMC6555444 DOI: 10.18632/aging.101955] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 05/03/2019] [Indexed: 12/12/2022]
Abstract
Aging is associated with a genome-wide change of DNA methylation (DNAm). "DNAm age" is defined as the predicted chronological age by the age estimator based on DNAm. The estimator is called the epigenetic clock. The molecular mechanism underlining the epigenetic clock is still unknown. Here, we evaluated the effects of hypoxia and two immortalization factors, hTERT and SV40-LargeT (LT), on the DNAm age of human fibroblasts in vitro. We detected the cell division-associated progression of DNAm age after >10 population doublings. Moreover, the progression of DNAm age was slower under hypoxia (1% oxygen) compared to normoxia (21% oxygen), suggesting that oxygen levels determine the speed of the epigenetic aging. We show that the speed of cell division-associated DNAm age progression depends on the chronological age of the cell donor. hTERT expression did not arrest cell division-associated progression of DNAm age in most cells. SV40LT expression produced inconsistent effects, including rejuvenation of DNAm age. Our results show that a) oxygen and the targets of SV40LT (e.g. p53) modulate epigenetic aging rates and b) the chronological age of donor cells determines the speed of mitosis-associated DNAm age progression in daughter cells.
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140
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Horvath S, Lu AT, Cohen H, Raj K. Rapamycin retards epigenetic ageing of keratinocytes independently of its effects on replicative senescence, proliferation and differentiation. Aging (Albany NY) 2020; 11:3238-3249. [PMID: 31136303 PMCID: PMC6555449 DOI: 10.18632/aging.101976] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/15/2019] [Indexed: 12/22/2022]
Abstract
The advent of epigenetic clocks has prompted questions about the place of epigenetic ageing within the current understanding of ageing biology. It was hitherto unclear whether epigenetic ageing represents a distinct mode of ageing or a manifestation of a known characteristic of ageing. We report here that epigenetic ageing is not affected by replicative senescence, telomere length, somatic cell differentiation, cellular proliferation rate or frequency. It is instead retarded by rapamycin, the potent inhibitor of the mTOR complex which governs many pathways relating to cellular metabolism. Rapamycin, however, is also an effective inhibitor of cellular senescence. Hence cellular metabolism underlies two independent arms of ageing - cellular senescence and epigenetic ageing. The demonstration that a compound that targets metabolism can slow epigenetic ageing provides a long-awaited point-of-entry into elucidating the molecular pathways that underpin the latter. Lastly, we report here an in vitro assay, validated in humans, that recapitulates human epigenetic ageing that can be used to investigate and identify potential interventions that can inhibit or retard it.
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Affiliation(s)
- Steve Horvath
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.,Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ake T Lu
- Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Howard Cohen
- Elizabeth House Medical Practice, Warlingham, Surrey CR6 9LF, United Kingdom
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, United Kingdom
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141
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Sehl ME, Carroll JE, Horvath S, Bower JE. The acute effects of adjuvant radiation and chemotherapy on peripheral blood epigenetic age in early stage breast cancer patients. NPJ Breast Cancer 2020; 6:23. [PMID: 32566744 PMCID: PMC7293278 DOI: 10.1038/s41523-020-0161-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 04/30/2020] [Indexed: 02/07/2023] Open
Abstract
Survival has increased in early stage breast cancer (BC), and the late effects of treatment persist for decades. Molecular mechanisms underlying the acceleration of age-related diseases after chemotherapy and radiotherapy are poorly understood. We examined epigenetic changes in peripheral whole blood cells in early stage BC patients undergoing surgery followed by adjuvant radiotherapy, or surgery followed by adjuvant chemotherapy and radiotherapy. DNA methylation experiments were performed on whole blood samples collected before and after adjuvant therapy. Methylation profiles were used to estimate four measures of epigenetic age acceleration-intrinsic, extrinsic, phenotypic, and Grim-and cell counts. We found significant increases in extrinsic, phenotypic, and Grim epigenetic age acceleration and in estimated proportions of senescent T lymphocytes from pre- to post-treatment. When examining differential effects by treatment category, most of these increases were significant only in women undergoing radiation alone. Further studies are needed to examine whether these effects are related to the risk of cognitive and functional decline in BC survivors.
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Affiliation(s)
- Mary E. Sehl
- Division of Hematology-Oncology, Department of Medicine, David Geffen School of Medicine, Los Angeles, CA USA
- Department of Biomathematics, David Geffen School of Medicine, Los Angeles, CA USA
- UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA USA
| | - Judith E. Carroll
- UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, Los Angeles, CA USA
- Cousins Center for Psychoneuroimmunology, UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, Los Angeles, CA USA
- Department of Biostatistics, Fielding School of Public Health, Los Angeles, CA USA
| | - Julienne E. Bower
- UCLA Jonsson Comprehensive Cancer Center, Los Angeles, CA USA
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, Los Angeles, CA USA
- Cousins Center for Psychoneuroimmunology, UCLA Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA USA
- Department of Psychology, University of California, Los Angeles, CA 90095 USA
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142
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Queen NJ, Hassan QN, Cao L. Improvements to Healthspan Through Environmental Enrichment and Lifestyle Interventions: Where Are We Now? Front Neurosci 2020; 14:605. [PMID: 32655354 PMCID: PMC7325954 DOI: 10.3389/fnins.2020.00605] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 05/18/2020] [Indexed: 12/11/2022] Open
Abstract
Environmental enrichment (EE) is an experimental paradigm that is used to explore how a complex, stimulating environment can impact overall health. In laboratory animal experiments, EE housing conditions typically include larger-than-standard cages, abundant bedding, running wheels, mazes, toys, and shelters which are rearranged regularly to further increase stimulation. EE has been shown to improve multiple aspects of health, including but not limited to metabolism, learning and cognition, anxiety and depression, and immunocompetence. Recent advances in lifespan have led some researchers to consider aging as a risk factor for disease. As such, there is a pressing need to understand the processes by which healthspan can be increased. The natural and predictable changes during aging can be reversed or decreased through EE and its underlying mechanisms. Here, we review the use of EE in laboratory animals to understand mechanisms involved in aging, and comment on relative areas of strength and weakness in the current literature. We additionally address current efforts toward applying EE-like lifestyle interventions to human health to extend healthspan. Although increasing lifespan is a clear goal of medical research, improving the quality of this added time also deserves significant attention. Despite hurdles in translating experimental results toward clinical application, we argue there is great potential in using features of EE toward improving human healthy life expectancy or healthspan, especially in the context of increased global longevity.
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Affiliation(s)
- Nicholas J. Queen
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
| | - Quais N. Hassan
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
- Medical Scientist Training Program, College of Medicine, The Ohio State University, Columbus, OH, United States
| | - Lei Cao
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University, Columbus, OH, United States
- The Ohio State University Comprehensive Cancer Center, Columbus, OH, United States
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143
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Chouliaras L, Kumar GS, Thomas AJ, Lunnon K, Chinnery PF, O'Brien JT. Epigenetic regulation in the pathophysiology of Lewy body dementia. Prog Neurobiol 2020; 192:101822. [PMID: 32407744 DOI: 10.1016/j.pneurobio.2020.101822] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 04/09/2020] [Accepted: 05/06/2020] [Indexed: 12/18/2022]
Abstract
Lewy body dementia encompasses both dementia with Lewy bodies and Parkinson's disease dementia. Although both are common causes of dementia, they remain relatively understudied. The review summarises the clinico-pathologic characteristics of Lewy Body dementia and discusses the genetic and environmental evidence contributing to the risk of developing the condition. Considering that the pathophysiology of Lewy body dementia is not yet fully understood, here we focus on the role of epigenetic mechanisms as potential key mediators of gene-environment interactions in the development of the disease. We examine available important data on genomics, epigenomics, gene expression and proteomic studies in Lewy body dementia on human post-mortem brain and peripheral tissues. Genetic variation and epigenetic modifications in key genes involved in the disorder, such as apolipoprotein E (APOE), α-synuclein (SNCA) and glucocerobrosidase (GBA), suggest a central involvement of epigenetics in DLB but conclusive evidence is scarce. This is due to limitations of existing literature, such as small sample sizes, lack of replication and lack of studies interrogating cell-type specific epigenetic modifications in the brain. Future research in the field can improve the understanding of this common but complex and rapidly progressing type of dementia and potentially open early diagnostic and effective therapeutic targets.
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Affiliation(s)
| | - Gautham S Kumar
- Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Alan J Thomas
- Institute of Neuroscience, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, UK
| | - Katie Lunnon
- College of Medicine and Health, University of Exeter Medical School, Exeter University, Exeter, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences and MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - John T O'Brien
- Department of Psychiatry, University of Cambridge, Cambridge, UK
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144
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Cano A, Sánchez-López E, Ettcheto M, López-Machado A, Espina M, Souto EB, Galindo R, Camins A, García ML, Turowski P. Current advances in the development of novel polymeric nanoparticles for the treatment of neurodegenerative diseases. Nanomedicine (Lond) 2020; 15:1239-1261. [PMID: 32370600 DOI: 10.2217/nnm-2019-0443] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Effective intervention is essential to combat the coming epidemic of neurodegenerative (ND) diseases. Nanomedicine can overcome restrictions of CNS delivery imposed by the blood-brain barrier, and thus be instrumental in preclinical discovery and therapeutic intervention of ND diseases. Polymeric nanoparticles (PNPs) have shown great potential and versatility to encapsulate several compounds simultaneously in controlled drug-delivery systems and target them to the deepest brain regions. Here, we critically review recent advances in the development of drugs incorporated into PNPs and summarize the molecular changes and functional effects achieved in preclinical models of the most common ND disorders. We also briefly discuss the many challenges remaining to translate these findings and technological advances successfully to current clinical settings.
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Affiliation(s)
- Amanda Cano
- Department of Pharmacy, Pharmaceutical Technology & Physical Chemistry, Faculty of Pharmacy & Food Sciences, University of Barcelona, Barcelona, Spain.,Institute of Nanoscience & Nanotechnology (IN2UB), Barcelona, Spain.,Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Elena Sánchez-López
- Department of Pharmacy, Pharmaceutical Technology & Physical Chemistry, Faculty of Pharmacy & Food Sciences, University of Barcelona, Barcelona, Spain.,Institute of Nanoscience & Nanotechnology (IN2UB), Barcelona, Spain.,Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Miren Ettcheto
- Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Department of Pharmacology, Toxicology & Therapeutic Chemistry, Faculty of Pharmacy & Food Sciences, University of Barcelona, Barcelona, Spain.,Unit of Biochemistry & Pharmacology, Faculty of Medicine & Health Sciences, University of Rovira i Virgili, Reus (Tarragona), Spain
| | - Ana López-Machado
- Department of Pharmacy, Pharmaceutical Technology & Physical Chemistry, Faculty of Pharmacy & Food Sciences, University of Barcelona, Barcelona, Spain.,Institute of Nanoscience & Nanotechnology (IN2UB), Barcelona, Spain
| | - Marta Espina
- Department of Pharmacy, Pharmaceutical Technology & Physical Chemistry, Faculty of Pharmacy & Food Sciences, University of Barcelona, Barcelona, Spain.,Institute of Nanoscience & Nanotechnology (IN2UB), Barcelona, Spain
| | - Eliana B Souto
- Department of Pharmaceutical Technology, Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal.,CEB, Centre of Biological Engineering, University of Minho, Campus de Gualtar 4710-057, Braga, Portugal
| | - Ruth Galindo
- Department of Pharmacy, Pharmaceutical Technology & Physical Chemistry, Faculty of Pharmacy & Food Sciences, University of Barcelona, Barcelona, Spain.,Institute of Nanoscience & Nanotechnology (IN2UB), Barcelona, Spain.,Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Unit of Synthesis & Biomedical Applications of Peptides, Department of Biomedical Chemistry, Institute for Advanced Chemistry of Catalonia, Consejo Superior de Investigaciones Científicas (IQAC-CSIC), Barcelona, Spain
| | - Antonio Camins
- Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Madrid, Spain.,Department of Pharmacology, Toxicology & Therapeutic Chemistry, Faculty of Pharmacy & Food Sciences, University of Barcelona, Barcelona, Spain
| | - Maria Luisa García
- Department of Pharmacy, Pharmaceutical Technology & Physical Chemistry, Faculty of Pharmacy & Food Sciences, University of Barcelona, Barcelona, Spain.,Institute of Nanoscience & Nanotechnology (IN2UB), Barcelona, Spain.,Biomedical Research Networking Centre in Neurodegenerative Diseases (CIBERNED), Madrid, Spain
| | - Patric Turowski
- UCL Institute of Ophthalmology, University College of London, London, UK
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145
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Okazaki S, Numata S, Otsuka I, Horai T, Kinoshita M, Sora I, Ohmori T, Hishimoto A. Decelerated epigenetic aging associated with mood stabilizers in the blood of patients with bipolar disorder. Transl Psychiatry 2020; 10:129. [PMID: 32366819 PMCID: PMC7198548 DOI: 10.1038/s41398-020-0813-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 04/15/2020] [Accepted: 04/21/2020] [Indexed: 02/07/2023] Open
Abstract
There is high mortality among patients with bipolar disorder (BD). Studies have reported accelerated biological aging in patients with BD. Recently, Horvath and Hannum et al. independently developed DNA methylation (DNAm) profiles as "epigenetic clocks," which are the most accurate biological age estimate. This led to the development of two accomplished measures of epigenetic age acceleration (EAA) using blood samples, namely, intrinsic and extrinsic EAA (IEAA and EEAA, respectively). IEAA, which is based on Horvath's clock, is independent of blood cell counts and indicates cell-intrinsic aging. On the other hand, EEAA, which is based on Hannum's clock, is associated with age-dependent changes in blood cell counts and indicates immune system aging. Further, Lu et al. developed the "GrimAge" clock, which can strongly predict the mortality risk, and DNAm-based telomere length (DNAmTL). We used a DNAm dataset from whole blood samples obtained from 30 patients with BD and 30 healthy controls. We investigated Horvath EAA, IEAA, Hannum EAA, EEAA, Grim EAA, DNAmTL, and DNAm-based blood cell composition. Compared with controls, there was a decrease in Horvath EAA and IEAA in patients with BD. Further, there was a significant decrease in Horvath EAA and IEAA in patients with BD taking medication combinations of mood stabilizers (including lithium carbonate, sodium valproate, and carbamazepine) than in those taking no medication/monotherapy. This study provides novel evidence indicating decelerated epigenetic aging associated with mood stabilizers in patients with BD.
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Affiliation(s)
- Satoshi Okazaki
- grid.31432.370000 0001 1092 3077Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Shusuke Numata
- grid.267335.60000 0001 1092 3579Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Ikuo Otsuka
- grid.31432.370000 0001 1092 3077Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tadasu Horai
- grid.31432.370000 0001 1092 3077Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Makoto Kinoshita
- grid.267335.60000 0001 1092 3579Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Ichiro Sora
- grid.31432.370000 0001 1092 3077Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Tetsuro Ohmori
- grid.267335.60000 0001 1092 3579Department of Psychiatry, Graduate School of Biomedical Sciences, Tokushima University, Tokushima, Japan
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.
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146
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Chuang YH, Lu AT, Paul KC, Folle AD, Bronstein JM, Bordelon Y, Horvath S, Ritz B. Longitudinal Epigenome-Wide Methylation Study of Cognitive Decline and Motor Progression in Parkinson's Disease. JOURNAL OF PARKINSONS DISEASE 2020; 9:389-400. [PMID: 30958317 DOI: 10.3233/jpd-181549] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND DNA methylation studies in Parkinson's disease (PD) thus far have focused on disease susceptibility but not progression. OBJECTIVE In this epigenome-wide association study (EWAS), we aim to identify methylation markers associated with faster cognitive decline or motor progression in PD. METHODS We included 232 PD patients from the Parkinson's Environment and Gene follow-up study who provided blood samples at enrolment. Information on cognitive and motor function was collected using the Mini-Mental State Examination (MMSE) and Unified Parkinson's Disease Rating Scale (UPDRS). For EWAS analyses, we used a robust measure of correlation: biweight midcorrelations, t-tests, and Cox proportional hazard models. We also conducted weighted correlation network analysis (WGCNA) to identify CpG modules associated with cognitive decline or motor progression in PD. RESULTS Among 197 individuals of European ancestry, with our EWAS approach we identified 7 genome-wide significant CpGs associated with a MMSE 4-point decline and 8 CpGs associated with faster motor progression (i.e., rate of UPDRS increase ≥5-point/year). The most interesting CpGs for cognitive decline include cg17445913 in KCNB1 (cor = 0.36, p = 6.85×10-7) and cg02920897 in DLEU2 (cor = 0.34, p = 3.23×10-6), while for motor progression it was cg01754178 in PTPRN2 (cor = - 0.34, p = 2.07×10-6). In WGCNA, motor progression related modules were enriched for genes related to neuronal synaptic functions, Wnt signaling pathway, and mitochondrial apoptosis. CONCLUSIONS Our study provides the first epigenetic evidence that differential methylation in genes previously identified as being associated with cognitive impairment, neuronal synaptic function, Wnt signaling pathway, and mitochondrial apoptosis is associated with cognitive and motor progression in PD.
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Affiliation(s)
- Yu-Hsuan Chuang
- Department of Epidemiology, Fielding School of Public Health (FSPH), University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Kimberly C Paul
- Department of Epidemiology, Fielding School of Public Health (FSPH), University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Aline D Folle
- Department of Epidemiology, Fielding School of Public Health (FSPH), University of California Los Angeles (UCLA), Los Angeles, CA, USA
| | - Jeff M Bronstein
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Yvette Bordelon
- Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.,Department of Biostatistics, FSPH, UCLA, Los Angeles, CA, USA
| | - Beate Ritz
- Department of Epidemiology, Fielding School of Public Health (FSPH), University of California Los Angeles (UCLA), Los Angeles, CA, USA.,Department of Neurology, David Geffen School of Medicine, UCLA, Los Angeles, CA, USA.,Department of Environmental Health, FSPH, UCLA, Los Angeles, CA, USA
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147
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Huang J, Bai L, Cui B, Wu L, Wang L, An Z, Ruan S, Yu Y, Zhang X, Chen J. Leveraging biological and statistical covariates improves the detection power in epigenome-wide association testing. Genome Biol 2020; 21:88. [PMID: 32252795 PMCID: PMC7132874 DOI: 10.1186/s13059-020-02001-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 03/17/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Epigenome-wide association studies (EWAS), which seek the association between epigenetic marks and an outcome or exposure, involve multiple hypothesis testing. False discovery rate (FDR) control has been widely used for multiple testing correction. However, traditional FDR control methods do not use auxiliary covariates, and they could be less powerful if the covariates could inform the likelihood of the null hypothesis. Recently, many covariate-adaptive FDR control methods have been developed, but application of these methods to EWAS data has not yet been explored. It is not clear whether these methods can significantly improve detection power, and if so, which covariates are more relevant for EWAS data. RESULTS In this study, we evaluate the performance of five covariate-adaptive FDR control methods with EWAS-related covariates using simulated as well as real EWAS datasets. We develop an omnibus test to assess the informativeness of the covariates. We find that statistical covariates are generally more informative than biological covariates, and the covariates of methylation mean and variance are almost universally informative. In contrast, the informativeness of biological covariates depends on specific datasets. We show that the independent hypothesis weighting (IHW) and covariate adaptive multiple testing (CAMT) method are overall more powerful, especially for sparse signals, and could improve the detection power by a median of 25% and 68% on real datasets, compared to the ST procedure. We further validate the findings in various biological contexts. CONCLUSIONS Covariate-adaptive FDR control methods with informative covariates can significantly increase the detection power for EWAS. For sparse signals, IHW and CAMT are recommended.
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Affiliation(s)
- Jinyan Huang
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China.
| | - Ling Bai
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Bowen Cui
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Liang Wu
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Liwen Wang
- Department of General Surgery, Rui-Jin Hospital, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Zhiyin An
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Shulin Ruan
- State Key Laboratory of Medical Genomics, Shanghai Institute of Hematology, National Research Center for Translational Medicine, Rui-Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Jiao Tong University, 197 Ruijin Er Road, Shanghai, 200025, China
| | - Yue Yu
- Division of Digital Health Sciences, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA
| | - Xianyang Zhang
- Department of Statistics, Texas A&M University, Blocker 449D, College Station, TX, 77843, USA.
| | - Jun Chen
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research and Center for Individualized Medicine, Mayo Clinic, 200 1st St SW, Rochester, MN, 55905, USA.
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148
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Lu AT, Quach A, Wilson JG, Reiner AP, Aviv A, Raj K, Hou L, Baccarelli AA, Li Y, Stewart JD, Whitsel EA, Assimes TL, Ferrucci L, Horvath S. DNA methylation GrimAge strongly predicts lifespan and healthspan. Aging (Albany NY) 2020; 11:303-327. [PMID: 30669119 PMCID: PMC6366976 DOI: 10.18632/aging.101684] [Citation(s) in RCA: 985] [Impact Index Per Article: 246.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/22/1969] [Indexed: 12/16/2022]
Abstract
It was unknown whether plasma protein levels can be estimated based on DNA methylation (DNAm) levels, and if so, how the resulting surrogates can be consolidated into a powerful predictor of lifespan. We present here, seven DNAm-based estimators of plasma proteins including those of plasminogen activator inhibitor 1 (PAI-1) and growth differentiation factor 15. The resulting predictor of lifespan, DNAm GrimAge (in units of years), is a composite biomarker based on the seven DNAm surrogates and a DNAm-based estimator of smoking pack-years. Adjusting DNAm GrimAge for chronological age generated novel measure of epigenetic age acceleration, AgeAccelGrim.Using large scale validation data from thousands of individuals, we demonstrate that DNAm GrimAge stands out among existing epigenetic clocks in terms of its predictive ability for time-to-death (Cox regression P=2.0E-75), time-to-coronary heart disease (Cox P=6.2E-24), time-to-cancer (P= 1.3E-12), its strong relationship with computed tomography data for fatty liver/excess visceral fat, and age-at-menopause (P=1.6E-12). AgeAccelGrim is strongly associated with a host of age-related conditions including comorbidity count (P=3.45E-17). Similarly, age-adjusted DNAm PAI-1 levels are associated with lifespan (P=5.4E-28), comorbidity count (P= 7.3E-56) and type 2 diabetes (P=2.0E-26). These DNAm-based biomarkers show the expected relationship with lifestyle factors including healthy diet and educational attainment.Overall, these epigenetic biomarkers are expected to find many applications including human anti-aging studies.
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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
| | - Austin Quach
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Abraham Aviv
- Center of Development and Aging, New Jersey Medical School, Rutgers State University of New Jersey, Newark, NJ 07103, USA
| | - Kenneth Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, United Kingdom
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Andrea A Baccarelli
- Laboratory of Environmental Epigenetics, Departments of Environmental Health Sciences Epidemiology, Columbia University Mailman School of Public Health, New York, NY 10032, USA
| | - Yun Li
- Departments of Genetics, Biostatistics, Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA
| | - James D Stewart
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC 27599, USA.,Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC 27516, USA
| | - Themistocles L Assimes
- Department of Medicine (Division of Cardiovascular Medicine), Stanford University School of Medicine, Stanford, CA 94305, USA.,VA Palo Alto Health Care System, Palo Alto, CA 94304, USA
| | - Luigi Ferrucci
- Longitudinal Studies Section, Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, USA, Baltimore, MD 21224, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA.,Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA 90095, USA
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149
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Gensous N, Garagnani P, Santoro A, Giuliani C, Ostan R, Fabbri C, Milazzo M, Gentilini D, di Blasio AM, Pietruszka B, Madej D, Bialecka-Debek A, Brzozowska A, Franceschi C, Bacalini MG. One-year Mediterranean diet promotes epigenetic rejuvenation with country- and sex-specific effects: a pilot study from the NU-AGE project. GeroScience 2020; 42:687-701. [PMID: 31981007 PMCID: PMC7205853 DOI: 10.1007/s11357-019-00149-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Mediterranean diet has been proposed to promote healthy aging, but its effects on aging biomarkers have been poorly investigated. We evaluated the impact of a 1-year Mediterranean-like diet in a pilot study including 120 elderly healthy subjects from the NU-AGE study (60 Italians, 60 Poles) by measuring the changes in their epigenetic age, assessed by Horvath's clock. We observed a trend towards epigenetic rejuvenation of participants after nutritional intervention. The effect was statistically significant in the group of Polish females and in subjects who were epigenetically older at baseline. A genome-wide association study of epigenetic age changes after the intervention did not return significant (adjusted p value < 0.05) loci. However, we identified small-effect alleles (nominal p value < 10-4), mapping in genes enriched in pathways related to energy metabolism, regulation of cell cycle, and of immune functions. Together, these findings suggest that Mediterranean diet can promote epigenetic rejuvenation but with country-, sex-, and individual-specific effects, thus highlighting the need for a personalized approach to nutritional interventions.
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Affiliation(s)
- Noémie Gensous
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy.
- Center for Applied Biomedical Research (CRBA), St. Orsola-Malpighi University Hospital, Bologna, Italy.
- Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet at Huddinge University Hospital, S-141 86, Stockholm, Sweden.
- CNR Institute of Molecular Genetics "Luigi Luca Cavalli-Sforza", Unit of Bologna, Bologna, Italy.
| | - Aurelia Santoro
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Cristina Giuliani
- Department of Biological, Geological, and Environmental Sciences (BiGeA), Laboratory of Molecular Anthropology and Centre for Genome Biology, University of Bologna, Bologna, Italy
| | - Rita Ostan
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Cristina Fabbri
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Maddalena Milazzo
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
| | - Davide Gentilini
- Department of Brain and Behavioral Sciences, University of Pavia, Pavia, Italy
- Istituto Auxologico Italiano IRCCS, Cusano Milanino, Milan, Italy
| | | | - Barbara Pietruszka
- Department of Human Nutrition, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Dawid Madej
- Department of Human Nutrition, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Agata Bialecka-Debek
- Department of Human Nutrition, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Anna Brzozowska
- Department of Human Nutrition, Warsaw University of Life Sciences-SGGW, Warsaw, Poland
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES), Alma Mater Studiorum - University of Bologna, Via San Giacomo 12, 40126, Bologna, Italy
- Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky Univeristy, Nizhny Novgorod, Russia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, Bologna, Italy
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150
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Salameh Y, Bejaoui Y, El Hajj N. DNA Methylation Biomarkers in Aging and Age-Related Diseases. Front Genet 2020; 11:171. [PMID: 32211026 PMCID: PMC7076122 DOI: 10.3389/fgene.2020.00171] [Citation(s) in RCA: 136] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 02/13/2020] [Indexed: 12/11/2022] Open
Abstract
Recent research efforts provided compelling evidence of genome-wide DNA methylation alterations in aging and age-related disease. It is currently well established that DNA methylation biomarkers can determine biological age of any tissue across the entire human lifespan, even during development. There is growing evidence suggesting epigenetic age acceleration to be strongly linked to common diseases or occurring in response to various environmental factors. DNA methylation based clocks are proposed as biomarkers of early disease risk as well as predictors of life expectancy and mortality. In this review, we will summarize key advances in epigenetic clocks and their potential application in precision health. We will also provide an overview of progresses in epigenetic biomarker discovery in Alzheimer's, type 2 diabetes, and cardiovascular disease. Furthermore, we will highlight the importance of prospective study designs to identify and confirm epigenetic biomarkers of disease.
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Affiliation(s)
| | | | - Nady El Hajj
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar
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