101
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Voisin S, Harvey NR, Haupt LM, Griffiths LR, Ashton KJ, Coffey VG, Doering TM, Thompson JLM, Benedict C, Cedernaes J, Lindholm ME, Craig JM, Rowlands DS, Sharples AP, Horvath S, Eynon N. An epigenetic clock for human skeletal muscle. J Cachexia Sarcopenia Muscle 2020; 11:887-898. [PMID: 32067420 PMCID: PMC7432573 DOI: 10.1002/jcsm.12556] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/15/2020] [Accepted: 01/30/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Ageing is associated with DNA methylation changes in all human tissues, and epigenetic markers can estimate chronological age based on DNA methylation patterns across tissues. However, the construction of the original pan-tissue epigenetic clock did not include skeletal muscle samples and hence exhibited a strong deviation between DNA methylation and chronological age in this tissue. METHODS To address this, we developed a more accurate, muscle-specific epigenetic clock based on the genome-wide DNA methylation data of 682 skeletal muscle samples from 12 independent datasets (18-89 years old, 22% women, 99% Caucasian), all generated with Illumina HumanMethylation (HM) arrays (HM27, HM450, or HMEPIC). We also took advantage of the large number of samples to conduct an epigenome-wide association study of age-associated DNA methylation patterns in skeletal muscle. RESULTS The newly developed clock uses 200 cytosine-phosphate-guanine dinucleotides to estimate chronological age in skeletal muscle, 16 of which are in common with the 353 cytosine-phosphate-guanine dinucleotides of the pan-tissue clock. The muscle clock outperformed the pan-tissue clock, with a median error of only 4.6 years across datasets (vs. 13.1 years for the pan-tissue clock, P < 0.0001) and an average correlation of ρ = 0.62 between actual and predicted age across datasets (vs. ρ = 0.51 for the pan-tissue clock). Lastly, we identified 180 differentially methylated regions with age in skeletal muscle at a false discovery rate < 0.005. However, gene set enrichment analysis did not reveal any enrichment for gene ontologies. CONCLUSIONS We have developed a muscle-specific epigenetic clock that predicts age with better accuracy than the pan-tissue clock. We implemented the muscle clock in an r package called Muscle Epigenetic Age Test available on Bioconductor to estimate epigenetic age in skeletal muscle samples. This clock may prove valuable in assessing the impact of environmental factors, such as exercise and diet, on muscle-specific biological ageing processes.
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Affiliation(s)
- Sarah Voisin
- Institute for Health and Sport, Victoria University, Melbourne, Australia
| | - Nicholas R Harvey
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia.,Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Larisa M Haupt
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Lyn R Griffiths
- Genomics Research Centre, Institute of Health and Biomedical Innovation, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Kevin J Ashton
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia
| | - Vernon G Coffey
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia
| | - Thomas M Doering
- Faculty of Health Sciences & Medicine, Bond University, Gold Coast, Australia.,School of Health, Medical and Applied Sciences, Central Queensland University, Rockhampton, Australia
| | | | - Christian Benedict
- Sleep Research Laboratory, Department of Neuroscience, Uppsala University, Uppsala, Sweden
| | | | - Malene E Lindholm
- Department of Medicine, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jeffrey M Craig
- Centre for Molecular and Medical Research, Deakin University, Geelong, Australia.,Epigenetics, Murdoch Children's Research Institute, Royal Children's Hospital, Melbourne, Australia
| | - David S Rowlands
- School of Sport, Exercise and Nutrition, Massey University, Wellington, New Zealand
| | - Adam P Sharples
- Department of Physical Performance, Norwegian School of Sport Sciences, Oslo, Norway.,Stem Cells, Ageing and Molecular Physiology Unit, Exercise Metabolism and Adaptation Research Group, Research Institute for Sport and Exercise Sciences, Liverpool John Moores University, Liverpool, UK
| | - Steve Horvath
- Department of Human Genetics and Biostatistics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Nir Eynon
- Institute for Health and Sport, Victoria University, Melbourne, Australia
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102
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McKenna BG, Hendrix CL, Brennan PA, Smith AK, Stowe ZN, Newport DJ, Knight AK. Maternal prenatal depression and epigenetic age deceleration: testing potentially confounding effects of prenatal stress and SSRI use. Epigenetics 2020; 16:327-337. [PMID: 32660321 DOI: 10.1080/15592294.2020.1795604] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Previous studies suggest epigenetic alterations may contribute to the association between maternal prenatal depression and adverse offspring outcomes. Developmental researchers have recently begun to examine these associations in relation to epigenetic age acceleration/deceleration, a biomarker of developmental risk that reflects the deviation between epigenetic age and chronological age. In the perinatal period, preliminary studies indicate that maternal prenatal depression may lead to epigenetic age deceleration in newborns, which may predict adverse developmental outcomes. The present study examined the relationship between maternal prenatal exposures (i.e., depression, stress, and SSRI use) and offspring epigenetic age deceleration in 303 mother-offspring dyads. Women were recruited in the first trimester of pregnancy and followed longitudinally until delivery. Maternal depression, perceived stress, and SSRI use were assessed at each prenatal visit. Newborn epigenetic age was determined via cord blood samples. Results indicated maternal prenatal stress was not associated with newborn epigenetic age deceleration (ΔR2 = 0.002; p = 0.37). Maternal prenatal depression was associated with decelerated epigenetic age (ΔR2 = 0.01, p = 0.04), but this relationship did not hold when accounting for maternal use of SSRIs (ΔR2 = 0.002, p = 0.43). Conversely, maternal SSRI use significantly predicted newborn epigenetic age deceleration over and above the influence of maternal depression (ΔR2 = 0.03, p = 0.001). These findings suggest maternal prenatal SSRI use may significantly contribute to the previously documented association between maternal prenatal depression and epigenetic age deceleration. Further studies are needed to examine how these epigenetic differences at birth may contribute to adverse outcomes in later development.
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Affiliation(s)
| | | | | | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University , Atlanta, GA, USA.,Department of Psychiatry and Behavioral Sciences, Emory University , Atlanta, GA, USA
| | - Zachary N Stowe
- Department of Psychiatry, University of Wisconsin , Madison, WI, USA
| | - D Jeffrey Newport
- Department of Psychiatry, University of Texas at Austin , Austin, TX, USA
| | - Anna K Knight
- Department of Gynecology and Obstetrics, Emory University , Atlanta, GA, USA
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103
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Guo J, Wu C, Zhang J, Qi X, Lv S, Jiang S, Zhou T, Lu D, Feng C, Chang X, Zhang Y, Cao Y, Wang G, Zhou Z. Prenatal exposure to mixture of heavy metals, pesticides and phenols and IQ in children at 7 years of age: The SMBCS study. ENVIRONMENT INTERNATIONAL 2020; 139:105692. [PMID: 32251899 DOI: 10.1016/j.envint.2020.105692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 03/24/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE Prenatal exposure to heavy metals, pesticides and phenols has been suggested to interfere with neurodevelopment, but the neurotoxicity of their mixtures is still unclear. We aimed to elucidate the associations of maternal urinary concentrations of selected chemical mixtures with intelligence quotient (IQ) in children. METHODS Maternal urinary concentrations of selected heavy metals, pesticide metabolites, and phenols were quantified in pregnant women who participated in the Sheyang Mini Birth Cohort Study (SMBCS) from June 2009 to January 2010. At age 7 years, child's IQ score was assessed using the Chinese version of Wechsler Intelligence Scale for Children (C-WISC) by trained pediatricians. Generalized linear regression models (GLM), Bayesian kernel machine regression (BKMR) models and elastic net regression (ENR) models were used to assess the associations of urinary concentrations individual chemicals and their mixtures with IQ scores of the 7-year-old children. RESULTS Of 326 mother-child pairs, single-chemical models indicated that prenatal urinary concentrations of lead (Pb) and bisphenol A (BPA) were significantly negatively associated with full intelligence quotient (FIQ) among children aged 7 years [β = -2.31, 95% confidence interval (CI): -4.13, -0.48; p = 0.013, sex interaction p-value = 0.076; β = -1.18, 95% CI: -2.21, -0.15; p = 0.025; sex interaction p-value = 0.296, for Pb and BPA, respectively]. Stratified analysis by sex indicated that the associations were only statistically significant in boys. In multi-chemical BKMR and ENR models, statistically significant inverse association was found between prenatal urinary Pb level and boy's FIQ scores at 7 years. Furthermore, BKMR analysis indicated that the overall mixture was associated with decreases in boy's IQ when all the chemicals' concentrations were at their 75th percentiles or higher, compared to at their 50th percentiles. ENR models revealed that maternal urinary Pb levels were statistically significantly associated with lower FIQ scores (β = -2.20, 95% CI: -4.20, -0.20; p = 0.031). CONCLUSIONS Prenatal exposure to selected chemical mixtures may affect intellectual performance at 7 years of age, particularly in boys. Pb and BPA were suspected as primary chemicals associated with child neurodevelopment.
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Affiliation(s)
- Jianqiu Guo
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education/Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Chunhua Wu
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education/Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China.
| | - Jiming Zhang
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education/Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Xiaojuan Qi
- Zhejiang Provincial Center for Disease Control and Prevention, No. 3399 Binsheng Road, Hangzhou 310051, China
| | - Shenliang Lv
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education/Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Shuai Jiang
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education/Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Tong Zhou
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education/Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Dasheng Lu
- Shanghai Municipal Center for Disease Control and Prevention, No. 1380 Zhongshan West Road, Shanghai 200336, China
| | - Chao Feng
- Shanghai Municipal Center for Disease Control and Prevention, No. 1380 Zhongshan West Road, Shanghai 200336, China
| | - Xiuli Chang
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education/Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Yubin Zhang
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education/Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China
| | - Yang Cao
- Clinical Epidemiology and Biostatistics, School of Medical Sciences, Örebro University, Örebro 70182, Sweden
| | - Guoquan Wang
- Shanghai Municipal Center for Disease Control and Prevention, No. 1380 Zhongshan West Road, Shanghai 200336, China
| | - Zhijun Zhou
- School of Public Health/Key Laboratory of Public Health Safety of Ministry of Education/Key Lab of Health Technology Assessment, National Health Commission of the People's Republic of China, Fudan University, No. 130 Dong'an Road, Shanghai 200032, China.
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104
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York TP, Latendresse SJ, Jackson-Cook C, Lapato DM, Moyer S, Wolen AR, Roberson-Nay R, Do EK, Murphy SK, Hoyo C, Fuemmeler BF, Strauss JF. Replicated umbilical cord blood DNA methylation loci associated with gestational age at birth. Epigenetics 2020; 15:1243-1258. [PMID: 32448018 DOI: 10.1080/15592294.2020.1767277] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
DNA methylation is highly sensitive to in utero perturbations and has an established role in both embryonic development and regulation of gene expression. The foetal genetic component has been previously shown to contribute significantly to the timing of birth, yet little is known about the identity and behaviour of individual genes. The aim of this study was to test the extent genome-wide DNA methylation levels in umbilical cord blood were associated with gestational age at birth (GA). Findings were validated in an independent sample and evidence for the regulation of gene expression was evaluated for cis gene relationships in specimens with multi-omic data. Genome-wide DNA methylation, measured by the Illumina Infinium Human Methylation 450 K BeadChip, was associated with GA for 2,372 CpG probes (5% FDR) in both the Pregnancy, Race, Environment, Genes (PREG) and Newborn Epigenetic Study (NEST) cohorts. Significant probes mapped to 1,640 characterized genes and an association with nearby gene expression measures obtained by the Affymetrix HG-133A microarray was found for 11 genes. Differentially methylated positions were enriched for actively transcribed and enhancer chromatin states, were predominately located outside of CpG islands, and mapped to genes enriched for inflammation and innate immunity ontologies. In both PREG and NEST, the first principal component derived from these probes explained approximately one-half (58.1% and 47.8%, respectively) of the variation in GA. Gene pathways identified are consistent with the hypothesis of pathogen detection and response by the immune system to elicit premature labour as a consequence of unscheduled inflammation.
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Affiliation(s)
- Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University , Richmond, VA, USA
| | - Shawn J Latendresse
- Department of Psychology and Neuroscience, Baylor University , Waco, TX, USA
| | - Colleen Jackson-Cook
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University , Richmond, VA, USA.,Department of Pathology, Virginia Commonwealth University , Richmond, VA, USA
| | - Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA
| | - Sara Moyer
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA
| | - Aaron R Wolen
- Transplant Research Institute, Department of Surgery, University of Tennessee Health Science Center , Memphis, TN, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University , Richmond, VA, USA
| | - Elizabeth K Do
- Department of Health Behavior and Policy, Virginia Commonwealth University , Richmond, VA, USA
| | - Susan K Murphy
- Department of Obstetrics and Gynecology, Duke University , Durham, North Carolina, USA
| | - Catherine Hoyo
- Epidemiology and Environmental Epigenomics Laboratory, Center for Human Health and the Environment, North Carolina State University , Raleigh, NC, USA
| | - Bernard F Fuemmeler
- Department of Health Behavior and Policy, Virginia Commonwealth University , Richmond, VA, USA
| | - Jerome F Strauss
- Department of Human and Molecular Genetics, Virginia Commonwealth University , Richmond, VA, USA.,Department of Obstetrics and Gynecology, Virginia Commonwealth University , Richmond, VA, USA
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105
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Raj K, Horvath S. Current perspectives on the cellular and molecular features of epigenetic ageing. Exp Biol Med (Maywood) 2020; 245:1532-1542. [PMID: 32276545 DOI: 10.1177/1535370220918329] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
IMPACT STATEMENT The field of epigenetic ageing is relatively new, and the speed of its expansion presents a challenge in keeping abreast with new discoveries and their implications. Several reviews have already addressed the great number of pathologies, health conditions, life-style, and external stressors that are associated with changes to the rate of epigenetic ageing. While these associations highlight and affirm the ability of epigenetic clock to capture biologically meaningful changes associated with age, they do not inform us about the underlying mechanisms. In this very early period since the development of the clock, there have been rather limited experimental research that are aimed at uncovering the mechanism. Hence, the perspective that we proffer is derived from available but nevertheless limited lines of evidence that together provide a seemingly coherent narrative that can be tested. This, we believe would be helpful towards uncovering the workings of the epigenetic clock.
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Affiliation(s)
- Kenneth Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, Oxfordshire OX11 0RQ, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, CA 90095, USA and Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, CA 90095, USA
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106
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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: 141] [Impact Index Per Article: 35.3] [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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107
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Hannon E, Schendel D, Ladd-Acosta C, Grove J, Hansen CS, Hougaard DM, Bresnahan M, Mors O, Hollegaard MV, Bækvad-Hansen M, Hornig M, Mortensen PB, Børglum AD, Werge T, Pedersen MG, Nordentoft M, Buxbaum JD, Daniele Fallin M, Bybjerg-Grauholm J, Reichenberg A, Mill J. Variable DNA methylation in neonates mediates the association between prenatal smoking and birth weight. Philos Trans R Soc Lond B Biol Sci 2020; 374:20180120. [PMID: 30966880 DOI: 10.1098/rstb.2018.0120] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
There is great interest in the role epigenetic variation induced by non-genetic exposures may play in the context of health and disease. In particular, DNA methylation has previously been shown to be highly dynamic during the earliest stages of development and is influenced by in utero exposures such as maternal smoking and medication. In this study we sought to identify the specific DNA methylation differences in blood associated with prenatal and birth factors, including birth weight, gestational age and maternal smoking. We quantified neonatal methylomic variation in 1263 infants using DNA isolated from a unique collection of archived blood spots taken shortly after birth (mean = 6.08 days; s.d. = 3.24 days). An epigenome-wide association study (EWAS) of gestational age and birth weight identified 4299 and 18 differentially methylated positions (DMPs) respectively, at an experiment-wide significance threshold of p < 1 × 10-7. Our EWAS of maternal smoking during pregnancy identified 110 DMPs in neonatal blood, replicating previously reported genomic loci, including AHRR. Finally, we tested the hypothesis that DNA methylation mediates the relationship between maternal smoking and lower birth weight, finding evidence that methylomic variation at three DMPs may link exposure to outcome. These findings complement an expanding literature on the epigenomic consequences of prenatal exposures and obstetric factors, confirming a link between the maternal environment and gene regulation in neonates. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.
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Affiliation(s)
- Eilis Hannon
- 1 University of Exeter Medical School, University of Exeter , Exeter , UK
| | - Diana Schendel
- 2 Department of Public Health, Aarhus University , Aarhus , Denmark.,3 National Centre for Register-Based Research, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark
| | - Christine Ladd-Acosta
- 9 Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD , USA.,10 Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD , USA
| | - Jakob Grove
- 4 Centre for Integrative Sequencing, iSEQ, Aarhus University , Aarhus , Denmark.,5 Department of Biomedicine - Human Genetics, Aarhus University , Aarhus , Denmark.,6 Bioinformatics Research Centre, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,12 Centre for Genomics and Personalized Medicine , Aarhus , Denmark
| | - Christine Søholm Hansen
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark.,14 Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services , Copenhagen , Denmark
| | - David Michael Hougaard
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark
| | - Michaeline Bresnahan
- 15 Center for Infection and Immunity, Columbia University Mailman School of Public Health , New York, NY , USA
| | - Ole Mors
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,17 Psychosis Research Unit, Aarhus University Hospital , Risskov , Denmark
| | - Mads Vilhelm Hollegaard
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark
| | - Marie Bækvad-Hansen
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark
| | - Mady Hornig
- 15 Center for Infection and Immunity, Columbia University Mailman School of Public Health , New York, NY , USA.,16 Department of Epidemiology, Columbia University Mailman School of Public Health , New York, NY , USA
| | - Preben Bo Mortensen
- 3 National Centre for Register-Based Research, Aarhus University , Aarhus , Denmark.,7 Centre for Integrated Register-based Research, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark
| | - Anders D Børglum
- 4 Centre for Integrative Sequencing, iSEQ, Aarhus University , Aarhus , Denmark.,5 Department of Biomedicine - Human Genetics, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,12 Centre for Genomics and Personalized Medicine , Aarhus , Denmark
| | - Thomas Werge
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,14 Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services , Copenhagen , Denmark.,18 Department of Clinical Medicine, Mental Health Center Copenhagen, University of Copenhagen , Copenhagen , Denmark
| | - Marianne Giørtz Pedersen
- 3 National Centre for Register-Based Research, Aarhus University , Aarhus , Denmark.,7 Centre for Integrated Register-based Research, Aarhus University , Aarhus , Denmark.,8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark
| | - Merete Nordentoft
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,19 Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen , Copenhagen , Denmark
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- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark
| | - Joseph D Buxbaum
- 20 Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai , New York, NY , USA
| | - M Daniele Fallin
- 10 Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD , USA.,11 Department of Mental Health, Johns Hopkins Bloomberg School of Public Health , Baltimore, MD , USA
| | - Jonas Bybjerg-Grauholm
- 8 The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH , Aarhus , Denmark.,13 Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut , Copenhagen , Denmark
| | - Abraham Reichenberg
- 20 Seaver Autism Center for Research and Treatment, Department of Psychiatry, Icahn School of Medicine at Mount Sinai , New York, NY , USA
| | - Jonathan Mill
- 1 University of Exeter Medical School, University of Exeter , Exeter , UK
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108
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Merid SK, Novoloaca A, Sharp GC, Küpers LK, Kho AT, Roy R, Gao L, Annesi-Maesano I, Jain P, Plusquin M, Kogevinas M, Allard C, Vehmeijer FO, Kazmi N, Salas LA, Rezwan FI, Zhang H, Sebert S, Czamara D, Rifas-Shiman SL, Melton PE, Lawlor DA, Pershagen G, Breton CV, Huen K, Baiz N, Gagliardi L, Nawrot TS, Corpeleijn E, Perron P, Duijts L, Nohr EA, Bustamante M, Ewart SL, Karmaus W, Zhao S, Page CM, Herceg Z, Jarvelin MR, Lahti J, Baccarelli AA, Anderson D, Kachroo P, Relton CL, Bergström A, Eskenazi B, Soomro MH, Vineis P, Snieder H, Bouchard L, Jaddoe VW, Sørensen TIA, Vrijheid M, Arshad SH, Holloway JW, Håberg SE, Magnus P, Dwyer T, Binder EB, DeMeo DL, Vonk JM, Newnham J, Tantisira KG, Kull I, Wiemels JL, Heude B, Sunyer J, Nystad W, Munthe-Kaas MC, Räikkönen K, Oken E, Huang RC, Weiss ST, Antó JM, Bousquet J, Kumar A, Söderhäll C, Almqvist C, Cardenas A, Gruzieva O, Xu CJ, Reese SE, Kere J, Brodin P, Solomon O, Wielscher M, Holland N, Ghantous A, Hivert MF, Felix JF, Koppelman GH, London SJ, Melén E. Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age. Genome Med 2020; 12:25. [PMID: 32114984 PMCID: PMC7050134 DOI: 10.1186/s13073-020-0716-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 01/30/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Preterm birth and shorter duration of pregnancy are associated with increased morbidity in neonatal and later life. As the epigenome is known to have an important role during fetal development, we investigated associations between gestational age and blood DNA methylation in children. METHODS We performed meta-analysis of Illumina's HumanMethylation450-array associations between gestational age and cord blood DNA methylation in 3648 newborns from 17 cohorts without common pregnancy complications, induced delivery or caesarean section. We also explored associations of gestational age with DNA methylation measured at 4-18 years in additional pediatric cohorts. Follow-up analyses of DNA methylation and gene expression correlations were performed in cord blood. DNA methylation profiles were also explored in tissues relevant for gestational age health effects: fetal brain and lung. RESULTS We identified 8899 CpGs in cord blood that were associated with gestational age (range 27-42 weeks), at Bonferroni significance, P < 1.06 × 10- 7, of which 3343 were novel. These were annotated to 4966 genes. After restricting findings to at least three significant adjacent CpGs, we identified 1276 CpGs annotated to 325 genes. Results were generally consistent when analyses were restricted to term births. Cord blood findings tended not to persist into childhood and adolescence. Pathway analyses identified enrichment for biological processes critical to embryonic development. Follow-up of identified genes showed correlations between gestational age and DNA methylation levels in fetal brain and lung tissue, as well as correlation with expression levels. CONCLUSIONS We identified numerous CpGs differentially methylated in relation to gestational age at birth that appear to reflect fetal developmental processes across tissues. These findings may contribute to understanding mechanisms linking gestational age to health effects.
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Affiliation(s)
- Simon Kebede Merid
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Alexei Novoloaca
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Gemma C Sharp
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Leanne K Küpers
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Division of Human Nutrition and Health, Wageningen University & Research, Wageningen, the Netherlands
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Alvin T Kho
- Computational Health Informatics Program, Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Ritu Roy
- Computational Biology And Informatics, University of California, San Francisco, San Francisco, CA, USA
- HDF Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA, USA
| | - Lu Gao
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Isabella Annesi-Maesano
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Pooja Jain
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
| | - Michelle Plusquin
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Hasselt, Belgium
| | - Manolis Kogevinas
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Catherine Allard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
| | - Florianne O Vehmeijer
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Nabila Kazmi
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, USA
| | - Faisal I Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield, Bedfordshire, MK43 0AL, UK
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Sylvain Sebert
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Genomic of Complex diseases, School of Public Health, Imperial College London, London, UK
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
| | - Sheryl L Rifas-Shiman
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Phillip E Melton
- School of Pharmacy and Biomedical Sciences, Faculty of Health Sciences, Curtin University, Bentley, Australia
- Curtin/UWA Centre for Genetic Origins of Health and Disease, School of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Western Australia, Perth, Australia
| | - Debbie A Lawlor
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Carrie V Breton
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Karen Huen
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Nour Baiz
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Luigi Gagliardi
- Division of Neonatology and Pediatrics, Ospedale Versilia, Viareggio, AUSL Toscana Nord Ovest, Pisa, Italy
| | - Tim S Nawrot
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
- Department of Public Health & Primary Care, Leuven University, Leuven, Belgium
| | - Eva Corpeleijn
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Patrice Perron
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Medicine, Université de Sherbrooke, Sherbrooke, Canada
| | - Liesbeth Duijts
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Ellen Aagaard Nohr
- Research Unit for Gynaecology and Obstetrics, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mariona Bustamante
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Susan L Ewart
- College of Veterinary Medicine, Michigan State University, East Lansing, MI, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, USA
| | - Shanshan Zhao
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | | | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marjo-Riitta Jarvelin
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Jari Lahti
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Turku Institute for Advanced Studies, University of Turku, Turku, Finland
| | - Andrea A Baccarelli
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University Medical Center, New York, NY, USA
| | - Denise Anderson
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- Bristol NIHR Biomedical Research Centre, Bristol, UK
| | - Anna Bergström
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Brenda Eskenazi
- Center for Environmental Research and Children's Health (CERCH), University of California, Berkeley, Berkeley, CA, USA
| | - Munawar Hussain Soomro
- Sorbonne Université and INSERM, Epidemiology of Allergic and Respiratory Diseases Department (EPAR), Pierre Louis Institute of Epidemiology and Public Health (IPLESP UMRS 1136), Saint-Antoine Medical School, Paris, France
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Luigi Bouchard
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Department of Biochemistry, Université de Sherbrooke, Sherbrooke, QC, Canada
- Department of medical biology, CIUSSS-SLSJ, Saguenay, QC, Canada
| | - Vincent W Jaddoe
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Thorkild I A Sørensen
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Novo Nordisk Foundation Center for Basic Metabolic Research, Section on Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Department of Public Health, Section of Epidemiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martine Vrijheid
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - S Hasan Arshad
- Clinical & Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK
- The David Hide Asthma and Allergy Research Centre, Newport, Isle of Wight, UK
| | - John W Holloway
- Human Development & Health, Faculty of Medicine, University of Southampton, Southampton, UK
| | | | - Per Magnus
- Norwegian Institute of Public Health, Oslo, Norway
| | - Terence Dwyer
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK
- Murdoch Children's Research Institute, Australia Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Melbourne, Australia
| | - Elisabeth B Binder
- Department of Translational Research in Psychiatry, Max-Planck-Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, USA
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - John Newnham
- Faculty of Health and Medical Sciences, UWA Medical School, University of Western Australia, Perth, Australia
| | - Kelan G Tantisira
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Inger Kull
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs' Children's Hospital, Södersjukhuset, 118 83, Stockholm, Sweden
| | - Joseph L Wiemels
- Center for Genetic Epidemiology, University of Southern California, Los Angeles, USA
| | - Barbara Heude
- INSERM, UMR1153 Epidemiology and Biostatistics Sorbonne Paris Cité Center (CRESS), Research Team on Early life Origins of Health (EarOH), Paris Descartes University, Paris, France
| | - Jordi Sunyer
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | | | - Monica C Munthe-Kaas
- Norwegian Institute of Public Health, Oslo, Norway
- Department of Pediatric Oncology and Hematology, Oslo University Hospital, Oslo, Norway
| | | | - Emily Oken
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
| | - Rae-Chi Huang
- Telethon Kids Institute, University of Western Australia, Perth, Australia
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Josep Maria Antó
- ISGlobal, Barcelona Institute for Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
- IMIM (Hospital del Mar Medical Research Institute), Barcelona, Spain
| | - Jean Bousquet
- University Hospital, Montpellier, France
- Department of Dermatology, Charité, Berlin, Germany
| | - Ashish Kumar
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- University of Basel, Basel, Switzerland
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Cilla Söderhäll
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Catarina Almqvist
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Pediatric Allergy and Pulmonology Unit at Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Andres Cardenas
- Division of Environmental Health Sciences, School of Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
- Centre for Occupational and Environmental Medicine, Stockholm, Stockholm Region, Sweden
| | - Cheng-Jian Xu
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Sarah E Reese
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Folkhälsa Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki Finland, Helsinki, Finland
| | - Petter Brodin
- Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
- Department of Newborn Medicine, Karolinska University Hospital, Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
| | - Olivia Solomon
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Matthias Wielscher
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK
| | - Nina Holland
- Children's Environmental Health Laboratory, University of California, Berkeley, Berkeley, CA, USA
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer, Lyon, France
| | - Marie-France Hivert
- Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke (CHUS), Sherbrooke, QC, Canada
- Division of Chronic Disease Research Across the Lifecourse (CoRAL), Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA
- Diabetes Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Janine F Felix
- The Generation R Study Group, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
- Department of Pediatrics, Erasmus MC, University Medical Center Rotterdam, Rotterdam, the Netherlands
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, GRIAC Research Institute Groningen, Groningen, The Netherlands
| | - Stephanie J London
- Department of Health and Human Services, National Institute of Environmental Health Sciences, National Institutes of Health, RTP, Durham, NC, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
- Department of Clinical Sciences and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.
- Sachs' Children's Hospital, South General Hospital, Stockholm, Sweden.
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Linnér A, Almgren M. Epigenetic programming-The important first 1000 days. Acta Paediatr 2020; 109:443-452. [PMID: 31603247 DOI: 10.1111/apa.15050] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 09/07/2019] [Accepted: 10/08/2019] [Indexed: 12/13/2022]
Abstract
The perinatal period is a time of fast physiological change, including epigenetic programming. Adverse events may lead to epigenetic changes, with implications for health and disease. Our review covers the basics of clinical epigenetics and explores the latest research, including the role of epigenetic processes in complex disease phenotypes, such as neurodevelopmental, neurodegenerative and immunological disorders. Some studies suggest that epigenetic alterations are linked to early life environmental stressors, including mode of delivery, famine, psychosocial stress, severe institutional deprivation and childhood abuse. CONCLUSION: Epigenetic modifications due to perinatal environmental exposures can lead to lifelong, but potentially reversible, phenotypic alterations and disease.
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Affiliation(s)
- Agnes Linnér
- Department of Women’s and Children’s Health Karolinska Institutet Stockholm Sweden
| | - Malin Almgren
- Department of Clinical Neuroscience Karolinska Institutet Stockholm Sweden
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110
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Phang M, Ross J, Raythatha JH, Dissanayake HU, McMullan RL, Kong Y, Hyett J, Gordon A, Molloy P, Skilton MR. Epigenetic aging in newborns: role of maternal diet. Am J Clin Nutr 2020; 111:555-561. [PMID: 31942922 DOI: 10.1093/ajcn/nqz326] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/09/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Epigenetic aging is associated with higher risk of cardiovascular disease, cancer, and all-cause mortality and may be a mechanistic link between early-life exposures, such as maternal dietary characteristics during pregnancy, and risk of adult disease. OBJECTIVES We sought to determine the early-life risk factors for newborn epigenetic aging, specifically maternal dietary macronutrient intake, and whether epigenetic aging is associated with cardiovascular health markers in the newborn. METHODS Epigenetic age acceleration of 169 newborns was measured from saliva using the Horvath age calculator. Maternal diet during pregnancy was assessed using food-frequency questionnaires. RESULTS Newborns with positive age acceleration were more likely to be female and have greater body fatness. Maternal intakes of saturated fat [6.2 wk epigenetic age acceleration (95% CI: 1.0, 11.3) per 5% of energy; P = 0.02] and monounsaturated fat [12.4 wk (95% CI: 4.2, 20.5) per 5% of energy; P = 0.003] were associated with higher epigenetic age acceleration in the newborn. The strongest association of individual fatty acids were for palmitoleic acid (25.3 wk; 95% CI: 11.4, 39.2; P = 0.0004), oleic acid (2.2 wk; 95% CI: 0.8, 3.6; P = 0.002), and palmitic acid (2.9 wk; 95% CI: 1.0, 4.9; P = 0.004) per 1% of energy intake. Vitamin D supplementation was associated with lower epigenetic age acceleration (-8.1 wk; 95% CI: -14.5, -1.7; P = 0.01). Epigenetic age acceleration was associated with aortic intima-media thickness in preterm infants [1.0 µm (95% CI: 0.2, 1.8) per week of epigenetic age acceleration; P = 0.01], but not among those born at term (P = 0.78). Epigenetic age acceleration was not associated with heart rate variability in either preterm or term born infants (both P > 0.2). CONCLUSIONS This study provides evidence of maternal dietary characteristics that are associated with epigenetic aging in the offspring. Prospective intervention studies are required to determine whether such associations are causal.
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Affiliation(s)
- Melinda Phang
- Boden Collaboration for Obesity, Nutrition, Exercise, and Eating Disorders, University of Sydney, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Jason Ross
- CSIRO Health and Biosecurity, Sydney, Australia
| | - Jineel H Raythatha
- Boden Collaboration for Obesity, Nutrition, Exercise, and Eating Disorders, University of Sydney, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Hasthi U Dissanayake
- Boden Collaboration for Obesity, Nutrition, Exercise, and Eating Disorders, University of Sydney, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia.,Sleep Research Group, University of Sydney, Sydney, Australia
| | - Rowena L McMullan
- Boden Collaboration for Obesity, Nutrition, Exercise, and Eating Disorders, University of Sydney, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia.,Royal Prince Alfred Hospital, Sydney, Australia
| | - Yang Kong
- Boden Collaboration for Obesity, Nutrition, Exercise, and Eating Disorders, University of Sydney, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Jon Hyett
- Royal Prince Alfred Hospital, Sydney, Australia
| | - Adrienne Gordon
- Sydney Medical School, University of Sydney, Sydney, Australia.,Royal Prince Alfred Hospital, Sydney, Australia
| | | | - Michael R Skilton
- Boden Collaboration for Obesity, Nutrition, Exercise, and Eating Disorders, University of Sydney, Sydney, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
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111
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Chen L, Wagner CL, Dong Y, Wang X, Shary JR, Huang Y, Hollis BW, Zhu H. Effects of Maternal Vitamin D3 Supplementation on Offspring Epigenetic Clock of Gestational Age at Birth: A Post-hoc Analysis of a Randomized Controlled Trial. Epigenetics 2020; 15:830-840. [PMID: 32089064 DOI: 10.1080/15592294.2020.1734148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Vitamin D could be beneficial for healthy ageing in humans. We previously found that vitamin D supplementation may slow down epigenetic ageing in young African American adults. We tested new epigenetic clocks developed for neonates among a multiethnic population, and tested the hypothesis that maternal vitamin D supplementation would slow down the epigenetic gestational age acceleration (GAA) in newborn babies. Ninety-two pregnant women (aged 29.6 ± 4.8 y; 21% African Americans, 28% Hispanics) were randomized to receive 4000 IU/day vitamin D3 or placebo, plus prenatal vitamins containing 400 IU vitamin D3 during pregnancy in a randomized controlled trial (RCT). Cord blood genome-wide methylation analysis was performed on the Illumina Infinium MethylationEPIC Beadchip. DNA methylation gestational age was calculated based on two calculations developed by Knight and Bohlin. DNA methylation gestational ages calculated by Knight's clock and Bohlin' clock were highly correlated with the gestational age in the placebo group (correlation coefficients = 0.88, p s< 0.001, respectively). GAA was associated with higher birth weight (p = 0.039). In the entire cohort, vitamin D3 supplementation was not associated with GAA (p > 0.05). However, vitamin D3 supplementation decreased GAA by both Knight's clock (β = -0.89, p = 0.047) and Bohlin's clock (β = -0.71, p = 0.005) in the African American participants. Maternal vitamin D3 supplementation may slow down the epigenetic gestational ageing process in African American neonates. Long-term follow-up studies are warranted to determine the role of epigenetic age acceleration in the growth and development of offspring.
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Affiliation(s)
- Li Chen
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
| | - Carol L Wagner
- Department of Pediatrics, Medical University of South Carolina ,SC, USA
| | - Yanbin Dong
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
| | - Xiaoling Wang
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
| | - Judith R Shary
- Department of Pediatrics, Medical University of South Carolina ,SC, USA
| | - Ying Huang
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
| | - Bruce W Hollis
- Department of Pediatrics, Medical University of South Carolina ,SC, USA
| | - Haidong Zhu
- Georgia Prevention Institute, Department of Medicine, Medical College of Georgia, Augusta University , Augusta, GA, USA
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Barišić A, Kolak M, Peterlin A, Tul N, Gašparović Krpina M, Ostojić S, Peterlin B, Pereza N. DNMT3B rs1569686 and rs2424913 gene polymorphisms are associated with positive family history of preterm birth and smoking status. Croat Med J 2020; 61:8-17. [PMID: 32118373 PMCID: PMC7063552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 12/20/2019] [Indexed: 12/17/2023] Open
Abstract
AIM To evaluate the association between spontaneous preterm birth (SPTB) and DNA methyltransferase (DNMT)1, 3A, 3B, and 3L gene polymorphisms, and their contribution to the clinical characteristics of women with SPTB and their newborns. METHODS This case-control study, conducted in 2018, enrolled 162 women with SPTB and 162 women with term delivery. DNMT1 rs2228611, DNMT3A rs1550117, DNMT3B rs1569686, DNMT3B rs2424913, and DNMT3L rs2070565 single nucleotide polymorphisms were genotyped using polymerase chain reaction and restriction fragment length polymorphism methods. The clinical characteristics included in the analysis were family history of preterm birth, maternal smoking, maternal age, gestational week at delivery, and fetal birth weight. RESULTS DNMT gene polymorphisms were not significantly associated with SPTB. DNMT3B rs1569686 and rs2424913 minor alleles (T) were significantly more frequent in women with familial PTB than in women with non-familial PTB, increasing the odds for familial PTB 3.30 and 3.54 times under dominant genetic models. They were also significantly more frequent in women with SPTB who smoked before pregnancy, reaching the most significant association under additive genetic models (odds ratio 6.86, 95% confidence interval 2.25-20.86, P<0.001; odds ratio 3.77, 95% confidence interval 1.36-10.52, P=0.011, respectively). CONCLUSIONS DNMT3B rs1569686 and rs2424913 gene polymorphisms might be associated with positive family history of PTB and smoking status.
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Affiliation(s)
| | | | | | | | | | | | | | - Nina Pereza
- Nina Pereza, Department of Medical Biology and Genetics, Faculty of Medicine, University of Rijeka, B. Branchetta 20, 51000 Rijeka, Croatia,
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113
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Ferrucci L, Gonzalez‐Freire M, Fabbri E, Simonsick E, Tanaka T, Moore Z, Salimi S, Sierra F, de Cabo R. Measuring biological aging in humans: A quest. Aging Cell 2020; 19:e13080. [PMID: 31833194 PMCID: PMC6996955 DOI: 10.1111/acel.13080] [Citation(s) in RCA: 326] [Impact Index Per Article: 81.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 10/22/2019] [Accepted: 10/27/2019] [Indexed: 12/16/2022] Open
Abstract
The global population of individuals over the age of 65 is growing at an unprecedented rate and is expected to reach 1.6 billion by 2050. Most older individuals are affected by multiple chronic diseases, leading to complex drug treatments and increased risk of physical and cognitive disability. Improving or preserving the health and quality of life of these individuals is challenging due to a lack of well-established clinical guidelines. Physicians are often forced to engage in cycles of "trial and error" that are centered on palliative treatment of symptoms rather than the root cause, often resulting in dubious outcomes. Recently, geroscience challenged this view, proposing that the underlying biological mechanisms of aging are central to the global increase in susceptibility to disease and disability that occurs with aging. In fact, strong correlations have recently been revealed between health dimensions and phenotypes that are typical of aging, especially with autophagy, mitochondrial function, cellular senescence, and DNA methylation. Current research focuses on measuring the pace of aging to identify individuals who are "aging faster" to test and develop interventions that could prevent or delay the progression of multimorbidity and disability with aging. Understanding how the underlying biological mechanisms of aging connect to and impact longitudinal changes in health trajectories offers a unique opportunity to identify resilience mechanisms, their dynamic changes, and their impact on stress responses. Harnessing how to evoke and control resilience mechanisms in individuals with successful aging could lead to writing a new chapter in human medicine.
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Affiliation(s)
- Luigi Ferrucci
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Marta Gonzalez‐Freire
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Elisa Fabbri
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
- Department of Medical and Surgical SciencesUniversity of BolognaBolognaItaly
| | - Eleanor Simonsick
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Toshiko Tanaka
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Zenobia Moore
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
| | - Shabnam Salimi
- Department of Epidemiology and Public HealthUniversity of Maryland School of MedicineBaltimoreMDUSA
| | - Felipe Sierra
- Division of Aging BiologyNational Institute on AgingNIHBethesdaMDUSA
| | - Rafael de Cabo
- Translational Gerontology BranchBiomedical Research CenterNational Institute on AgingNational Institutes of HealthBaltimoreMDUSA
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Maternal cardiometabolic factors and genetic ancestry influence epigenetic aging of the placenta. J Dev Orig Health Dis 2020; 12:34-41. [PMID: 31948495 DOI: 10.1017/s2040174419000801] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Disruption of physiological aging of the placenta can lead to pregnancy complications and increased risk for cardiometabolic diseases during childhood and adulthood. Maternal metabolic and genetic factors need to operate in concert with placental development for optimal pregnancy outcome. However, it is unknown whether maternal cardiometabolic status and genetic ancestry contribute to differences in placental epigenetic age acceleration (PAA). We investigated whether maternal prepregnancy obesity, gestational weight gain (GWG), blood pressure, and genetic ancestry influence PAA. Among 301 pregnant women from 4 race/ethnic groups who provided placenta samples at delivery as part of the National Institute of Child Health and Human Development Fetal Growth Studies, placental DNA methylation age was estimated using 62 CpGs known to predict placental aging. PAA was defined to be the difference between placental DNA methylation age and gestational age at birth. Percentage of genetic ancestries was estimated using genotype data. We found that a 1 kg/week increase in GWG was associated with up to 1.71 (95% CI: -3.11, -0.32) week lower PAA. Offspring Native American ancestry and African ancestry were associated, respectively, with higher and lower PAA among Hispanics, and maternal East Asian ancestry was associated with lower PAA among Asians (p < 0.05). Among mothers with a male offspring, blood pressure was associated with lower PAA across all three trimesters (p < 0.05), prepregnancy obesity compared to normal weight was associated with 1.24 (95% CI: -2.24, -0.25) week lower PAA. In summary, we observed that maternal cardiometabolic factors and genetic ancestry influence placental epigenetic aging and some of these influences may be male offspring-specific.
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115
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Hüls A, Czamara D. Methodological challenges in constructing DNA methylation risk scores. Epigenetics 2020; 15:1-11. [PMID: 31318318 PMCID: PMC6961658 DOI: 10.1080/15592294.2019.1644879] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/28/2019] [Accepted: 07/09/2019] [Indexed: 12/23/2022] Open
Abstract
Polygenic approaches often access more variance of complex traits than is possible by single variant approaches. For genotype data, genetic risk scores (GRS) are widely used for risk prediction as well as in association and interaction studies. Recently, interest has been growing in transferring GRS approaches to DNA methylation data (methylation risk scores, MRS), which can be used 1) as biomarkers for environmental exposures, 2) in association analyses in which single CpG sites do not achieve significance, 3) as dimension reduction approach in interaction and mediation analyses, and 4) to predict individual risks of disease or treatment success. Most GRS approaches can directly be transferred to methylation data. However, since methylation data is more sensitive to confounding, e.g. by age and tissue, it is more complex to find appropriate external weights. In this review, we will outline the adaption of current GRS approaches to methylation data and highlight occurring challenges.
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Affiliation(s)
- Anke Hüls
- Department of Human Genetics, Emory University, Atlanta, GA, USA
- Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, and Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Darina Czamara
- Department of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
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116
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Bergallo M, Marozio L, Botta G, Tancredi A, Daprà V, Galliano I, Montanari P, Coscia A, Benedetto C, Tovo PA. Human Endogenous Retroviruses Are Preferentially Expressed in Mononuclear Cells From Cord Blood Than From Maternal Blood and in the Fetal Part of Placenta. Front Pediatr 2020; 8:244. [PMID: 32478020 PMCID: PMC7240011 DOI: 10.3389/fped.2020.00244] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 04/20/2020] [Indexed: 12/11/2022] Open
Abstract
Background: Placenta shows high transcription levels of human endogenous retroviruses (HERVs) that are overexpressed during embryonic and fetal development. Methods: In order to gather further information on the degree of HERV activation in maternal and fetal tissues we assessed the transcription levels of pol genes of HERV-H, -K, and -W in PBMCs of newborns and their mothers as well as in chorion (fetal part) and decidua basalis (maternal part) of the placenta using a real time PCR assay. Results: Transcripts of pol genes of the three HERV families were significantly higher in mononuclear cells from cord blood than from maternal blood and in the fetal part than in the maternal part of the placenta. Conclusions: The HERV over-expressions in cells and tissues of the offspring are further clues that they play pivotal physiologic roles during early life events and suggest that HERV-driven abnormalities of pregnancy and fetal development may derive mostly from the conceptus, not from the mother.
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Affiliation(s)
- Massimiliano Bergallo
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy.,Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Luca Marozio
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, Turin, Italy
| | - Giovanni Botta
- Department of Pathology AOU Città della Salute e della Scienza di Torino, Turin, Italy
| | - Annalisa Tancredi
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, Turin, Italy
| | - Valentina Daprà
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy.,Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Ilaria Galliano
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy.,Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Paola Montanari
- Pediatric Laboratory, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy.,Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Alessandra Coscia
- Neonatology Unit, Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
| | - Chiara Benedetto
- Department of Surgical Sciences, Obstetrics and Gynecology 1, University of Turin, Turin, Italy
| | - Pier Angelo Tovo
- Department of Pediatric Sciences and Public Health, University of Turin, Turin, Italy
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117
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Bright HD, Howe LD, Khouja JN, Simpkin AJ, Suderman M, O'Keeffe LM. Epigenetic gestational age and trajectories of weight and height during childhood: a prospective cohort study. Clin Epigenetics 2019; 11:194. [PMID: 31842976 PMCID: PMC6916215 DOI: 10.1186/s13148-019-0761-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2019] [Accepted: 10/09/2019] [Indexed: 11/21/2022] Open
Abstract
Background Differences between an individual’s estimated epigenetic gestational age (EGA) and their actual gestational age (GA) are defined as gestational age acceleration (GAA). GAA is associated with increased birthweight and birth length. Whether these associations persist through childhood is yet to be investigated. Methods We examined the association between GAA and trajectories of height and weight from birth to 10 years (n = 785) in a British birth cohort study, the Avon Longitudinal Study of Parents and Children (ALSPAC). EGA of participants was estimated using DNA methylation data from cord blood using a recently developed prediction model. GAA of participants, measured in weeks, was calculated as the residuals from a regression model of EGA on actual GA. Analyses were performed using linear spline multilevel models and adjusted for maternal age, maternal pre-pregnancy BMI, maternal smoking during pregnancy, and maternal education. Results In adjusted analyses, offspring with a one-week greater GAA were born on average 0.14 kg heavier (95% confidence interval (CI) 0.09, 0.19) and 0.55 cm taller (95% CI 0.33, 0.78) at birth. These differences in weight persisted up to approximately age 9 months but thereafter began to attenuate. From age 5 years onwards, the association between GAA and weight reversed such that GAA was associated with lower weight and this association strengthened with age (mean difference at age 10 years − 0.60 kg, 95% CI − 1.19, − 0.01). Differences in height persisted only up to age 9 months (mean difference at 9 months 0.15 cm, 95% CI − 0.09, 0.39). From age 9 months to age 10 years, offspring with a one-week greater GAA were of comparable height with those with no GAA (mean difference at age 10 years − 0.07 cm, 95% CI − 0.64, 0.50). Conclusions Gestational age acceleration is associated with increased birth weight and length and these differences persist to age 9 months. From age 5 years onwards, the association of GAA and weight reverses such that by age 10 years, greater GAA is associated with lower childhood weight. Further work is required to examine whether the weight effects of GAA strengthen through adolescence and into early adulthood.
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Affiliation(s)
- Harold D Bright
- Bristol Medical School, Faculty of Health Sciences, University of Bristol, First Floor, 5 Tyndall Avenue, Bristol, BS8 1UD, UK.
| | - Laura D Howe
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Jasmine N Khouja
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,School of Psychological Science at the University of Bristol, 12a Priory Road, Bristol, BS8 1TU, UK
| | - Andrew J Simpkin
- School of Mathematics, Statistics and Applied Mathematics, National University of Ireland, University Road, Galway, H91 TK33, Ireland
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
| | - Linda M O'Keeffe
- MRC Integrative Epidemiology Unit at the University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Oakfield House, Oakfield Grove, Bristol, BS8 2BN, UK
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118
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Palma-Gudiel H, Fañanás L, Horvath S, Zannas AS. Psychosocial stress and epigenetic aging. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2019; 150:107-128. [PMID: 32204828 DOI: 10.1016/bs.irn.2019.10.020] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aging is the single most important risk factor for diseases that are currently the leading causes of morbidity and mortality. However, there is considerable inter-individual variability in risk for aging-related disease, and studies suggest that biological age can be influenced by multiple factors, including exposure to psychosocial stress. Among markers of biological age that can be affected by stress, the present article focuses on the so-called measures of epigenetic aging: DNA methylation-based age predictors that are measured in a range of tissues, including the brain, and can predict lifespan and healthspan. We review evidence linking exposure to diverse types of psychosocial stress, including early-life stress, cumulative stressful experiences, and low socioeconomic status, with accelerated epigenetic aging as a putative mediator of the effects of psychosocial environment on health and disease. The chapter also discusses methodological differences that may contribute to discordant findings across studies to date and plausible mechanisms that may underlie the effects of stress on the aging epigenome. Future studies examining the effects of adversity on epigenetic and other indicators of biological weathering may provide important insights into the pathogenesis of aging-related disease states.
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Affiliation(s)
- Helena Palma-Gudiel
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona (UB), Barcelona, Spain; Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Madrid, Spain
| | - Lourdes Fañanás
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona (UB), Barcelona, Spain; Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Madrid, Spain
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, United States; Department of Biostatistics, Fielding School of Public Health, University of California Los Angeles, Los Angeles, CA, United States
| | - Anthony S Zannas
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, United States; Department of Genetics, University of North Carolina, Chapel Hill, NC, United States; Department of Psychiatry and Behavioral Sciences, Duke University Medical Center, Durham, NC, United States; Institute for Trauma Recovery, University of North Carolina School of Medicine, Chapel Hill, NC, United States; Neuroscience Curriculum, University of North Carolina, Chapel Hill, NC, United States.
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119
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Schmeer C, Kretz A, Wengerodt D, Stojiljkovic M, Witte OW. Dissecting Aging and Senescence-Current Concepts and Open Lessons. Cells 2019; 8:cells8111446. [PMID: 31731770 PMCID: PMC6912776 DOI: 10.3390/cells8111446] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 11/12/2019] [Accepted: 11/13/2019] [Indexed: 01/10/2023] Open
Abstract
In contrast to the programmed nature of development, it is still a matter of debate whether aging is an adaptive and regulated process, or merely a consequence arising from a stochastic accumulation of harmful events that culminate in a global state of reduced fitness, risk for disease acquisition, and death. Similarly unanswered are the questions of whether aging is reversible and can be turned into rejuvenation as well as how aging is distinguishable from and influenced by cellular senescence. With the discovery of beneficial aspects of cellular senescence and evidence of senescence being not limited to replicative cellular states, a redefinition of our comprehension of aging and senescence appears scientifically overdue. Here, we provide a factor-based comparison of current knowledge on aging and senescence, which we converge on four suggested concepts, thereby implementing the newly emerging cellular and molecular aspects of geroconversion and amitosenescence, and the signatures of a genetic state termed genosenium. We also address the possibility of an aging-associated secretory phenotype in analogy to the well-characterized senescence-associated secretory phenotype and delineate the impact of epigenetic regulation in aging and senescence. Future advances will elucidate the biological and molecular fingerprints intrinsic to either process.
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Affiliation(s)
- Christian Schmeer
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
- Correspondence:
| | - Alexandra Kretz
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Diane Wengerodt
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
| | - Milan Stojiljkovic
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
| | - Otto W. Witte
- Hans-Berger Department of Neurology, Jena University Hospital, 07747 Jena, Thuringia, Germany; (A.K.); (D.W.); (M.S.); (O.W.W.)
- Jena Center for Healthy Ageing, Jena University Hospital, 07747 Jena, Thuringia, Germany
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120
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Prenatal exposure to traffic-related air pollution, the gestational epigenetic clock, and risk of early-life allergic sensitization. J Allergy Clin Immunol 2019; 144:1729-1731.e5. [PMID: 31470034 DOI: 10.1016/j.jaci.2019.07.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 07/18/2019] [Accepted: 07/26/2019] [Indexed: 01/29/2023]
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121
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Engebretsen S, Bohlin J. Statistical predictions with glmnet. Clin Epigenetics 2019; 11:123. [PMID: 31443682 PMCID: PMC6708235 DOI: 10.1186/s13148-019-0730-1] [Citation(s) in RCA: 458] [Impact Index Per Article: 91.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 08/16/2019] [Indexed: 11/28/2022] Open
Abstract
Elastic net type regression methods have become very popular for prediction of certain outcomes in epigenome-wide association studies (EWAS). The methods considered accept biased coefficient estimates in return for lower variance thus obtaining improved prediction accuracy. We provide guidelines on how to obtain parsimonious models with low mean squared error and include easy to follow walk-through examples for each step in R.
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Affiliation(s)
- Solveig Engebretsen
- Division for Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway.,Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Jon Bohlin
- Division for Infection Control and Environmental Health, Department of Infectious Disease Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway. .,Centre for Fertility and Health (CEFH), Norwegian Institute of Public Health, Oslo, Norway. .,Faculty of Veterinary Science, Department of Production Animals, Norwegian University of Life Science, Ås, Norway.
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122
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Falick Michaeli T, Spiro A, Sabag O, Karavani G, Yagel S, Eventov-Friedman S, Cedar H, Bergman Y, Gielchinsky Y. Determining gestational age using genome methylation profile: A novel approach for fetal medicine. Prenat Diagn 2019; 39:1005-1010. [PMID: 31330572 DOI: 10.1002/pd.5535] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 07/03/2019] [Accepted: 07/11/2019] [Indexed: 01/09/2023]
Abstract
Gestational age determination by traditional tools (last menstrual period, ultrasonography measurements and Ballard Maturational Assessment in newborns) has major limitations and therefore there is a need to find different approaches. In this study, we looked for a molecular marker that can be used to determine the accurate gestational age of the newborn. To this end, we performed reduced representation bisulfite sequencing (RRBS) on 41 cord blood and matching placenta samples from women between 25 and 40 weeks of gestation and generated an epigenetic clock based on the methylation level at different loci in the genome. We identified a set of 332 differentially methylated regions (DMRs) that undergo demethylation in late gestational age in cord blood cells and can predict the gestational age (r = -.7, P = 2E-05). Once the set of 411 DMRs that undergo de novo methylation in late gestational age was used in combination with the first set, it generated a more accurate clock (R = .77, P = 1.87E-05). We have compared gestational age determined by Ballard score assessment with our epigenetic clock and found high concordance. Taken together, this study demonstrates that DNA methylation can accurately predict gestational age and thus may serve as a good clinical predictor.
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Affiliation(s)
- Tal Falick Michaeli
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Adam Spiro
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Ofra Sabag
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Gilad Karavani
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Simha Yagel
- Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | | | - Howard Cedar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Yehudit Bergman
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel
| | - Yuval Gielchinsky
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Hebrew University Medical School, Jerusalem, Israel.,Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
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123
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Tekola-Ayele F, Workalemahu T, Gorfu G, Shrestha D, Tycko B, Wapner R, Zhang C, Louis GMB. Sex differences in the associations of placental epigenetic aging with fetal growth. Aging (Albany NY) 2019; 11:5412-5432. [PMID: 31395791 PMCID: PMC6710059 DOI: 10.18632/aging.102124] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Accepted: 07/21/2019] [Indexed: 12/15/2022]
Abstract
Identifying factors that influence fetal growth in a sex-specific manner can help unravel mechanisms that explain sex differences in adverse neonatal outcomes and in-utero origins of cardiovascular disease disparities. Premature aging of the placenta, a tissue that supports fetal growth and exhibits sex-specific epigenetic changes, is associated with pregnancy complications. Using DNA methylation-based age estimator, we investigated the sex-specific relationship of placental epigenetic aging with fetal growth across 13-40 weeks gestation, neonatal size, and risk of low birth weight. Placental epigenetic age acceleration (PAA), the difference between DNA methylation age and gestational age, was associated with reduced fetal weight among males but with increased fetal weight among females. PAA was inversely associated with fetal weight, abdominal circumference, and biparietal diameter at 32-40 weeks among males but was positively associated with all growth measures among females across 13-40 weeks. A 1-week increase in PAA was associated with 2-fold (95% CI 1.2, 3.2) increased odds for low birth weight and 1.5-fold (95% CI 1.1, 2.0) increased odds for small-for-gestational age among males. In all, fetal growth was significantly reduced in males but not females exposed to a rapidly aging placenta. Epigenetic aging of the placenta may underlie sex differences in neonatal outcomes.
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Affiliation(s)
- Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Tsegaselassie Workalemahu
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Gezahegn Gorfu
- Department of Clinical Laboratory Science, College of Nursing and Allied Health Sciences, Howard University, Washington, DC 20059, USA
| | - Deepika Shrestha
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Benjamin Tycko
- Hackensack-Meridian Health Center for Discovery and Innovation and the Hackensack-Meridian Health School of Medicine at Seton Hall University, Nutley, NJ 07110, USA
| | - Ronald Wapner
- Department of Obstetrics and Gynecology, Columbia University, New York, NY 10032, USA
| | - Cuilin Zhang
- Epidemiology Branch, Division of Intramural Population Health Research, National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Germaine M. Buck Louis
- Dean’s Office, College of Health and Human Services, George Mason University, Fairfax, VA 22030, USA
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124
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Li C, Gao W, Gao Y, Yu C, Lv J, Lv R, Duan J, Sun Y, Guo X, Cao W, Li L. Age prediction of children and adolescents aged 6-17 years: an epigenome-wide analysis of DNA methylation. Aging (Albany NY) 2019; 10:1015-1026. [PMID: 29754148 PMCID: PMC5990383 DOI: 10.18632/aging.101445] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/08/2018] [Indexed: 02/06/2023]
Abstract
The DNA methylation age, a good reflection of human aging process, has been used to predict chronological age of adults and newborns. However, the prediction model for children and adolescents was absent. In this study, we aimed to generate a prediction model of chronological age for children and adolescents aged 6-17 years by using age-specific DNA methylation patterns from 180 Chinese twin individuals. We identified 6,350 age-related CpGs from the epigenome-wide association analysis (N=179). 116 known age-related sites in children were confirmed. 83 novel CpGs were selected as predictors from all age-related loci by elastic net regression and they could accurately predict the chronological age of the pediatric population, with a correlation of 0.99 and the error of 0.23 years in the training dataset (N=90). The predictive accuracy in the testing dataset (N=89) was high (correlation=0.93, error=0.62 years). Among the 83 predictors, 49 sites were novel probes not existing on the Illumina 450K BeadChip. The top two predictors of age were on the PRKCB and REG4 genes, which are associated with diabetes and cancer, respectively. Our results suggest that the chronological age can be accurately predicted among children and adolescents aged 6-17 years by 83 newly identified CpG sites.
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Affiliation(s)
- Chunxiao Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Wenjing Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Ying Gao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Canqing Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Jun Lv
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Ruoran Lv
- Beijing Center for Disease Control and Prevention, Beijing 100013, China
| | - Jiali Duan
- Beijing Center for Disease Control and Prevention, Beijing 100013, China
| | - Ying Sun
- Beijing Center for Disease Control and Prevention, Beijing 100013, China
| | - Xianghui Guo
- Chaoyang District Center for Disease Control and Prevention, Beijing 100021, China
| | - Weihua Cao
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
| | - Liming Li
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China
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125
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Abstract
Identifying and validating molecular targets of interventions that extend the human health span and lifespan has been difficult, as most clinical biomarkers are not sufficiently representative of the fundamental mechanisms of ageing to serve as their indicators. In a recent breakthrough, biomarkers of ageing based on DNA methylation data have enabled accurate age estimates for any tissue across the entire life course. These 'epigenetic clocks' link developmental and maintenance processes to biological ageing, giving rise to a unified theory of life course. Epigenetic biomarkers may help to address long-standing questions in many fields, including the central question: why do we age?
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126
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Lee Y, Choufani S, Weksberg R, Wilson SL, Yuan V, Burt A, Marsit C, Lu AT, Ritz B, Bohlin J, Gjessing HK, Harris JR, Magnus P, Binder AM, Robinson WP, Jugessur A, Horvath S. Placental epigenetic clocks: estimating gestational age using placental DNA methylation levels. Aging (Albany NY) 2019; 11:4238-4253. [PMID: 31235674 PMCID: PMC6628997 DOI: 10.18632/aging.102049] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 06/17/2019] [Indexed: 12/12/2022]
Abstract
The human pan-tissue epigenetic clock is widely used for estimating age across the entire lifespan, but it does not lend itself well to estimating gestational age (GA) based on placental DNAm methylation (DNAm) data. We replicate previous findings demonstrating a strong correlation between GA and genome-wide DNAm changes. Using substantially more DNAm arrays (n=1,102 in the training set) than a previous study, we present three new placental epigenetic clocks: 1) a robust placental clock (RPC) which is unaffected by common pregnancy complications (e.g., gestational diabetes, preeclampsia), and 2) a control placental clock (CPC) constructed using placental samples from pregnancies without known placental pathology, and 3) a refined RPC for uncomplicated term pregnancies. These placental clocks are highly accurate estimators of GA based on placental tissue; e.g., predicted GA based on RPC is highly correlated with actual GA (r>0.95 in test data, median error less than one week). We show that epigenetic clocks derived from cord blood or other tissues do not accurately estimate GA in placental samples. While fundamentally different from Horvath's pan-tissue epigenetic clock, placental clocks closely track fetal age during development and may have interesting applications.
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Affiliation(s)
- Yunsung Lee
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
| | - Sanaa Choufani
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Rosanna Weksberg
- Genetics and Genome Biology Program, Research Institute, The Hospital for Sick Children and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - Samantha L. Wilson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Victor Yuan
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Amber Burt
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Carmen Marsit
- Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, GA 30322, USA
| | - Ake T. Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Beate Ritz
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Jon Bohlin
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Håkon K. Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Jennifer R. Harris
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Alexandra M. Binder
- Department of Epidemiology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Wendy P. Robinson
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- B.C. Children’s Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - 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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127
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Li P, Marshall L, Oh G, Jakubowski JL, Groot D, He Y, Wang T, Petronis A, Labrie V. Epigenetic dysregulation of enhancers in neurons is associated with Alzheimer's disease pathology and cognitive symptoms. Nat Commun 2019; 10:2246. [PMID: 31113950 PMCID: PMC6529540 DOI: 10.1038/s41467-019-10101-7] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 04/18/2019] [Indexed: 12/23/2022] Open
Abstract
Epigenetic control of enhancers alters neuronal functions and may be involved in Alzheimer’s disease (AD). Here, we identify enhancers in neurons contributing to AD by comprehensive fine-mapping of DNA methylation at enhancers, genome-wide. We examine 1.2 million CpG and CpH sites in enhancers in prefrontal cortex neurons of individuals with no/mild, moderate, and severe AD pathology (n = 101). We identify 1224 differentially methylated enhancer regions; most of which are hypomethylated at CpH sites in AD neurons. CpH methylation losses occur in normal aging neurons, but are accelerated in AD. Integration of epigenetic and transcriptomic data demonstrates a pro-apoptotic reactivation of the cell cycle in post-mitotic AD neurons. Furthermore, AD neurons have a large cluster of significantly hypomethylated enhancers in the DSCAML1 gene that targets BACE1. Hypomethylation of these enhancers in AD is associated with an upregulation of BACE1 transcripts and an increase in amyloid plaques, neurofibrillary tangles, and cognitive decline. Epigenetic control of enhancers may contribute to neurological disease. Here the authors carry out genome-wide analysis of DNA methylation in neurons isolated postmortem from patients with Alzheimer’s disease.
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Affiliation(s)
- Peipei Li
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Lee Marshall
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Gabriel Oh
- Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada
| | - Jennifer L Jakubowski
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA
| | - Daniel Groot
- Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada
| | - Yu He
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Ting Wang
- Department of Genetics, Washington University in St. Louis, St. Louis, MO, 63130, USA
| | - Arturas Petronis
- Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada.,Institute of Biotechnology, Life Sciences Center, Vilnius University, LT-10257, Vilnius, Lithuania
| | - Viviane Labrie
- Center for Neurodegenerative Science, Van Andel Research Institute, Grand Rapids, MI, 49503, USA. .,Centre for Addiction and Mental Health, Toronto, M5T 1R8, ON, Canada. .,Division of Psychiatry and Behavioral Medicine, College of Human Medicine, Michigan State University, Grand Rapids, MI, 49503, USA.
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128
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Gillespie SL, Hardy LR, Anderson CM. Patterns of DNA methylation as an indicator of biological aging: State of the science and future directions in precision health promotion. Nurs Outlook 2019; 67:337-344. [PMID: 31248628 DOI: 10.1016/j.outlook.2019.05.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 05/13/2019] [Accepted: 05/15/2019] [Indexed: 12/13/2022]
Abstract
BACKGROUND A rapidly expanding literature suggests that individuals of the same chronological age show significant variation in biological age. PURPOSE The purpose of this article is to review the literature surrounding epigenetic age as estimated by DNA methylation, involving the addition or removal of methyl groups to DNA that can alter gene expression without changing the DNA sequence. METHODS This state of the science literature review summarizes current approaches in epigenetic age determination and applications of aging algorithms. FINDINGS A number of algorithms estimate epigenetic age using DNA methylation markers, primarily among adults. Algorithm application has focused on determining predictive value for risk of disease and death and identifying antecedents to age acceleration. Several studies have incorporated epigenetic age to evaluate intervention effectiveness. DISCUSSION As the research community continues to refine aging algorithms, there may be opportunity to promote health from a precision health perspective.
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Affiliation(s)
- Shannon L Gillespie
- Martha S. Pitzer Center for Women, Children, & Youth, College of Nursing, The Ohio State University, Columbus, OH.
| | - Lynda R Hardy
- Center for Research and Health Analytics, College of Nursing, The Ohio State University, Columbus, OH
| | - Cindy M Anderson
- Martha S. Pitzer Center for Women, Children, & Youth, College of Nursing, The Ohio State University, Columbus, OH
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129
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Palma-Gudiel H, Eixarch E, Crispi F, Morán S, Zannas AS, Fañanás L. Prenatal adverse environment is associated with epigenetic age deceleration at birth and hypomethylation at the hypoxia-responsive EP300 gene. Clin Epigenetics 2019; 11:73. [PMID: 31072398 PMCID: PMC6507133 DOI: 10.1186/s13148-019-0674-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Accepted: 04/26/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Obstetric complications have long been retrospectively associated with a wide range of short- and long-term health consequences, including neurodevelopmental alterations such as those observed in schizophrenia and other psychiatric disorders. However, prospective studies assessing fetal well-being during pregnancy tend to focus on perinatal complications as the final outcome of interest, while there is a scarcity of postnatal follow-up studies. In this study, the cerebroplacental ratio (CPR), a hemodynamic parameter reflecting fetal adaptation to hypoxic conditions, was analyzed in a sample of monozygotic monochorionic twins (60 subjects), part of them with prenatal complications, with regard to (i) epigenetic age acceleration, and (ii) DNA methylation at genes included in the polygenic risk score (PRS) for schizophrenia, and highly expressed in placental tissue. RESULTS Decreased CPR measured during the third trimester was associated with epigenetic age deceleration (β = 0.21, t = 3.362, p = 0.002). Exploration of DNA methylation at placentally expressed genes of the PRS for schizophrenia revealed methylation at cg06793497 (EP300 gene) to be associated with CPR (β = 0.021, t = 4.385; p = 0.00008, FDR-adjusted p = 0.11). This association was reinforced by means of an intrapair analysis in monozygotic twins discordant for prenatal suffering (β = 0.027, t = 3.924, p = 0.001). CONCLUSIONS Prenatal adverse environment during the third trimester of pregnancy is associated with both (i) developmental immaturity in terms of epigenetic age, and (ii) decreased CpG-specific methylation in a gene involved in hypoxia response and schizophrenia genetic liability.
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Affiliation(s)
- Helena Palma-Gudiel
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona (UB), Avda. Diagonal 643 2n A, 08028, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Madrid, Spain
| | - Elisenda Eixarch
- Fetal i+D Fetal Medicine Research Center, BCNatal-Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Déu), Institut Clínic de Ginecologia, Obstetrícia i Neonatologia, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain.,Center for Biomedical Research on Rare Diseases (CIBER-ER), Madrid, Spain
| | - Fátima Crispi
- Fetal i+D Fetal Medicine Research Center, BCNatal-Barcelona Center for Maternal-Fetal and Neonatal Medicine (Hospital Clínic and Hospital Sant Joan de Déu), Institut Clínic de Ginecologia, Obstetrícia i Neonatologia, Institut d'Investigacions Biomèdiques August Pi i Sunyer, Universitat de Barcelona, Barcelona, Spain.,Center for Biomedical Research on Rare Diseases (CIBER-ER), Madrid, Spain
| | - Sebastián Morán
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Anthony S Zannas
- Departments of Psychiatry and Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Lourdes Fañanás
- Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology, University of Barcelona (UB), Avda. Diagonal 643 2n A, 08028, Barcelona, Spain. .,Centro de Investigación Biomédica en Red en Salud Mental (CIBERSAM), Madrid, Spain.
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130
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Everson TM, Marsit CJ, Michael O'Shea T, Burt A, Hermetz K, Carter BS, Helderman J, Hofheimer JA, McGowan EC, Neal CR, Pastyrnak SL, Smith LM, Soliman A, DellaGrotta SA, Dansereau LM, Padbury JF, Lester BM. Epigenome-wide Analysis Identifies Genes and Pathways Linked to Neurobehavioral Variation in Preterm Infants. Sci Rep 2019; 9:6322. [PMID: 31004082 PMCID: PMC6474865 DOI: 10.1038/s41598-019-42654-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 04/03/2019] [Indexed: 02/07/2023] Open
Abstract
Neonatal molecular biomarkers of neurobehavioral responses (measures of brain-behavior relationships), when combined with neurobehavioral performance measures, could lead to better predictions of long-term developmental outcomes. To this end, we examined whether variability in buccal cell DNA methylation (DNAm) associated with neurobehavioral profiles in a cohort of infants born less than 30 weeks postmenstrual age (PMA) and participating in the Neonatal Neurobehavior and Outcomes in Very Preterm Infants (NOVI) Study (N = 536). We tested whether epigenetic age, age acceleration, or DNAm levels at individual loci differed between infants based on their NICU Network Neurobehavioral Scale (NNNS) profile classifications. We adjusted for recruitment site, infant sex, PMA, and tissue heterogeneity. Infants with an optimally well-regulated NNNS profile had older epigenetic age compared to other NOVI infants (β1 = 0.201, p-value = 0.026), but no significant difference in age acceleration. In contrast, infants with an atypical NNNS profile had differential methylation at 29 CpG sites (FDR < 10%). Some of the genes annotated to these CpGs included PLA2G4E, TRIM9, GRIK3, and MACROD2, which have previously been associated with neurological structure and function, or with neurobehavioral disorders. These findings contribute to the existing evidence that neonatal epigenetic variations may be informative for infant neurobehavior.
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Affiliation(s)
- Todd M Everson
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, United States.
| | - Carmen J Marsit
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - T Michael O'Shea
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Amber Burt
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Karen Hermetz
- Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, United States
| | - Brian S Carter
- Department of Pediatrics-Neonatology, Children's Mercy Hospital, Kansas City, MO, United States
| | - Jennifer Helderman
- Department of Pediatrics, Wake Forest School of Medicine, Winston Salem, NC, United States
| | - Julie A Hofheimer
- Department of Pediatrics, University of North Carolina School of Medicine, Chapel Hill, NC, United States
| | - Elisabeth C McGowan
- Department of Pediatrics, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
| | - Charles R Neal
- Department of Pediatrics, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, United States
| | - Steven L Pastyrnak
- Department of Pediatrics, Spectrum Health-Helen Devos Hospital, Grand Rapids, MI, United States
| | - Lynne M Smith
- Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, United States
| | - Antoine Soliman
- Department of Pediatrics, Miller Children's and Women's Hospital Long Beach, Long Beach, CA, United States
| | - Sheri A DellaGrotta
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
| | - Lynne M Dansereau
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
| | - James F Padbury
- Department of Pediatrics, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
| | - Barry M Lester
- Department of Pediatrics, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
- Brown Center for the Study of Children at Risk, Brown Alpert Medical School and Women and Infants Hospital, Providence, RI, United States
- Department of Psychiatry and Human Behavior, Brown Alpert Medical School, Providence, RI, United States
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131
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Synchrony and asynchrony between an epigenetic clock and developmental timing. Sci Rep 2019; 9:3770. [PMID: 30842553 PMCID: PMC6403397 DOI: 10.1038/s41598-019-39919-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2018] [Accepted: 01/28/2019] [Indexed: 12/23/2022] Open
Abstract
Epigenetic changes have been used to estimate chronological age across the lifespan, and some studies suggest that epigenetic "aging" clocks may already operate in developing tissue. To better understand the relationship between developmental stage and epigenetic age, we utilized the highly regular sequence of development found in the mammalian neural retina and a well-established epigenetic aging clock based on DNA methylation. Our results demonstrate that the epigenetic age of fetal retina is highly correlated with chronological age. We further establish that epigenetic aging progresses normally in vitro, suggesting that epigenetic aging is a property of individual tissues. This correlation is also retained in stem cell-derived retinal organoids, but is accelerated in individuals with Down syndrome, a progeroid-like condition. Overall, our results suggest that epigenetic aging begins as early as a few weeks post-conception, in fetal tissues, and the mechanisms underlying the phenomenon of epigenetic aging might be studied in developing organs.
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132
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Wu Y, Lin X, Lim IY, Chen L, Teh AL, MacIsaac JL, Tan KH, Kobor MS, Chong YS, Gluckman PD, Karnani N. Analysis of two birth tissues provides new insights into the epigenetic landscape of neonates born preterm. Clin Epigenetics 2019; 11:26. [PMID: 30744680 PMCID: PMC6371604 DOI: 10.1186/s13148-018-0599-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/17/2018] [Indexed: 01/04/2023] Open
Abstract
Background Preterm birth (PTB), defined as child birth before completion of 37 weeks of gestation, is a major challenge in perinatal health care and can bear long-term medical and financial burden. Over a million children die each year due to PTB complications, and those who survive can face developmental delays. Unfortunately, our understanding of the molecular pathways associated with PTB remains limited. There is a growing body of evidence suggesting the role of DNA methylation (DNAm) in mediating the effects of PTB on future health outcomes. Thus, epigenome-wide association studies (EWAS), where DNAm sites are examined for associations with PTB, can help shed light on the biological mechanisms linking the two. Results In an Asian cohort of 1019 infants (68 preterm, 951 full term), we examined and compared the associations between PTB and genome-wide DNAm profiles using both cord tissue (n = 1019) and cord blood (n = 332) samples on Infinium HumanMethylation450 arrays. PTB was significantly associated (P < 5.8e−7) with DNAm at 296 CpGs (209 genes) in the cord blood. Over 95% of these CpGs were replicated in other PTB/gestational age EWAS conducted in (cord) blood. This replication was apparent even across populations of different ethnic origin (Asians, Caucasians, and African Americans). More than a third of these 296 CpGs were replicated in at least 4 independent studies, thereby identifying a robust set of PTB-linked epigenetic signatures in cord blood. Interrogation of cord tissue in addition to cord blood provided novel insights into the epigenetic status of the neonates born preterm. Overall, 994 CpGs (608 genes, P < 3.7e−7) associated with PTB in cord tissue, of which only 10 of these CpGs were identified in the analysis using cord blood. Genes from cord tissue showed enrichment of molecular pathways related to fetal growth and development, while those from cord blood showed enrichment of immune response pathways. A substantial number of PTB-associated CpGs from both the birth tissues were also associated with gestational age. Conclusions Our findings provide insights into the epigenetic landscape of neonates born preterm, and that its status is captured more comprehensively by interrogation of more than one neonatal tissue in tandem. Both these neonatal tissues are clinically relevant in their unique ways and require careful consideration in identification of biomarkers related to PTB and gestational age. Trial registration This birth cohort is a prospective observational study designed to study the developmental origins of health and disease, and was retrospectively registered on 1 July 2010 under the identifier NCT01174875. Electronic supplementary material The online version of this article (10.1186/s13148-018-0599-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yonghui Wu
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Xinyi Lin
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Duke-NUS Medical School, Singapore, Singapore
| | - Ives Yubin Lim
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Li Chen
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Ai Ling Teh
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore
| | - Julia L MacIsaac
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Kok Hian Tan
- KK Women's and Children's Hospital, Singapore, Singapore
| | - Michael S Kobor
- Department of Medical Genetics, Centre for Molecular Medicine and Therapeutics, Child and Family Research Institute, University of British Columbia, Vancouver, Canada
| | - Yap Seng Chong
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Peter D Gluckman
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore.,Centre for Human Evolution, Adaptation and Disease, Liggins Institute, University of Auckland, Auckland, New Zealand
| | - Neerja Karnani
- Singapore Institute for Clinical Sciences, A*STAR, 30 Medical Drive, Singapore, 117609, Singapore. .,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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133
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Epigenetic age acceleration is associated with allergy and asthma in children in Project Viva. J Allergy Clin Immunol 2019; 143:2263-2270.e14. [PMID: 30738172 DOI: 10.1016/j.jaci.2019.01.034] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 01/14/2019] [Accepted: 01/17/2019] [Indexed: 01/10/2023]
Abstract
BACKGROUND Epigenetic clocks have been suggested to capture one feature of the complexity between aging and the epigenome. However, little is known about the epigenetic clock in childhood allergy and asthma. OBJECTIVE We sought to examine associations of DNA methylation age (DNAmAge) and epigenetic age acceleration with childhood allergy and asthma. METHODS We calculated DNAmAge and age acceleration at birth, early childhood, and midchildhood based on the IlluminaHumanMethylation450BeadChip in Project Viva. We evaluated epigenetic clock associations with allergy and asthma using covariate-adjusted linear and logistic regressions. We attempted to replicate our findings in the Genetics of Asthma in Costa Rica Study. RESULTS At midchildhood (mean age, 7.8 years) in Project Viva, DNAmAge and age acceleration were cross-sectionally associated with greater total serum IgE levels and greater odds of atopic sensitization. Every 1-year increase in intrinsic epigenetic age acceleration was associated with a 1.22 (95% CI, 1.07-1.39), 1.17 (95% CI, 1.03-1.34), and 1.29 (95% CI, 1.12-1.49) greater odds of atopic sensitization and environmental and food allergen sensitization. DNAmAge and extrinsic epigenetic age acceleration were also cross-sectionally associated with current asthma at midchildhood. DNAmAge and age acceleration at birth and early childhood were not associated with midchildhood allergy or asthma. The midchildhood association between age acceleration and atopic sensitization were replicated in an independent data set. CONCLUSIONS Because the epigenetic clock might reflect immune and developmental components of biological aging, our study suggests pathways through which molecular epigenetic mechanisms of immunity, development, and maturation can interact along the age axis and associate with childhood allergy and asthma by midchildhood.
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134
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Abstract
Purpose of review This review demonstrates the growing body of evidence connecting DNA methylation to prior exposure. It highlights the potential to use DNA methylation patterns as a feasible, stable, and accurate biomarker of past exposure, opening new opportunities for environmental and gene-environment interaction studies among existing banked samples. Recent findings We present the evidence for association between past exposure, including prenatal exposures, and DNA methylation measured at a later time in the life course. We demonstrate the potential utility of DNA methylation-based biomarkers of past exposure using results from multiple studies of smoking as an example. Multiple studies show the ability to accurately predict prenatal smoking exposure based on DNA methylation measured at birth, in childhood, and even adulthood. Separate sets of DNA methylation loci have been used to predict past personal smoking exposure (postnatal) as well. Further, it appears that these two types of exposures, prenatal and previous personal exposure, can be isolated from each other. There is also a suggestion that quantitative methylation scores may be useful for estimating dose. We highlight the remaining needs for rigor in methylation biomarker development including analytic challenges as well as the need for development across multiple developmental windows, multiple tissue types, and multiple ancestries. Summary If fully developed, DNA methylation-based biomarkers can dramatically shift our ability to carry out environmental and genetic-environmental epidemiology using existing biobanks, opening up unprecedented opportunities for environmental health.
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135
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Ashapkin VV, Kutueva LI, Vanyushin BF. Epigenetic Clock: Just a Convenient Marker or an Active Driver of Aging? ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1178:175-206. [PMID: 31493228 DOI: 10.1007/978-3-030-25650-0_10] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A global DNA hypomethylation and local changes in the methylation levels of specific DNA loci occur during aging in mammals. Global hypomethylation mainly affects highly methylated repeat sequences, such as transposable elements; it is an essentially stochastic process usually referred to as "epigenetic drift." Specific changes in DNA methylation affect various genome sequences and could be either hypomethylation or hypermethylation, but the prevailing tendencies are hypermethylation of promoter sequences associated with CpG islands and hypomethylation of CpG poor genes. Methylation levels of multiple CpG sites display a strong correlation to age common between individuals of the same species. Collectively, methylation of such CpG sites could be used as "epigenetic clocks" to predict biological age. Furthermore, the discrepancy between epigenetic and chronological ages could be predictive of all-cause mortality and multiple age-associated diseases. Random changes in DNA methylation (epigenetic drift) could also affect the aging phenotype, causing accidental changes in gene expression and increasing the transcriptional noise between cells of the same tissue. Both effects could become detrimental to tissue functioning and cause a gradual decline in organ function during aging. Strong evidence shows that epigenetic systems contribute to lifespan control in various organisms. Similar to other cell systems, the epigenome is prone to gradual degradation due to the genome damage, stressful agents and other aging factors. However, unlike mutations and many other hallmarks of aging, age-related epigenetic changes could be fully or partially reversed to a "young" state.
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Affiliation(s)
- Vasily V Ashapkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia.
| | - Lyudmila I Kutueva
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Boris F Vanyushin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russia
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136
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Transcriptional activity of human endogenous retroviruses is higher at birth in inversed correlation with gestational age. INFECTION GENETICS AND EVOLUTION 2018; 68:273-279. [PMID: 30578937 DOI: 10.1016/j.meegid.2018.12.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/13/2018] [Accepted: 12/15/2018] [Indexed: 11/23/2022]
Abstract
Human endogenous retroviruses (HERVs) have been studied in relation to the onset and/or progression of several diseases. However, increasing evidence highlights that they also have important physiologic roles, for instance they are involved in preimplantation embryonic growth and in placentation. We assessed the transcriptional activity of HERVs in PBMCs of healthy newborns, infants and children to gather further information on their potential physiological roles. mRNA expression of HERV-H, K and W was evaluated in PBMCs of 63 preterm newborns, 47 term newborns, 38 infants (1-24 months of age), and 36 children (25-131 months of age) using a PCR real time Taqman amplification assay and normalization to glyceraldehyde-3-phosphate dehydrogenase (GAPDH). The expression levels of HERV-H, K, and W were significantly higher at birth than in infancy and childhood. Furthermore, HERV activation was highest in preterm newborns and a significant inverse correlation was found between HERV transcripts and duration of pregnancy. The overexpression of HERVs at birth in inversed correlation with gestational age are further clues of their potential involvement in early life events.
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137
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Population DNA methylation studies in the Developmental Origins of Health and Disease (DOHaD) framework. J Dev Orig Health Dis 2018; 10:306-313. [PMID: 30101736 DOI: 10.1017/s2040174418000442] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Epigenetic changes represent a potential mechanism underlying associations of early-life exposures and later life health outcomes. Population-based cohort studies starting in early life are an attractive framework to study the role of such changes. DNA methylation is the most studied epigenetic mechanism in population research. We discuss the application of DNA methylation in early-life population studies, some recent findings, key challenges and recommendations for future research. Studies into DNA methylation within the Developmental Origins of Health and Disease framework generally either explore associations between prenatal exposures and offspring DNA methylation or associations between offspring DNA methylation in early life and later health outcomes. Only a few studies to date have integrated prospective exposure, epigenetic and phenotypic data in order to explicitly test the role of DNA methylation as a potential biological mediator of environmental effects on health outcomes. Population epigenetics is an emerging field which has challenges in terms of methodology and interpretation of the data. Key challenges include tissue specificity, cell type adjustment, issues of power and comparability of findings, genetic influences, and exploring causality and functional consequences. Ongoing studies are working on addressing these issues. Large collaborative efforts of prospective cohorts are emerging, with clear benefits in terms of optimizing power and use of resources, and in advancing methodology. In the future, multidisciplinary approaches, within and beyond longitudinal birth and preconception cohorts will advance this complex, but highly promising, the field of research.
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138
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Salas LA, Wiencke JK, Koestler DC, Zhang Z, Christensen BC, Kelsey KT. Tracing human stem cell lineage during development using DNA methylation. Genome Res 2018; 28:1285-1295. [PMID: 30072366 PMCID: PMC6120629 DOI: 10.1101/gr.233213.117] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 07/27/2018] [Indexed: 12/22/2022]
Abstract
Stem cell maturation is a fundamental, yet poorly understood aspect of human development. We devised a DNA methylation signature deeply reminiscent of embryonic stem cells (a fetal cell origin signature, FCO) to interrogate the evolving character of multiple human tissues. The cell fraction displaying this FCO signature was highly dependent upon developmental stage (fetal versus adult), and in leukocytes, it described a dynamic transition during the first 5 yr of life. Significant individual variation in the FCO signature of leukocytes was evident at birth, in childhood, and throughout adult life. The genes characterizing the signature included transcription factors and proteins intimately involved in embryonic development. We defined and applied a DNA methylation signature common among human fetal hematopoietic progenitor cells and have shown that this signature traces the lineage of cells and informs the study of stem cell heterogeneity in humans under homeostatic conditions.
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Affiliation(s)
- Lucas A Salas
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA
| | - John K Wiencke
- Department of Neurological Surgery, Institute for Human Genetics, University of California San Francisco, San Francisco, California 94158, USA
| | - Devin C Koestler
- Department of Biostatistics, University of Kansas Medical Center, Kansas City, Kansas 66160, USA
| | - Ze Zhang
- Department of Epidemiology, Brown University, Providence, Rhode Island 02912, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island 02912, USA
| | - Brock C Christensen
- Department of Epidemiology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA.,Department of Molecular and Systems Biology, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA.,Department of Community and Family Medicine, Geisel School of Medicine, Dartmouth College, Lebanon, New Hampshire 03756, USA
| | - Karl T Kelsey
- Department of Epidemiology, Brown University, Providence, Rhode Island 02912, USA.,Department of Pathology and Laboratory Medicine, Brown University, Providence, Rhode Island 02912, USA
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139
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Relationship between Epigenetic Maturity and Respiratory Morbidity in Preterm Infants. J Pediatr 2018; 198:168-173.e2. [PMID: 29705119 PMCID: PMC6261285 DOI: 10.1016/j.jpeds.2018.02.074] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/26/2018] [Accepted: 02/28/2018] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To assess associations between epigenetic maturity of extremely preterm babies (born at less than 28 weeks of gestation), neonatal interventions, and respiratory outcomes, including the administration of surfactant and postnatal corticosteroids, duration of assisted ventilation, and development of bronchopulmonary dysplasia (BPD). STUDY DESIGN DNA was extracted from neonatal blood spots collected after birth from 143 extremely preterm infants born 1991-1992 in Victoria, Australia and used to determined DNA methylation (DNAm). A DNAm based gestational age was determined using our previously published method. The residual of DNAm gestational age and clinically estimated gestational age (referred to as "gestational age acceleration") was used as a measure to assess developmental maturity. Associations between gestational age acceleration and respiratory interventions and morbidities were determined. RESULTS Infants with higher gestational age acceleration were less likely to receive surfactant (P = .009) or postnatal corticosteroids (P = .008), had fewer days of assisted ventilation (P = .01), and had less BPD (P = .02). Respiratory measures are known to correlate with gestational age; however, models comparing each with clinically estimated gestational age were improved by the addition of the gestational age acceleration measure in the model. CONCLUSIONS Gestational age acceleration correlates with respiratory interventions and outcomes of extremely preterm babies. Surfactant and postnatal corticosteroid use, assisted ventilation days, and BPD rates were all lower in babies who were epigenetically more mature than their obstetrically estimated gestational age. This suggests that gestational age acceleration is a clinically relevant metric of developmental maturity.
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140
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Khouja JN, Simpkin AJ, O'Keeffe LM, Wade KH, Houtepen LC, Relton CL, Suderman M, Howe LD. Epigenetic gestational age acceleration: a prospective cohort study investigating associations with familial, sociodemographic and birth characteristics. Clin Epigenetics 2018; 10:86. [PMID: 29983833 PMCID: PMC6020346 DOI: 10.1186/s13148-018-0520-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/14/2018] [Indexed: 11/20/2022] Open
Abstract
Background Gestational age at delivery is associated with health and social outcomes. Recently, cord blood DNA methylation data has been used to predict gestational age. The discrepancy between gestational age predicted from DNA methylation and determined by ultrasound or last menstrual period is known as gestational age acceleration. This study investigated associations of sex, socioeconomic status, parental behaviours and characteristics and birth outcomes with gestational age acceleration. Results Using data from the Avon Longitudinal Study of Parents and Children (n = 863), we found that pre-pregnancy maternal overweight and obesity were associated with greater gestational age acceleration (mean difference = 1.6 days, 95% CI 0.7 to 2.6, and 2.9 days, 95% CI 1.3 to 4.4, respectively, compared with a body mass index < 25 kg/m2, p < .001). There was evidence of an association between male sex and greater gestational age acceleration. Greater gestational age acceleration was associated with higher birthweight, birth length and head circumference of the child (mean differences per week higher gestational age acceleration: birthweight 0.1 kg, 95% CI 0.1 to 0.2, p < .001; birth length 0.4 cm, 95% CI 0.2 to 0.7, p < .001; head circumference 0.2 cm, 95% CI 0.1 to − 0.4, p < .001). There was evidence of an association between gestational age acceleration and mode of delivery (assisted versus unassisted delivery, odds ratio = 0.9 per week higher gestational age acceleration, 95% CI 0.7, 1.3 (p = .05); caesarean section versus unassisted delivery, odds ratio = 0.6, 95% CI 0.4 to 0.9 per week higher gestational age acceleration (p = .05)). There was no evidence of association for other parental and perinatal characteristics. Conclusions The associations of higher maternal body mass index and larger birth size with greater gestational age acceleration may imply that maternal overweight and obesity is associated with more rapid development of the fetus in utero. The implications of gestational age acceleration for postnatal health warrant further investigation. Electronic supplementary material The online version of this article (10.1186/s13148-018-0520-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jasmine N Khouja
- 1MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, England.,2Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, England.,3School of Experimental Psychology at the University of Bristol, Bristol, England
| | - Andrew J Simpkin
- 1MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, England.,2Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, England
| | - Linda M O'Keeffe
- 1MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, England.,2Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, England
| | - Kaitlin H Wade
- 1MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, England.,2Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, England
| | - Lotte C Houtepen
- 1MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, England.,2Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, England
| | - Caroline L Relton
- 1MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, England.,2Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, England
| | - Matthew Suderman
- 1MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, England.,2Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, England
| | - Laura D Howe
- 1MRC Integrative Epidemiology Unit at the University of Bristol, Bristol, England.,2Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, England
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141
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Bauer M. Cell-type-specific disturbance of DNA methylation pattern: a chance to get more benefit from and to minimize cohorts for epigenome-wide association studies. Int J Epidemiol 2018; 47:917-927. [DOI: 10.1093/ije/dyy029] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/02/2023] Open
Affiliation(s)
- Mario Bauer
- Department of Environmental Immunology, Helmholtz Centre for Environmental Research, UFZ, Permoserst, 15, 04318 Leipzig, Germany
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142
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El Hajj N, Haertle L, Dittrich M, Denk S, Lehnen H, Hahn T, Schorsch M, Haaf T. DNA methylation signatures in cord blood of ICSI children. Hum Reprod 2018; 32:1761-1769. [PMID: 28575352 PMCID: PMC5850272 DOI: 10.1093/humrep/dex209] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/15/2017] [Indexed: 12/12/2022] Open
Abstract
STUDY QUESTION Does ICSI induce specific DNA methylation changes in the resulting offspring? SUMMARY ANSWER Although several thousand analyzed CpG sites (throughout the genome) displayed significant between-group methylation differences, both ICSI and spontaneously conceived children varied within the normal range of methylation variation. WHAT IS KNOWN ALREADY Children conceived by ART have increased risks for medical problems at birth and to the extent of present knowledge also in later life (i.e. impaired metabolic and cardiovascular functions). One plausible mechanism mediating these ART effects are epigenetic changes originating in the germ cells and/or early embryos and persisting during further development. STUDY DESIGN, SIZE, DURATION We compared the cord blood methylomes and candidate gene methylation patterns of newborns conceived through ICSI or spontaneously. PARTICIPANTS/MATERIALS, SETTING, METHODS Umbilical cord bloods were obtained from healthy newborn singletons conceived spontaneously (53 samples), through ICSI (89) or IVF (34). Bisulfite-converted DNA samples of 48 ICSI and 46 control pregnancies were used for genome-wide analyses with Illumina's 450K methylation arrays. Candidate genes from the methylation screen were analyzed in all three groups by bisulfite pyrosequencing. MAIN RESULTS AND THE ROLE OF CHANCE Altogether, 4730 (0.11%) of 428 227 analyzed CpG sites exhibited significant between-group methylation differences, but all with small (β < 10%) or very small (β < 1%) effect size. ICSI children showed a significantly decreased DNA methylation age at birth, lagging approximately half a week behind the controls. ART-susceptible CpGs were enriched in CpG islands with low methylation values (0-20%) and in imprinting control regions (ICRs). Eighteen promoter regions (six in microRNA and SNORD RNA genes), four CpG islands (three in genes including one long non-coding RNA), and two ICRs contained multiple significant sites. Three differentially methylated regions were studied in more detail by bisulfite pyrosequencing. ATG4C and SNORD114-9 could be validated in an independent ICSI group, following adjustment for maternal age and other confounding factors. ATG4C was also significant in the IVF group. LARGE SCALE DATA N/A. LIMITATIONS, REASONS FOR CAUTION The observed epigenetic effects are small and there are numerous potential confounding factors such as parental age and infertility. Although our study meets current standards for epigenetic screens, sample size is still two orders of magnitude below that of genome-wide association studies. WIDER IMPLICATIONS OF THE FINDINGS Our study suggests an impact of ICSI on the offspring's epigenome(s), which may contribute to phenotypic variation and disease susceptibility in ART children. Epigenetic regulation of gene expression by different classes of non-coding RNAs may be a key mechanism for developmental programming through ART. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by a research grant (no. 692185) from the European Union (ERA of ART). There are no competing interests.
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Affiliation(s)
- Nady El Hajj
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Larissa Haertle
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany.,Department of Bioinformatics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Sarah Denk
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
| | - Harald Lehnen
- Department of Gynecology and Obstetrics, Municipal Clinics, Hubertusstrasse 100, 41239 Mönchengladbach, Germany
| | - Thomas Hahn
- Fertility Center, Mainzer Strasse 98-102, 65189 Wiesbaden, Germany
| | - Martin Schorsch
- Fertility Center, Mainzer Strasse 98-102, 65189 Wiesbaden, Germany
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, 97074 Würzburg, Germany
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143
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Lapato DM, Moyer S, Olivares E, Amstadter AB, Kinser PA, Latendresse SJ, Jackson-Cook C, Roberson-Nay R, Strauss JF, York TP. Prospective longitudinal study of the pregnancy DNA methylome: the US Pregnancy, Race, Environment, Genes (PREG) study. BMJ Open 2018; 8:e019721. [PMID: 29743320 PMCID: PMC5942473 DOI: 10.1136/bmjopen-2017-019721] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 01/15/2018] [Accepted: 02/16/2018] [Indexed: 01/08/2023] Open
Abstract
PURPOSE The goal of the Pregnancy, Race, Environment, Genes study was to understand how social and environmental determinants of health (SEDH), pregnancy-specific environments (PSE) and biological processes influence the timing of birth and account for the racial disparity in preterm birth. The study followed a racially diverse longitudinal cohort throughout pregnancy and included repeated measures of PSE and DNA methylation (DNAm) over the course of gestation and up to 1 year into the postpartum period. PARTICIPANTS All women were between 18 and 40 years of age with singleton pregnancies and no diagnosis of diabetes or indication of assisted reproductive technology. Both mother and father had to self-identify as either African-American (AA) or European-American (EA). Maternal peripheral blood samples along with self-report questionnaires measuring SEDH and PSE factors were collected at four pregnancy visits, and umbilical cord blood was obtained at birth. A subset of participants returned for two additional postpartum visits, during which additional questionnaires and maternal blood samples were collected. The pregnancy and postpartum extension included n=240 (AA=126; EA=114) and n=104 (AA=50; EA=54), respectively. FINDINGS TO DATE One hundred seventy-seven women (AA=89, EA=88) met full inclusion criteria out of a total of 240 who were initially enrolled. Of the 63 participants who met exclusion criteria after enrolment, 44 (69.8%) were associated with a medical reason. Mean gestational age at birth was significantly shorter for the AA participants by 5.1 days (M=272.5 (SD=10.5) days vs M=277.6 (SD=8.3)). FUTURE PLANS Future studies will focus on identifying key environmental factors that influence DNAm change across pregnancy and account for racial differences in preterm birth.
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Affiliation(s)
- Dana M Lapato
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Sara Moyer
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
| | | | - Ananda B Amstadter
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Patricia A Kinser
- Department of Family and Community Health Nursing, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Shawn J Latendresse
- Department of Psychology and Neuroscience, Baylor University, Waco, Texas, USA
| | - Colleen Jackson-Cook
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Roxann Roberson-Nay
- Department of Psychiatry, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Jerome F Strauss
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
| | - Timothy P York
- Department of Human and Molecular Genetics, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
- Department of Obstetrics and Gynecology, Virginia Commonwealth University, Richmond, Virginia, USA
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144
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The Epigenetic Clock at Birth: Associations With Maternal Antenatal Depression and Child Psychiatric Problems. J Am Acad Child Adolesc Psychiatry 2018; 57:321-328.e2. [PMID: 29706161 PMCID: PMC6277971 DOI: 10.1016/j.jaac.2018.02.011] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 02/09/2018] [Accepted: 03/09/2018] [Indexed: 11/23/2022]
Abstract
OBJECTIVE Maternal antenatal depression may compromise the fetal developmental milieu and contribute to individual differences in aging and disease trajectories in later life. We evaluated the association between maternal antenatal depression and a novel biomarker of aging at birth, namely epigenetic gestational age (GA) based on fetal cord blood methylation data. We also examined whether this biomarker prospectively predicts and mediates maternal effects on early childhood psychiatric problems. METHOD A total of 694 mothers from the Prediction and Prevention of Preeclampsia and Intrauterine Growth Restriction (PREDO) Study provided information on history of depression diagnosed before pregnancy; 581 completed the Center for Epidemiological Studies Depression Scale throughout pregnancy, and 407 completed the Child Behavior Checklist at child's age 3.7 years (SD = 0.75 year). DNA methylation (DNAm) GA of fetal cord blood DNA was based on the methylation profile of 148 selected cytosine linked to guanine by phosphate (CpG) sites. Epigenetic GA was calculated as the arithmetic difference between DNAm GA and chronological GA and adjusted for chronological GA. RESULTS Maternal history of depression diagnosed before pregnancy (mean difference = -0.25 SD units, 95% CI = -0.46 to -0.03) and greater antenatal depressive symptoms (-0.08 SD unit per 1-SD unit increase, 95% CI = -0.16 to -0.004) were associated with child's lower epigenetic GA. Child's lower epigenetic GA, in turn, prospectively predicted total and internalizing problems and partially mediated the effects of maternal antenatal depression on internalizing problems in boys. CONCLUSION Maternal antenatal depression is associated with lower epigenetic GA in offspring. This lower epigenetic GA seems to be associated with a developmental disadvantage for boys, who, in early childhood, show greater psychiatric problems.
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145
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Zhou W, Dinh HQ, Ramjan Z, Weisenberger DJ, Nicolet CM, Shen H, Laird PW, Berman BP. DNA methylation loss in late-replicating domains is linked to mitotic cell division. Nat Genet 2018; 50:591-602. [PMID: 29610480 PMCID: PMC5893360 DOI: 10.1038/s41588-018-0073-4] [Citation(s) in RCA: 202] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 01/24/2018] [Indexed: 12/31/2022]
Abstract
DNA methylation loss occurs frequently in cancer genomes, primarily within lamina-associated, late-replicating regions termed Partially Methylated Domains (PMDs). We profiled 39 diverse primary tumors and 8 matched adjacent tissues using Whole-Genome Bisulfite Sequencing (WGBS), and analyzed them alongside 343 additional human and 206 mouse WGBS datasets. We identified a local CpG sequence context associated with preferential hypomethylation in PMDs. Analysis of CpGs in this context (“Solo-WCGWs”) revealed previously undetected PMD hypomethylation in almost all healthy tissue types. PMD hypomethylation increased with age, beginning during fetal development, and appeared to track the accumulation of cell divisions. In cancer, PMD hypomethylation depth correlated with somatic mutation density and cell-cycle gene expression, consistent with its reflection of mitotic history, and suggesting its application as a mitotic clock. We propose that late replication leads to lifelong progressive methylation loss, which acts as a biomarker for cellular aging and which may contribute to oncogenesis.
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Affiliation(s)
- Wanding Zhou
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA
| | - Huy Q Dinh
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | | | - Daniel J Weisenberger
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Charles M Nicolet
- USC Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA, USA
| | - Hui Shen
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA.
| | - Peter W Laird
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, MI, USA.
| | - Benjamin P Berman
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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146
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Hannon E, Schendel D, Ladd-Acosta C, Grove J, Hansen CS, Andrews SV, Hougaard DM, Bresnahan M, Mors O, Hollegaard MV, Bækvad-Hansen M, Hornig M, Mortensen PB, Børglum AD, Werge T, Pedersen MG, Nordentoft M, Buxbaum J, Daniele Fallin M, Bybjerg-Grauholm J, Reichenberg A, Mill J. Elevated polygenic burden for autism is associated with differential DNA methylation at birth. Genome Med 2018; 10:19. [PMID: 29587883 PMCID: PMC5872584 DOI: 10.1186/s13073-018-0527-4] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2017] [Accepted: 02/20/2018] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD involves both inherited and environmental risk factors, with epigenetic processes hypothesized as one mechanism by which both genetic and non-genetic variation influence gene regulation and pathogenesis. The aim of this study was to identify DNA methylation biomarkers of ASD detectable at birth. METHODS We quantified neonatal methylomic variation in 1263 infants-of whom ~ 50% went on to subsequently develop ASD-using DNA isolated from archived blood spots taken shortly after birth. We used matched genotype data from the same individuals to examine the molecular consequences of ASD-associated genetic risk variants, identifying methylomic variation associated with elevated polygenic burden for ASD. In addition, we performed DNA methylation quantitative trait loci (mQTL) mapping to prioritize target genes from ASD GWAS findings. RESULTS We identified robust epigenetic signatures of gestational age and prenatal tobacco exposure, confirming the utility of DNA methylation data generated from neonatal blood spots. Although we did not identify specific loci showing robust differences in neonatal DNA methylation associated with later ASD, there was a significant association between increased polygenic burden for autism and methylomic variation at specific loci. Each unit of elevated ASD polygenic risk score was associated with a mean increase in DNA methylation of - 0.14% at two CpG sites located proximal to a robust GWAS signal for ASD on chromosome 8. CONCLUSIONS This study is the largest analysis of DNA methylation in ASD undertaken and the first to integrate genetic and epigenetic variation at birth. We demonstrate the utility of using a polygenic risk score to identify molecular variation associated with disease, and of using mQTL to refine the functional and regulatory variation associated with ASD risk variants.
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Affiliation(s)
- Eilis Hannon
- University of Exeter Medical School, University of Exeter, RILD Building, Level 4, Barrack Rd, Exeter, EX2 5DW UK
| | - Diana Schendel
- Department of Public Health, Aarhus University, Aarhus, Denmark
| | - Christine Ladd-Acosta
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Jakob Grove
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Christine Søholm Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
| | - Shan V. Andrews
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - David Michael Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michaeline Bresnahan
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, USA
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
| | - Mads Vilhelm Hollegaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Mady Hornig
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | - Preben Bo Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University; Aarhus University Hospital, Risskov, Denmark
- National Centre for Register-Based Research, Aarhus University, Aarhus, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Anders D. Børglum
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Centre for Integrative Sequencing, iSEQ, Aarhus University, Aarhus, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Institute of Biological Psychiatry, MHC Sct. Hans, Mental Health Services Copenhagen, Roskilde, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Marianne Giørtz Pedersen
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Psychosis Research Unit, Aarhus University Hospital, Risskov, Denmark
- Centre for Integrated Register-based Research, Aarhus University, Aarhus, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Mental Health Services in the Capital Region of Denmark, Mental Health Center Copenhagen, University of Copenhagen, Copenhagen, Denmark
| | - Joseph Buxbaum
- Department of Psychiatry, Mount Sinai School of Medicine, New York City, USA
| | - M. Daniele Fallin
- Wendy Klag Center for Autism and Developmental Disabilities, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
- Center for Infection and Immunity, Columbia University Mailman School of Public Health, New York, USA
- Department of Psychiatry, Columbia University, New York, USA
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD USA
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrative Psychiatric Research, Aarhus, Denmark
- Center for Neonatal Screening, Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Abraham Reichenberg
- Department of Psychiatry, Mount Sinai School of Medicine, New York City, USA
| | - Jonathan Mill
- University of Exeter Medical School, University of Exeter, RILD Building, Level 4, Barrack Rd, Exeter, EX2 5DW UK
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147
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Declerck K, Vanden Berghe W. Back to the future: Epigenetic clock plasticity towards healthy aging. Mech Ageing Dev 2018; 174:18-29. [PMID: 29337038 DOI: 10.1016/j.mad.2018.01.002] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2017] [Revised: 01/08/2018] [Accepted: 01/10/2018] [Indexed: 12/22/2022]
Abstract
Aging is the most important risk factor for major human lifestyle diseases, including cancer, neurological and cardiometabolic disorders. Due to the complex interplay between genetics, lifestyle and environmental factors, some individuals seem to age faster than others, whereas centenarians seem to have a slower aging process. Therefore, a biochemical biomarker reflecting the relative biological age would be helpful to predict an individual's health status and aging disease risk. Although it is already known for years that cumulative epigenetic changes occur upon aging, DNA methylation patterns were only recently used to construct an epigenetic clock predictor for biological age, which is a measure of how well your body functions compared to your chronological age. Moreover, the epigenetic DNA methylation clock signature is increasingly applied as a biomarker to estimate aging disease susceptibility and mortality risk. Finally, the epigenetic clock signature could be used as a lifestyle management tool to monitor healthy aging, to evaluate preventive interventions against chronic aging disorders and to extend healthy lifespan. Dissecting the mechanism of the epigenetic aging clock will yield valuable insights into the aging process and how it can be manipulated to improve health span.
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Affiliation(s)
- Ken Declerck
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Belgium
| | - Wim Vanden Berghe
- Laboratory of Protein Chemistry, Proteomics and Epigenetic Signaling (PPES), Department of Biomedical Sciences, University of Antwerp (UA), Belgium.
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148
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Bush NR, Jones-Mason K, Coccia M, Caron Z, Alkon A, Thomas M, Coleman-Phox K, Wadhwa PD, Laraia BA, Adler NE, Epel ES. Effects of pre- and postnatal maternal stress on infant temperament and autonomic nervous system reactivity and regulation in a diverse, low-income population. Dev Psychopathol 2017; 29:1553-1571. [PMID: 29162167 PMCID: PMC5726291 DOI: 10.1017/s0954579417001237] [Citation(s) in RCA: 82] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
We examined the prospective associations of objective and subjective measures of stress during pregnancy with infant stress reactivity and regulation, an early-life predictor of psychopathology. In a racially and ethnically diverse low-income sample of 151 mother-infant dyads, maternal reports of stressful life events (SLE) and perceived stress (PS) were collected serially over gestation and the early postpartum period. Infant reactivity and regulation at 6 months of age was assessed via maternal report of temperament (negativity, surgency, and regulation) and infant parasympathetic nervous system physiology (respiratory sinus arrhythmia [RSA]) during the Still Face Paradigm. Regression models predicting infant temperament showed higher maternal prenatal PS predicted lower surgency and self-regulation but not negativity. Regression models predicting infant physiology showed higher numbers of SLE during gestation predicted greater RSA reactivity and weaker recovery. Tests of interactions revealed SLE predicted RSA reactivity only at moderate to high levels of PS. Thus, findings suggest objective and subjective measures of maternal prenatal stress uniquely predict infant behavior and physiology, adjusting for key pre- and postnatal covariates, and advance the limited evidence for such prenatal programming within high-risk populations. Assessing multiple levels of maternal stress and offspring stress reactivity and regulation provides a richer picture of intergenerational transmission of adversity.
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Affiliation(s)
- Nicole R. Bush
- Department of Psychiatry, Center for Health and Community, Weill Neurosciences Institute, University of California, San Francisco
- Department of Pediatrics, University of California, San Francisco
| | - Karen Jones-Mason
- Department of Psychiatry, Center for Health and Community, Weill Neurosciences Institute, University of California, San Francisco
| | - Michael Coccia
- Department of Psychiatry, Center for Health and Community, Weill Neurosciences Institute, University of California, San Francisco
| | - Zoe Caron
- Department of Psychiatry, Center for Health and Community, Weill Neurosciences Institute, University of California, San Francisco
| | - Abbey Alkon
- Department of Nursing, University of California, San Francisco
| | - Melanie Thomas
- Department of Psychiatry, Zuckerberg San Francisco General Hospital and Trauma Center, University of California, San Francisco
| | - Kim Coleman-Phox
- Department of Psychiatry, Center for Health and Community, Weill Neurosciences Institute, University of California, San Francisco
| | - Pathik D. Wadhwa
- School of Medicine, Development, Health and Disease Research Program, University of California, Irvine
| | | | - Nancy E. Adler
- Department of Psychiatry, Center for Health and Community, Weill Neurosciences Institute, University of California, San Francisco
| | - Elissa S. Epel
- Department of Psychiatry, Center for Health and Community, Weill Neurosciences Institute, University of California, San Francisco
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149
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Abstract
AbstractAnimal models of early postnatal mother–infant interactions have highlighted the importance of tactile contact for biobehavioral outcomes via the modification of DNA methylation (DNAm). The role of normative variation in contact in early human development has yet to be explored. In an effort to translate the animal work on tactile contact to humans, we applied a naturalistic daily diary strategy to assess the link between maternal contact with infants and epigenetic signatures in children 4–5 years later, with respect to multiple levels of child-level factors, including genetic variation and infant distress. We first investigated DNAm at four candidate genes: the glucocorticoid receptor gene, nuclear receptor subfamily 3, group C, member 1 (NR3C1), μ-opioid receptor M1 (OPRM1) and oxytocin receptor (OXTR; related to the neurobiology of social bonds), and brain-derived neurotrophic factor (BDNF; involved in postnatal plasticity). Although no candidate gene DNAm sites significantly associated with early postnatal contact, when we next examined DNAm across the genome, differentially methylated regions were identified between high and low contact groups. Using a different application of epigenomic information, we also quantified epigenetic age, and report that for infants who received low contact from caregivers, greater infant distress was associated with younger epigenetic age. These results suggested that early postnatal contact has lasting associations with child biology.
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150
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Budinger GRS, Kohanski RA, Gan W, Kobor MS, Amaral LA, Armanios M, Kelsey KT, Pardo A, Tuder R, Macian F, Chandel N, Vaughan D, Rojas M, Mora AL, Kovacs E, Duncan SR, Finkel T, Choi A, Eickelberg O, Chen D, Agusti A, Selman M, Balch WE, Busse P, Lin A, Morimoto R, Sznajder JI, Thannickal VJ. The Intersection of Aging Biology and the Pathobiology of Lung Diseases: A Joint NHLBI/NIA Workshop. J Gerontol A Biol Sci Med Sci 2017; 72:1492-1500. [PMID: 28498894 PMCID: PMC5861849 DOI: 10.1093/gerona/glx090] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 05/10/2017] [Indexed: 12/31/2022] Open
Abstract
Death from chronic lung disease is increasing and chronic obstructive pulmonary disease has become the third leading cause of death in the United States in the past decade. Both chronic and acute lung diseases disproportionately affect elderly individuals, making it likely that these diseases will become more frequent and severe as the worldwide population ages. Chronic lung diseases are associated with substantial morbidity, frequently resulting in exercise limiting dyspnea, immobilization, and isolation. Therefore, effective strategies to prevent or treat lung disease are likely to increase healthspan as well as life span. This review summarizes the findings of a joint workshop sponsored by the NIA and NHLBI that brought together investigators focused on aging and lung biology. These investigators encouraged the use of genetic systems and aged animals in the study of lung disease and the development of integrative systems-based platforms that can dynamically incorporate data sets that describe the genomics, transcriptomics, epigenomics, metabolomics, and proteomics of the aging lung in health and disease. Further research was recommended to integrate benchmark biological hallmarks of aging in the lung with the pathobiology of acute and chronic lung diseases with divergent pathologies for which advanced age is the most important risk factor.
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Affiliation(s)
- GR Scott Budinger
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Ronald A Kohanski
- Division of Aging Biology, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | - Weiniu Gan
- Division of Lung Diseases, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Michael S Kobor
- Center for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, Canada
| | - Luis A Amaral
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, Illinois
| | - Mary Armanios
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Karl T Kelsey
- Departments of Epidemiology, Laboratory Medicine & Pathology, Brown University, Providence, Rhode Island
| | - Annie Pardo
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, México
| | - Rubin Tuder
- Department of Medicine, Division of Pulmonary Sciences and Critical Care Medicine, University of Colorado at Denver Health Sciences Center, Denver, Colorado
| | - Fernando Macian
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Navdeep Chandel
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Douglas Vaughan
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
| | - Mauricio Rojas
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Ana L Mora
- Division of Pulmonary, Allergy and Critical Care Medicine, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania
| | - Elizabeth Kovacs
- Department of Surgery, University of Colorado at Denver Health Sciences Center, Denver, Colorado
| | | | - Toren Finkel
- Center for Molecular Medicine, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland
| | - Augustine Choi
- Weill Cornell Medical College, Division of Pulmonary and Critical Care Medicine, Weill Department of Medicine, New York, New York
| | - Oliver Eickelberg
- Pulmonary Sciences and Critical Care Medicine, University of Colorado, Anschutz Medical Campus
| | - Danica Chen
- Program in Metabolic Biology, Nutritional Sciences & Toxicology, University of California, Berkeley, California
| | - Alvar Agusti
- Respiratory Institute, Hospital Clinic, IDIBAPS, University of Barcelona, CIBERES, Spain
| | - Moises Selman
- Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Tlalpan, México
| | - William E Balch
- Department of Chemical Physiology, Department of Cell and Molecular Biology, The Skaggs Institute of Chemical Biology, The Scripps Research Institute, La Jolla, California
| | - Paula Busse
- Division of Clinical Immunology, Department of Medicine, Mount Sinai School of Medicine, New York, New York
| | - Anning Lin
- Ben May Department for Cancer Research, University of Chicago, Chicago, Illinois
| | - Richard Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, Illinois
| | - Jacob I Sznajder
- Feinberg School of Medicine, Division of Pulmonary and Critical Care Medicine, Northwestern University, Chicago, Illinois
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