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Short AK, Weber R, Kamei N, Wilcox Thai C, Arora H, Mortazavi A, Stern HS, Glynn L, Baram TZ. Individual longitudinal changes in DNA-methylome identify signatures of early-life adversity and correlate with later outcome. Neurobiol Stress 2024; 31:100652. [PMID: 38962694 PMCID: PMC11219970 DOI: 10.1016/j.ynstr.2024.100652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/02/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Adverse early-life experiences (ELA) affect a majority of the world's children. Whereas the enduring impact of ELA on cognitive and emotional health is established, there are no tools to predict vulnerability to ELA consequences in an individual child. Epigenetic markers including peripheral-cell DNA-methylation profiles may encode ELA and provide predictive outcome markers, yet the interindividual variance of the human genome and rapid changes in DNA methylation in childhood pose significant challenges. Hoping to mitigate these challenges we examined the relation of several ELA dimensions to DNA methylation changes and outcome using a within-subject longitudinal design and a high methylation-change threshold. DNA methylation was analyzed in buccal swab/saliva samples collected twice (neonatally and at 12 months) in 110 infants. We identified CpGs differentially methylated across time for each child and determined whether they associated with ELA indicators and executive function at age 5. We assessed sex differences and derived a sex-dependent 'impact score' based on sites that most contributed to methylation changes. Changes in methylation between two samples of an individual child reflected age-related trends and correlated with executive function years later. Among tested ELA dimensions and life factors including income to needs ratios, maternal sensitivity, body mass index and infant sex, unpredictability of parental and household signals was the strongest predictor of executive function. In girls, high early-life unpredictability interacted with methylation changes to presage executive function. Thus, longitudinal, within-subject changes in methylation profiles may provide a signature of ELA and a potential predictive marker of individual outcome.
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Affiliation(s)
- Annabel K. Short
- Department of Anatomy and Neurobiology, ersity of California- Irvine, Irvine, CA, 92697, USA
- Departments of Pediatrics and Neurology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Ryan Weber
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Noriko Kamei
- Department of Anatomy and Neurobiology, ersity of California- Irvine, Irvine, CA, 92697, USA
| | - Christina Wilcox Thai
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Hina Arora
- Department of Statistics, University of California-Irvine, Irvine, CA, 92697, USA
| | - Ali Mortazavi
- Department of Developmental and Cell Biology, University of California-Irvine, Irvine, CA, 92697, USA
| | - Hal S. Stern
- Department of Statistics, University of California-Irvine, Irvine, CA, 92697, USA
| | - Laura Glynn
- Department of Psychology, Chapman University, Orange, CA, 92866, USA
| | - Tallie Z. Baram
- Department of Anatomy and Neurobiology, ersity of California- Irvine, Irvine, CA, 92697, USA
- Departments of Pediatrics and Neurology, University of California-Irvine, Irvine, CA, 92697, USA
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Khodasevich D, Holland N, Harley KG, Eskenazi B, Barcellos LF, Cardenas A. Prenatal exposure to environmental phenols and phthalates and altered patterns of DNA methylation in childhood. ENVIRONMENT INTERNATIONAL 2024; 190:108862. [PMID: 38972116 DOI: 10.1016/j.envint.2024.108862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 06/13/2024] [Accepted: 06/28/2024] [Indexed: 07/09/2024]
Abstract
INTRODUCTION Epigenetic marks are key biomarkers linking the prenatal environment to health and development. However, DNA methylation associations and persistence of marks for prenatal exposure to multiple Endocrine Disrupting Chemicals (EDCs) in human populations have not been examined in great detail. METHODS We measured Bisphenol-A (BPA), triclosan, benzophenone-3 (BP3), methyl-paraben, propyl-paraben, and butyl-paraben, as well as 11 phthalate metabolites, in two pregnancy urine samples, at approximately 13 and 26 weeks of gestation in participants of the Center for the Health Assessment of Mothers and Children of Salinas (CHAMACOS) study (N = 309). DNA methylation of cord blood at birth and child peripheral blood at ages 9 and 14 years was measured with 450K and EPIC arrays. Robust linear regression was used to identify differentially methylated probes (DMPs), and comb-p was used to identify differentially methylated regions (DMRs) in association with pregnancy-averaged EDC concentrations. Quantile g-computation was used to assess associations of the whole phenol/phthalate mixture with DMPs and DMRs. RESULTS Prenatal BPA exposure was associated with 1 CpG among males and Parabens were associated with 10 CpGs among females at Bonferroni-level significance in cord blood. Other suggestive DMPs (unadjusted p-value < 1 × 10-6) and several DMRs associated with the individual phenols and whole mixture were also identified. A total of 10 CpG sites at least suggestively associated with BPA, Triclosan, BP3, Parabens, and the whole mixture in cord blood were found to persist into adolescence in peripheral blood. CONCLUSIONS We found sex-specific associations between prenatal phenol exposure and DNA methylation, particularly with BPA in males and Parabens in females. Additionally, we found several DMPs that maintained significant associations with prenatal EDC exposures at age 9 and age 14 years.
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Affiliation(s)
- Dennis Khodasevich
- Division of Environmental Health Sciences, Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Nina Holland
- Center for Environmental Research and Community Health (CERCH), Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Kim G Harley
- Center for Environmental Research and Community Health (CERCH), Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Brenda Eskenazi
- Center for Environmental Research and Community Health (CERCH), Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Lisa F Barcellos
- Division of Epidemiology, Berkeley Public Health, University of California, Berkeley, Berkeley, CA, USA
| | - Andres Cardenas
- Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA.
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Wang G, Xu R, Zhang B, Hong X, Bartell TR, Pearson C, Liang L, Wang X. Impact of intrauterine exposure to maternal diabetes on preterm birth: fetal DNA methylation alteration is an important mediator. Clin Epigenetics 2023; 15:59. [PMID: 37029435 PMCID: PMC10082529 DOI: 10.1186/s13148-023-01473-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 03/21/2023] [Indexed: 04/09/2023] Open
Abstract
BACKGROUND In utero exposure to diabetes has been shown to contribute to preterm birth, though the underlying biological mechanisms are yet to be fully elucidated. Fetal epigenetic variations established in utero may be a possible pathway. This study aimed to investigate whether in utero exposure to diabetes was associated with a change in newborn DNA methylation, and whether the identified CpG sites mediate the association between diabetes and preterm birth in a racially diverse birth cohort population. METHODS This study included 954 mother-newborn pairs. Methylation levels in the cord blood were determined using the Illumina Infinium MethylationEPIC BeadChip 850 K array platform. In utero exposure to diabetes was defined by the presence of maternal pregestational or gestational diabetes. Preterm birth was defined as gestational age at birth less than 37 weeks. Linear regression analysis was employed to identify differentially methylated CpG sites. Differentially methylated regions were identified using the DMRcate Package. RESULTS 126 (13%) newborns were born to mothers with diabetes in pregnancy and 173 (18%) newborns were born preterm, while 41 newborns were born both preterm and to mothers with diabetes in pregnancy. Genomic-wide CpG analysis found that eighteen CpG sites in cord blood were differentially methylated by maternal diabetes status at an FDR threshold of 5%. These significant CpG sites were mapped to 12 known genes, one of which was annotated to gene Major Histocompatibility Complex, Class II, DM Beta (HLA-DMB). Consistently, one of the two identified significant methylated regions overlapped with HLA-DMB. The identified differentially methylated CpG sites mediated the association between diabetes in pregnancy and preterm birth by 61%. CONCLUSIONS In this US birth cohort, we found that maternal diabetes was associated with altered fetal DNA methylation patterns, which substantially explained the link between diabetes and preterm birth.
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Affiliation(s)
- Guoying Wang
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205-2179, USA.
| | - Richard Xu
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Boyang Zhang
- Department of Biostatistics, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA
| | - Xiumei Hong
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205-2179, USA
| | - Tami R Bartell
- Patrick M. Magoon Institute for Healthy Communities, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Colleen Pearson
- Department of Pediatrics, Boston University Chobanian & Avedisian School of Medicine and Boston Medical Center, Boston, MA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Xiaobin Wang
- Center on Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD, 21205-2179, USA
- Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
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Gim JA. Integrative Approaches of DNA Methylation Patterns According to Age, Sex and Longitudinal Changes. Curr Genomics 2023; 23:385-399. [PMID: 37920553 PMCID: PMC10173416 DOI: 10.2174/1389202924666221207100513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 10/04/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
Background In humans, age-related DNA methylation has been studied in blood, tissues, buccal swabs, and fibroblasts, and changes in DNA methylation patterns according to age and sex have been detected. To date, approximately 137,000 samples have been analyzed from 14,000 studies, and the information has been uploaded to the NCBI GEO database. Methods A correlation between age and methylation level and longitudinal changes in methylation levels was revealed in both sexes. Here, 20 public datasets derived from whole blood were analyzed using the Illumina BeadChip. Batch effects with respect to the time differences were correlated. The overall change in the pattern was provided as the inverse of the coefficient of variation (COV). Results Of the 20 datasets, nine were from a longitudinal study. All data had age and sex as common variables. Comprehensive details of age-, sex-, and longitudinal change-based DNA methylation levels in the whole blood sample were elucidated in this study. ELOVL2 and FHL2 showed the maximum correlation between age and DNA methylation. The methylation patterns of genes related to mental health differed according to age. Age-correlated genes have been associated with malformations (anteverted nostril, craniofacial abnormalities, and depressed nasal bridge) and drug addiction (drug habituation and smoking). Conclusion Based on 20 public DNA methylation datasets, methylation levels according to age and longitudinal changes by sex were identified and visualized using an integrated approach. The results highlight the molecular mechanisms underlying the association of sex and biological age with changes in DNA methylation, and the importance of optimal genomic information management.
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Affiliation(s)
- Jeong-An Gim
- Medical Science Research Center, College of Medicine, Korea University Guro Hospital, Seoul 08308, Republic of Korea
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Baker EC, San AE, Cilkiz KZ, Littlejohn BP, Cardoso RC, Ghaffari N, Long CR, Riggs PK, Randel RD, Welsh TH, Riley DG. Inter-Individual Variation in DNA Methylation Patterns across Two Tissues and Leukocytes in Mature Brahman Cattle. BIOLOGY 2023; 12:biology12020252. [PMID: 36829529 PMCID: PMC9953534 DOI: 10.3390/biology12020252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 01/31/2023] [Accepted: 02/01/2023] [Indexed: 02/09/2023]
Abstract
Quantifying the natural inter-individual variation in DNA methylation patterns is important for identifying its contribution to phenotypic variation, but also for understanding how the environment affects variability, and for incorporation into statistical analyses. The inter-individual variation in DNA methylation patterns in female cattle and the effect that a prenatal stressor has on such variability have yet to be quantified. Thus, the objective of this study was to utilize methylation data from mature Brahman females to quantify the inter-individual variation in DNA methylation. Pregnant Brahman cows were transported for 2 h durations at days 60 ± 5; 80 ± 5; 100 ± 5; 120 ± 5; and 140 ± 5 of gestation. A non-transport group was maintained as a control. Leukocytes, amygdala, and anterior pituitary glands were harvested from eight cows born from the non-transport group (Control) and six from the transport group (PNS) at 5 years of age. The DNA harvested from the anterior pituitary contained the greatest variability in DNA methylation of cytosine-phosphate-guanine (mCpG) sites from both the PNS and Control groups, and the amygdala had the least. Numerous variable mCpG sites were associated with retrotransposable elements and highly repetitive regions of the genome. Some of the genomic features that had high variation in DNA methylation are involved in immune responses, signaling, responses to stimuli, and metabolic processes. The small overlap of highly variable CpG sites and features between tissues and leukocytes supports the role of variable DNA methylation in regulating tissue-specific gene expression. Many of the CpG sites that exhibited high variability in DNA methylation were common between the PNS and Control groups within a tissue, but there was little overlap in genomic features with high variability. The interaction between the prenatal environment and the genome could be responsible for the differences in location of the variable DNA methylation.
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Affiliation(s)
- Emilie C. Baker
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
| | - Audrey E. San
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research, College Station, TX 77845, USA
- Texas A&M AgriLife Research & Extension Center at Overton, Overton, TX 75684, USA
| | - Kubra Z. Cilkiz
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
| | - Brittni P. Littlejohn
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research & Extension Center at Overton, Overton, TX 75684, USA
| | - Rodolfo C. Cardoso
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
| | - Noushin Ghaffari
- Department of Computer Science, Prairie View A&M University, Prairie View, TX 77446, USA
| | - Charles R. Long
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research & Extension Center at Overton, Overton, TX 75684, USA
| | - Penny K. Riggs
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
| | - Ronald D. Randel
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research & Extension Center at Overton, Overton, TX 75684, USA
| | - Thomas H. Welsh
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Texas A&M AgriLife Research, College Station, TX 77845, USA
| | - David G. Riley
- Department of Animal Science, Texas A&M University, College Station, TX 77845, USA
- Correspondence:
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Campagna MP, Xavier A, Lechner-Scott J, Maltby V, Scott RJ, Butzkueven H, Jokubaitis VG, Lea RA. Epigenome-wide association studies: current knowledge, strategies and recommendations. Clin Epigenetics 2021; 13:214. [PMID: 34863305 PMCID: PMC8645110 DOI: 10.1186/s13148-021-01200-8] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/19/2021] [Indexed: 02/06/2023] Open
Abstract
The aetiology and pathophysiology of complex diseases are driven by the interaction between genetic and environmental factors. The variability in risk and outcomes in these diseases are incompletely explained by genetics or environmental risk factors individually. Therefore, researchers are now exploring the epigenome, a biological interface at which genetics and the environment can interact. There is a growing body of evidence supporting the role of epigenetic mechanisms in complex disease pathophysiology. Epigenome-wide association studies (EWASes) investigate the association between a phenotype and epigenetic variants, most commonly DNA methylation. The decreasing cost of measuring epigenome-wide methylation and the increasing accessibility of bioinformatic pipelines have contributed to the rise in EWASes published in recent years. Here, we review the current literature on these EWASes and provide further recommendations and strategies for successfully conducting them. We have constrained our review to studies using methylation data as this is the most studied epigenetic mechanism; microarray-based data as whole-genome bisulphite sequencing remains prohibitively expensive for most laboratories; and blood-based studies due to the non-invasiveness of peripheral blood collection and availability of archived DNA, as well as the accessibility of publicly available blood-cell-based methylation data. Further, we address multiple novel areas of EWAS analysis that have not been covered in previous reviews: (1) longitudinal study designs, (2) the chip analysis methylation pipeline (ChAMP), (3) differentially methylated region (DMR) identification paradigms, (4) methylation quantitative trait loci (methQTL) analysis, (5) methylation age analysis and (6) identifying cell-specific differential methylation from mixed cell data using statistical deconvolution.
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Affiliation(s)
- Maria Pia Campagna
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
| | - Alexandre Xavier
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Jeannette Lechner-Scott
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Department of Neurology, Division of Medicine, John Hunter Hospital, Newcastle, Australia
| | - Vicky Maltby
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
| | - Rodney J Scott
- Centre for Information Based Medicine, Hunter Medical Research Institute, Newcastle, Australia
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia
- Division of Molecular Medicine, New South Wales Health Pathology North, Newcastle, Australia
| | - Helmut Butzkueven
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Vilija G Jokubaitis
- Department of Neuroscience, Central Clinical School, Monash University, Melbourne, Australia
- Department of Neurology, Alfred Health, Melbourne, Australia
| | - Rodney A Lea
- School of Biomedical Sciences and Pharmacy, University of Newcastle, Newcastle, Australia.
- Centre for Genomics and Personalised Health, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Australia.
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Gutierrez MJ, Perez GF, Gomez JL, Rodriguez-Martinez CE, Castro-Rodriguez JA, Nino G. Genes, environment, and developmental timing: New insights from translational approaches to understand early origins of respiratory diseases. Pediatr Pulmonol 2021; 56:3157-3165. [PMID: 34388306 PMCID: PMC8858026 DOI: 10.1002/ppul.25598] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 06/17/2021] [Accepted: 06/22/2021] [Indexed: 12/24/2022]
Abstract
Over the past decade, "omics" approaches have advanced our understanding of the molecular programming of the airways in humans. Several studies have identified potential molecular mechanisms that contribute to early life epigenetic reprogramming, including DNA methylation, histone modifications, microRNAs, and the homeostasis of the respiratory mucosa (epithelial function and microbiota). Current evidence supports the notion that early infancy is characterized by heightened susceptibility to airway genetic reprogramming in response to the first exposures in life, some of which can have life-long consequences. Here, we summarize and analyze the latest insights from studies that support a novel epigenetic paradigm centered on human maturational and developmental programs including three cardinal elements: genes, environment, and developmental timing. The combination of these factors is likely responsible for the functional trajectory of the respiratory system at the molecular, functional, and clinical levels.
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Affiliation(s)
- Maria J Gutierrez
- Division of Pediatric Allergy and Immunology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Geovanny F Perez
- Division of Pediatric Pulmonology, Oishei Children's Hospital, University at Buffalo, Buffalo, New York, USA
| | - Jose L Gomez
- Department of Internal Medicine, Section of Pulmonary, Critical Care, and Sleep Medicine, Yale School of Medicine, New Haven, Connecticut, USA
| | - Carlos E Rodriguez-Martinez
- Department of Pediatrics, Universidad Nacional de Colombia, Bogota, Colombia.,Department of Pediatric Pulmonology and Pediatric Critical Care Medicine, School of Medicine, Universidad El Bosque, Bogota, Colombia
| | - Jose A Castro-Rodriguez
- Department of Pediatric Pulmonology, School of Medicine, Pontificia Universidad Catolica de Chile, Santiago, Chile
| | - Gustavo Nino
- Division of Pediatric Pulmonary and Sleep Medicine, Children's National Hospital, George Washington University, Washington D.C., USA
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Gallego-Paüls M, Hernández-Ferrer C, Bustamante M, Basagaña X, Barrera-Gómez J, Lau CHE, Siskos AP, Vives-Usano M, Ruiz-Arenas C, Wright J, Slama R, Heude B, Casas M, Grazuleviciene R, Chatzi L, Borràs E, Sabidó E, Carracedo Á, Estivill X, Urquiza J, Coen M, Keun HC, González JR, Vrijheid M, Maitre L. Variability of multi-omics profiles in a population-based child cohort. BMC Med 2021; 19:166. [PMID: 34289836 PMCID: PMC8296694 DOI: 10.1186/s12916-021-02027-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Multiple omics technologies are increasingly applied to detect early, subtle molecular responses to environmental stressors for future disease risk prevention. However, there is an urgent need for further evaluation of stability and variability of omics profiles in healthy individuals, especially during childhood. METHODS We aimed to estimate intra-, inter-individual and cohort variability of multi-omics profiles (blood DNA methylation, gene expression, miRNA, proteins and serum and urine metabolites) measured 6 months apart in 156 healthy children from five European countries. We further performed a multi-omics network analysis to establish clusters of co-varying omics features and assessed the contribution of key variables (including biological traits and sample collection parameters) to omics variability. RESULTS All omics displayed a large range of intra- and inter-individual variability depending on each omics feature, although all presented a highest median intra-individual variability. DNA methylation was the most stable profile (median 37.6% inter-individual variability) while gene expression was the least stable (6.6%). Among the least stable features, we identified 1% cross-omics co-variation between CpGs and metabolites (e.g. glucose and CpGs related to obesity and type 2 diabetes). Explanatory variables, including age and body mass index (BMI), explained up to 9% of serum metabolite variability. CONCLUSIONS Methylation and targeted serum metabolomics are the most reliable omics to implement in single time-point measurements in large cross-sectional studies. In the case of metabolomics, sample collection and individual traits (e.g. BMI) are important parameters to control for improved comparability, at the study design or analysis stage. This study will be valuable for the design and interpretation of epidemiological studies that aim to link omics signatures to disease, environmental exposures, or both.
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Affiliation(s)
- Marta Gallego-Paüls
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Carles Hernández-Ferrer
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Mariona Bustamante
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Xavier Basagaña
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Jose Barrera-Gómez
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Chung-Ho E Lau
- MRC Centre for Environment and Health, School of Public Health, Imperial College London, London, UK
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington, London, UK
| | - Alexandros P Siskos
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer and Division of Systems Medicine, Department of Metabolism, Digestion & Reproduction, Imperial College London, London, UK
| | - Marta Vives-Usano
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Carlos Ruiz-Arenas
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - John Wright
- Bradford Institute for Health Research, Bradford Teaching Hospitals NHS Foundation Trust, Bradford, UK
| | - Remy Slama
- Team of Environmental Epidemiology applied to Reproduction and Respiratory Health, Institute for Advanced Biosciences (IAB), Inserm, CNRS, Université Grenoble Alpes, Grenoble, France
| | - Barbara Heude
- Université de Paris, Centre for Research in Epidemiology and Statistics (CRESS), INSERM, INRAE, F-75004, Paris, France
| | - Maribel Casas
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | | | - Leda Chatzi
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Eva Borràs
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Eduard Sabidó
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Ángel Carracedo
- Medicine Genomics Group, Centro de Investigación Biomédica en Red Enfermedades Raras (CIBERER), University of Santiago de Compostela, CEGEN-PRB3, Santiago de Compostela, Spain
- Galician Foundation of Genomic Medicine, Instituto de Investigación Sanitaria de Santiago de Compostela (IDIS), Servicio Gallego de Salud (SERGAS), Santiago de Compostela, Galicia, Spain
| | - Xavier Estivill
- Center for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Jose Urquiza
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Muireann Coen
- Division of Systems Medicine, Department of Metabolism, Digestion and Reproduction, Imperial College London, South Kensington, London, UK
- Oncology Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Hector C Keun
- Cancer Metabolism & Systems Toxicology Group, Division of Cancer, Department of Surgery & Cancer and Division of Systems Medicine, Department of Metabolism, Digestion & Reproduction, Imperial College London, London, UK
| | - Juan R González
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Martine Vrijheid
- ISGlobal, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain
| | - Léa Maitre
- ISGlobal, Barcelona, Spain.
- Universitat Pompeu Fabra (UPF), Barcelona, Spain.
- Consorcio de Investigacion Biomedica en Red de Epidemiologia y Salud Publica (CIBERESP), Madrid, Spain.
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9
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Mourtzi N, Sertedaki A, Charmandari E. Glucocorticoid Signaling and Epigenetic Alterations in Stress-Related Disorders. Int J Mol Sci 2021; 22:5964. [PMID: 34073101 PMCID: PMC8198182 DOI: 10.3390/ijms22115964] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/26/2021] [Accepted: 05/29/2021] [Indexed: 12/31/2022] Open
Abstract
Stress is defined as a state of threatened or perceived as threatened homeostasis. The well-tuned coordination of the stress response system is necessary for an organism to respond to external or internal stressors and re-establish homeostasis. Glucocorticoid hormones are the main effectors of stress response and aberrant glucocorticoid signaling has been associated with an increased risk for psychiatric and mood disorders, including schizophrenia, post-traumatic stress disorder and depression. Emerging evidence suggests that life-stress experiences can alter the epigenetic landscape and impact the function of genes involved in the regulation of stress response. More importantly, epigenetic changes induced by stressors persist over time, leading to increased susceptibility for a number of stress-related disorders. In this review, we discuss the role of glucocorticoids in the regulation of stress response, the mechanism through which stressful experiences can become biologically embedded through epigenetic alterations, and we underline potential associations between epigenetic changes and the development of stress-related disorders.
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Affiliation(s)
- Niki Mourtzi
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (N.M.); (A.S.)
| | - Amalia Sertedaki
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (N.M.); (A.S.)
| | - Evangelia Charmandari
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, “Aghia Sophia” Children’s Hospital, National and Kapodistrian University of Athens Medical School, 11527 Athens, Greece; (N.M.); (A.S.)
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
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10
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Hu J, Zhao FY, Huang B, Ran J, Chen MY, Liu HL, Deng YS, Zhao X, Han XF. An Eight-CpG-based Methylation Classifier for Preoperative Discriminating Early and Advanced-Late Stage of Colorectal Cancer. Front Genet 2021; 11:614160. [PMID: 33519917 PMCID: PMC7838682 DOI: 10.3389/fgene.2020.614160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/14/2020] [Indexed: 11/28/2022] Open
Abstract
Aim To develop and validate a CpG-based classifier for preoperative discrimination of early and advanced-late stage colorectal cancer (CRC). Methods We identified an epigenetic signature based on methylation status of multiple CpG sites (CpGs) from 372 subjects in The Cancer Genome Atlas (TCGA) CRC cohort, and an external cohort (GSE48684) with 64 subjects by LASSO regression algorithm. A classifier derived from the methylation signature was used to establish a multivariable logistic regression model to predict the advanced-late stage of CRC. A nomogram was further developed by incorporating the classifier and some independent clinical risk factors, and its performance was evaluated by discrimination and calibration analysis. The prognostic value of the classifier was determined by survival analysis. Furthermore, the diagnostic performance of several CpGs in the methylation signature was evaluated. Results The eight-CpG-based methylation signature discriminated early stage from advanced-late stage CRC, with a satisfactory AUC of more than 0.700 in both the training and validation sets. This methylation classifier was identified as an independent predictor for CRC staging. The nomogram showed favorable predictive power for preoperative staging, and the C-index reached 0.817 (95% CI: 0.753–0.881) and 0.817 (95% CI: 0.721–0.913) in another training set and validation set respectively, with good calibration. The patients stratified in the high-risk group by the methylation classifier had significantly worse survival outcome than those in the low-risk group. Combination diagnosis utilizing only four of the eight specific CpGs performed well, even in CRC patients with low CEA level or at early stage. Conclusions Our classifier is a valuable predictive indicator that can supplement established methods for more accurate preoperative staging and also provides prognostic information for CRC patients. Besides, the combination of multiple CpGs has a high value in the diagnosis of CRC.
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Affiliation(s)
- Ji Hu
- Department of General Surgery, The First People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Fu-Ying Zhao
- Department of Medical Laboratory, The First People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Bin Huang
- Department of General Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Jing Ran
- Department of Pathology, The First People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Mei-Yuan Chen
- Department of General Surgery, The First People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Hai-Lin Liu
- Department of Clinical Pharmacy, The First People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - You-Song Deng
- Department of General Surgery, The First People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
| | - Xia Zhao
- Department of Microbiology, Army Medical University, Chongqing, China
| | - Xiao-Fan Han
- Department of General Surgery, The First People's Hospital of Chongqing Liang Jiang New Area, Chongqing, China
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11
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Shen T, Li X, Chen L, Chen Z, Tan T, Hua T, Chen B, Yuan Y, Zhang Z, Kuney L, Xu Z. The relationship of tryptophan hydroxylase-2 methylation to early-life stress and its impact on short-term antidepressant treatment response. J Affect Disord 2020; 276:850-858. [PMID: 32738671 DOI: 10.1016/j.jad.2020.07.111] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 06/26/2020] [Accepted: 07/06/2020] [Indexed: 01/13/2023]
Abstract
INTRODUCTION The gene tryptophan hydroxylase 2 (TPH2) encodes the associated rate-limiting enzyme in the biosynthesis 5-HT (serotonin). Early life stress and adult variability in TPH2 can correspond with diminished response to antidepressants for patients with major depressive disorder (MDD). DNA methylation is an epigenetic mechanism mediating gene expression, often tempered by environmental factors. Here, we investigate the influence of TPH2 methylation combined with stress on response to antidepressants within the first two weeks of treatment initiation. METHODS 291 Han Chinese patients with major depressive disorder and 100 healthy controls comprised the study population. The Life Events Scale (LES) and the Childhood Trauma Questionnaire (CTQ) rated recent and early-life stress. The primary outcome equaled a reduction by ≥ 50% from the Hamilton Depression Rating Scale-17 (HAMD-17) after 2 weeks of treatment. The Illumina HiSeq platform assessed methylation status in 38 CpG sites located upstream and downstream of 11 TPH2 polymorphism sites. RESULTS In 291 patients and 100 healthy controls, 3 CpG sites predict antidepressant treatment response per sex (TPH2-7-142, p=0.012; TPH2-1-43, p=0.033; TPH2-5-203, p=0.036). High-level CTQ scores relate significantly to DNA hypomethylation at CpG-site TPH2-8-237 in males (false discovery rate [FDR]-corrected p=0.038). Additionally, the interaction of hypermethylation in two CpG sites and elevated early-life stress may reduce antidepressant response (TPH2-5-203, FDR corrected p=0.010; TPH2-10-60, FDR corrected p=0.001). CONCLUSIONS Our study suggests that TPH2 methylation and its interaction with early-life stress may impair antidepressant response, suggesting that pharmaco-epigenetic studies could identify epigenetic biomarkers for antidepressant response.
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Affiliation(s)
- Tian Shen
- Department of Psychosomatics and Psychiatry, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, PR China
| | - Xingyu Li
- Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Institute of Life Sciences, Southeast University, Nanjing 210096, PR China
| | - Lei Chen
- Department of Psychosomatics and Psychiatry, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, PR China
| | - Zimu Chen
- Department of Psychosomatics and Psychiatry, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, PR China
| | - Tingting Tan
- Department of Psychosomatics and Psychiatry, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, PR China
| | - Tiantian Hua
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, PR China
| | - Bingwei Chen
- Department of Epidemiology and Biostatistics, School of Public Health, Southeast University, Nanjing 210009, PR China
| | - Yonggui Yuan
- Department of Psychosomatics and Psychiatry, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, PR China
| | - Zhijun Zhang
- Department of Neurology, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, PR China
| | - Liz Kuney
- Psychiatry Department, State University of New York Upstate Medical University, Syracuse, NY 13210, USA
| | - Zhi Xu
- Department of Psychosomatics and Psychiatry, Zhongda Hospital, School of Medicine, Southeast University, Nanjing 210009, PR China.
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12
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Diaz M, Garde E, Lopez-Bermejo A, de Zegher F, Ibañez L. Differential DNA methylation profile in infants born small-for-gestational-age: association with markers of adiposity and insulin resistance from birth to age 24 months. BMJ Open Diabetes Res Care 2020; 8:8/1/e001402. [PMID: 33106332 PMCID: PMC7592237 DOI: 10.1136/bmjdrc-2020-001402] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 07/04/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
INTRODUCTION Prenatal growth restraint followed by rapid postnatal weight gain increases lifelong diabetes risk. Epigenetic dysregulation in critical windows could exert long-term effects on metabolism and confer such risk. RESEARCH DESIGN AND METHODS We conducted a genome-wide DNA methylation profiling in peripheral blood from infants born appropriate-for-gestational-age (AGA, n=30) or small-for-gestational-age (SGA, n=21, with postnatal catch-up) at age 12 months, to identify new genes that may predispose to metabolic dysfunction. Candidate genes were validated by bisulfite pyrosequencing in the entire cohort. All infants were followed since birth; cord blood methylation profiling was previously reported. Endocrine-metabolic variables and body composition (dual-energy X-ray absorptiometry) were assessed at birth and at 12 and 24 months. RESULTS GPR120 (cg14582356, cg01272400, cg23654127, cg03629447), NKX6.1 (cg22598426, cg07688460, cg17444738, cg12076463, cg10457539), CPT1A (cg14073497, cg00941258, cg12778395) and IGFBP 4 (cg15471812) genes were hypermethylated (GPR120, NKX6.1 were also hypermethylated in cord blood), whereas CHGA (cg13332653, cg15480367, cg05700406), FABP5 (cg00696973, cg10563714, cg16128701), CTRP1 (cg19231170, cg19472078, cg0164309, cg07162665, cg17758081, cg18996910, cg06709009), GAS6 (N/A), ONECUT1 (cg14217069, cg02061705, cg26158897, cg06657050, cg15446043) and SLC2A8 (cg20758474, cg19021975, cg11312566, cg12281690, cg04016166, cg03804985) genes were hypomethylated in SGA infants. These genes were related to β-cell development and function, inflammation, and glucose and lipid metabolism and associated with body mass index, body composition, and markers of insulin resistance at 12 and 24 months. CONCLUSION In conclusion, at 12 months, abnormal methylation of GPR120 and NKX6.1 persists and new epigenetic marks further involved in adipogenesis and energy homeostasis arise in SGA infants. These abnormalities may contribute to metabolic dysfunction and diabetes risk later in life.
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Affiliation(s)
- Marta Diaz
- Endocrinology Department, Institut Pediàtric Hospital Sant Joan de Déu, University of Barcelona, Esplugues, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Edurne Garde
- Endocrinology Department, Institut Pediàtric Hospital Sant Joan de Déu, University of Barcelona, Esplugues, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
| | - Abel Lopez-Bermejo
- Department of Pediatrics, Dr. Josep Trueta Hospital and Girona Institute for Biomedical Research, Girona, Spain
| | - Francis de Zegher
- Department of Development & Regeneration, University of Leuven, Leuven, Flanders, Belgium
| | - Lourdes Ibañez
- Endocrinology Department, Institut Pediàtric Hospital Sant Joan de Déu, University of Barcelona, Esplugues, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), ISCIII, Madrid, Spain
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13
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Gutierrez MJ, Nino G, Hong X, Wang X. Epigenomics and Early Life Human Humoral Immunity: Novel Paradigms and Research Opportunities. Front Immunol 2020; 11:1766. [PMID: 32983086 PMCID: PMC7492271 DOI: 10.3389/fimmu.2020.01766] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 07/01/2020] [Indexed: 12/24/2022] Open
Abstract
The molecular machinery controlling immune development has been extensively investigated. Studies in animal models and adult individuals have revealed fundamental mechanisms of disease and have been essential to understanding how humans sense and respond to cellular stress, tissue damage, pathogens and their environment. Nonetheless, our understanding of how immune responses originate during human development is just starting to emerge. In particular, studies to unveil how environmental and other non-heritable factors shape the immune system at the beginning of life offer great promise to yield important knowledge about determinants of normal inter-individual immune variation and to prevent and treat many human diseases. In this review, we summarize our current understanding of some of the mechanisms determining early life antibody production as a model of an immune process with sequential molecular checkpoints susceptible to influence by non-heritable factors. We discuss the potential of epigenomics as a valuable approach that may reveal not only relevant gene-environment interactions but important clues about immune developmental processes and homeostasis in early life. We then highlight the novel paradigm of human immunology as a complex field that nowadays requires a longitudinal systems-biology approach to understand normal variation and developmental changes during the first few years of life.
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Affiliation(s)
- Maria J Gutierrez
- Division of Pediatric Allergy, Immunology and Rheumatology, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Gustavo Nino
- Division of Pediatric Pulmonary and Sleep Medicine, Children's National Medical Center, George Washington University, Washington, DC, United States.,Center for Genetic Medicine, Children's National Medical Center, Washington, DC, United States
| | - Xiumei Hong
- Department of Population, Family and Reproductive Health, Center on Early Life Origins of Disease, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States
| | - Xiaobin Wang
- Department of Population, Family and Reproductive Health, Center on Early Life Origins of Disease, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, United States.,Division of General Pediatrics and Adolescent Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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14
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Prats-Puig A, García-Retortillo S, Puig-Parnau M, Vasileva F, Font-Lladó R, Xargay-Torrent S, Carreras-Badosa G, Mas-Parés B, Bassols J, López-Bermejo A. DNA Methylation Reorganization of Skeletal Muscle-Specific Genes in Response to Gestational Obesity. Front Physiol 2020; 11:938. [PMID: 32848869 PMCID: PMC7412435 DOI: 10.3389/fphys.2020.00938] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 12/25/2022] Open
Abstract
The goals were to investigate in umbilical cord tissue if gestational obesity: (1) was associated with changes in DNA methylation of skeletal muscle-specific genes; (2) could modulate the co-methylation interactions among these genes. Additionally, we assessed the associations between DNA methylation levels and infant's variables at birth and at age 6. DNA methylation was measured in sixteen pregnant women [8-gestational obesity group; 8-control group] in umbilical cord using the Infinium Methylation EPIC Bead Chip microarray. Differentially methylated CpGs were identified with Beta Regression Models [false discovery rate (FDR) < 0.05 and an Odds Ratio > 1.5 or < 0.67]. DNA methylation interactions between CpGs of skeletal muscle-specific genes were studied using data from Pearson correlation matrices. In order to quantify the interactions within each network, the number of links was computed. This identification analysis reported 38 differential methylated CpGs within skeletal muscle-specific genes (comprising 4 categories: contractibility, structure, myokines, and myogenesis). Compared to control group, gestational obesity (1) promotes hypermethylation in highly methylated genes and hypomethylation in low methylated genes; (2) CpGs in regions close to transcription sites and with high CpG density are hypomethylated while regions distant to transcriptions sites and with low CpG density are hypermethylated; (3) diminishes the number of total interactions in the co-methylation network. Interestingly, the associations between infant's fasting glucose at age 6 and MYL6, MYH11, TNNT3, TPM2, CXCL2, and NCAM1 were still relevant after correcting for multiple testing. In conclusion, our study showed a complex interaction between gestational obesity and the epigenetic status of muscle-specific genes in umbilical cord tissue. Additionally, gestational obesity may alter the functional co-methylation connectivity of CpG within skeletal muscle-specific genes interactions, our results revealing an extensive reorganization of methylation in response to maternal overweight. Finally, changes in methylation levels of skeletal muscle specific genes may have persistent effects on the offspring of mothers with gestational obesity.
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Affiliation(s)
- Anna Prats-Puig
- University School of Health and Sport (EUSES), University of Girona, Girona, Spain
| | - Sergi García-Retortillo
- University School of Health and Sport (EUSES), University of Girona, Girona, Spain
- Complex Systems in Sport, National Institute of Physical Education and Sport of Catalonia (INEFC), Universitat de Barcelona (UB), Barcelona, Spain
| | - Miquel Puig-Parnau
- University School of Health and Sport (EUSES), University of Girona, Girona, Spain
| | - Fidanka Vasileva
- Faculty of Physical Education, Sport and Health, Ss. Cyril and Methodius University, Skopje, North Macedonia
| | - Raquel Font-Lladó
- University School of Health and Sport (EUSES), University of Girona, Girona, Spain
| | - Sílvia Xargay-Torrent
- Pediatric Endocrinology, Girona Institute for Biomedical Research, Dr. Josep Trueta Hospital, Girona, Spain
| | - Gemma Carreras-Badosa
- Pediatric Endocrinology, Girona Institute for Biomedical Research, Dr. Josep Trueta Hospital, Girona, Spain
| | - Berta Mas-Parés
- Maternal & Fetal Metabolic Research, Girona Institute for Biomedical Research, Salt, Spain
| | - Judit Bassols
- Maternal & Fetal Metabolic Research, Girona Institute for Biomedical Research, Salt, Spain
| | - Abel López-Bermejo
- Pediatric Endocrinology, Girona Institute for Biomedical Research, Dr. Josep Trueta Hospital, Girona, Spain
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15
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Gutierrez MJ, Nino G, Hong X, Wang X. Epigenetic Dynamics of the Infant Immune System Reveals a Tumor Necrosis Factor Superfamily Signature in Early Human Life. EPIGENOMES 2020; 4. [PMID: 32922965 PMCID: PMC7486026 DOI: 10.3390/epigenomes4030012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
DNA methylation (DNAm) is an essential mechanism governing normal development in humans. Although most DNAm patterns in blood cells are established in utero, the genes associated with immune function undergo postnatal DNAm modifications, and the characterization of this subset of genes is incomplete. Accordingly, we used available longitudinal DNAm datasets from a large birth cohort in the U.S. to further identify postnatal DNAm variation in peripheral leukocytes from 105 children (n = 105) between birth and the first two years of life, as determined by postnatal changes in β values (with the percentage of methylation ranging from 0 to 1.0 at individual CpG sites). Our study is an extension of a previous analysis performed by our group and identified that: (1) as previously described, DNAm patterns at most CpG sites were established before birth and only a small group of genes underwent DNAm modifications postnatally, (2) this subset includes multiple immune genes critical for lymphocyte development, and (3) several members of the tumor necrosis factor receptor and cytokine superfamilies with essential roles in immune cell activation, survival, and lymphoid tissue development were among those with a larger postnatal variation. This study describes the precise epigenetic DNA methylation marks in important immune genes that change postnatally and raises relevant questions about the role of DNAm during postnatal immune development in early childhood.
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Affiliation(s)
- Maria J. Gutierrez
- Division of Pediatric Allergy, Immunology and Rheumatology, Department of Pediatrics, Johns Hopkins University, Baltimore, MD 21287, USA
- Correspondence:
| | - Gustavo Nino
- Division of Pediatric Pulmonary and Sleep Medicine, Children’s National Medical Center, George Washington University, Washington, DC 20010, USA;
- Center for Genetic Medicine, Children’s National Medical Center, Washington, DC 20010, USA
| | - Xiumei Hong
- Center on the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA; (X.H.); (X.W.)
| | - Xiaobin Wang
- Center on the Early Life Origins of Disease, Department of Population, Family and Reproductive Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA; (X.H.); (X.W.)
- Division of General Pediatrics & Adolescent Medicine, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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16
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Ikegame T, Bundo M, Okada N, Murata Y, Koike S, Sugawara H, Saito T, Ikeda M, Owada K, Fukunaga M, Yamashita F, Koshiyama D, Natsubori T, Iwashiro N, Asai T, Yoshikawa A, Nishimura F, Kawamura Y, Ishigooka J, Kakiuchi C, Sasaki T, Abe O, Hashimoto R, Iwata N, Yamasue H, Kato T, Kasai K, Iwamoto K. Promoter Activity-Based Case-Control Association Study on SLC6A4 Highlighting Hypermethylation and Altered Amygdala Volume in Male Patients With Schizophrenia. Schizophr Bull 2020; 46:1577-1586. [PMID: 32556264 PMCID: PMC7846196 DOI: 10.1093/schbul/sbaa075] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Associations between altered DNA methylation of the serotonin transporter (5-HTT)-encoding gene SLC6A4 and early life adversity, mood and anxiety disorders, and amygdala reactivity have been reported. However, few studies have examined epigenetic alterations of SLC6A4 in schizophrenia (SZ). We examined CpG sites of SLC6A4, whose DNA methylation levels have been reported to be altered in bipolar disorder, using 3 independent cohorts of patients with SZ and age-matched controls. We found significant hypermethylation of a CpG site in SLC6A4 in male patients with SZ in all 3 cohorts. We showed that chronic administration of risperidone did not affect the DNA methylation status at this CpG site using common marmosets, and that in vitro DNA methylation at this CpG site diminished the promoter activity of SLC6A4. We then genotyped the 5-HTT-linked polymorphic region (5-HTTLPR) and investigated the relationship among 5-HTTLPR, DNA methylation, and amygdala volume using brain imaging data. We found that patients harboring low-activity 5-HTTLPR alleles showed hypermethylation and they showed a negative correlation between DNA methylation levels and left amygdala volumes. These results suggest that hypermethylation of the CpG site in SLC6A4 is involved in the pathophysiology of SZ, especially in male patients harboring low-activity 5-HTTLPR alleles.
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Affiliation(s)
- Tempei Ikegame
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Miki Bundo
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan,PRESTO, Japan Science and Technology Agency, Tokyo, Japan
| | - Naohiro Okada
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo Institutes for Advanced Study (UTIAS), The University of Tokyo, Tokyo, Japan
| | - Yui Murata
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Shinsuke Koike
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,UTokyo Institute for Diversity and Adaptation of Human Mind (UTIDAHM), The University of Tokyo, Tokyo, Japan
| | - Hiroko Sugawara
- Department of Neuropsychiatry, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Takeo Saito
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Masashi Ikeda
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Keiho Owada
- Department of Child Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Masaki Fukunaga
- Division of Cerebral Integration, National Institute for Physiological Sciences, Aichi, Japan
| | - Fumio Yamashita
- Division of Ultrahigh Field MRI, Institute for Biomedical Sciences, Iwate Medical University, Iwate, Japan
| | - Daisuke Koshiyama
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsunobu Natsubori
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Norichika Iwashiro
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tatsuro Asai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Akane Yoshikawa
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Schizophrenia Research Project, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Fumichika Nishimura
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | | | | | - Chihiro Kakiuchi
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Tsukasa Sasaki
- Laboratory of Health Education, Graduate School of Education, The University of Tokyo, Tokyo, Japan
| | - Osamu Abe
- Department of Radiology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ryota Hashimoto
- Department of Pathology of Mental Diseases, National Institute of Mental Health, National Center of Neurology and Psychiatry, Tokyo, Japan,Department of Psychiatry, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Nakao Iwata
- Department of Psychiatry, Fujita Health University School of Medicine, Aichi, Japan
| | - Hidenori Yamasue
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan,Department of Psychiatry, Hamamatsu University School of Medicine, Shizuoka, Japan
| | - Tadafumi Kato
- Laboratory for Molecular Dynamics of Mental Disorders, RIKEN CBS, Saitama, Japan
| | - Kiyoto Kasai
- Department of Neuropsychiatry, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Kazuya Iwamoto
- Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan,To whom correspondence should be addressed; Department of Molecular Brain Science, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-ku, Kumamoto 860-8556, Japan; tel: +81-96-373-5062, fax: +81-96-373-5062, e-mail:
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17
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Stonawski V, Roetner J, Goecke TW, Fasching PA, Beckmann MW, Kornhuber J, Kratz O, Moll GH, Eichler A, Heinrich H, Frey S. Genome-Wide DNA Methylation Patterns in Children Exposed to Nonpharmacologically Treated Prenatal Depressive Symptoms: Results From 2 Independent Cohorts. Epigenet Insights 2020; 13:2516865720932146. [PMID: 32596638 PMCID: PMC7298426 DOI: 10.1177/2516865720932146] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/01/2020] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Maternal depressive symptoms are a common phenomenon during pregnancy and are related to negative outcomes for child development and health. Modifications in child DNA methylation are discussed as an underlying mechanism for the association between prenatal depressive symptoms and alterations in child outcomes. However, formerly reported genome-wide associations have yet to be replicated. METHODS In an epigenome-wide association study (EWAS), alterations of DNA methylation related to maternal prenatal depressive symptoms were investigated in buccal cell samples from 174 children (n = 52 exposed to prenatal depressive symptoms; 6-9 years old) of the German longitudinal study FRAMES-FRANCES. Whole blood samples from the independent, age-comparable ARIES subsample of the ARIES/ALSPAC study (n = 641; n = 159 exposed to prenatal depressive symptoms; 7-8 years old) were examined as a confirmation sample. Depressive symptoms were assessed with the Edinburgh Postnatal Depression Scale. DNA methylation was analyzed with the Infinium Human Methylation 450k BeadChip. Modifications in single CpGs, regions, and biological pathways were investigated. Results were adjusted for age and birth outcomes as well as postnatal and current maternal depressive symptoms. Analyses were performed for the whole sample as well as separated for sex. RESULTS The EWAS yielded no differentially methylated CpG or region as well as no accordance between samples withstanding correction for multiple testing. In pathway analyses, no overlapping functional domain was found to be enriched for either sample. A comparison of current and former findings suggests some overlapping methylation modifications from infancy to childhood. Results suggest that there might be sex-specific differential methylation, which should be further investigated in additional studies. CONCLUSIONS The current, mainly nonsignificant, results challenge the assumption of consistent modifications of DNA methylation in children exposed to prenatal depressive symptoms. Despite the relatively small sample size used in this study, this lack of significant results may reflect diverse issues of environmental epigenetic studies, which need to be addressed in future research.
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Affiliation(s)
- Valeska Stonawski
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Jakob Roetner
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Tamme W Goecke
- Department of Gynecology and Obstetrics,
University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg
(FAU), Erlangen, Germany
- Department of Obstetrics and
Gynaecology, RoMed Hospital Rosenheim, Rosenheim, Germany
| | - Peter A Fasching
- Department of Gynecology and Obstetrics,
University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg
(FAU), Erlangen, Germany
| | - Matthias W Beckmann
- Department of Gynecology and Obstetrics,
University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg
(FAU), Erlangen, Germany
| | - Johannes Kornhuber
- Department of Psychiatry and
Psychotherapy, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Oliver Kratz
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Gunther H Moll
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | - Anna Eichler
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
| | | | - Stefan Frey
- Department of Child and Adolescent
Mental Health, University Hospital Erlangen, Friedrich-Alexander University
Erlangen-Nürnberg (FAU), Erlangen, Germany
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18
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Sunny SK, Zhang H, Rezwan FI, Relton CL, Henderson AJ, Merid SK, Melén E, Hallberg J, Arshad SH, Ewart S, Holloway JW. Changes of DNA methylation are associated with changes in lung function during adolescence. Respir Res 2020; 21:80. [PMID: 32264874 PMCID: PMC7140357 DOI: 10.1186/s12931-020-01342-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/25/2020] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Adolescence is a significant period for the gender-dependent development of lung function. Prior studies have shown that DNA methylation (DNA-M) is associated with lung function and DNA-M at some cytosine-phosphate-guanine dinucleotide sites (CpGs) changes over time. This study examined whether changes of DNA-M at lung-function-related CpGs are associated with changes in lung function during adolescence for each gender, and if so, the biological significance of the detected CpGs. METHODS Genome-scale DNA-M was measured in peripheral blood samples at ages 10 (n = 330) and 18 years (n = 476) from the Isle of Wight (IOW) birth cohort in United Kingdom, using Illumina Infinium arrays (450 K and EPIC). Spirometry was conducted at both ages. A training and testing method was used to screen 402,714 CpGs for their potential associations with lung function. Linear regressions were applied to assess the association of changes in lung function with changes of DNA-M at those CpGs potentially related to lung function. Adolescence-related and personal and family-related confounders were included in the model. The analyses were stratified by gender. Multiple testing was adjusted by controlling false discovery rate of 0.05. Findings were further examined in two independent birth cohorts, the Avon Longitudinal Study of Children and Parents (ALSPAC) and the Children, Allergy, Milieu, Stockholm, Epidemiology (BAMSE) cohort. Pathway analyses were performed on genes to which the identified CpGs were mapped. RESULTS For females, 42 CpGs showed statistically significant associations with change in FEV1/FVC, but none for change in FEV1 or FVC. No CpGs were identified for males. In replication analyses, 16 and 21 of the 42 CpGs showed the same direction of associations among the females in the ALSPAC and BAMSE cohorts, respectively, with 11 CpGs overlapping across all the three cohorts. Through pathway analyses, significant biological processes were identified that have previously been related to lung function development. CONCLUSIONS The detected 11 CpGs in all three cohorts have the potential to serve as the candidate epigenetic markers for changes in lung function during adolescence in females.
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Affiliation(s)
- Shadia Khan Sunny
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152 USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health, School of Public Health, University of Memphis, Memphis, TN 38152 USA
| | - Faisal I. Rezwan
- School of Water, Energy and Environment, Cranfield University, Cranfield Bedfordshire, MK43 0AL England
| | - Caroline L. Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, BS8 2BN UK
| | - A. John Henderson
- Population Health Sciences, University of Bristol, Bristol, BS8 2BN UK
| | - Simon Kebede Merid
- Department of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
| | - Erik Melén
- Department of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs’ Children’s Hospital, Stockholm, Sweden
| | - Jenny Hallberg
- Department of Clinical Sciences and Education Södersjukhuset, Karolinska Institutet, Stockholm, Sweden
- Sachs’ Children’s Hospital, Stockholm, Sweden
| | - S. Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD UK
- The David Hide Asthma and Allergy Research Centre, St Mary’s Hospital, Parkhurst Road, Newport, Isle of Wight PO30 5TG UK
| | - Susan Ewart
- Large Animal Clinical Sciences, Michigan State University, East Lansing, MI USA
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton, SO16 6YD UK
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19
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Hematopoietic cellular aging is not accelerated during the first 2 years of life in children born preterm. Pediatr Res 2020; 88:903-909. [PMID: 32170191 PMCID: PMC7086539 DOI: 10.1038/s41390-020-0833-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/10/2020] [Accepted: 02/19/2020] [Indexed: 11/08/2022]
Abstract
BACKGROUND Prematurity in itself and exposure to neonatal intensive care triggers inflammatory processes and oxidative stress, leading to risk for disease later in life. The effects on cellular aging processes are incompletely understood. METHODS Relative telomere length (RTL) was measured by qPCR in this longitudinal cohort study with blood samples taken at birth and at 2 years of age from 60 children (16 preterm and 44 term). Viral respiratory infections the first year were evaluated. Epigenetic biological DNA methylation (DNAm) age was predicted based on methylation array data in 23 children (11 preterm and 12 term). RTL change/year and DNAm age change/year was compared in preterm and term during the 2 first years of life. RESULTS Preterm infants had longer telomeres than term born at birth and at 2 years of age, but no difference in telomere attrition rate could be detected. Predicted epigenetic DNAm age was younger in preterm infants, but rate of DNAm aging was similar in both groups. CONCLUSIONS Despite early exposure to risk factors for accelerated cellular aging, children born preterm exhibited preserved telomeres. Stress during the neonatal intensive care period did not reflect accelerated epigenetic DNAm aging. Early-life aging was not explained by preterm birth. IMPACT Preterm birth is associated with elevated disease risk later in life. Preterm children often suffer from inflammation early in life. Stress-related telomere erosion during neonatal intensive care has been proposed. Inflammation-accelerated biological aging in preterm is unknown. We find no accelerated aging due to prematurity or infections during the first 2 years of life.
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20
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Liu J, Zhao W, Ammous F, Turner ST, Mosley TH, Zhou X, Smith JA. Longitudinal analysis of epigenome-wide DNA methylation reveals novel smoking-related loci in African Americans. Epigenetics 2019; 14:171-184. [PMID: 30764717 DOI: 10.1080/15592294.2019.1581589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022] Open
Abstract
Changes in DNA methylation may be a potential mechanism that mediates the effects of smoking on physiological function and subsequent disease risk. Given the dynamic nature of the epigenome, longitudinal studies are indispensable for investigating smoking-induced methylation changes over time. Using blood samples collected approximately five years apart in 380 African Americans (mean age 60.7 years) from the Genetic Epidemiology Network of Arteriopathy (GENOA) study, we measured DNA methylation levels using Illumina HumanMethylation BeadChips. We evaluated the association between Phase 1 smoking status and rate of methylation change, using generalized estimating equation models. Among the 6958 CpG sites examined, smoking status was associated with methylation change for 22 CpGs (false discovery rate q < 0.1), with the majority (91%) becoming less methylated over time. Methylation change was greater in ever smokers than never smokers, and the absolute differences in rates of change ranged from 0.18 to 0.77 per decade in M value, equivalent to a β value change of 0.013 to 0.047 per decade. Significant enrichment was observed for CpG islands, enhancers, and DNAse hypersensitivity sites (p < 0.05). Although biological pathway analyses were not significant, most of the 22 CpGs were within genes known to be associated with cardiovascular disease, cancers, and aging. In conclusion, we identified epigenetic signatures for cigarette smoking that may have been missed in cross-sectional analyses, providing insight into the epigenetic effect of smoking and highlighting the importance of longitudinal analysis in understanding the dynamic human epigenome.
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Affiliation(s)
- Jiaxuan Liu
- a Department of Epidemiology , School of Public Health, University of Michigan , Ann Arbor , MI , USA
| | - Wei Zhao
- a Department of Epidemiology , School of Public Health, University of Michigan , Ann Arbor , MI , USA
| | - Farah Ammous
- a Department of Epidemiology , School of Public Health, University of Michigan , Ann Arbor , MI , USA
| | - Stephen T Turner
- b Division of Nephrology and Hypertension , Mayo Clinic , Rochester , MN , USA
| | - Thomas H Mosley
- c Memory Impairment and Neurodegenerative Dementia (MIND) Center , University of Mississippi Medical Center , Jackson , MS , USA
| | - Xiang Zhou
- d Department of Biostatistics , School of Public Health, University of Michigan , Ann Arbor , MI , USA
| | - Jennifer A Smith
- a Department of Epidemiology , School of Public Health, University of Michigan , Ann Arbor , MI , USA.,e Survey Research Center, Institute for Social Research , University of Michigan , Ann Arbor , MI , USA
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21
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Viitaniemi HM, Verhagen I, Visser ME, Honkela A, van Oers K, Husby A. Seasonal Variation in Genome-Wide DNA Methylation Patterns and the Onset of Seasonal Timing of Reproduction in Great Tits. Genome Biol Evol 2019; 11:970-983. [PMID: 30840074 PMCID: PMC6447391 DOI: 10.1093/gbe/evz044] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/05/2019] [Indexed: 02/06/2023] Open
Abstract
In seasonal environments, timing of reproduction is a trait with important fitness consequences, but we know little about the molecular mechanisms that underlie the variation in this trait. Recently, several studies put forward DNA methylation as a mechanism regulating seasonal timing of reproduction in both plants and animals. To understand the involvement of DNA methylation in seasonal timing of reproduction, it is necessary to examine within-individual temporal changes in DNA methylation, but such studies are very rare. Here, we use a temporal sampling approach to examine changes in DNA methylation throughout the breeding season in female great tits (Parus major) that were artificially selected for early timing of breeding. These females were housed in climate-controlled aviaries and subjected to two contrasting temperature treatments. Reduced representation bisulfite sequencing on red blood cell derived DNA showed genome-wide temporal changes in more than 40,000 out of the 522,643 CpG sites examined. Although most of these changes were relatively small (mean within-individual change of 6%), the sites that showed a temporal and treatment-specific response in DNA methylation are candidate sites of interest for future studies trying to understand the link between DNA methylation patterns and timing of reproduction.
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Affiliation(s)
- Heidi M Viitaniemi
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
| | - Irene Verhagen
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Marcel E Visser
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Antti Honkela
- Helsinki Institute for Information Technology HIIT, Department of Mathematics and Statistics, University of Helsinki, Finland
- Department of Public Health, University of Helsinki, Finland
| | - Kees van Oers
- Department of Animal Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Wageningen, The Netherlands
| | - Arild Husby
- Organismal and Evolutionary Biology Research Programme, University of Helsinki, Finland
- Department of Ecology and Genetics, EBC, Uppsala University, Sweden
- Centre for Biodiversity Dynamics, NTNU, Trondheim, Norway
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22
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Alfano R, Guida F, Galobardes B, Chadeau-Hyam M, Delpierre C, Ghantous A, Henderson J, Herceg Z, Jain P, Nawrot TS, Relton C, Vineis P, Castagné R, Plusquin M. Socioeconomic position during pregnancy and DNA methylation signatures at three stages across early life: epigenome-wide association studies in the ALSPAC birth cohort. Int J Epidemiol 2019; 48:30-44. [PMID: 30590607 PMCID: PMC6443021 DOI: 10.1093/ije/dyy259] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 11/06/2018] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Socioeconomic experiences are recognized determinants of health, and recent work has shown that social disadvantages in early life may induce sustained biological changes at molecular level that are detectable later in life. However, the dynamics and persistence of biological embedding of socioeconomic position (SEP) remains vastly unexplored. METHODS Using the data from the ALSPAC birth cohort, we performed epigenome-wide association studies of DNA methylation changes at three life stages (birth, n = 914; childhood at mean age 7.5 years, n = 973; and adolescence at mean age 15.5 years, n = 974), measured using the Illumina HumanMethylation450 Beadchip, in relation to pregnancy SEP indicators (maternal and paternal education and occupation). RESULTS Across the four early life SEP metrics investigated, only maternal education was associated with methylation levels at birth, and four CpGs mapped to SULF1, GLB1L2 and RPUSD1 genes were identified [false discovery rate (FDR)-corrected P-value <0.05]. No epigenetic signature was found associated with maternal education in child samples, but methylation levels at 20 CpG loci were found significantly associated with maternal education in adolescence. Although no overlap was found between the differentially methylated CpG sites at different ages, we identified two CpG sites at birth and during adolescence which are 219 bp apart in the SULF1 gene that encodes an heparan sulphatase involved in modulation of signalling pathways. Using data from an independent birth cohort, the ENVIRONAGE cohort, we were not able to replicate these findings. CONCLUSIONS Taken together, our results suggest that parental SEP, and particularly maternal education, may influence the offspring's methylome at birth and adolescence.
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Affiliation(s)
- Rossella Alfano
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Florence Guida
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
| | - Bruna Galobardes
- Department of Population Health Sciences, University of Bristol, Bristol, UK
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences (IRAS), Utrecht University, Utrecht, The Netherlands
| | - Cyrille Delpierre
- INSERM, UMR1027, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Akram Ghantous
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - John Henderson
- Department of Population Health Sciences, University of Bristol, Bristol, UK
| | - Zdenko Herceg
- Epigenetics Group, International Agency for Research on Cancer (IARC), Lyon, France
| | - Pooja Jain
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- NIHR-Health Protection Research Unit, Respiratory Infections and Immunity, Imperial College London, London, UK
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Caroline Relton
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Paolo Vineis
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- IIGM, Italian Institute for Genomic Medicine, Turin, Italy
| | - Raphaële Castagné
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- INSERM, UMR1027, Université Toulouse III-Paul Sabatier, Toulouse, France
| | - Michelle Plusquin
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK
- Medical Research Council-Health Protection Agency Centre for Environment and Health, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
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23
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Abstract
DNA methylation is an epigenetic mechanism most commonly associated with transcriptional repression. While it is clear that DNA methylation can silence HIV proviral expression in in vitro latency models, its correlation with HIV persistence and expression in vivo is ambiguous, particularly in persons living with HIV (PLWH) receiving antiretroviral therapy (ART). DNA methylation is an epigenetic mechanism most commonly associated with transcriptional repression. While it is clear that DNA methylation can silence HIV proviral expression in in vitro latency models, its correlation with HIV persistence and expression in vivo is ambiguous, particularly in persons living with HIV (PLWH) receiving antiretroviral therapy (ART). Several factors potentially contribute to discrepancies between results in the literature, including differences in integration sites, functional proviral load, sampling bias, and stochastic PCR amplification. Recent studies into genomic features of cytosine methylation sites in mammalian genes offer potentially significant insights into this mechanism. Here, we discuss the importance of these factors in the context of the HIV.
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24
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Pérez RF, Santamarina P, Tejedor JR, Urdinguio RG, Álvarez-Pitti J, Redon P, Fernández AF, Fraga MF, Lurbe E. Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes. J Transl Med 2019; 17:15. [PMID: 30626398 PMCID: PMC6327427 DOI: 10.1186/s12967-018-1751-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 12/17/2018] [Indexed: 01/08/2023] Open
Abstract
Background Early life is a period of drastic epigenetic remodeling in which the epigenome is especially sensitive to extrinsic and intrinsic influence. However, the epigenome-wide dynamics of the DNA methylation changes that occur during this period have not been sufficiently characterized in longitudinal studies. Methods To this end, we studied the DNA methylation status of more than 750,000 CpG sites using Illumina MethylationEPIC arrays on 33 paired blood samples from 11 subjects at birth and at 5 and 10 years of age, then characterized the chromatin context associated with these loci by integrating our data with histone, chromatin-state and enhancer-element external datasets, and, finally, validated our results through bisulfite pyrosequencing in two independent longitudinal cohorts of 18 additional subjects. Results We found abundant DNA methylation changes (110,726 CpG sites) during the first lustrum of life, while far fewer alterations were observed in the subsequent 5 years (460 CpG sites). However, our analysis revealed persistent DNA methylation changes at 240 CpG sites, indicating that there are genomic locations of considerable epigenetic change beyond immediate birth. The chromatin context of hypermethylation changes was associated with repressive genomic locations and genes with developmental and cell signaling functions, while hypomethylation changes were linked to enhancer regions and genes with immunological and mRNA and protein metabolism functions. Significantly, our results show that genes that suffer simultaneous hyper- and hypomethylation are functionally distinct from exclusively hyper- or hypomethylated genes, and that enhancer-associated methylation is different in hyper- and hypomethylation scenarios, with hypomethylation being more associated to epigenetic changes at blood tissue-specific enhancer elements. Conclusions These data show that epigenetic remodeling is dramatically reduced after the first 5 years of life. However, there are certain loci which continue to manifest DNA methylation changes, pointing towards a possible functionality beyond early development. Furthermore, our results deepen the understanding of the genomic context associated to hyper- or hypomethylation alterations during time, suggesting that hypomethylation of blood tissue-specific enhancer elements could be of importance in the establishment of functional states in blood tissue during early-life. Electronic supplementary material The online version of this article (10.1186/s12967-018-1751-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Raúl F Pérez
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain.,Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain
| | - Pablo Santamarina
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain.,Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain
| | - Juan Ramón Tejedor
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Rocío G Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Julio Álvarez-Pitti
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain.,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Pau Redon
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain.,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA)-Instituto de Investigación Sanitaria del Principado de Asturias (ISPA)-Hospital Universitario Central de Asturias (HUCA), 33011, Oviedo, Asturias, Spain
| | - Mario F Fraga
- Nanomedicine Group, Nanomaterials and Nanotechnology Research Center (CINN-CSIC), Universidad de Oviedo, 33940, Oviedo, Asturias, Spain.
| | - Empar Lurbe
- Servicio de Pediatría, Consorcio Hospital General Universitario de Valencia, 46014, Valencia, Spain. .,Centros de Investigación Biomédica en Red de Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain.
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25
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Li Y, Deng Y, Deng C, Xie L, Yu L, Liu L, Yuan Y, Liu H, Dai L. Association of long interspersed nucleotide element-1 and interferon regulatory factor 6 methylation changes with nonsyndromic cleft lip with or without cleft palate. Oral Dis 2018; 25:215-222. [PMID: 30153397 DOI: 10.1111/odi.12965] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 06/09/2018] [Accepted: 07/04/2018] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To examine the possible associations between methylation changes in the promoter regions of long interspersed nucleotide element-1 (LINE-1) and interferon regulatory factor 6 gene (IRF6) and nonsyndromic cleft lip with or without cleft palate (NSCL/P). METHODS A case-control investigation was performed to compare 37 infants affected by NSCL/Ps with 60 babies without cleft malformations. Their genomic DNA samples were obtained, and the LINE-1 and IRF6 methylation levels were measured by using Sequenom MassArray. Unconditional logistic regression was adopted to estimate the odds ratio. RESULTS Infants with NSCL/Ps had a higher methylation level at LINE-1 and IRF6 promoter regions than controls. High levels of LINE-1 (≥64.07%) and IRF6 (≥6.46%) methylation were associated with an increased risk of NSCL/P (LINE-1, OR = 2.63, 95% CI: 1.07-6.57; IRF6, OR = 4.73, 95% CI: 2.10-13.07), and the associations remained to be significant after adjusting for potential confounders. Similar associations were also found for cleft lip only, cleft lip, and palate. CONCLUSION Our study suggested that aberrant methylation of LINE-1 and IRF6 might contribute to the development of NSCL/Ps. Further studies are needed to replicate the findings.
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Affiliation(s)
- Yanhua Li
- Obstetric and Gynecologic Department, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Ying Deng
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Changfei Deng
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Liang Xie
- Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Li Yu
- Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.,Pediatric Department, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Lijun Liu
- Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.,Pediatric Department, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Yumei Yuan
- Hengyang Women and Children Hospital, Hengyang, China
| | - Hanmin Liu
- Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China.,Pediatric Department, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Li Dai
- National Center for Birth Defects Monitoring, West China Second University Hospital, Sichuan University, Chengdu, China.,Key Laboratory of Obstetrics & Gynecology and Pediatric Diseases and Birth Defects of the Ministry of Education, West China Second University Hospital, Sichuan University, Chengdu, China
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Ciuculete DM, Boström AE, Tuunainen AK, Sohrabi F, Kular L, Jagodic M, Voisin S, Mwinyi J, Schiöth HB. Changes in methylation within the STK32B promoter are associated with an increased risk for generalized anxiety disorder in adolescents. J Psychiatr Res 2018; 102:44-51. [PMID: 29604450 DOI: 10.1016/j.jpsychires.2018.03.008] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 12/20/2022]
Abstract
Generalized anxiety disorder (GAD) is highly prevalent among adolescents. An early detection of individuals at risk may prevent later psychiatric condition. Genome-wide studies investigating single nucleotide polymorphisms (SNPs) concluded that a focus on epigenetic mechanisms, which mediate the impact of environmental factors, could more efficiently help the understanding of GAD pathogenesis. We investigated the relationship between epigenetic shifts in blood and the risk to develop GAD, evaluated by the Development and Well-Being Assessment (DAWBA) score, in 221 otherwise healthy adolescents. Our analysis focused specifically on methylation sites showing high inter-individual variation but low tissue-specific variation, in order to infer a potential correlation between results obtained in blood and brain. Two statistical methods were applied, 1) a linear model with limma and 2) a likelihood test followed by Bonferroni correction. Methylation findings were validated in a cohort of 160 adults applying logistic models against the outcome variable "anxiety treatment obtained in the past" and studied in a third cohort with regards to associated expression changes measured in monocytes. One CpG site showed 1% increased methylation in adolescents at high risk of GAD (cg16333992, padj. = 0.028, estimate = 3.22), as confirmed in the second cohort (p = 0.031, estimate = 1.32). The identified and validated CpG site is located within the STK32B promoter region and its methylation level was positively associated with gene expression. Gene ontology analysis revealed that STK32B is involved in stress response and defense response. Our results provide evidence that shifts in DNA methylation are associated with a modulated risk profile for GAD in adolescence.
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Affiliation(s)
- Diana M Ciuculete
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden.
| | - Adrian E Boström
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Anna-Kaisa Tuunainen
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Farah Sohrabi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Lara Kular
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Maja Jagodic
- Department of Clinical Neuroscience, Center for Molecular Medicine, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Sarah Voisin
- Institute of Sport, Exercise and Active Living, Victoria University, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Jessica Mwinyi
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
| | - Helgi B Schiöth
- Department of Neuroscience, Functional Pharmacology, Uppsala University, BMC, Box 593, 751 24 Uppsala, Sweden
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Freire-Aradas A, Phillips C, Girón-Santamaría L, Mosquera-Miguel A, Gómez-Tato A, Casares de Cal MÁ, Álvarez-Dios J, Lareu MV. Tracking age-correlated DNA methylation markers in the young. Forensic Sci Int Genet 2018; 36:50-59. [PMID: 29933125 DOI: 10.1016/j.fsigen.2018.06.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Revised: 06/08/2018] [Accepted: 06/11/2018] [Indexed: 01/03/2023]
Abstract
DNA methylation is the most extensively studied epigenetic signature, with a large number of studies reporting age-correlated CpG sites in overlapping genes. However, most of these studies lack sample coverage of individuals under 18 years old and therefore little is known about the progression of DNA methylation patterns in children and adolescents. In the present study we aimed to select candidate age-correlated DNA methylation markers based on public datasets from Illumina BeadChip arrays and previous publications, then to explore the resulting markers in 209 blood samples from donors aged between 2 to 18 years old using the EpiTYPER® DNA methylation analysis system. Results from our analyses identified six genes highly correlated with age in the young, in particular the gene KCNAB3, which indicates its potential as a highly informative and specific age biomarker for childhood and adolescence. We outline a preliminary age prediction model based on quantile regression that uses data from the six CpG sites most strongly correlated with age ranges extended to include children and adolescents.
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Affiliation(s)
- Ana Freire-Aradas
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
| | - Christopher Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Lorena Girón-Santamaría
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Ana Mosquera-Miguel
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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28
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Plusquin M, Chadeau-Hyam M, Ghantous A, Alfano R, Bustamante M, Chatzi L, Cuenin C, Gulliver J, Herceg Z, Kogevinas M, Nawrot TS, Pizzi C, Porta D, Relton CL, Richiardi L, Robinson O, Sunyer J, Vermeulen R, Vriens A, Vrijheid M, Henderson J, Vineis P. DNA Methylome Marks of Exposure to Particulate Matter at Three Time Points in Early Life. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:5427-5437. [PMID: 29597345 DOI: 10.1021/acs.est.7b06447] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Maternal exposure to airborne particulate matter (PM) has been associated with restricted fetal growth and reduced birthweight. Here, we performed methylome-wide analyses of cord and children's blood DNA in relation to residential exposure to PM smaller than 10 μm (PM10). This study included participants of the Avon Longitudinal Study of Pregnancy and Childhood (ALSPAC, cord blood, n = 780; blood at age 7, n = 757 and age 15-17, n = 850) and the EXPOsOMICS birth cohort consortium including cord blood from ENVIR ONAGE ( n = 197), INMA ( n = 84), Piccolipiù ( n = 99) and Rhea ( n = 75). We could not identify significant CpG sites, by meta-analyzing associations between maternal PM10 exposure during pregnancy and DNA methylation in cord blood, nor by studying DNA methylation and concordant annual exposure at 7 and 15-17 years. The CpG cg21785536 was inversely associated with PM10 exposure using a longitudinal model integrating the three studied age groups (-1.2% per 10 μg/m3; raw p-value = 3.82 × 10-8). Pathway analyses on the corresponding genes of the 100 strongest associated CpG sites of the longitudinal model revealed enriched pathways relating to the GABAergic synapse, p53 signaling and NOTCH1. We provided evidence that residential PM10 exposure in early life affects methylation of the CpG cg21785536 located on the EGF Domain Specific O-Linked N-Acetylglucosamine Transferase gene.
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Affiliation(s)
- Michelle Plusquin
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
| | - Marc Chadeau-Hyam
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
- Institute for Risk Assessment Sciences (IRAS), Division of Environmental Epidemiology , Utrecht University , Utrecht , The Netherlands
| | - Akram Ghantous
- International Agency for Research on Cancer (IARC) , 150 Cours Albert-Thomas , 69008 Lyon , France
| | - Rossella Alfano
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
| | - Mariona Bustamante
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology , Barcelona , Spain
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) , Madrid , Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL) , Barcelona , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona, Catalonia , Spain
| | - Leda Chatzi
- Department of Preventive Medicine , University of Southern California , Los Angeles , California 90007 , United States
- Department of Social Medicine , University of Crete , Heraklion, Crete , Greece
| | - Cyrille Cuenin
- International Agency for Research on Cancer (IARC) , 150 Cours Albert-Thomas , 69008 Lyon , France
| | - John Gulliver
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC) , 150 Cours Albert-Thomas , 69008 Lyon , France
| | - Manolis Kogevinas
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) , Madrid , Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL) , Barcelona , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona, Catalonia , Spain
- IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Spain
| | - Tim S Nawrot
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
- Environment & Health Unit Leuven University , Leuven , Belgium
| | - Costanza Pizzi
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences , University of Turin and CPO-Piemonte , Torino , Italy
| | - Daniela Porta
- Department of Epidemiology of the Lazio Regional Health Service , Rome , Italy
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, Department of Population Health Sciences, Bristol Medical School , University of Bristol , Bristol , U.K
| | - Lorenzo Richiardi
- Cancer Epidemiology Unit-CERMS, Department of Medical Sciences , University of Turin and CPO-Piemonte , Torino , Italy
| | - Oliver Robinson
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
| | - Jordi Sunyer
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) , Madrid , Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL) , Barcelona , Spain
- IMIM (Hospital del Mar Medical Research Institute) , Barcelona , Spain
| | - Roel Vermeulen
- Medical Research Council-Health Protection Agency Centre for Environment and Health , Imperial College London , London , United Kingdom
- Institute for Risk Assessment Sciences (IRAS), Division of Environmental Epidemiology , Utrecht University , Utrecht , The Netherlands
| | - Annette Vriens
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
| | - Martine Vrijheid
- Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP) , Madrid , Spain
- ISGlobal, Centre for Research in Environmental Epidemiology (CREAL) , Barcelona , Spain
- Universitat Pompeu Fabra (UPF) , Barcelona, Catalonia , Spain
| | - John Henderson
- Department of Population Health Sciences, Bristol Medical School , University of Bristol , Bristol , U.K
| | - Paolo Vineis
- Centre for Environmental Sciences , Hasselt University , Hasselt , Belgium
- Department of Epidemiology and Biostatistics, The School of Public Health , Imperial College London , London , United Kingdom
- IIGM, Italian Institute for Genomic Medicine , Turin , Italy
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Simpkin AJ, Howe LD, Tilling K, Gaunt TR, Lyttleton O, McArdle WL, Ring SM, Horvath S, Smith GD, Relton CL. The epigenetic clock and physical development during childhood and adolescence: longitudinal analysis from a UK birth cohort. Int J Epidemiol 2018; 46:549-558. [PMID: 28089957 PMCID: PMC5722033 DOI: 10.1093/ije/dyw307] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/23/2016] [Indexed: 12/31/2022] Open
Abstract
Background: Statistical models that use an individual’s DNA methylation levels to estimate their age (known as epigenetic clocks) have recently been developed, with 96% correlation found between epigenetic and chronological age. We postulate that differences between estimated and actual age [age acceleration (AA)] can be used as a measure of developmental age in early life. Methods: We obtained DNA methylation measures at three time points (birth, age 7 years and age 17 years) in 1018 children from the Avon Longitudinal Study of Parents and Children (ALSPAC). Using an online calculator, we estimated epigenetic age, and thus AA, for each child at each time point. We then investigated whether AA was prospectively associated with repeated measures of height, weight, body mass index (BMI), bone mineral density, bone mass, fat mass, lean mass and Tanner stage. Results: Positive AA at birth was associated with higher average fat mass [1321 g per year of AA, 95% confidence interval (CI) 386, 2256 g] from birth to adolescence (i.e. from age 0–17 years) and AA at age 7 was associated with higher average height (0.23 cm per year of AA, 95% CI 0.04, 0.41 cm). Conflicting evidence for the role of AA (at birth and in childhood) on changes during development was also found, with higher AA being positively associated with changes in weight, BMI and Tanner stage, but negatively with changes in height and fat mass. Conclusions: We found evidence that being ahead of one’s epigenetic age acceleration is related to developmental characteristics during childhood and adolescence. This demonstrates the potential for using AA as a measure of development in future research.
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Affiliation(s)
- Andrew J Simpkin
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Laura D Howe
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Kate Tilling
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Oliver Lyttleton
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Wendy L McArdle
- School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Steve Horvath
- School of Public Health, University of California Los Angeles, Los Angeles, CA, USA.,David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Bristol, UK
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30
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Agarwal P, Morriseau TS, Kereliuk SM, Doucette CA, Wicklow BA, Dolinsky VW. Maternal obesity, diabetes during pregnancy and epigenetic mechanisms that influence the developmental origins of cardiometabolic disease in the offspring. Crit Rev Clin Lab Sci 2018; 55:71-101. [DOI: 10.1080/10408363.2017.1422109] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Prasoon Agarwal
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
| | - Taylor S. Morriseau
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
| | - Stephanie M. Kereliuk
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
| | - Christine A. Doucette
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
- Department of Physiology & Pathophysiology, University of Manitoba, Winnipeg, Canada
| | - Brandy A. Wicklow
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
- Department of Pediatrics & Child Health, University of Manitoba, Winnipeg, Canada
| | - Vernon W. Dolinsky
- Department of Pharmacology & Therapeutics, University of Manitoba, Winnipeg, Canada
- Diabetes Research Envisioned and Accomplished in Manitoba (DREAM) Research Theme of the Children’s Hospital Research Institute of Manitoba, University of Manitoba, Winnipeg, Canada
- Manitoba Developmental Origins of Chronic Diseases in Children Network (DEVOTION), University of Manitoba, Winnipeg, Canada
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31
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Naumova OY, Dozier M, Dobrynin PV, Grigorev K, Wallin A, Jeltova I, Lee M, Raefski A, Grigorenko EL. Developmental dynamics of the epigenome: A longitudinal study of three toddlers. Neurotoxicol Teratol 2017; 66:125-131. [PMID: 29247702 DOI: 10.1016/j.ntt.2017.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 11/20/2017] [Accepted: 12/08/2017] [Indexed: 12/23/2022]
Abstract
Epigenetic regulation plays an important role in development, at the embryonic stages and later during the lifespan. Some epigenetic marks are highly conserved throughout the lifespan whereas others are closely associated with specific age periods and/or particular environmental factors. Little is known about the dynamics of epigenetic regulation during childhood, especially during the period of rapid early development. Our study was aimed to determine whether the developmental program at the early stages of human development is accompanied by significant changes in the systems of genome regulation, specifically, by genome-wide changes in DNA methylation. Using a sequencing approach (MBD-seq) we investigated genome-wide DNA methylation patterns in the T-lymphocytes of three healthy toddlers at two timepoints within the second year of life. Pairwise comparison of the methylation patterns across the individuals and time points was conducted to determine common longitudinal changes in the DNA methylation patterns. Despite relatively high interindividual variability in their epigenetic profiles and the dynamics of these profiles during the second year of life, all children showed consistent changes in the DNA methylation patterns of genes involved in the control of the immune system and genes related to the development of the CNS. Thereby, we provide evidence that early development might be accompanied by epigenetic changes in specific functional groups of genes; many such epigenetic changes appear to be related to the rapid development of the CNS.
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Affiliation(s)
- Oxana Yu Naumova
- Dept. of Psychology, University of Houston, Houston, TX, USA; Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia; Dept. of Psychology, Saint Petersburg State University, St. Petersburg, Russia
| | - Mary Dozier
- Dept. of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Pavel V Dobrynin
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Kirill Grigorev
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg, Russia
| | - Allison Wallin
- Dept. of Psychological and Brain Sciences, University of Delaware, Newark, DE, USA
| | - Ida Jeltova
- Private Psychological Practice, Ridgewood, NJ, USA
| | - Maria Lee
- Child Study Center, Yale University, New Haven, CT, USA
| | - Adam Raefski
- Child Study Center, Yale University, New Haven, CT, USA
| | - Elena L Grigorenko
- Dept. of Psychology, University of Houston, Houston, TX, USA; Dept. of Psychology, Saint Petersburg State University, St. Petersburg, Russia; Child Study Center, Yale University, New Haven, CT, USA; Office of the Rector, Moscow State University of Psychology and Education, Moscow, Russia.
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32
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DNA Methylation Patterns in Cord Blood of Neonates Across Gestational Age: Association With Cell-Type Proportions. Nurs Res 2017; 66:115-122. [PMID: 28125511 PMCID: PMC5345885 DOI: 10.1097/nnr.0000000000000210] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Background A statistical methodology is available to estimate the proportion of cell types (cellular heterogeneity) in adult whole blood specimens used in epigenome-wide association studies (EWAS). However, there is no methodology to estimate the proportion of cell types in umbilical cord blood (also a heterogeneous tissue) used in EWAS. Objectives The objectives of this study were to determine whether differences in DNA methylation (DNAm) patterns in umbilical cord blood are the result of blood cell type proportion changes that typically occur across gestational age and to demonstrate the effect of cell type proportion confounding by comparing preterm infants exposed and not exposed to antenatal steroids. Methods We obtained DNAm profiles of cord blood using the Illumina HumanMethylation27k BeadChip array for 385 neonates from the Boston Birth Cohort. We estimated cell type proportions for six cell types using the deconvolution method developed by Houseman et al. (2012). Results The cell type proportion estimates segregated into two groups that were significantly different by gestational age, indicating that gestational age was associated with cell type proportion. Among infants exposed to antenatal steroids, the number of differentially methylated CpGs dropped from 127 to 1 after controlling for cell type proportion. Discussion EWAS utilizing cord blood are confounded by cell type proportion. Careful study design including correction for cell type proportion and interpretation of results of EWAS using cord blood are critical.
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33
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Kochmanski J, Montrose L, Goodrich JM, Dolinoy DC. Environmental Deflection: The Impact of Toxicant Exposures on the Aging Epigenome. Toxicol Sci 2017; 156:325-335. [PMID: 28087834 PMCID: PMC6256948 DOI: 10.1093/toxsci/kfx005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Epigenetic drift and age-related methylation have both been used in the literature to describe changes in DNA methylation that occurs with aging. However, ambiguity remains regarding the exact definition of both of these terms, and neither of these fields of study explicitly considers the impact of environmental factors on the aging epigenome. Recent twin studies have demonstrated longitudinal, pair-specific discordance in DNA methylation patterns, suggesting an effect of the environment on age-related methylation and/or epigenetic drift. Supporting this idea, other new reports have shown clear environment- and toxicant-mediated shifts away from the baseline rates of age-related methylation and epigenetic drift within an organism, a process we now term "environmental deflection." By defining and delineating environmental deflection, this contemporary review aims to highlight the effects of specific toxicological factors on the rate of DNA methylation changes that occur over the life course. In an effort to inform future epigenetics-based toxicology studies, a field of research now classified as toxicoepigenetics, we provide clear definitions and examples of "epigenetic drift" and "age-related methylation," summarize the recent evidence for environmental deflection of the aging epigenome, and discuss the potential functional effects of environmental deflection.
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Affiliation(s)
| | | | | | - Dana C. Dolinoy
- Environmental Health Sciences
- Nutritional Sciences, School of Public Health, University of Michigan, Washington Heights, Ann Arbor, Michigan 48109
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34
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Epigenome-wide association study of DNA methylation in panic disorder. Clin Epigenetics 2017; 9:6. [PMID: 28149334 PMCID: PMC5270210 DOI: 10.1186/s13148-016-0307-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Accepted: 12/26/2016] [Indexed: 12/22/2022] Open
Abstract
Background Panic disorder (PD) is considered to be a multifactorial disorder emerging from interactions among multiple genetic and environmental factors. To date, although genetic studies reported several susceptibility genes with PD, few of them were replicated and the pathogenesis of PD remains to be clarified. Epigenetics is considered to play an important role in etiology of complex traits and diseases, and DNA methylation is one of the major forms of epigenetic modifications. In this study, we performed an epigenome-wide association study of PD using DNA methylation arrays so as to investigate the possibility that different levels of DNA methylation might be associated with PD. Methods The DNA methylation levels of CpG sites across the genome were examined with genomic DNA samples (PD, N = 48, control, N = 48) extracted from peripheral blood. Methylation arrays were used for the analysis. β values, which represent the levels of DNA methylation, were normalized via an appropriate pipeline. Then, β values were converted to M values via the logit transformation for epigenome-wide association study. The relationship between each DNA methylation site and PD was assessed by linear regression analysis with adjustments for the effects of leukocyte subsets. Results Forty CpG sites showed significant association with PD at 5% FDR correction, though the differences of the DNA methylation levels were relatively small. Most of the significant CpG sites (37/40 CpG sites) were located in or around CpG islands. Many of the significant CpG sites (27/40 CpG sites) were located upstream of genes, and all such CpG sites with the exception of two were hypomethylated in PD subjects. A pathway analysis on the genes annotated to the significant CpG sites identified several pathways, including “positive regulation of lymphocyte activation.” Conclusions Although future studies with larger number of samples are necessary to confirm the small DNA methylation abnormalities associated with PD, there is a possibility that several CpG sites might be associated, together as a group, with PD. Electronic supplementary material The online version of this article (doi:10.1186/s13148-016-0307-1) contains supplementary material, which is available to authorized users.
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35
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Oelsner KT, Guo Y, To SBC, Non AL, Barkin SL. Maternal BMI as a predictor of methylation of obesity-related genes in saliva samples from preschool-age Hispanic children at-risk for obesity. BMC Genomics 2017; 18:57. [PMID: 28068899 PMCID: PMC5223358 DOI: 10.1186/s12864-016-3473-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 12/26/2016] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The study of epigenetic processes and mechanisms present a dynamic approach to assess complex individual variation in obesity susceptibility. However, few studies have examined epigenetic patterns in preschool-age children at-risk for obesity despite the relevance of this developmental stage to trajectories of weight gain. We hypothesized that salivary DNA methylation patterns of key obesogenic genes in Hispanic children would 1) correlate with maternal BMI and 2) allow for identification of pathways associated with children at-risk for obesity. RESULTS Genome-wide DNA methylation was conducted on 92 saliva samples collected from Hispanic preschool children using the Infinium Illumina HumanMethylation 450 K BeadChip (Illumina, San Diego, CA, USA), which interrogates >484,000 CpG sites associated with ~24,000 genes. The analysis was limited to 936 genes that have been associated with obesity in a prior GWAS Study. Child DNA methylation at 17 CpG sites was found to be significantly associated with maternal BMI, with increased methylation at 12 CpG sites and decreased methylation at 5 CpG sites. Pathway analysis revealed methylation at these sites related to homocysteine and methionine degradation as well as cysteine biosynthesis and circadian rhythm. Furthermore, eight of the 17 CpG sites reside in genes (FSTL1, SORCS2, NRF1, DLC1, PPARGC1B, CHN2, NXPH1) that have prior known associations with obesity, diabetes, and the insulin pathway. CONCLUSIONS Our study confirms that saliva is a practical human tissue to obtain in community settings and in pediatric populations. These salivary findings indicate potential epigenetic differences in Hispanic preschool children at risk for pediatric obesity. Identifying early biomarkers and understanding pathways that are epigenetically regulated during this critical stage of child development may present an opportunity for prevention or early intervention for addressing childhood obesity. TRIAL REGISTRATION The clinical trial protocol is available at ClinicalTrials.gov ( NCT01316653 ). Registered 3 March 2011.
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Affiliation(s)
- Kathryn Tully Oelsner
- College of Medicine, Medical University of South Carolina, 96 Jonathan Lucas St, Suite 601, MSC 617, Charleston, SC 29425 USA
| | - Yan Guo
- Center for Quantitative Research, School of Medicine, Vanderbilt University, 2220 Pierce Ave, 571 Preston Research Building, Nashville, TN USA
| | - Sophie Bao-Chieu To
- Department of Biological Sciences, Vanderbilt University, 1210 BSB, 465 21st Ave S, Nashville, TN USA
| | - Amy L. Non
- Department of Anthropology, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093 USA
| | - Shari L. Barkin
- Department of Pediatrics, Vanderbilt University School of Medicine, 2200 Children’s Way, Doctor’s Office Tower 8232, Nashville, TN 37232-9225 USA
- Pediatric Obesity Research, Diabetes Research and Training Center, Vanderbilt University School of Medicine, 2200 Children’s Way, Doctor’s Office Tower 8232, Nashville, TN 37232-9225 USA
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36
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Provenzi L, Giorda R, Beri S, Montirosso R. SLC6A4 methylation as an epigenetic marker of life adversity exposures in humans: A systematic review of literature. Neurosci Biobehav Rev 2016; 71:7-20. [DOI: 10.1016/j.neubiorev.2016.08.021] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Revised: 07/18/2016] [Accepted: 08/23/2016] [Indexed: 12/29/2022]
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Extensive Epigenetic Changes Accompany Terminal Differentiation of Mouse Hepatocytes After Birth. G3-GENES GENOMES GENETICS 2016; 6:3701-3709. [PMID: 27652892 PMCID: PMC5100869 DOI: 10.1534/g3.116.034785] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
DNA methylation is traditionally thought to be established during early development and to remain mostly unchanged thereafter in healthy tissues, although recent studies have shown that this epigenetic mark can be more dynamic. Epigenetic changes occur in the liver after birth, but the timing and underlying biological processes leading to DNA methylation changes are not well understood. We hypothesized that this epigenetic reprogramming was the result of terminal differentiation of hepatocyte precursors. Using genomic approaches, we characterized the DNA methylation patterns in mouse liver from E18.5 until adulthood to determine if the timing of the DNA methylation change overlaps with hepatocyte terminal differentiation, and to examine the genomic context of these changes and identify the regulatory elements involved. Out of 271,325 CpGs analyzed throughout the genome, 214,709 CpGs changed DNA methylation by more than 5% (e.g., from 5 to 10% methylation) between E18.5 and 9 wk of age, and 18,863 CpGs changed DNA methylation by more than 30%. Genome-scale data from six time points between E18.5 and P20 show that DNA methylation changes coincided with the terminal differentiation of hepatoblasts into hepatocytes. We also showed that epigenetic reprogramming occurred primarily in intergenic enhancer regions while gene promoters were less affected. Our data suggest that normal postnatal hepatic development and maturation involves extensive epigenetic remodeling of the genome, and that enhancers play a key role in controlling the transition from hepatoblasts to fully differentiated hepatocytes. Our study provides a solid foundation to support future research aimed at further revealing the role of epigenetics in stem cell biology.
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Rounge TB, Page CM, Lepistö M, Ellonen P, Andreassen BK, Weiderpass E. Genome-wide DNA methylation in saliva and body size of adolescent girls. Epigenomics 2016; 8:1495-1505. [DOI: 10.2217/epi-2016-0045] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Aim: We performed an epigenome-wide association study within the Finnish Health in Teens cohort to identify differential DNA methylation and its association with BMI in adolescents. Materials & methods: Differential DNA methylation analyses of 3.1 million CpG sites were performed in saliva samples from 50 lean and 50 heavy adolescent girls by genome-wide targeted bisulfite-sequencing. Results: We identified 100 CpG sites with p-values < 0.000524, seven regions by ‘bumphunting’ and five CpG islands that differed significantly between the two groups. The ten CpG sites and regions most strongly associated with BMI substantially overlapped with obesity- and insulin-related genes, including MC2R, IGFBPL1, IP6K1 and IGF2BP1. Conclusion: Our findings suggest an association between the saliva methylome and BMI in adolescence.
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Affiliation(s)
- Trine B Rounge
- Genetic Epidemiology Group, Folkhälsan Research Center, Helsinki, Finland
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway
| | - Christian M Page
- Department of Neurology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Department of Noncommunicable Diseases, Norwegian Institute of Public Health, Oslo, Norway
| | - Maija Lepistö
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Bettina K Andreassen
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway
| | - Elisabete Weiderpass
- Genetic Epidemiology Group, Folkhälsan Research Center, Helsinki, Finland
- Department of Research, Cancer Registry of Norway, Institute of Population-Based Cancer Research, Oslo, Norway
- Department of Medical Epidemiology & Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Department of Community Medicine, Faculty of Health Sciences, University of Tromsø, The Arctic University of Norway, Tromsø, Norway
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Urdinguio RG, Torró MI, Bayón GF, Álvarez-Pitti J, Fernández AF, Redon P, Fraga MF, Lurbe E. Longitudinal study of DNA methylation during the first 5 years of life. J Transl Med 2016; 14:160. [PMID: 27259700 PMCID: PMC4891837 DOI: 10.1186/s12967-016-0913-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 05/18/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early life epigenetic programming influences adult health outcomes. Moreover, DNA methylation levels have been found to change more rapidly during the first years of life. Our aim was the identification and characterization of the CpG sites that are modified with time during the first years of life. We hypothesize that these DNA methylation changes would lead to the detection of genes that might be epigenetically modulated by environmental factors during early childhood and which, if disturbed, might contribute to susceptibility to diseases later in life. METHODS The study of the DNA methylation pattern of 485577 CpG sites was performed on 30 blood samples from 15 subjects, collected both at birth and at 5 years old, using Illumina(®) Infinium 450 k array. To identify differentially methylated CpG (dmCpG) sites, the methylation status of each probe was examined using linear models and the Empirical Bayes Moderated t test implemented in the limma package of R/Bioconductor. Surogate variable analysis was used to account for batch effects. RESULTS DNA methylation levels significantly changed from birth to 5 years of age in 6641 CpG sites. Of these, 36.79 % were hypermethylated and were associated with genes related mainly to developmental ontology terms, while 63.21 % were hypomethylated probes and associated with genes related to immune function. CONCLUSIONS Our results suggest that DNA methylation alterations with age during the first years of life might play a significant role in development and the regulation of leukocyte-specific functions. This supports the idea that blood leukocytes experience genome remodeling related to their interaction with environmental factors, underlining the importance of environmental exposures during the first years of life and suggesting that new strategies should be take into consideration for disease prevention.
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Affiliation(s)
- Rocio G Urdinguio
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain.,Nanomaterials and Nanotechnology Research Center (CINN)-Spanish Council for Scientific Research (CSIC), (CINN-CSIC), Avenida de la Vega 4-6, 33940, El Entrego, Spain
| | - María Isabel Torró
- Servicio de Pediatría, Consorcio Hospital General Universitario, Universidad de Valencia, Avda. Tres Cruces s/n, 46014, Valencia, Spain.,CIBER Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Gustavo F Bayón
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Julio Álvarez-Pitti
- Servicio de Pediatría, Consorcio Hospital General Universitario, Universidad de Valencia, Avda. Tres Cruces s/n, 46014, Valencia, Spain.,CIBER Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Agustín F Fernández
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain
| | - Pau Redon
- Servicio de Pediatría, Consorcio Hospital General Universitario, Universidad de Valencia, Avda. Tres Cruces s/n, 46014, Valencia, Spain.,CIBER Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain
| | - Mario F Fraga
- Cancer Epigenetics Laboratory, Institute of Oncology of Asturias (IUOPA), HUCA, Universidad de Oviedo, Oviedo, Spain. .,Nanomaterials and Nanotechnology Research Center (CINN)-Spanish Council for Scientific Research (CSIC), (CINN-CSIC), Avenida de la Vega 4-6, 33940, El Entrego, Spain.
| | - Empar Lurbe
- Servicio de Pediatría, Consorcio Hospital General Universitario, Universidad de Valencia, Avda. Tres Cruces s/n, 46014, Valencia, Spain. .,CIBER Fisiopatología Obesidad y Nutrición (CB06/03), Instituto de Salud Carlos III, Madrid, Spain.
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40
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Cacabelos R, Torrellas C. Epigenetics of Aging and Alzheimer's Disease: Implications for Pharmacogenomics and Drug Response. Int J Mol Sci 2015; 16:30483-543. [PMID: 26703582 PMCID: PMC4691177 DOI: 10.3390/ijms161226236] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/16/2015] [Accepted: 12/08/2015] [Indexed: 02/07/2023] Open
Abstract
Epigenetic variability (DNA methylation/demethylation, histone modifications, microRNA regulation) is common in physiological and pathological conditions. Epigenetic alterations are present in different tissues along the aging process and in neurodegenerative disorders, such as Alzheimer’s disease (AD). Epigenetics affect life span and longevity. AD-related genes exhibit epigenetic changes, indicating that epigenetics might exert a pathogenic role in dementia. Epigenetic modifications are reversible and can potentially be targeted by pharmacological intervention. Epigenetic drugs may be useful for the treatment of major problems of health (e.g., cancer, cardiovascular disorders, brain disorders). The efficacy and safety of these and other medications depend upon the efficiency of the pharmacogenetic process in which different clusters of genes (pathogenic, mechanistic, metabolic, transporter, pleiotropic) are involved. Most of these genes are also under the influence of the epigenetic machinery. The information available on the pharmacoepigenomics of most drugs is very limited; however, growing evidence indicates that epigenetic changes are determinant in the pathogenesis of many medical conditions and in drug response and drug resistance. Consequently, pharmacoepigenetic studies should be incorporated in drug development and personalized treatments.
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Affiliation(s)
- Ramón Cacabelos
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
| | - Clara Torrellas
- EuroEspes Biomedical Research Center, Institute of Medical Science and Genomic Medicine, 15165-Bergondo, Corunna, Spain.
- Chair of Genomic Medicine, Camilo José Cela University, 28692-Madrid, Spain.
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41
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Genome-wide DNA methylation map of human neutrophils reveals widespread inter-individual epigenetic variation. Sci Rep 2015; 5:17328. [PMID: 26612583 PMCID: PMC4661471 DOI: 10.1038/srep17328] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 10/29/2015] [Indexed: 11/13/2022] Open
Abstract
The extent of variation in DNA methylation patterns in healthy individuals is not yet well documented. Identification of inter-individual epigenetic variation is important for understanding phenotypic variation and disease susceptibility. Using neutrophils from a cohort of healthy individuals, we generated base-resolution DNA methylation maps to document inter-individual epigenetic variation. We identified 12851 autosomal inter-individual variably methylated fragments (iVMFs). Gene promoters were the least variable, whereas gene body and upstream regions showed higher variation in DNA methylation. The iVMFs were relatively enriched in repetitive elements compared to non-iVMFs, and were associated with genome regulation and chromatin function elements. Further, variably methylated genes were disproportionately associated with regulation of transcription, responsive function and signal transduction pathways. Transcriptome analysis indicates that iVMF methylation at differentially expressed exons has a positive correlation and local effect on the inclusion of that exon in the mRNA transcript.
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Aberrant 5'-CpG Methylation of Cord Blood TNFα Associated with Maternal Exposure to Polybrominated Diphenyl Ethers. PLoS One 2015; 10:e0138815. [PMID: 26406892 PMCID: PMC4583495 DOI: 10.1371/journal.pone.0138815] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 09/03/2015] [Indexed: 02/01/2023] Open
Abstract
Growing evidence suggests that maternal exposures to endocrine disrupting chemicals during pregnancy may lead to poor pregnancy outcomes and increased fetal susceptibility to adult diseases. Polybrominated diphenyl ethers (PBDEs), which are ubiquitously used flame-retardants, could leach into the environment; and become persistent organic pollutants via bioaccumulation. In the United States, blood PBDE levels in adults range from 30–100 ng/g- lipid but the alarming health concern revolves around children who have reported blood PBDE levels 3 to 9-fold higher than adults. PBDEs disrupt endocrine, immune, reproductive and nervous systems. However, the mechanism underlying its adverse health effect is not fully understood. Epigenetics is a possible biological mechanism underlying maternal exposure-child health outcomes by regulating gene expression without changes in the DNA sequence. We sought to examine the relationship between maternal exposure to environmental PBDEs and promoter methylation of a proinflammatory gene, tumor necrosis factor alpha (TNFα). We measured the maternal blood PBDE levels and cord blood TNFα promoter methylation levels on 46 paired samples of maternal and cord blood from the Boston Birth Cohort (BBC). We showed that decreased cord blood TNFα methylation associated with high maternal PBDE47 exposure. CpG site-specific methylation showed significantly hypomethylation in the girl whose mother has a high blood PBDE47 level. Consistently, decreased TNFα methylation associated with an increase in TNFα protein level in cord blood. In conclusion, our finding provided evidence that in utero exposure to PBDEs may epigenetically reprogram the offspring’s immunological response through promoter methylation of a proinflammatory gene.
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43
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Omic personality: implications of stable transcript and methylation profiles for personalized medicine. Genome Med 2015; 7:88. [PMID: 26391122 PMCID: PMC4578259 DOI: 10.1186/s13073-015-0209-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 07/22/2015] [Indexed: 01/18/2023] Open
Abstract
Background Personalized medicine is predicated on the notion that individual biochemical and genomic profiles are relatively constant in times of good health and to some extent predictive of disease or therapeutic response. We report a pilot study quantifying gene expression and methylation profile consistency over time, addressing the reasons for individual uniqueness, and its relation to N = 1 phenotypes. Methods Whole blood samples from four African American women, four Caucasian women, and four Caucasian men drawn from the Atlanta Center for Health Discovery and Well Being study at three successive 6-month intervals were profiled by RNA-Seq, miRNA-Seq, and Illumina Methylation 450 K arrays. Standard regression approaches were used to evaluate the proportion of variance for each type of omic measure among individuals, and to quantify correlations among measures and with clinical attributes related to wellness. Results Longitudinal omic profiles were in general highly consistent over time, with an average of 67 % variance in transcript abundance, 42 % in CpG methylation level (but 88 % for the most differentiated CpG per gene), and 50 % in miRNA abundance among individuals, which are all comparable to 74 % variance among individuals for 74 clinical traits. One third of the variance could be attributed to differential blood cell type abundance, which was also fairly stable over time, and a lesser amount to expression quantitative trait loci (eQTL) effects. Seven conserved axes of covariance that capture diverse aspects of immune function explained over half of the variance. These axes also explained a considerable proportion of individually extreme transcript abundance, namely approximately 100 genes that were significantly up-regulated or down-regulated in each person and were in some cases enriched for relevant gene activities that plausibly associate with clinical attributes. A similar fraction of genes had individually divergent methylation levels, but these did not overlap with the transcripts, and fewer than 20 % of genes had significantly correlated methylation and gene expression. Conclusions People express an “omic personality” consisting of peripheral blood transcriptional and epigenetic profiles that are constant over the course of a year and reflect various types of immune activity. Baseline genomic profiles can provide a window into the molecular basis of traits that might be useful for explaining medical conditions or guiding personalized health decisions. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0209-4) contains supplementary material, which is available to authorized users.
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44
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Zhang N, Zhao S, Zhang SH, Chen J, Lu D, Shen M, Li C. Intra-Monozygotic Twin Pair Discordance and Longitudinal Variation of Whole-Genome Scale DNA Methylation in Adults. PLoS One 2015; 10:e0135022. [PMID: 26248206 PMCID: PMC4527769 DOI: 10.1371/journal.pone.0135022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 07/16/2015] [Indexed: 02/04/2023] Open
Abstract
Monozygotic twins share identical genomic DNA and are indistinguishable using conventional genetic markers. Increasing evidence indicates that monozygotic twins are epigenetically distinct, suggesting that a comparison between DNA methylation patterns might be useful to approach this forensic problem. However, the extent of epigenetic discordance between healthy adult monozygotic twins and the stability of CpG loci within the same individual over a short time span at the whole-genome scale are not well understood. Here, we used Infinium HumanMethylation450 Beadchips to compare DNA methylation profiles using blood collected from 10 pairs of monozygotic twins and 8 individuals sampled at 0, 3, 6, and 9 months. Using an effective and unbiased method for calling differentially methylated (DM) CpG sites, we showed that 0.087%–1.530% of the CpG sites exhibit differential methylation in monozygotic twin pairs. We further demonstrated that, on whole-genome level, there has been no significant epigenetic drift within the same individuals for up to 9 months, including one monozygotic twin pair. However, we did identify a subset of CpG sites that vary in DNA methylation over the 9-month period. The magnitude of the intra-pair or longitudinal methylation discordance of the CpG sites inside the CpG islands is greater than those outside the CpG islands. The CpG sites located on shores appear to be more suitable for distinguishing between MZ twins.
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Affiliation(s)
- Na Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Shumin Zhao
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
| | - Su-Hua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Jinzhong Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Min Shen
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
- * E-mail:
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Lévesque ML, Casey KF, Szyf M, Ismaylova E, Ly V, Verner MP, Suderman M, Brendgen M, Vitaro F, Dionne G, Boivin M, Tremblay RE, Booij L. Genome-wide DNA methylation variability in adolescent monozygotic twins followed since birth. Epigenetics 2015; 9:1410-21. [PMID: 25437055 DOI: 10.4161/15592294.2014.970060] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
DNA methylation patterns are characterized by highly conserved developmental programs, but allow for divergent gene expression resulting from stochastic epigenetic drift or divergent environments. Genome-wide methylation studies in monozygotic (MZ) twins are providing insight into the extent of epigenetic variation that occurs, irrespective of genotype. However, little is known about the variability of DNA methylation patterns in adolescence, a period involving significant and rapid physical, emotional, social, and neurodevelopmental change. Here, we assessed genome-wide DNA methylation using the 450 K Illumina BeadChip in a sample of 37 MZ twin pairs followed longitudinally since birth to investigate: 1) the extent of variation in DNA methylation in identical genetic backgrounds in adolescence and; 2) whether these variations are randomly distributed or enriched in particular functional pathways. We also assessed stability of DNA methylation over 3-6 months to distinguish stable trait-like and variable state-like genes. A pathway analysis found high within-pair variability in genes associated with development, cellular mechanisms, tissue and cell morphology, and various disorders. Test-retest analyses performed in a sub-sample of 8 twin pairs demonstrated enrichment in gene pathways involved in organismal development, cellular growth and proliferation, cell signaling, and particular disorders. The variability found in functional gene pathways may plausibly underlie phenotypic differences in this adolescent MZ twin sample. Furthermore, we assessed stability of methylation over 3-6 months and found that some genes were stable while others were unstable, suggesting that the methylome remains dynamic in adolescence and that dynamic sites tend to be organized in certain gene pathways.
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46
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Simpkin AJ, Suderman M, Gaunt TR, Lyttleton O, McArdle WL, Ring SM, Tilling K, Davey Smith G, Relton CL. Longitudinal analysis of DNA methylation associated with birth weight and gestational age. Hum Mol Genet 2015; 24:3752-63. [PMID: 25869828 PMCID: PMC4459393 DOI: 10.1093/hmg/ddv119] [Citation(s) in RCA: 108] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/04/2015] [Indexed: 01/14/2023] Open
Abstract
Gestational age (GA) and birth weight have been implicated in the determination of long-term health. It has been hypothesized that changes in DNA methylation may mediate these long-term effects. We obtained DNA methylation profiles from cord blood and peripheral blood at ages 7 and 17 in the same children from the Avon Longitudinal Study of Parents and Children. Repeated-measures data were used to investigate changes in birth-related methylation during childhood and adolescence. Ten developmental phenotypes (e.g. height) were analysed to identify possible mediation of health effects by DNA methylation. In cord blood, methylation at 224 CpG sites was found to be associated with GA and 23 CpG sites with birth weight. Methylation changed in the majority of these sites over time, but neither birth characteristic was strongly associated with methylation at age 7 or 17 (using a conservative correction for multiple testing of P < 1.03 × 10(-7)), suggesting resolution of differential methylation by early childhood. Associations were observed between birth weight-associated CpG sites and phenotypic characteristics in childhood. One strong association involved birth weight, methylation of a CpG site proximal to the NFIX locus and bone mineral density at age 17. Analysis of serial methylation from birth to adolescence provided evidence for a lack of persistence of methylation differences beyond early childhood. Sites associated with birth weight were linked to developmental genes and have methylation levels which are associated with developmental phenotypes. Replication and interrogation of causal relationships are needed to substantiate whether methylation differences at birth influence the association between birth weight and development.
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Affiliation(s)
- Andrew J Simpkin
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol,
| | - Matthew Suderman
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol
| | - Oliver Lyttleton
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK and
| | - Wendy L McArdle
- School of Social and Community Medicine, University of Bristol, Bristol BS8 2BN, UK and
| | - Susan M Ring
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol
| | - Kate Tilling
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol
| | - Caroline L Relton
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne NE1 3BZ, UK
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Ollikainen M, Ismail K, Gervin K, Kyllönen A, Hakkarainen A, Lundbom J, Järvinen EA, Harris JR, Lundbom N, Rissanen A, Lyle R, Pietiläinen KH, Kaprio J. Genome-wide blood DNA methylation alterations at regulatory elements and heterochromatic regions in monozygotic twins discordant for obesity and liver fat. Clin Epigenetics 2015; 7:39. [PMID: 25866590 PMCID: PMC4393626 DOI: 10.1186/s13148-015-0073-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 03/11/2015] [Indexed: 12/16/2022] Open
Abstract
Background The current epidemic of obesity and associated diseases calls for swift actions to better understand the mechanisms by which genetics and environmental factors affect metabolic health in humans. Monozygotic (MZ) twin pairs showing discordance for obesity suggest that epigenetic influences represent one such mechanism. We studied genome-wide leukocyte DNA methylation variation in 30 clinically healthy young adult MZ twin pairs discordant for body mass index (BMI; average within-pair BMI difference: 5.4 ± 2.0 kg/m2). Results There were no differentially methylated cytosine-guanine (CpG) sites between the co-twins discordant for BMI. However, stratification of the twin pairs based on the level of liver fat accumulation revealed two epigenetically highly different groups. Significant DNA methylation differences (n = 1,236 CpG sites (CpGs)) between the co-twins were only observed if the heavier co-twins had excessive liver fat (n = 13 twin pairs). This unhealthy pattern of obesity was coupled with insulin resistance and low-grade inflammation. The differentially methylated CpGs included 23 genes known to be associated with obesity, liver fat, type 2 diabetes mellitus (T2DM) and metabolic syndrome, and potential novel metabolic genes. Differentially methylated CpG sites were overrepresented at promoters, insulators, and heterochromatic and repressed regions. Based on predictions by overlapping histone marks, repressed and weakly transcribed sites were significantly more often hypomethylated, whereas sites with strong enhancers and active promoters were hypermethylated. Further, significant clustering of differentially methylated genes in vitamin, amino acid, fatty acid, sulfur, and renin-angiotensin metabolism pathways was observed. Conclusions The methylome in leukocytes is altered in obesity associated with metabolic disturbances, and our findings indicate several novel candidate genes and pathways in obesity and obesity-related complications. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0073-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Miina Ollikainen
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Khadeeja Ismail
- Department of Public Health, University of Helsinki, Helsinki, Finland
| | - Kristina Gervin
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Anjuska Kyllönen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Antti Hakkarainen
- Department of Radiology, HUS Medical Imaging Center, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Jesper Lundbom
- Department of Radiology, HUS Medical Imaging Center, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Elina A Järvinen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Jennifer R Harris
- Division of Epidemiology, The Norwegian Institute of Public Health, Oslo, Norway
| | - Nina Lundbom
- Department of Radiology, HUS Medical Imaging Center, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland
| | - Aila Rissanen
- Department of Psychiatry, Helsinki University Central Hospital, Helsinki, Finland.,Endocrinology, Abdominal Center, Helsinki University Central Hospital, Helsinki, Finland
| | - Robert Lyle
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Kirsi H Pietiläinen
- Obesity Research Unit, Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland.,Endocrinology, Abdominal Center, Helsinki University Central Hospital, Helsinki, Finland.,Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland
| | - Jaakko Kaprio
- Department of Public Health, University of Helsinki, Helsinki, Finland.,Institute for Molecular Medicine FIMM, University of Helsinki, Helsinki, Finland.,Department of Mental Health and Substance Abuse Services, National Institute for Health and Welfare, Helsinki, Finland
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Nemoda Z, Massart R, Suderman M, Hallett M, Li T, Coote M, Cody N, Sun ZS, Soares CN, Turecki G, Steiner M, Szyf M. Maternal depression is associated with DNA methylation changes in cord blood T lymphocytes and adult hippocampi. Transl Psychiatry 2015; 5:e545. [PMID: 25849984 PMCID: PMC4462598 DOI: 10.1038/tp.2015.32] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 12/27/2014] [Accepted: 02/09/2015] [Indexed: 12/19/2022] Open
Abstract
Depression affects 10-15% of pregnant women and has been associated with preterm delivery and later developmental, behavioural and learning disabilities. We tested the hypothesis that maternal depression is associated with DNA methylation alterations in maternal T lymphocytes, neonatal cord blood T lymphocytes and adult offspring hippocampi. Genome-wide DNA methylation of CD3+ T lymphocytes isolated from 38 antepartum maternal and 44 neonatal cord blood samples were analyzed using Illumina Methylation 450 K microarrays. Previously obtained methylation data sets using methylated DNA immunoprecipitation and array-hybridization of 62 postmortem hippocampal samples of adult males were re-analyzed to test associations with history of maternal depression. We found 145 (false discovery rate (FDR) q<0.05) and 2520 (FDR q<0.1) differentially methylated CG-sites in cord blood T lymphocytes of neonates from the maternal depression group as compared with the control group. However, no significant DNA methylation differences were detected in the antepartum maternal T lymphocytes of our preliminary data set. We also detected 294 differentially methylated probes (FDR q<0.1) in hippocampal samples associated with history of maternal depression. We observed a significant overlap (P=0.002) of 33 genes with changes in DNA methylation in T lymphocytes of neonates and brains of adult offspring. Many of these genes are involved in immune system functions. Our results show that DNA methylation changes in offspring associated with maternal depression are detectable at birth in the immune system and persist to adulthood in the brain. This is consistent with the hypothesis that system-wide epigenetic changes are involved in life-long responses to maternal depression in the offspring.
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Affiliation(s)
- Z Nemoda
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada,Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, QC, Canada
| | - R Massart
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada,Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, QC, Canada
| | - M Suderman
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada,Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, QC, Canada,McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada
| | - M Hallett
- McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada
| | - T Li
- Women's Health Concerns Clinic, St Joseph's Healthcare, Hamilton, ON, Canada
| | - M Coote
- Women's Health Concerns Clinic, St Joseph's Healthcare, Hamilton, ON, Canada
| | - N Cody
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Z S Sun
- Behavioral Genetics Center, Institute of Psychology, Chinese Academy of Sciences, Beijing, China
| | - C N Soares
- Women's Health Concerns Clinic, St Joseph's Healthcare, Hamilton, ON, Canada,Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada,Department of Obstetrics and Gynecology, McMaster University, Hamilton, ON, Canada
| | - G Turecki
- McGill Group for Suicide Studies, Douglas Mental Health University Institute, Montreal, QC, Canada
| | - M Steiner
- Women's Health Concerns Clinic, St Joseph's Healthcare, Hamilton, ON, Canada,Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada,Department of Obstetrics and Gynecology, McMaster University, Hamilton, ON, Canada,Departments of Psychiatry and Behavioural Neurosciences and Obstetrics and Gynecology, McMaster University, 301 James Street South, Hamilton, ON, Canada L8P 3B6 E-mail:
| | - M Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada,Sackler Program for Epigenetics and Psychobiology, McGill University, Montreal, QC, Canada,McGill Centre for Bioinformatics, McGill University, Montreal, QC, Canada,Department of Pharmacology and Therapeutics, McGill University Medical School, 3655 Sir William Osler Promenade #1309, Montreal, QC, Canada H3G 1Y6. E-mail:
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49
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Acevedo N, Reinius LE, Vitezic M, Fortino V, Söderhäll C, Honkanen H, Veijola R, Simell O, Toppari J, Ilonen J, Knip M, Scheynius A, Hyöty H, Greco D, Kere J. Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes. Clin Epigenetics 2015; 7:34. [PMID: 25874017 PMCID: PMC4396570 DOI: 10.1186/s13148-015-0064-6] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 02/24/2015] [Indexed: 12/15/2022] Open
Abstract
Background Age-related changes in DNA methylation occurring in blood leukocytes during early childhood may reflect epigenetic maturation. We hypothesized that some of these changes involve gene networks of critical relevance in leukocyte biology and conducted a prospective study to elucidate the dynamics of DNA methylation. Serial blood samples were collected at 3, 6, 12, 24, 36, 48 and 60 months after birth in ten healthy girls born in Finland and participating in the Type 1 Diabetes Prediction and Prevention Study. DNA methylation was measured using the HumanMethylation450 BeadChip. Results After filtering for the presence of polymorphisms and cell-lineage-specific signatures, 794 CpG sites showed significant DNA methylation differences as a function of age in all children (41.6% age-methylated and 58.4% age-demethylated, Bonferroni-corrected P value <0.01). Age-methylated CpGs were more frequently located in gene bodies and within +5 to +50 kilobases (kb) of transcription start sites (TSS) and enriched in developmental, neuronal and plasma membrane genes. Age-demethylated CpGs were associated to promoters and DNAse-I hypersensitivity sites, located within −5 to +5 kb of the nearest TSS and enriched in genes related to immunity, antigen presentation, the polycomb-group protein complex and cytoplasm. Conclusions This study reveals that susceptibility loci for complex inflammatory diseases (for example, IRF5, NOD2, and PTGER4) and genes encoding histone modifiers and chromatin remodeling factors (for example, HDAC4, KDM2A, KDM2B, JARID2, ARID3A, and SMARCD3) undergo DNA methylation changes in leukocytes during early childhood. These results open new perspectives to understand leukocyte maturation and provide a catalogue of CpG sites that may need to be corrected for age effects when performing DNA methylation studies in children. Electronic supplementary material The online version of this article (doi:10.1186/s13148-015-0064-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nathalie Acevedo
- Department of Medicine Solna, Translational Immunology Unit, Karolinska University Hospital, Stockholm, Sweden ; Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Lovisa E Reinius
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Morana Vitezic
- Department of Biology, Bioinformatics Centre, University of Copenhagen, Copenhagen, Denmark
| | - Vittorio Fortino
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Hanna Honkanen
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Riitta Veijola
- Department of Pediatrics, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Olli Simell
- Department of Pediatrics, Turku University Hospital, Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Jorma Toppari
- Department of Physiology and Pediatrics, Turku University Hospital, University of Turku, Turku, Finland
| | - Jorma Ilonen
- Immunogenetics Laboratory, University of Turku, Finland and Department of Clinical Microbiology, University of Eastern Finland, Kuopio, Finland
| | - Mikael Knip
- Children's Hospital, Helsinki University Central Hospital, University of Helsinki, Helsinki, Finland ; Department of Paediatrics, Tampere University Hospital, Tampere, Finland ; Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Annika Scheynius
- Department of Medicine Solna, Translational Immunology Unit, Karolinska University Hospital, Stockholm, Sweden
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland ; Fimlab Laboratories, Tampere, Finland
| | - Dario Greco
- Unit of Systems Toxicology, Finnish Institute of Occupational Health, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Stockholm, Sweden ; Folkhälsan Institute of Genetics, Helsinki, and Research Programs Unit, University of Helsinki, Helsinki, Finland
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50
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Dukal H, Frank J, Lang M, Treutlein J, Gilles M, Wolf IA, Krumm B, Massart R, Szyf M, Laucht M, Deuschle M, Rietschel M, Witt SH. New-born females show higher stress- and genotype-independent methylation of SLC6A4 than males. Borderline Personal Disord Emot Dysregul 2015; 2:8. [PMID: 26401310 PMCID: PMC4579500 DOI: 10.1186/s40479-015-0029-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Accepted: 03/24/2015] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Research has demonstrated an association between exposure to early life stress and an increased risk of psychiatric disorders in later life, in particular depression. However, the mechanism through which early life stress contributes to disease development remains unclear. Previous studies have reported an association between early life stress and altered methylation of the serotonin transporter gene (SLC6A4), a key candidate gene for several psychiatric disorders. These differences in methylation are influenced by sex and genetic variation in the SLC6A4-linked polymorphic region (5-HTTLPR). Furthermore, one study indicated that stress during pregnancy may induce methylation changes in SLC6A4 in the newborn. The present study is the first to investigate whether early life stress during pregnancy impacts on SLC6A4 methylation in newborns, taking into account the influence of genetic variation and sex. METHODS Cord blood was obtained from newborns with high (n = 45) or low (n = 45) early life stress, defined as maternal stress during pregnancy. The effect on methylation of early life stress, 5-HTTLPR genotype, and sex was assessed at four cytosin-phosphate-guanine dinucleotide (CpG) sites in the promoter associated CpG island north shore (CpG 1 to 4). The epigenetic analyses focused on these CpG sites, since research has shown that CpG island shore methylation has functional consequences. RESULTS Significant sex-specific methylation was observed, with females displaying higher methylation levels than males (p < 0.001). Importantly, this effect was influenced by neither early life stress nor genotype. CONCLUSIONS The present data suggest that sex-specific methylation of SLC6A4 is present at birth, and is independent of early life stress and 5-HTTLPR genotype. This may contribute to the sex-specific prevalence of depression.
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Affiliation(s)
- Helene Dukal
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Maren Lang
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Maria Gilles
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Isabell Ac Wolf
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Bertram Krumm
- Department of Biostatistics, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Renaud Massart
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC Canada
| | - Moshe Szyf
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC Canada
| | - Manfred Laucht
- Department of Child and Adolescent Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Michael Deuschle
- Department of Psychiatry and Psychotherapy, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim, Germany
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