Epigenome-Wide Associations of Placental DNA Methylation and Behavioral and Emotional Difficulties in Children at 3 Years of Age

The placenta is a key organ for fetal and brain development. Its epigenome can be regarded as a biochemical record of the prenatal environment and a potential mechanism of its association with the future health of the fetus. We investigated associations between placental DNA methylation levels and child behavioral and emotional difficulties, assessed at 3 years of age using the Strengths and Difficulties Questionnaire (SDQ) in 441 mother–child dyads from the EDEN cohort. Hypothesis-driven and exploratory analyses (on differentially methylated probes (EWAS) and regions (DMR)) were adjusted for confounders, technical factors, and cell composition estimates, corrected for multiple comparisons, and stratified by child sex. Hypothesis-driven analyses showed an association of cg26703534 (AHRR) with emotional symptoms, and exploratory analyses identified two probes, cg09126090 (intergenic region) and cg10305789 (PPP1R16B), as negatively associated with peer relationship problems, as well as 33 DMRs, mostly positively associated with at least one of the SDQ subscales. Among girls, most associations were seen with emotional difficulties, whereas in boys, DMRs were as much associated with emotional than behavioral difficulties. This study provides the first evidence of associations between placental DNA methylation and child behavioral and emotional difficulties. Our results suggest sex-specific associations and might provide new insights into the mechanisms of neurodevelopment.

[1]  K. Strandberg-Larsen,et al.  Smoking during pregnancy and children’s emotional and behavioural trajectories , 2022, The European Journal of Public Health.

[2]  R. Slama,et al.  Maternal blood pressure associates with placental DNA methylation both directly and through alterations in cell-type composition , 2022, BMC Medicine.

[3]  S. Entringer,et al.  Reliability of a novel approach for reference-based cell type estimation in human placental DNA methylation studies , 2022, Cellular and Molecular Life Sciences.

[4]  C. Nievergelt,et al.  Epigenome-wide meta-analysis of PTSD symptom severity in three military cohorts implicates DNA methylation changes in genes involved in immune system and oxidative stress , 2021, Molecular Psychiatry.

[5]  Rosalind J Wright,et al.  Associations between infant sex and DNA methylation across umbilical cord blood, artery, and placenta samples , 2021, Epigenetics.

[6]  M. Scher.  “The First Thousand Days” Define a Fetal/Neonatal Neurology Program , 2021, Frontiers in Pediatrics.

[7]  R. Slama,et al.  Pregnancy exposure to synthetic phenols and placental DNA methylation — An epigenome-wide association study in male infants from the EDEN cohort , 2021, Environmental pollution.

[8]  K. Georgiades,et al.  Prevalence of childhood mental disorders in high-income countries: a systematic review and meta-analysis to inform policymaking , 2021, Evidence-Based Mental Health.

[9]  A. Sakhi,et al.  Associations between a mixture of phenols and phthalates and child behaviour in a French mother-child cohort with repeated assessment of exposure. , 2021, Environment international.

[10]  C. Cecil,et al.  Genome-wide DNA methylation patterns associated with general psychopathology in children , 2021, Journal of psychiatric research.

[11]  Carolyn J. Brown,et al.  A cross-cohort analysis of autosomal DNA methylation sex differences in the term placenta , 2021, Biology of Sex Differences.

[12]  J. Lepeule,et al.  Epigenetic Alterations of Maternal Tobacco Smoking during Pregnancy: A Narrative Review , 2021, International journal of environmental research and public health.

[13]  J. González,et al.  Early-life environmental exposure determinants of child behavior in Europe: A longitudinal, population-based study , 2021, Environment international.

[14]  M. Sirota,et al.  Large-scale placenta DNA methylation integrated analysis reveals fetal sex-specific differentially methylated CpG sites and regions , 2021, Scientific Reports.

[15]  R. Lister,et al.  Maternal Hyperglycemia Induces Changes in Gene Expression and Morphology in Mouse Placentas. , 2021, Gynecology & reproductive health.

[16]  M. Rietschel,et al.  Meta-analysis of epigenome-wide associations between DNA methylation at birth and childhood cognitive skills , 2020, bioRxiv.

[17]  M. Mon-Williams,et al.  Prenatal exposure to a wide range of environmental chemicals and child behaviour between 3 and 7 years of age – An exposome-based approach in 5 European cohorts , 2020, The Science of the total environment.

[18]  R. Kessler,et al.  Epigenome-wide meta-analysis of PTSD across 10 military and civilian cohorts identifies methylation changes in AHRR , 2020, Nature Communications.

[19]  R. Slama,et al.  Immediate and durable effects of maternal tobacco consumption alter placental DNA methylation in enhancer and imprinted gene-containing regions , 2020, BMC Medicine.

[20]  W. Robinson,et al.  Cell-specific characterization of the placental methylome , 2020, BMC genomics.

[21]  F. Tekola-Ayele,et al.  DNA methylation loci in placenta associated with birthweight and expression of genes relevant for early development and adult diseases , 2020, Clinical Epigenetics.

[22]  M. Hivert,et al.  Placental NEGR1 DNA methylation is associated with BMI and neurodevelopment in preschool-age children , 2020, Epigenetics.

[23]  C. Rosenfeld.  The placenta‐brain‐axis , 2020, Journal of neuroscience research.

[24]  A. Brandeburová,et al.  Update on Sexual Dimorphism in Brain Structure–Function Interrelationships: A Literature Review , 2019, Applied Psychophysiology and Biofeedback.

[25]  A. Moffett,et al.  Development of the human placenta , 2019, Development.

[26]  C. Bult,et al.  The Alliance of Genome Resources: Building a Modern Data Ecosystem for Model Organism Databases , 2019, Genetics.

[27]  C. Marsit,et al.  Placental methylation signatures from maternal smoking during pregnancy and potential impacts on fetal growth , 2019, Environmental Epidemiology.

[28]  Brian D. Bennett,et al.  Comparison of smoking-related DNA methylation between newborns from prenatal exposure and adults from personal smoking , 2019, Epigenomics.

[29]  K. Hao,et al.  Placental DNA methylation signatures of maternal smoking during pregnancy and potential impacts on fetal growth , 2019, Nature Communications.

[30]  S. Mostafavi,et al.  Accurate ethnicity prediction from placental DNA methylation data , 2019, bioRxiv.

[31]  K. Hao,et al.  Maternal circadian disruption is associated with variation in placental DNA methylation , 2019, PloS one.

[32]  W. Robinson,et al.  Association of a placental Interleukin-6 genetic variant (rs1800796) with DNA methylation, gene expression and risk of acute chorioamnionitis , 2019, BMC Medical Genetics.

[33]  I. Hertz-Picciotto,et al.  Placental DNA methylation levels at CYP2E1 and IRS2 are associated with child outcome in a prospective autism study , 2018, bioRxiv.

[34]  Laura E. Pryor,et al.  Early childcare type predicts children’s emotional and behavioural trajectories into middle childhood. Data from the EDEN mother–child cohort study , 2018, Journal of Epidemiology & Community Health.

[35]  J. Schwartz,et al.  Pregnancy exposure to atmospheric pollution and meteorological conditions and placental DNA methylation. , 2018, Environment international.

[36]  Theodore D. Satterthwaite,et al.  Sex differences in the developing brain: insights from multimodal neuroimaging , 2018, Neuropsychopharmacology.

[37]  M. Ogundele.  Behavioural and emotional disorders in childhood: A brief overview for paediatricians , 2018, World journal of clinical pediatrics.

[38]  L. C. Bidwell,et al.  Prenatal substance exposure and offspring development: Does DNA methylation play a role? , 2018, Neurotoxicology and teratology.

[39]  B. Penninx,et al.  HPA Axis Genes, and Their Interaction with Childhood Maltreatment, are Related to Cortisol Levels and Stress-Related Phenotypes , 2017, Neuropsychopharmacology.

[40]  J. Holbrook,et al.  Is cellular heterogeneity merely a confounder to be removed from epigenome-wide association studies? , 2017, Epigenomics.

[41]  Tom R. Gaunt,et al.  Neonatal DNA methylation and early-onset conduct problems: A genome-wide, prospective study , 2017, Development and Psychopathology.

[42]  Xiaolin Zhou,et al.  Identifying new susceptibility genes on dopaminergic and serotonergic pathways for the framing effect in decision-making , 2017, Social cognitive and affective neuroscience.

[43]  Marie-France Hivert,et al.  Persistent DNA methylation changes associated with prenatal mercury exposure and cognitive performance during childhood , 2017, Scientific Reports.

[44]  C. Marsit,et al.  Sexual epigenetic dimorphism in the human placenta: implications for susceptibility during the prenatal period. , 2017, Epigenomics.

[45]  E. Fikrig,et al.  Multiple UBXN family members inhibit retrovirus and lentivirus production and canonical NFκΒ signaling by stabilizing IκBα , 2017, PLoS pathogens.

[46]  Shijie C. Zheng,et al.  A comparison of reference-based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies , 2017, bioRxiv.

[47]  T. Bianco-Miotto,et al.  Cord Blood DNA Methylation Biomarkers for Predicting Neurodevelopmental Outcomes , 2016, Genes.

[48]  G. Burton,et al.  Placental Origins of Chronic Disease. , 2016, Physiological reviews.

[49]  A. Woodman,et al.  Comparison of Normal and Pre-Eclamptic Placental Gene Expression: A Systematic Review with Meta-Analysis , 2016, PloS one.

[50]  B. Lester,et al.  Regions of variable DNA methylation in human placenta associated with newborn neurobehavior , 2016, Epigenetics.

[51]  Nicholas J Timpson,et al.  A genome‐wide approach to children's aggressive behavior: The EAGLE consortium , 2016, American journal of medical genetics. Part B, Neuropsychiatric genetics : the official publication of the International Society of Psychiatric Genetics.

[52]  Tsippi Iny Stein,et al.  The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analyses , 2016, Current protocols in bioinformatics.

[53]  P. Gustafsson,et al.  The Strengths and Difficulties Questionnaire (SDQ) for preschool children—a Swedish validation , 2016, Nordic journal of psychiatry.

[54]  G. Vilagut,et al.  Screening for Depression in the General Population with the Center for Epidemiologic Studies Depression (CES-D): A Systematic Review with Meta-Analysis , 2016, PloS one.

[55]  Charles Auffray,et al.  DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis. , 2016, American journal of human genetics.

[56]  R. Slama,et al.  Cohort Profile Cohort Profile : The EDEN mother-child cohort on the prenatal and early postnatal determinants of child health and development , 2015 .

[57]  R. Z. Pinto,et al.  Prenatal Alcohol Exposure, FASD, and Child Behavior: A Meta-analysis , 2016, Pediatrics.

[58]  C. Marsit,et al.  Reference-free deconvolution of DNA methylation data and mediation by cell composition effects , 2016, bioRxiv.

[59]  Brenda Eskenazi,et al.  Sex differences in DNA methylation assessed by 450 K BeadChip in newborns , 2015, BMC Genomics.

[60]  E. Silverman,et al.  The impact of genetic variation and cigarette smoke on DNA methylation in current and former smokers from the COPDGene study , 2015, Epigenetics.

[61]  B. Lester,et al.  Placental epigenetic patterning of glucocorticoid response genes is associated with infant neurodevelopment. , 2015, Epigenomics.

[62]  N. Schork,et al.  Understanding and predicting suicidality using a combined genomic and clinical risk assessment approach , 2015, Molecular Psychiatry.

[63]  C. Galéra,et al.  Maternal Depression Trajectories and Children's Behavior at Age 5 Years. , 2015, The Journal of pediatrics.

[64]  B. Lester,et al.  Examining the joint contribution of placental NR3C1 and HSD11B2 methylation for infant neurobehavior , 2015, Psychoneuroendocrinology.

[65]  B. Trainor,et al.  Environmental Health Factors and Sexually Dimorphic Differences in Behavioral Disruptions , 2014, Current Environmental Health Reports.

[66]  Mark D. Robinson,et al.  Statistical methods for detecting differentially methylated loci and regions , 2014, Front. Genet..

[67]  J. Ryan,et al.  Postnatal stability, tissue, and time specific effects of AHRR methylation change in response to maternal smoking in pregnancy , 2014, Epigenetics.

[68]  B. Lester,et al.  Sex-specific associations between placental leptin promoter DNA methylation and infant neurobehavior , 2014, Psychoneuroendocrinology.

[69]  Francesco Marabita,et al.  A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data , 2012, Bioinform..

[70]  Brent S. Pedersen,et al.  Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values , 2012, Bioinform..

[71]  Susan K. Murphy,et al.  450K Epigenome-Wide Scan Identifies Differential DNA Methylation in Newborns Related to Maternal Smoking during Pregnancy , 2012, Environmental health perspectives.

[72]  C. Bromer,et al.  Genetic and epigenetic variation of the glucocorticoid receptor (NR3C1) in placenta and infant neurobehavior. , 2012, Developmental psychobiology.

[73]  F. Champagne,et al.  Epigenetic and Neurodevelopmental Perspectives on Variation in Parenting Behavior , 2012, Parenting, science and practice.

[74]  B. Lester,et al.  Placental 11-Beta Hydroxysteroid Dehydrogenase Methylation Is Associated with Newborn Growth and a Measure of Neurobehavioral Outcome , 2012, PloS one.

[75]  A. Carter,et al.  Assessment of Behavioral and Emotional Problems in Infancy: A Systematic Review , 2012, Clinical child and family psychology review.

[76]  P. Levitt,et al.  Fetal, maternal, and placental sources of serotonin and new implications for developmental programming of the brain , 2011, Neuroscience.

[77]  A. Gabory,et al.  Developmental programming and epigenetics. , 2011, The American journal of clinical nutrition.

[78]  M. Holmes,et al.  Prenatal Excess Glucocorticoid Exposure and Adult Affective Disorders: A Role for Serotonergic and Catecholamine Pathways , 2011, Neuroendocrinology.

[79]  R. Leibel,et al.  Roles of the placenta in fetal brain development , 2011, Proceedings of the National Academy of Sciences.

[80]  John Wei,et al.  Identify Risk Genes for ADHD Rare Copy Number Variation Discovery and Cross-Disorder Comparisons , 2011 .

[81]  Sanaa Choufani,et al.  Cell specific patterns of methylation in the human placenta , 2011, Epigenetics.

[82]  Tsviya Olender,et al.  GeneCards Version 3: the human gene integrator , 2010, Database J. Biol. Databases Curation.

[83]  D. Lamping,et al.  When to Use Broader Internalising and Externalising Subscales Instead of the Hypothesised Five Subscales on the Strengths and Difficulties Questionnaire (SDQ): Data from British Parents, Teachers and Children , 2010, Journal of abnormal child psychology.

[84]  C. Victora,et al.  Worldwide Timing of Growth Faltering: Revisiting Implications for Interventions , 2010, Pediatrics.

[85]  P. Slagboom,et al.  The epigenome: Archive of the prenatal environment , 2009, Epigenetics.

[86]  V. Kovess,et al.  The strengths and difficulties questionnaire: validation study in French school-aged children and cross-cultural comparisons , 2009, Social Psychiatry and Psychiatric Epidemiology.

[87]  B. Horta,et al.  The worldwide prevalence of ADHD: a systematic review and metaregression analysis. , 2007, The American journal of psychiatry.

[88]  D. J. Barker.  The origins of the developmental origins theory , 2007, Journal of internal medicine.

[89]  J. Seckl,et al.  The Mother or the Fetus? 11β-Hydroxysteroid Dehydrogenase Type 2 Null Mice Provide Evidence for Direct Fetal Programming of Behavior by Endogenous Glucocorticoids , 2006, The Journal of Neuroscience.

[90]  S G Selevan,et al.  Identifying critical windows of exposure for children's health. , 2000, Environmental health perspectives.

[91]  R. Goodman.  The Strengths and Difficulties Questionnaire: a research note. , 1997, Journal of child psychology and psychiatry, and allied disciplines.

[92]  L. Radloff.  The CES-D Scale , 1977 .

[93]  Z. Šidák.  Rectangular Confidence Regions for the Means of Multivariate Normal Distributions , 1967 .

[94]  R. Hurley,et al.  Sexual Dimorphism in Brain Development: Influence on Affective Disorders. , 2021, The Journal of neuropsychiatry and clinical neurosciences.

[95]  Amy L. Salisbury,et al.  Epigenetic Regulation of Placental NR3C1: Mechanism Underlying Prenatal Programming of Infant Neurobehavior by Maternal Smoking? , 2016, Child development.

[96]  T. Bale,et al.  The Placenta as a Mediator of Stress Effects on Neurodevelopmental Reprogramming , 2016, Neuropsychopharmacology.

[97]  A. Aldao,et al.  Gender differences in emotion expression in children: a meta-analytic review. , 2013, Psychological bulletin.

[98]  Brian Biehs,et al.  Statistical Applications in Genetics and Molecular Biology Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics , 2011 .

[99]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .