Prenatal Exposure to Maternal Cigarette Smoking and DNA Methylation: Epigenome-Wide Association in a Discovery Sample of Adolescents and Replication in an Independent Cohort at Birth through 17 Years of Age

Background: Prenatal exposure to maternal cigarette smoking (prenatal smoke exposure) had been associated with altered DNA methylation (DNAm) at birth. Objective: We examined whether such alterations are present from birth through adolescence. Methods: We used the Infinium HumanMethylation450K BeadChip to search across 473,395 CpGs for differential DNAm associated with prenatal smoke exposure during adolescence in a discovery cohort (n = 132) and at birth, during childhood, and during adolescence in a replication cohort (n = 447). Results: In the discovery cohort, we found five CpGs in MYO1G (top-ranking CpG: cg12803068, p = 3.3 × 10–11) and CNTNAP2 (cg25949550, p = 4.0 × 10–9) to be differentially methylated between exposed and nonexposed individuals during adolescence. The CpGs in MYO1G and CNTNAP2 were associated, respectively, with higher and lower DNAm in exposed versus nonexposed adolescents. The same CpGs were differentially methylated at birth, during childhood, and during adolescence in the replication cohort. In both cohorts and at all developmental time points, the differential DNAm was in the same direction and of a similar magnitude, and was not altered appreciably by adjustment for current smoking by the participants or their parents. In addition, four of the five EWAS (epigenome-wide association study)–significant CpGs in the adolescent discovery cohort were also among the top sites of differential methylation in a previous birth cohort, and differential methylation of CpGs in CYP1A1, AHRR, and GFI1 observed in that study was also evident in our discovery cohort. Conclusions: Our findings suggest that modifications of DNAm associated with prenatal maternal smoking may persist in exposed offspring for many years—at least until adolescence. Citation: Lee KW, Richmond R, Hu P, French L, Shin J, Bourdon C, Reischl E, Waldenberger M, Zeilinger S, Gaunt T, McArdle W, Ring S, Woodward G, Bouchard L, Gaudet D, Davey Smith G, Relton C, Paus T, Pausova Z. 2015. Prenatal exposure to maternal cigarette smoking and DNA methylation: epigenome-wide association in a discovery sample of adolescents and replication in an independent cohort at birth through 17 years of age. Environ Health Perspect 123:193–199; http://dx.doi.org/10.1289/ehp.1408614

[1]  J. V. Moran,et al.  Dynamic interactions between transposable elements and their hosts , 2011, Nature Reviews Genetics.

[2]  Margaret A. Pericak-Vance,et al.  Individual common variants exert weak effects on the risk for autism spectrum disorders , 2012, Human molecular genetics.

[3]  Devin C. Koestler,et al.  DNA methylation arrays as surrogate measures of cell mixture distribution , 2012, BMC Bioinformatics.

[4]  C. Hsieh,et al.  Protein Binding Protects Sites on Stable Episomes and in the Chromosome from De Novo Methylation , 2001, Molecular and Cellular Biology.

[5]  A. Jeltsch.  Molecular enzymology of mammalian DNA methyltransferases. , 2006, Current topics in microbiology and immunology.

[6]  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.

[7]  Christian Gieger,et al.  Tobacco Smoking Leads to Extensive Genome-Wide Changes in DNA Methylation , 2013, PloS one.

[8]  T. Kakutani,et al.  Bursts of retrotransposition reproduced in Arabidopsis , 2009, Nature.

[9]  A. Guidotti,et al.  Nicotine decreases DNA methyltransferase 1 expression and glutamic acid decarboxylase 67 promoter methylation in GABAergic interneurons , 2008, Proceedings of the National Academy of Sciences.

[10]  W. Reik,et al.  Epigenetic Reprogramming in Plant and Animal Development , 2010, Science.

[11]  D. Lawlor,et al.  Cohort Profile: The ‘Children of the 90s’—the index offspring of the Avon Longitudinal Study of Parents and Children , 2012, International journal of epidemiology.

[12]  W. Xiao,et al.  Potential of DNMT and its Epigenetic Regulation for Lung Cancer Therapy , 2009, Current genomics.

[13]  K. Gunderson,et al.  High density DNA methylation array with single CpG site resolution. , 2011, Genomics.

[14]  J. Tost,et al.  Complete pipeline for Infinium(®) Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation. , 2012, Epigenomics.

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

[16]  Bernhard Korn,et al.  Tobacco-smoking-related differential DNA methylation: 27K discovery and replication. , 2011, American journal of human genetics.

[17]  Alexandra Wollum,et al.  Smoking prevalence and cigarette consumption in 187 countries, 1980-2012. , 2014, JAMA.

[18]  C. Power,et al.  Maternal smoking in pregnancy, adult adiposity and other risk factors for cardiovascular disease. , 2010, Atherosclerosis.

[19]  Rafael A. Irizarry,et al.  Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays , 2014, Bioinform..

[20]  A. Jeltsch,et al.  Structure and Function of Mammalian DNA Methyltransferases , 2011, Chembiochem : a European journal of chemical biology.

[21]  Arturas Petronis,et al.  Epigenetics as a unifying principle in the aetiology of complex traits and diseases , 2010, Nature.

[22]  B. Christensen,et al.  Association of secondhand smoke exposures with DNA methylation in bladder carcinomas , 2011, Cancer Causes & Control.

[23]  R. Dobson,et al.  Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood , 2012, Genome Biology.

[24]  Robert A Philibert,et al.  Demethylation of the aryl hydrocarbon receptor repressor as a biomarker for nascent smokers , 2012, Epigenetics.

[25]  M. Gillman,et al.  Maternal smoking during pregnancy and child overweight: systematic review and meta-analysis , 2008, International Journal of Obesity.

[26]  M. Esteller,et al.  Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome , 2011, Epigenetics.

[27]  K. Clark,et al.  The maternal and fetal physiologic effects of nicotine. , 1996, Seminars in perinatology.

[28]  Wei Xu,et al.  Candidate autism gene screen identifies critical role for cell-adhesion molecule CASPR2 in dendritic arborization and spine development , 2012, Proceedings of the National Academy of Sciences.

[29]  R. Harper,et al.  Cigarette Smoke Induces MUC5AC Protein Expression through the Activation of Sp1* , 2012, The Journal of Biological Chemistry.

[30]  J. R. Landis,et al.  The measurement of observer agreement for categorical data. , 1977, Biometrics.

[31]  Zdenka Pausova,et al.  Cigarette smoking and DNA methylation , 2013, Front. Genet..

[32]  D. Keefe,et al.  Telomere shortening and DNA damage of embryonic stem cells induced by cigarette smoke. , 2013, Reproductive toxicology.

[33]  Pau Farré,et al.  Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array , 2013, Epigenetics & Chromatin.

[34]  H. Leonhardt,et al.  Recruitment of DNA methyltransferase I to DNA repair sites. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Zachary D. Smith,et al.  A unique regulatory phase of DNA methylation in the early mammalian embryo , 2012, Nature.

[36]  H. Schillers,et al.  Myosin 1G (Myo1G) is a haematopoietic specific myosin that localises to the plasma membrane and regulates cell elasticity , 2010, FEBS letters.

[37]  Paolo Vineis,et al.  Epigenome-wide association study in the European Prospective Investigation into Cancer and Nutrition (EPIC-Turin) identifies novel genetic loci associated with smoking. , 2013, Human molecular genetics.

[38]  Alain Pitiot,et al.  Genes, maternal smoking, and the offspring brain and body during adolescence: Design of the Saguenay Youth Study , 2007, Human brain mapping.

[39]  A. Porcellini,et al.  DNA Damage, Homology-Directed Repair, and DNA Methylation , 2007, PLoS genetics.

[40]  George Davey Smith,et al.  Epigenetic Epidemiology of Common Complex Disease: Prospects for Prediction, Prevention, and Treatment , 2010, PLoS medicine.

[41]  P. Boffetta,et al.  Similar DNA methylation pattern in lung tumours from smokers and never-smokers with second-hand tobacco smoke exposure. , 2012, Mutagenesis.

[42]  Xiao Zhang,et al.  Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis , 2010, BMC Bioinformatics.

[43]  K. Bertrand,et al.  Induction of DNA Hypomethylation by Tumor Hypoxia , 2007, Epigenetics.

[44]  R. Weksberg,et al.  Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray , 2013, Epigenetics.

[45]  L. Aravind,et al.  Myosin 1G Is an Abundant Class I Myosin in Lymphocytes Whose Localization at the Plasma Membrane Depends on Its Ancient Divergent Pleckstrin Homology (PH) Domain (Myo1PH)* , 2010, The Journal of Biological Chemistry.

[46]  D. Dolinoy,et al.  Timing is everything , 2011, Epigenetics.

[47]  T. Paus,et al.  Prenatal Exposure to Maternal Cigarette Smoking and Accumulation of Intra‐abdominal Fat During Adolescence , 2010, Obesity.

[48]  J. D’Armiento,et al.  Identification of a cigarette smoke-responsive region in the distal MMP-1 promoter. , 2009, American journal of respiratory cell and molecular biology.