Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation.

Carrie V Breton,Weiliang Qui,Carole Ober,Kathleen C Barnes,Kimberly D Siegmund,Wenche Nystad,Andy Liu,Xinhui Wang,Bonnie R Joubert,Dan L Nicolae ,Robert F Lemanske ,Frank D Gilliland ,Robert C Strunk ,Stephanie J London ,Scott T Weiss ,Fernando D Martínez ,Siri Eldevik Håberg ,Vincent J Carey ,Benjamin A Raby

doi:10.1371/journal.pone.0099716

Abstract

BackgroundSmoking while pregnant is associated with a myriad of negative health outcomes in the child. Some of the detrimental effects may be due to epigenetic modifications, although few studies have investigated this hypothesis in detail.ObjectivesTo characterize site-specific epigenetic modifications conferred by prenatal smoking exposure within asthmatic children.MethodsUsing Illumina HumanMethylation27 microarrays, we estimated the degree of methylation at 27,578 distinct DNA sequences located primarily in gene promoters using whole blood DNA samples from the Childhood Asthma Management Program (CAMP) subset of Asthma BRIDGE childhood asthmatics (n = 527) ages 5–12 with prenatal smoking exposure data available. Using beta-regression, we screened loci for differential methylation related to prenatal smoke exposure, adjusting for gender, age and clinical site, and accounting for multiple comparisons by FDR.ResultsOf 27,578 loci evaluated, 22,131 (80%) passed quality control assessment and were analyzed. Sixty-five children (12%) had a history of prenatal smoke exposure. At an FDR of 0.05, we identified 19 CpG loci significantly associated with prenatal smoke, of which two replicated in two independent populations. Exposure was associated with a 2% increase in mean CpG methylation in FRMD4A (p = 0.01) and Cllorf52 (p = 0.001) compared to no exposure. Four additional genes, XPNPEP1, PPEF2, SMPD3 and CRYGN, were nominally associated in at least one replication group.ConclusionsThese data suggest that prenatal exposure to tobacco smoke is associated with reproducible epigenetic changes that persist well into childhood. However, the biological significance of these altered loci remains unknown.

Highlights

Smoking while pregnant is associated with a myriad of negative health outcomes both for the mother and for the fetus. [1] In utero tobacco smoke exposure (IUS) can damage the placental structure and function [2], is associated with changes in children’s neurodevelopment and behavior [3] as well as with impaired lung function and increased risk of developing asthma. [4,5,6] IUS-related deficits in lung function are larger for children with asthma. [7].One hypothesized mechanism through which IUS may act is by altering the epigenetic landscape within the developing fetus
Scientific reports are linking IUS exposure to alterations in the fetal epigenome, including changes in DNA methylation in numerous genes and tissue types. [8,9] To further investigate the association between IUS and epigenetics, we evaluated the association between IUS exposure and DNA methylation in the first phase of subjects participating in the Asthma BioRepository for Integrative Genomic Exploration (Asthma BRIDGE) study - a subset of asthmatic children originally from the Childhood Asthma Management Program (CAMP) trial. [10,11] We designed a study aimed at investigating DNA methylation in promoter regions of genes as these are the most pertinent regulatory regions for gene expression
The first phase of the Asthma BRIDGE multicenter initiative consisted of asthmatic subjects that were originally recruited as part of CAMP, the details of which have been described elsewhere. [10,11] Briefly, CAMP is a multicenter, randomized, doublemasked clinical trial to compare the long-term effectiveness and safety of 3 inhaled treatments for asthma: budesonide, nedocromil, and placebo

Summary

Introduction

Smoking while pregnant is associated with a myriad of negative health outcomes both for the mother and for the fetus. [1] In utero tobacco smoke exposure (IUS) can damage the placental structure and function [2], is associated with changes in children’s neurodevelopment and behavior [3] as well as with impaired lung function and increased risk of developing asthma. [4,5,6] IUS-related deficits in lung function are larger for children with asthma. [7].One hypothesized mechanism through which IUS may act is by altering the epigenetic landscape within the developing fetus. Smoking while pregnant is associated with a myriad of negative health outcomes both for the mother and for the fetus. [1] In utero tobacco smoke exposure (IUS) can damage the placental structure and function [2], is associated with changes in children’s neurodevelopment and behavior [3] as well as with impaired lung function and increased risk of developing asthma. [8,9] To further investigate the association between IUS and epigenetics, we evaluated the association between IUS exposure and DNA methylation in the first phase of subjects participating in the Asthma BioRepository for Integrative Genomic Exploration (Asthma BRIDGE) study - a subset of asthmatic children originally from the Childhood Asthma Management Program (CAMP) trial. Smoking while pregnant is associated with a myriad of negative health outcomes in the child. Some of the detrimental effects may be due to epigenetic modifications, few studies have investigated this hypothesis in detail

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Methods

Results

Discussion

Conclusion