450K Epigenome-Wide Scan Identifies Differential DNA Methylation in Newborns Related to Maternal Smoking during Pregnancy

Abstract

Background: Epigenetic modifications, such as DNA methylation, due to in utero exposures may play a critical role in early programming for childhood and adult illness. Maternal smoking is a major risk factor for multiple adverse health outcomes in children, but the underlying mechanisms are unclear.Objective: We investigated epigenome-wide methylation in cord blood of newborns in relation to maternal smoking during pregnancy.Methods: We examined maternal plasma cotinine (an objective biomarker of smoking) measured during pregnancy in relation to DNA methylation at 473,844 CpG sites (CpGs) in 1,062 newborn cord blood samples from the Norwegian Mother and Child Cohort Study (MoBa) using the Infinium HumanMethylation450 BeadChip (450K).Results: We found differential DNA methylation at epigenome-wide statistical significance (p-value < 1.06 × 10–7) for 26 CpGs mapped to 10 genes. We replicated findings for CpGs in AHRR, CYP1A1, and GFI1 at strict Bonferroni-corrected statistical significance in a U.S. birth cohort. AHRR and CYP1A1 play a key role in the aryl hydrocarbon receptor signaling pathway, which mediates the detoxification of the components of tobacco smoke. GFI1 is involved in diverse developmental processes but has not previously been implicated in responses to tobacco smoke.Conclusions: We identified a set of genes with methylation changes present at birth in children whose mothers smoked during pregnancy. This is the first study of differential methylation across the genome in relation to maternal smoking during pregnancy using the 450K platform. Our findings implicate epigenetic mechanisms in the pathogenesis of the adverse health outcomes associated with this important in utero exposure.

Offspring DNA methylation of the aryl-hydrocarbon receptor repressor gene is associated with maternal BMI, gestational age, and birth weight

“…However, close inspection of the data in Joubert et al revealed that 1 of the 4 differentially methylated CpG sites was more highly methylated among infants whose mothers were smokers. 12 Additionally, the magnitude of AHRR DNA methylation difference between mothers with undetectable vs. high cotinine levels at each of their 4 significant sites was of similar magnitude (»4%) as associations with our categorical predictors (2-3%). We did not analyze the same CpG sites as the smoking-associated CpG sites reported in prior studies but instead chose to maximize the CpG sites in the AHRR promoter region that our pyrosequencing assay would capture.…”

“…13 Others have demonstrated that these same methylation sites differed in the offspring of women who smoked during pregnancy, compared to offspring of non-smokers. 12,28 Prior studies demonstrating associations between smoking and AHRR DNA methylation used epigenome-wide methylation assays designed to discover previously unknown associations. 12,13 Given the results of these prior studies demonstrating that AHRR DNA methylation is modifiable during pregnancy, 12 we chose AHRR as a candidate gene to conduct a hypothesis-driven study of perinatal predictors of AHRR DNA methylation in cord blood.…”

“…9 Prenatal smoke exposure may also be associated with a higher risk of later obesity and cardiometabolic disorders. 10 Recent studies demonstrate that smoke exposure in adults 11 and among fetuses exposed to maternal smoking 12 is associated with altered leukocyte DNA methylation of the aryl-hydrocarbon receptor repressor (AHRR) gene, located on chromosome 5. 12,13 AHRR methylation is particularly interesting to study during pregnancy because the aryl-hydrocarbon receptor (AHR) is involved in metabolizing xenobiotics 14 that might affect fetal development.…”

DNA methylation and healthy human aging

“…This balance of responsiveness to stimuli and heritability results in a unique mechanism for lasting signatures of prior exposures that accumulate over the lifetime (Cortessis et al ., 2012; Feil & Fraga, 2012). As an example of a specific exposure that has been shown to leave a lasting signature, cigarette smoke has been linked to changes in DNA methylation at the AHRR locus both in smokers and in children of smokers (Saxonov et al ., 2006; Monick et al ., 2012; Joubert et al ., 2012; Shenker et al ., 2013; Sun et al ., 2013 Elliott et al ., 2014; Lee et al ., 2015; Shah et al ., 2014). Smoking‐associated DNA methylation changes have also been found in genes involved in inflammatory networks, important candidates in the risk of age‐related diseases such as heart disease and stroke (Breitling et al ., 2012; Dogan et al ., 2014).…”

Differential DNA methylation and PM2.5 species in a 450K epigenome-wide association study

“…Several studies have investigated the epigenome-wide association between smoking, an important PM source, and DNA methylation. Using the 450K platform and Bonferroni correction, Joubert et al 17 identified 26 CpGs with methylation changes in newborns related to maternal smoking during pregnancy in a large Norwegian birth cohort. Specifically, the authors documented changes at CpGs in cytochrome p450 1A1 (CYP1A1) and aryl-hydrocarbon receptor repressor (AHRR), genes known to play a key role in the aryl hydrocarbon receptor (AhR) signaling pathway that mediates the detoxification of components of tobacco smoke.…”