Variable DNA methylation in neonates mediates the association between prenatal smoking and birth weight

Abstract

There is great interest in the role epigenetic variation induced by non-genetic exposures may play in the context of health and disease. In particular, DNA methylation has previously been shown to be highly dynamic during the earliest stages of development and is influenced by in utero exposures such as maternal smoking and medication. In this study we sought to identify the specific DNA methylation differences in blood associated with prenatal and birth factors, including birth weight, gestational age and maternal smoking. We quantified neonatal methylomic variation in 1263 infants using DNA isolated from a unique collection of archived blood spots taken shortly after birth (mean = 6.08 days; s.d. = 3.24 days). An epigenome-wide association study (EWAS) of gestational age and birth weight identified 4299 and 18 differentially methylated positions (DMPs) respectively, at an experiment-wide significance threshold of p < 1 × 10^-7. Our EWAS of maternal smoking during pregnancy identified 110 DMPs in neonatal blood, replicating previously reported genomic loci, including AHRR. Finally, we tested the hypothesis that DNA methylation mediates the relationship between maternal smoking and lower birth weight, finding evidence that methylomic variation at three DMPs may link exposure to outcome. These findings complement an expanding literature on the epigenomic consequences of prenatal exposures and obstetric factors, confirming a link between the maternal environment and gene regulation in neonates. This article is part of the theme issue 'Developing differences: early-life effects and evolutionary medicine'.

Keywords: DNA methylation; birth weight; epigenome-wide association study; gestational age; maternal smoking; mediation analysis.

Figure 1.

Methylomic variation associated with birth weight and gestational age in neonates. Manhattan plots of p-values from an epigenome-wide association study (EWAS) of (a) birth weight (g) and (b) gestational age (weeks). The red (dashed) horizontal line indicates experiment-wide significance (p < 1 × 10⁻⁷); the blue (solid) horizontal line indicates a ‘discovery’ significance threshold (p < 5 × 10⁻⁵). Shown are scatterplots of the top-ranked differentially methylated positions (DMPs) associated with (c) birth weight (cg20076442) and (d) gestational age (cg11932158). (Online version in colour.)

Figure 2.

DNA methylation at birth is associated with maternal smoking during pregnancy. The red (dashed) horizontal line indicates experiment-wide significance (p < 1 × 10⁻⁷), the blue (solid) horizontal line indicates a ‘discovery’ significance threshold (p < 5 × 10⁻⁵). (a) Manhattan plots from an EWAS of maternal smoking. Boxplots of the three top-ranked DNA methylation sites associated with maternal smoking: (b) cg05575921, (c) cg09935388 and (d) cg12803068. Shown are unadjusted DNA methylation values.