Multifactorial analysis of the stochastic epigenetic variability in cord blood confirmed an impact of common behavioral and environmental factors but not of in vitro conception

Abstract

BackgroundAn increased incidence of imprint-associated disorders has been reported in babies born from assisted reproductive technology (ART). However, previous studies supporting an association between ART and an altered DNA methylation status of the conceived babies have been often conducted on a limited number of methylation sites and without correction for critical potential confounders. Moreover, all the previous studies focused on the identification of methylation changes shared among subjects while an evaluation of stochastic differences has never been conducted. This study aims to evaluate the effect of ART and other common behavioral or environmental factors associated with pregnancy on stochastic epigenetic variability using a multivariate approach.ResultsDNA methylation levels of cord blood from 23 in vitro and 41 naturally conceived children were analyzed using the Infinium HumanMethylation450 BeadChips. After multiple testing correction, no statistically significant difference emerged in the number of cord blood stochastic epigenetic variations or in the methylation levels between in vitro- and in vivo-conceived babies. Conversely, four multiple factor analysis dimensions summarizing common phenotypic, behavioral, or environmental factors (cord blood cell composition, pre or post conception supplementation of folates, birth percentiles, gestational age, cesarean section, pre-gestational mother’s weight, parents’ BMI and obesity status, presence of adverse pregnancy outcomes, mother’s smoking status, and season of birth) were significantly associated with stochastic epigenetic variability. The stochastic epigenetic variation analysis allowed the identification of a rare imprinting defect in the locus GNAS in one of the babies belonging to the control population, which would not have emerged using a classical case-control association analysis.ConclusionsWe confirmed the effect of several common behavioral or environmental factors on the epigenome of newborns and described for the first time an epigenetic effect related to season of birth. Children born after ART did not appear to have an increased risk of genome-wide changes in DNA methylation either at specific loci or randomly scattered throughout the genome. The inability to identify differences between cases and controls suggests that the number of stochastic epigenetic variations potentially induced by ART was not greater than that naturally produced in response to maternal behavior or other common environmental factors.Electronic supplementary materialThe online version of this article (10.1186/s13148-018-0510-3) contains supplementary material, which is available to authorized users.

Epigenetic mutation load is weakly correlated with epigenetic age acceleration

“…The calculation of SEM was consistent with a previously published and validated approach [ 24 , 26 , 31 ]. CpG with methylation levels three times the interquartile range above the third quartile or below the first quartile was identified as a SEM.…”

“…All DNA methylation data was extracted from blood samples with the Illumina Infinium platform (450K array for PEG1, FHS, and WHI studies; EPIC array for WHI). Following a published and validated approach [ 24 , 26 , 31 ], a SEM is observed for a given person at a specific CpG site if an individual’s methylation level is more than three times the interquartile range (IQR) lower than the 25 th percentile (Q1 – 3 × IQR), or more than three times the IQR higher than the 75 th percentile (Q3 + 3 × IQR). The 25 th and 75 th percentile, and correspondingly the IQR, for each CpG locus was estimated across all samples.…”

Epigenome Wide Association and Stochastic Epigenetic Mutation Analysis on Cord Blood of Preterm Birth

“…This finding might support the hypothesis that the increased burden of epigenetic errors might impair epigenetic regulatory mechanisms and predispose PTB babies to have adverse consequences in adulthood. Furthermore, recent findings described that several other exposure factors like folate supplementation can modulate the number of SEMs in the newborn [ 17 ], supporting the idea that it might be possible to control the burden of SEMs at birth thus reducing the risk of long-term adverse effects associated with PTB.…”

“…However, we can speculate that a part of the observed heterogeneity might be due to biological differences and presence of hidden pregnancy factors able to modulate DNA methylation. It is well known for example that a great number of maternal and paternal characteristics, environmental and behavioral exposure factors can significantly modulate the epigenome of the newborn [ 17 ]. Moreover, it cannot be excluded that a component of this heterogeneity might also reflect differences in preterm pathophysiology.…”

Does Endometriosis Influence the Embryo Quality and/or Development? Insights from a Large Retrospective Matched Cohort Study

“…In our laboratory, an embryo quality control is performed with a biannual frequency, together with other subjective evaluations (i.e., oocyte quality control, preimplantation diagnosis biopsy control) among the embryologists as previously described [31,35]. In any case, for this specific study, we choose to enroll in the study only cycles in which the quality of the embryos was evaluated every day by the same embryologist (P.V.)…”