Quality control and statistical modeling for environmental epigenetics: A study onin uterolead exposure and DNA methylation at birth

Abstract

DNA methylation data assayed using pyrosequencing techniques are increasingly being used in human cohort studies to investigate associations between epigenetic modifications at candidate genes and exposures to environmental toxicants and to examine environmentally-induced epigenetic alterations as a mechanism underlying observed toxicant-health outcome associations. For instance, in utero lead (Pb) exposure is a neurodevelopmental toxicant of global concern that has also been linked to altered growth in human epidemiological cohorts; a potential mechanism of this association is through alteration of DNA methylation (e.g., at growth-related genes). However, because the associations between toxicants and DNA methylation might be weak, using appropriate quality control and statistical methods is important to increase reliability and power of such studies. Using a simulation study, we compared potential approaches to estimate toxicant-DNA methylation associations that varied by how methylation data were analyzed (repeated measures vs. averaging all CpG sites) and by method to adjust for batch effects (batch controls vs. random effects). We demonstrate that correcting for batch effects using plate controls yields unbiased associations, and that explicitly modeling the CpG site-specific variances and correlations among CpG sites increases statistical power. Using the recommended approaches, we examined the association between DNA methylation (in LINE-1 and growth related genes IGF2, H19 and HSD11B2) and 3 biomarkers of Pb exposure (Pb concentrations in umbilical cord blood, maternal tibia, and maternal patella), among mother-infant pairs of the Early Life Exposures in Mexico to Environmental Toxicants (ELEMENT) cohort (n = 247). Those with 10 μg/g higher patella Pb had, on average, 0.61% higher IGF2 methylation (P = 0.05). Sex-specific trends between Pb and DNA methylation (P < 0.1) were observed among girls including a 0.23% increase in HSD11B2 methylation with 10 μg/g higher patella Pb.

Prenatal exposure to neurotoxic metals is associated with increased placental glucocorticoid receptor DNA methylation

“…No sex patterning in methylation was observed for As, Cd, or Hg. Previous work has shown some epigenetic patterning by sex in relation to prenatal As, Cd, and Pb exposures and DNA methylation, 26,40,50,51 though these studies reflect a heterogeneous mix of epigenome wide association studies, candidate gene examinations, and mouse models, rendering it difficult to compare our findings with published research. Thus, we suggest cautious interpretation of our sex-specific analysis and advise replication of these results.…”

Assisted reproductive technology alters deoxyribonucleic acid methylation profiles in bloodspots of newborn infants

“…Subsequent comparison of IUI, FH, or FZ with NAT identified differences between children born to parents undergoing infertility treatment and those born to fertile parents. Methylation changes between males and females within the same conception group were undertaken to examine how the epigenome might differ between genders (34)(35)(36).…”

Effects of Prenatal Exposure to Endocrine Disruptors and Toxic Metals on The Fetal Epigenome

“…Given the latent and persistent effects of early life exposure to Pb, epigenetic reprogramming has been posited to contribute to these effects. Maternal bone Pb levels have been significantly associated with LINE1 and Alu methylation, although cord blood Pb has not [58,59]. Maternal bone Pb represents cumulative exposure, suggesting that maternal cumulative Pb exposure is associated with altered global methylation.…”

“…However, results were not significant following multiple test correction [59]. Additional studies have focused on the sex-specific effects of Pb-induced epigenetic disruptions of the fetus.…”