DNA methylation as a potential mediator of the association between prenatal tobacco and alcohol exposure and child neurodevelopment in a South African birth cohort

Abstract

Prenatal tobacco exposure (PTE) and prenatal alcohol exposure (PAE) have been associated with an increased risk of delayed neurodevelopment in children as well as differential newborn DNA methylation (DNAm). However, the biological mechanisms connecting PTE and PAE, DNAm, and neurodevelopment are largely unknown. Here we aim to determine whether differential DNAm mediates the association between PTE and PAE and neurodevelopment at 6 (N = 112) and 24 months (N = 184) in children from the South African Drakenstein Child Health Study. PTE and PAE were assessed antenatally using urine cotinine measurements and the ASSIST questionnaire, respectively. Cord blood DNAm was measured using the EPIC and 450 K BeadChips. Neurodevelopment (cognitive, language, motor, adaptive behavior, socioemotional) was measured using the Bayley Scales of Infant and Toddler Development, Third Edition. We constructed methylation risk scores (MRS) for PTE and PAE and conducted causal mediation analysis (CMA) with these MRS as mediators. Next, we conducted a high-dimensional mediation analysis to identify individual CpG sites as potential mediators, followed by a CMA to estimate the average causal mediation effects (ACME) and total effect (TE). PTE and PAE were associated with neurodevelopment at 6 but not at 24 months. PTE MRS reached a prediction accuracy (R2) of 0.23 but did not significantly mediate the association between PTE and neurodevelopment. PAE MRS was not predictive of PAE (R2 = 0.006). For PTE, 31 CpG sites and eight CpG sites were identified as significant mediators (ACME and TE P < 0.05) for the cognitive and motor domains at 6 months, respectively. For PAE, 16 CpG sites and 1 CpG site were significant mediators for the motor and adaptive behavior domains at 6 months, respectively. Several of the associated genes, including MAD1L1, CAMTA1, and ALDH1A2 have been implicated in neurodevelopmental delay, suggesting that differential DNAm may partly explain the biological mechanisms underlying the relationship between PTE and PAE and child neurodevelopment.

Contributions of prenatal risk factors and neonatal epigenetics to cognitive outcome in children born very preterm.

“…Finally, we aimed to test whether DNA methylation mediated the pathway between prenatal risk and cognitive ability, using a combination of high-dimensional and causal mediation analyses. In line with emerging evidence (Abrishamcar et al, 2022;Feil et al, 2023), we hypothesized that we would find significant mediated pathways through one or more CpG site(s).…”

“…The majority of studies examining epigenetics as a mediator of environmental risk have used candidate gene approaches (for a review, see Barker et al, 2018). Two recent studies used HDMA to test whether DNA methylation mediated the associations between prenatal tobacco and alcohol exposure (Abrishamcar et al, 2022) and indoor air pollution (Feil et al, 2023) and child neurodevelopmental outcomes in a South African birth cohort. Similar to our findings, both prior studies identified significant epigenetic mediators, but only with the DACT (as opposed to HIMA) approaches.…”

“…We already obtained coefficients and p values for the M–O path (association between DNA methylation and child cognitive ability) in the first step of this analysis plan. Consistent with methods described elsewhere (Abrishamcar et al, 2022; Feil et al, 2023), we then filtered CpG sites from both the E–M and M–O paths using a p value threshold of .05. We additionally filtered coefficients based on their direction (i.e., positive or negative) to ensure an overall negative TE, given our hypothesis that increased prenatal risk would be associated with poorer child cognitive ability.…”

“…Like several prior studies, we only found significant mediation using one of two HDMA approaches. As others have pointed out, DACT may be better powered to detect significant mediators compared to HIMA (Abrishamcar et al, 2022;Feil et al, 2023). Alternatively, the increased power of the DACT method may be accompanied by a greater likelihood of false positive findings.…”

“…With the development of high-dimensional mediation methods in recent years (for a review, see Zeng et al, 2021), such studies are emerging. Two recent studies conducted in a South African birth cohort found that prenatal tobacco and alcohol exposure (Abrishamcar et al, 2022) and prenatal exposure to indoor air pollution (Feil et al, 2023) were related to infant and toddler cognitive development via their association with newborn DNA methylation at multiple CpGs sites, including methylation of genes and pathways implicated in fetal brain development, cognitive development, and neurodevelopmental delay. Thus, though this remains an emerging area of research, preliminary findings are promising and suggest the plausibility of DNA methylation as a potential molecular mediator linking prenatal risk factors to children’s cognitive development.…”