High-Dimensional Mediation Analysis: A New Method Applied to Maternal Smoking, Placental DNA Methylation, and Birth Outcomes

BACKGROUND: High-dimensional mediation analysis is an extension of unidimensional mediation analysis that includes multiple mediators, and increasingly it is being used to evaluate the indirect omics-layer effects of environmental exposures on health outcomes. Analyses involving high-dimensional mediators raise several statistical issues. Although many methods have recently been developed, no consensus has been reached about the optimal combination of approaches to high-dimensional mediation analyses. OBJECTIVES: We developed and validated a method for high-dimensional mediation analysis (HDMAX2) and applied it to evaluate the causal role of placental DNA methylation in the pathway between exposure to maternal smoking (MS) during pregnancy and gestational age (GA) and birth weight of the baby at birth. METHODS: HDMAX2 combines latent factor regression models for epigenome-wide association studies with max2 tests for mediation and considers CpGs and aggregated mediator regions (AMRs). HDMAX2 was carefully evaluated using simulated data and compared to state-of-the-art multidi-mensional epigenetic mediation methods. Then, HDMAX2 was applied to data from 470 women of the Etude des Determinants pre et postnatals du developpement de la sante de l'Enfant (EDEN) cohort. RESULTS: HDMAX2 demonstrated increased power in comparison with state-of-the-art multidimensional mediation methods and identified several AMRs not identified in previous mediation analyses of exposure to MS on birth weight and GA. The results provided evidence for a polygenic archi-tecture of the mediation pathway with a posterior estimate of the overall indirect effect of CpGs and AMRs equal to 44.5 g lower birth weight repre-senting 32.1% of the total effect [standard deviation oSD thorn = 60.7 g]. HDMAX2 also identified AMRs having simultaneous effects both on GA and on birth weight. Among the top hits of both GA and birth weight analyses, regions located in COASY, BLCAP, and ESRP2 also mediated the relationship between GA and birth weight, suggesting reverse causality in the relationship between GA and the methylome. DISCUSSION: HDMAX2 outperformed existing approaches and revealed an unsuspected complexity of the potential causal relationships between expo-sure to MS and birth weight at the epigenome-wide level. HDMAX2 is applicable to a wide range of tissues and omic layers. https://doi.org/10.1289/ EHP11559

Automated summary

High-dimensional mediation analysis is increasingly used to evaluate the indirect effects of environmental exposures on health outcomes. HDMAX2 is a new method that combines latent factor regression models and max2 tests to effectively analyze the causal role of maternal smoking during pregnancy on birth weight and gestational age. It demonstrated increased power compared to existing approaches and revealed a complex relationship between exposure and birth weight at the epigenome-wide level.