HDMAX2: A framework for High Dimensional Mediation Analysis with application to maternal smoking, placental DNA methylation and birth outcomes

Abstract

Background High-dimensional mediation analysis is an extension of unidimensional mediation analysis that includes multiple mediators, and is increasingly used in environmental epidemiology to evaluate the indirect epigenetic effects of environmental exposures on health outcomes. However, analyses involving high-dimensional mediators raise several statistical issues. While many methods have recently been developed to tackle those issues, no consensus has been reached about the optimal combination of approaches. Methods We developed HDMAX2, a new multi-step approach to mediation that combines latent factor regression models for epigenome-wide association studies with max-squared tests for mediation, and considers CpGs and aggregated mediator regions (AMR). HDMAX2 was carefully evaluated on simulated data, and compared to state-of-the- art multi-dimensional epigenetic mediation methods. Then it was applied to assess the indirect effects of exposure to maternal smoking (MS) on term birth weight (BW) and gestational age (GA) at delivery in a study of 470 women from the EDEN cohort. Results HDMAX2 resulted in increased power compared to state-of-the-art multi-dimensional mediation methods, and identified several AMRs not identified in previous mediation analyses of exposure to MS on BW and GA. The results provided evidence for a polygenic architecture of the causal pathway with an overall indirect effect of CpGs and AMRs of 44.5g lower BW (32.1% of the total effect size). HDMAX2 also identified AMRs having simultaneous effects both on GA and BW. Among the top hits of both GA and BW analyses, regions located in COASY, BLCAP and ESRP2 also mediated the relationship between GA on BW, suggesting a reverse causality in the relationship between GA and the methylome. Discussion This study brought up several statistical improvements of high-dimensional mediation analyses, which revealed an unsuspected complexity of the causal relationships between exposure to MS and BW at the epigenome-wide level. Mediation; high dimension; causal inference; epigenetics; DNA methylation; pregnancy