A region-based method for causal mediation analysis of DNA methylation data

Abstract

Exposure to environmental factors can affect DNA methylation at a 5'-cytosine-phosphate-guanine-3' (CpG) site or a genomic region, which can then affect an outcome. In other words, environmental effects on an outcome could be mediated by DNA methylation. To date, single CpG-site-based mediation analysis has been employed extensively. More recently, however, there has been considerable interest in studying differentially methylated regions (DMRs), both because DMRs are more likely to have functional effects than single CpG sites and because testing DMRs reduces multiple testing. In this report, we propose a novel causal mediation approach under the counterfactual framework to test the significance of total (TE), direct (DE), and indirect effects (IE) of predictors on response variable with a methylated region (MR) as the mediator (denoted as MR-Mediation). Functional linear transformation is used to reduce the possible high dimension of the CpG sites in a predefined MR and to account for their location information. In our simulation studies, MR-Mediation retained the desired Type I error rates for TE, DE, and IE tests. Furthermore, MR-Mediation had better power performance than testing mean methylation level as the mediator in most considered scenarios, especially for IE (i.e., mediated effect) test, which could be more interesting than the other two effect tests. We further illustrate our proposed method by analysing the methylation mediated effect of exposure to gun violence on total immunoglobulin E or atopic asthma among participants in the Epigenetic Variation and Childhood Asthma in Puerto Ricans study.

Keywords: Counterfactual framework; Mediation; Methylated region.

Figure 1.

Mediation model with DNA methylation as the mediator.

Figure 2.

QQ plot of the p-values from Setting (1) with (a) continuous outcome and (b) binary outcome. The first column shows DE results, the second column shows IE results, and the third column shows TE results. Each row shows one gene size (i.e., 10, 15, 20 or 40 CpG sites). Two approaches were compared: (1) MR-Mediation; and (2) Mean CpG methylation approach. A 95% pointwise confidence band (grey area) was computed under the assumption that the p-values were drawn independently from a uniform [0, 1] distribution.

Figure 3.

Power comparison for continuous outcome. (a) All positively effective CpG sites (100%+) and (b) 50% positively and 50% negatively effective CpG sites (50%+/50%–). The first column shows DE results, the second column shows IE results, and the third column shows TE results. Each row shows one gene size (i.e., 10, 15, 20, or 40 CpG sites). Two approaches were compared: (1) MR-Mediation; and (2) Mean CpG methylation approach.

Figure 4.

Power comparison for binary outcome. (a) All positively effective CpG sites (100%+) and (b) 50% positively and 50% negatively effective CpG sites (50%+/50%–). The first column shows DE results, the second column shows IE results, and the third column shows TE results. Each row shows one gene size (i.e., 10, 15, 20, or 40 CpG sites). Two approaches were compared: (1) MR-Mediation; and (2) Mean CpG methylation approach.