DNA Methylation and BMI: Investigating Identified Methylation Sites at HIF3A in a Causal Framework

Abstract

Multiple differentially methylated sites and regions associated with adiposity have now been identified in large-scale cross-sectional studies. We tested for replication of associations between previously identified CpG sites at HIF3A and adiposity in ∼1,000 mother-offspring pairs from the Avon Longitudinal Study of Parents and Children (ALSPAC). Availability of methylation and adiposity measures at multiple time points, as well as genetic data, allowed us to assess the temporal associations between adiposity and methylation and to make inferences regarding causality and directionality. Overall, our results were discordant with those expected if HIF3A methylation has a causal effect on BMI and provided more evidence for causality in the reverse direction (i.e., an effect of BMI on HIF3A methylation). These results are based on robust evidence from longitudinal analyses and were also partially supported by Mendelian randomization analysis, although this latter analysis was underpowered to detect a causal effect of BMI on HIF3A methylation. Our results also highlight an apparent long-lasting intergenerational influence of maternal BMI on offspring methylation at this locus, which may confound associations between own adiposity and HIF3A methylation. Further work is required to replicate and uncover the mechanisms underlying the direct and intergenerational effect of adiposity on DNA methylation.

Figure 1

Schematic diagrams of the causal inference methods being implemented in this study. A: Investigating longitudinal associations between BMI and HIF3A methylation. B: Investigating the dominant direction of causality in the association between BMI and HIF3A methylation with the use of bidirectional Mendelian randomization analysis. C: Investigating the intrauterine effect of maternal smoking on offspring DNA methylation with the use of a parental comparison design.

Figure 2

Triangulation approach for IV analyses used in this study. The observed association between the IV and the outcome (a) is compared with that expected given the association between the IV and the exposure (b) and the association between the exposure and the outcome (c).

Figure 3

Associations between maternal BMI and offspring methylation at birth at HIF3A CpG sites. Associations of maternal BMI and offspring cord blood methylation at birth at all 25 CpG sites at the HIF3A locus (mean change in methylation per unit increase in log-maternal prepregnancy BMI; error bars indicate 95% CIs). The locations of CpG sites on the HIF3A gene are mapped on the diagram below the graph. Blue blocks are exons, gray blocks are introns, green blocks are CpG islands, and red pins are CpG sites. The three sites previously identified in adult peripheral blood as associated with own BMI are highlighted with a red *. All sites associated with maternal BMI with a P value <0.05 in our analyses are highlighted with a blue *.

Figure 4

Associations between parental BMI and offspring DNA methylation at HIF3A. The error bars indicate the 95% CI. Maternal antenatal: n = 849 (birth) 904 (adolescence); paternal: n = 694 (birth) 742 (adolescence); mutually adjusted: n = 662 (birth) 708 (adolescence); maternal at follow-up: n = 819 (adolescence); maternal antenatal adjusted for maternal at follow-up: n = 763 (adolescence).