Placental multi-omics integration identifies candidate functional genes for birthweight

Abstract

Abnormal birthweight is associated with increased risk for cardiometabolic diseases in later life. Although the placenta is critical to fetal development and later life health, it has not been integrated into largescale functional genomics initiatives, and mechanisms of birthweight-associated variants identified by genome wide association studies (GWAS) are unclear. The goal of this study is to provide functional mechanistic insight into the causal pathway from a genetic variant to birthweight by integrating placental methylation and gene expression with established GWAS loci for birthweight. We identify placental DNA methylation and gene expression targets for several birthweight GWAS loci. The target genes are broadly enriched in cardiometabolic, immune response, and hormonal pathways. We find that methylation causally influences WNT3A, CTDNEP1, and RANBP2 expression in placenta. Multi-trait colocalization identifies PLEKHA1, FES, CTDNEP1, and PRMT7 as likely functional effector genes. These findings reveal candidate functional pathways that underpin the genetic regulation of birthweight via placental epigenetic and transcriptomic mechanisms. Clinical trial registration; ClinicalTrials.gov, NCT00912132.

Fig. 1. Overview of study workflow.

DNAm denotes DNA methylation, and eGene denotes an eQTL target gene in which gene expression in the placenta is regulated by a nearby genetic variant.

Fig. 2. Birthweight-associated genetic variants with co-occurring cis-eQTL and cis-mQTL effect.

a mQTL in the upper panel and eQTL in the lower panel. The red horizontal lines represent the 5% FDR threshold. CpGs and genes with labels correspond to loci in which a genetic variant was associated with both DNA methylation and gene expression. For ease of readability, only one CpG and one gene was labeled per locus. b Venn Diagram showing the number of birthweight GWAS loci that were found to be eQTL and mQTL in the placenta. c–e P is based on a two-sided Spearman correlation test performed between placental mQTL and eQTL association coefficients for all 197 eQTL-mQTL triplets (c), for 48 triplets consisting DNA methylation sites within the eQTL target genes (d), and for 23 triplets that overlap with blood eQTL from GTEx and mQTL from ARIES database (e). d, e Error bands in gray represent standard error of the mean.

Fig. 3. Causal inference test result.

a Pie-chart showing the number of eQTL-mQTL triplets predicted as “SEM” mediation representing SNP effect mediated via placental gene expression on nearby DNA methylation, “SME” mediation representing SNP effect mediated via placental DNA methylation on placental gene expression, “independent SE/SM” effect denoting SNP effect on placental DNA methylation and gene expression via independent pathways, and “unclassified” relationship. b, c Error bands in gray represent standard error of the mean and P is based on a two-sided Spearman correlation test. The dose-response correlation between eQTL and mQTL association coefficients was only significant for triplets with SEM or SME predicted causal relationship (b) but not with independent SE/SM relationship (c).

Fig. 4. Direction of the relationship between birthweight-associated SNP, DNA methylation and WNT3A gene expression in placenta.

a Association between all SNPs 100 kb up- and downstream of the birthweight GWAS SNP rs708122 and WNT3A gene expression (upper panel) and DNA methylation at cg02991924 (lower panel). The strongest association was found for the index SNP or its nearest linkage disequilibrium (LD) proxies. b rs708122 accounts for higher variance in DNA methylation than in WNT3A expression based on MR Steiger test. c, d Error bands in gray represent standard error of the mean and P is based on a two-sided Spearman correlation test. DNA methylation and WNT3A expression were not correlated. e, f Box plots indicate median (middle line), 25th, 75th percentile (box) and 5th and 95th percentile (whiskers) as well as outliers (single points). N = 71 individuals. rs708122 was associated with DNA methylation after regressing out WNT3A expression (e) (Kruskal Wallis test P = 3.06 × 10⁻⁷) but was not associated with residuals of WNT3A after regressing out DNA methylation (f) (Kruskal Wallis test P = 0.57).