Sex-differential DNA methylation and associated regulation networks in human brain implicated in the sex-biased risks of psychiatric disorders

Abstract

Many psychiatric disorders are characterized by a strong sex difference, but the mechanisms behind sex-bias are not fully understood. DNA methylation plays important roles in regulating gene expression, ultimately impacting sexually different characteristics of the human brain. Most previous literature focused on DNA methylation alone without considering the regulatory network and its contribution to sex-bias of psychiatric disorders. Since DNA methylation acts in a complex regulatory network to connect genetic and environmental factors with high-order brain functions, we investigated the regulatory networks associated with different DNA methylation and assessed their contribution to the risks of psychiatric disorders. We compiled data from 1408 postmortem brain samples in 3 collections to identify sex-differentially methylated positions (DMPs) and regions (DMRs). We identified and replicated thousands of DMPs and DMRs. The DMR genes were enriched in neuronal related pathways. We extended the regulatory networks related to sex-differential methylation and psychiatric disorders by integrating methylation quantitative trait loci (meQTLs), gene expression, and protein-protein interaction data. We observed significant enrichment of sex-associated genes in psychiatric disorder-associated gene sets. We prioritized 2080 genes that were sex-biased and associated with psychiatric disorders, such as NRXN1, NRXN2, NRXN3, FDE4A, and SHANK2. These genes are enriched in synapse-related pathways and signaling pathways, suggesting that sex-differential genes of these neuronal pathways may cause the sex-bias of psychiatric disorders.

Fig. 1

Overview of the study design

Fig. 2

Significance and difference of sex-differential DNA methylated positions. a Chromosome density plot of sex-differential DNA methylated positions, colored by the −log p value in 1 MB window size; b distribution of the effect size of DMPs (variation between male and female average methyaltion levels). The violin plots shows two DMP examples

Fig. 3

Sex-differential regulatory network. a Example of SNP–DMP–Gene groups. There are 12 SNP–DMP–Gene groups in this region on Chromosome 14: 24,895,387–24,912,111, involving two SNPs, five DMPs and three genes. The diagram shows the location of them while the cartoon diagram shows their relationship. The gray line represents meQTLs with FDR < 0.05. The blue lines represent negative correlation and red lines represent positive correlations. b Example of sex-differential PPI subnetworks. Every node represents a gene. The color of nodes represents differential methylation levels in corresponding promoters (Yellow: hypermethylated in the female; Blue: hypomethylated in female). The edges were built based on the protein-protein interaction in Pathway Common. The width of the edge is the estimation of effect sizes. Stars represent the candidate genes (Green: ASD candidate genes, Red: SCZ candidate genes, Purple: both ASD and SCZ candidate genes)

Fig. 4

A compressive overrepresentation of psychiatric candidate gene sets in sex-biased genes. a Overrepresentation of psychiatric candidate gene sets in DMR genes, DMP-correlated expressed genes, differentially expressed genes, and PPI network genes, clustered by the enrichment value. b Overrepresentation of psychiatric candidate gene sets in DMR genes and subset of DMR genes. The x-axis shows 34 gene sets divided based on the psychiatric disorder and labeled by type; the y-axis shows the DMR genes, DMP-correlated expressed genes and differentially expressed genes. The color of the box shows the odds ratio for enrichment (red for enrichment, blue for deletion). “*” indicates enrichment is statistically significant (p < 0.05), “**” indicates p < 0.001