Sexually Dimorphic Dna Methylation in Human Brain and Relevance to Psychiatric Disorders

Background The prevalence of many psychiatric disorders, including autism spectrum disorders (ASDs), depression, intellectual disability (ID), has presented clear sex differences. Sex-associated biomarkers in the brain may help to reveal the mechanisms involved in biology and etiology of psychiatric disorders. DNA methylation is sexually dimorphic and thus is a candidate for such biomarkers. We investigated sex-associated differential methylation at individual CpG loci (differential methylation positions, DMPs) and genomic regions (differentially methylated regions, DMRs), their corresponding genetic regulators (methylation quantitative trait loci, meQTLs), and regulatory target genes. We also tested co-methylated CpG sites for association with sex. Lastly, we investigated whether SNPs and genes involved in sex-dimorphic methylation were implicated in psychiatric disorders. Methods We systematically compared methylation in males and females in 697 human postmortem prefrontal cortex (PFC) samples, and another 210 samples to replicate the findings. Through DNA methylation profiling of 251 males and 446 females using Illumina 450K Methylation BeadChips, we applied an empirical Bayes method and DMRcate to investigate sexually DMPs and DMRs, respectively. We used weighted gene co-expression network analysis (WGCNA) to examine co-methylation sites related to sex. Combining the data of meQTLs and genome-wide expression methylation correlation pairs, we explored the genetic regulators of DMPs and DMRs and the target genes regulated by DMPs and DMRs. By examining the significant overlap between DMP/DMR target genes and genes associated with psychiatric disorders, we investigated the potential roles of sexually dimorphic DNA methylation on psychiatric disorders. Results We identified 13,352 DMPs and 4,490 DMRs, 5148/5344 (96%) of which are located on the X chromosome. Those DMRs spanned genes enriched for calcium signaling pathway (adjusted p = 2.3e-10) and neuroactive ligand-receptor interaction (adjusted p = 1.5e-9), and enriched for ASDs (adjusted p = 2.4e-18) and depression (adjusted p value=4.9e-10). There were 99,848 meQTLs and 1,066 DMP-expression pairs related to sexually dimorphic methylation. Co-methylation analysis identified a sex-associated module containing 4,825 DMPs. From 764 candidate genes with de novo mutations which have been reported in schizophrenia (SCZ), ASDs, epilepsy and ID, we found 112 DMR target genes, and 11 of them were reported in at least two disorders above. Among the previously reported 108 genome-wide significant SCZ-associated loci, we also found seven loci which could regulate the DMPs by meQTL. One SNP, rs7085104, could regulate the DMP and then affect the expression of C10orf32. Discussion To the best of our knowledge, this is the largest dataset to comprehensive analyze sexually dimorphic methylation in human brain. We identified 13,352 DMPs within 4,490 DMRs to be sexually dimorphic, and found one sex associated co-methylation module among 4,825 DMPs. Compared with previous studies, our results were more systematically investigated the DMPs which contained its upstream genetic regulators and downstream target genes’ expression. Furthermore, our findings of the association between the sexually dimorphic methylation and psychiatric disorders moved forward the understanding of the different prevalence of psychiatric disorders between males and females, and also provided a window to explain the GWAS signals.