Epigenome-wide association studies identify novel DNA methylation sites associated with PTSD: A meta-analysis of 23 military and civilian cohorts

Abstract

Background: The occurrence of post-traumatic stress disorder (PTSD) following a traumatic event is associated with biological differences that can represent the susceptibility to PTSD, the impact of trauma, or the sequelae of PTSD itself. These effects include differences in DNA methylation (DNAm), an important form of epigenetic gene regulation, at multiple CpG loci across the genome. Moreover, these effects can be shared or specific to both central and peripheral tissues. Here, we aim to identify blood DNAm differences associated with PTSD and characterize the underlying biological mechanisms by examining the extent to which they mirror associations across multiple brain regions.

Methods: As the Psychiatric Genomics Consortium (PGC) PTSD Epigenetics Workgroup, we conducted the largest cross-sectional meta-analysis of epigenome-wide association studies (EWASs) of PTSD to date, involving 5077 participants (2156 PTSD cases and 2921 trauma-exposed controls) from 23 civilian and military studies. PTSD diagnosis assessments were harmonized following the standardized guidelines established by the PGC-PTSD Workgroup. DNAm was assayed from blood using either Illumina HumanMethylation450 or MethylationEPIC (850K) BeadChips. A common QC pipeline was applied. Within each cohort, DNA methylation was regressed on PTSD, sex (if applicable), age, blood cell proportions, and ancestry. An inverse variance-weighted meta-analysis was performed. We conducted replication analyses in tissue from multiple brain regions, neuronal nuclei, and a cellular model of prolonged stress.

Results: We identified 11 CpG sites associated with PTSD in the overall meta-analysis (1.44e-09 < p < 5.30e-08), as well as 14 associated in analyses of specific strata (military vs civilian cohort, sex, and ancestry), including CpGs in AHRR and CDC42BPB. Many of these loci exhibit blood-brain correlation in methylation levels and cross-tissue associations with PTSD in multiple brain regions. Methylation at most CpGs correlated with their annotated gene expression levels.

Conclusions: This study identifies 11 PTSD-associated CpGs, also leverages data from postmortem brain samples, GWAS, and genome-wide expression data to interpret the biology underlying these associations and prioritize genes whose regulation differs in those with PTSD.

Keywords: DNA methylation; GWAS; PTSD; gene expression; postmortem brain; trauma.

Figure 1.. Manhattan Plot of the epigenome-wide association meta-analyses.

The x-axis depicts chromosomes and the location of each CpG site across the genome. The y-axis depicts the −log10 of the unadjusted p-value for the association with current PTSD. Each dot represents a CpG site. The solid blue line indicates the epigenome-wide statistical significance at p < 9.0e-8.

Fig 2.. Summary of all analyses and findings.

Figure combines CpGs from the main analysis (gold) and stratified analyses for sex, ancestry, and trauma type (light gold); and summarizes the results of blood and brain correlations (rose); cross-tissue associations for multiple brain regions (light blue), neuronal nuclei (blue), and a fibroblast model of prolonged stress (aqua), gene expression (purple); and genetic effects, including methylation quantitative trait loci (meQTL) analyses (light green) and genetic associations from the recent PGC-PTSD GWAS (dark green). Positive findings (p < 0.05) are indicated with the specific color of the respective category. Asterisk (*) indicates epigenome-wide significance (p < 9e-8). Gray represents the CpGs or genes were not present in the respective datasets. PFC: prefrontal cortex. EC: entorhinal cortex. STG: superior temporal gyrus. CER: cerebellum. dlPFC: dorsolateral prefrontal cortex. vmPFC: ventromedial prefrontal cortex. DG: dentate gyrus. 5mC: 5-Methylcytosine. 5hmC: 5-Hydroxymethylcytosine. GC: glucocorticoid.