Longitudinal epigenome-wide association studies of three male military cohorts reveal multiple CpG sites associated with post-traumatic stress disorder

Abstract

Background: Epigenetic mechanisms have been suggested to play a role in the development of post-traumatic stress disorder (PTSD). Here, blood-derived DNA methylation data (HumanMethylation450 BeadChip) collected prior to and following combat exposure in three cohorts of male military members were analyzed to assess whether DNA methylation profiles are associated with the development of PTSD. A total of 123 PTSD cases and 143 traumaexposed controls were included in the analyses. The Psychiatric Genomics Consortium (PGC) PTSD EWAS QC pipeline was used on all cohorts, and results were combined using a sample size weighted meta-analysis in a twostage design. In stage one, we jointly analyzed data of two new cohorts (N = 126 and 78) for gene discovery, and sought to replicate significant findings in a third, previously published cohort (N = 62) to assess the robustness of our results. In stage 2, we aimed at maximizing power for gene discovery by combining all three cohorts in a metaanalysis. Results: Stage 1 analyses identified four CpG sites in which, conditional on pre-deployment DNA methylation, postdeployment DNA methylation was significantly associated with PTSD status after epigenome-wide adjustment for multiple comparisons. The most significant (intergenic) CpG cg05656210 (p = 1.0 × 10 −08) was located on 5q31 and significantly replicated in the third cohort. In addition, 19 differentially methylated regions (DMRs) were identified, but failed replication. Stage 2 analyses identified three epigenome-wide significant CpGs, the intergenic CpG cg05656210 and two additional CpGs located in MAD1L1 (cg12169700) and HEXDC (cg20756026). Interestingly, cg12169700 had an underlying single nucleotide polymorphism (SNP) which was located within the same LD block as a recently identified PTSD-associated SNP in MAD1L1. Stage 2 analyses further identified 12 significant differential methylated regions (DMRs), 1 of which was located in MAD1L1 and 4 were situated in the human leukocyte antigen (HLA) region.

Molecular linkage between post-traumatic stress disorder and cognitive impairment: a targeted proteomics study of World Trade Center responders

“…Implicated in AD 83 Down 0.3241 0.5385 Up 0.0410 0.5904 Up 0.4513 0.5519 V-type proton ATPase subunit F (ATP6V1F) Involved in regulation of luminal or extracellular acidification, a crucial process for the normal physiological function of several organs, implicated in PTSD 42 , 43 Down 0.0613 0.6245 Down 0.0433 0.6486 Down 0.0405 0.6795 Brorin (VWC2) Involves in neural development, implicated in AD 39 Up 0.3971 0.5654 Up 0.0444 0.6572 Up 0.2008 0.6187 Desmoglein-3 (DSG3) Implicated in autoimmune disease 84 Up 0.2187 0.6137 Up 0.0452 0.6081 Up 0.2013 0.5853 DRAXIN Plays an important role in neural development Up 0.3633 0.5632 Up 0.0465 0.5996 Up 0.4593 0.5222 Cadherin-15 (CDH15) May contribute to the sorting of heterogeneous cell types. Implicated in PTSD 85 , cognitive impairment 86 Down 0.9755 0.5105 Down 0.3462 0.5609 Down 0.0024 0.7165 NEDD8-conjugating enzyme UBE2F (UBE2F) Implicated in stress response Up 0.1836 0.5203 Down 0.2715 0.6208 Down 0.0029 0.7572 ...…”

From genetics to systems biology of stress-related mental disorders

“…A longitudinal EWAS for PTSD which meta-analyzed 3 male military cohorts (123 cases and 143 controls) found 3 epigenome-wide significant CpGs-one of which was intergenic while the other 2 were located in genes MAD1L1 and HEXDC . In addition, 12 significant differential methylated regions (DMRs) were found; 4 of these regions were located in the human leukocyte antigen (HLA) and 1 was situated in MAD1L1 ( Snijders et al, 2020 ). Interestingly, as mentioned above in the “common variation” section, a SNP in MAD1LI was associated with PTSD in the largest PTSD GWAS ( Stein et al, 2021 ).…”

Immune system regulation and role of the human leukocyte antigen in posttraumatic stress disorder

“…Individuals with PTSD have increased methylation at a CpG site located in Toll-like receptor 8 ( TLR8 ) ( Smith et al, 2011 ), and decreased methylation at CpG sites located in dedicator of cytokinesis 2 ( DOCK2 ) ( Mehta et al, 2017 ), nuclear factor of activated T-cells ( NFATC4 ) ( Hammamieh et al, 2017 ), IL12B ( Bam et al, 2016b ) and aryl hydrocarbon receptor repressor ( AHRR ) ( Logue et al, 2020 ; Smith et al, 2020 ). Prospective studies investigating longitudinal methylation changes associated with PTSD implicated methylation changes in HEXDC and HLA-DPB1 ( Snijders et al, 2020 ), as well as enrichment in IL17 signaling pathway ( Rutten et al, 2018 ).…”

“…The PTSD-associated expression differences in HLA genes are consistent with reports from DNA methylation studies. A longitudinal meta-analysis of three male military cohorts reported that methylation levels across HLA-DPB1 and HLA-DRB1 regions are lower after deployment in individuals with PTSD ( Snijders et al, 2020 ). However, a recent study reported that PTSD was associated with increased methylation across HLA-DPB1 in a civilian cohort of predominantly African American women, whilst the association between PTSD and HLA-DPB1 methylation was in opposite direction in a military cohort of predominantly Caucasian males ( Katrinli et al, 2021 ).…”