bioRxiv Science⌕ Search

bioRxiv · 10.1101/594127

Methylomic profiles reveal sex-specific shifts in leukocyte composition associated with post-traumatic stress disorder

Abstract

Post-traumatic stress disorder (PTSD) is a debilitating mental disorder precipitated by trauma exposure. However, only some persons exposed to trauma develop PTSD. There are sex differences in risk; twice as many women as men, develop a lifetime diagnosis of PTSD. Methylomic profiles derived from peripheral blood are well-suited for investigating PTSD because DNA methylation (DNAm) encodes individual response to trauma and may play a key role in the immune dysregulation characteristic of PTSD pathophysiology. In the current study, we leveraged recent methodological advances to investigate sex-specific shifts in DNAm-based leukocyte composition that are associated with lifetime PTSD. We estimated leukocyte composition on a combined methylation array dataset (483 participants, [~]450k CpG sites) consisting of two civilian cohorts, the Detroit Neighborhood Health Study and Grady Trauma Project. Sex-stratified Mann-Whitney U test and two-way ANCOVA revealed that lifetime PTSD was associated with a small but significant elevation in monocyte proportions in males, but not in females (Holm-adjusted p-val < 0.05). No difference in monocyte proportions was observed between current and remitted PTSD cases in males, suggesting that this sex-specific peak shift reflects a long-standing trait of lifetime history of PTSD, rather than current state of PTSD. Associations with lifetime PTSD or PTSD status were not observed in any other leukocyte subtype and our finding in monocytes was confirmed using cell estimates based on a different deconvolution algorithm, suggesting that our sex-specific findings are robust across cell estimation approaches. Overall, our main finding of elevated monocyte proportions in males, but not in females with lifetime history of PTSD provides evidence for a sex-specific shift in peripheral blood leukocyte composition that is detectable in methylomic profiles and that reflects long-standing changes associated with PTSD diagnosis.

Source connections

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Kim, G. S., Smith, A., Xu, F., Michopoulos, V., Lori, A., Armstrong, D. L., Aiello, A. E., Koenen, K. C., Galea, S., Wildman, D. E., Uddin, M.. 2019-04-01. Methylomic profiles reveal sex-specific shifts in leukocyte composition associated with post-traumatic stress disorder. https://doi.org/10.1101/594127

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Genome-wide chromatin accessibility during early embryogenesis in a generalist cichlid fish

Background Lake Malawi's haplochromine cichlids are one of the most rapid and species-rich vertebrate adaptive radiations known, generating hundreds of species within < 1 million years, yet how regulatory regions shape their embryonic development remains poorly understood. Astatotilapia calliptera, a generalist riverine lineage and proxy for the ancestral stock that seeded this radiation, offers a developmental chromatin baseline against which regulatory divergence in specialised lineages can be compared. Results We generated genome-wide ATAC-seq profiles of A. calliptera embryos across three developmental stages (3, 7 and 12 days post-fertilisation, dpf), identifying 550,876-701,889 accessible chromatin peaks per stage. Accessible chromatin was enriched at gene promoters and at both highly conserved and accelerated conserved noncoding elements at every stage. The functional repertoire of accessible-promoter genes shifted across development, from early patterning at 3 dpf to the broadest regulatory repertoire at 7 dpf, and an increasingly neural- and locomotory-behaviour-enriched repertoire by 12 dpf, coinciding with post-hatching motor maturation. Differential accessibility showed that chromatin opening, rather than closing, dominates the earliest transitions (3 vs 7 and 3 vs 12 dpf), driven mostly by general metabolic genes, whereas the smaller, later 7 vs 12 dpf transition combined targeted gains at tissue-remodelling and apoptosis genes with losses at genes governing early neural and retinal patterning; almost all of these losses (96%) were at promoters that had opened between 3 and 7 dpf, indicating transient rather than sustained opening. Transcription factor (TF) footprinting identified stage-specific regulatory activity among developmentally important TFs, while the broader TF-promoter network remained topologically stable across all three stages, built around conserved hub regulators of core neural and sensory patterning genes e.g., SOX2, FOXG1, PTF1A, SOX10. This suggests that wiring is established early and largely maintained, following the hourglass model, with developmental progression driven by changes in activity of this conserved programme. Conclusions Together, these findings establish the first embryonic epigenomic resource for A. calliptera, revealing a developmental chromatin landscape of broad early opening and progressive functional specialisation, and providing a comparative framework for understanding how regulatory evolution has shaped Lake Malawi cichlid diversification.

genomics↗

Salinity adaptation in date palm (Phoenix dactylifera): evidence for selective sweeps at Salt Overly Sensitive (SOS) genes

The date palm is a high salinity tolerant fruit tree grown mainly in the region spanning from North Africa to parts of South Asia. Climate change models of this region indicate the possibility of increasing salinity in the future. The Salt Overly Sensitive (SOS) pathway is crucial for salinity tolerance in plants, serving as a primary defense mechanism by facilitating sodium exclusion. To better understand date palms' salt tolerance, we analyzed variation in SOS pathway genes in a set of 197 date palm genomes collected from across the range of cultivation. Here, we show evidence for selective sweeps in multiple SOS pathway genes. A single major pdSOS1 haplotype is at very high frequency in Eastern and Western subpopulations, with a minor, likely ancestral haplotype still present in both geographical locations. Allele-specific gene expression analysis showed differences in salt-treated roots between swept and ancestral haplotypes. Interestingly, sequence-based analysis of the pdSOS1 haplotype suggested a second, much earlier introgression event between P. theophrasti and date palm, though direction is unclear. This event happened before both the selective sweep and the previously reported recent introgression to date palm. We identified a MITE transposable element inserted into a pdSOS1 intron on the swept haplotype, and a similar insertion was found in an intron of the SOS2 paralog pdCIPK8. Both insertions are unique to date palm among Phoenix species. The pdCIPK8 haplotype containing the MITE is also at high frequency in both populations. Further analysis showed evidence for a selective sweep spanning the pdSOS3 region in the western population that shares similarity to an Eastern haplotype spanning the promoter region only. Slower extended haplotype homozygosity decay surrounding the genes in the western population suggests that the swept haplotype originated in the East and spread to the West in all cases. Altogether, our data provide evidence of selective sweeps in the date palm SOS pathway and may go to explaining how this species has developed such high salinity tolerance.

genomics↗

Genome evolution and glycosyltransferase diversification shape asperosaponin biosynthesis in Dipsacus asperoides

Deciphering the genomic and enzymatic features associated with high-abundance specialized metabolism is important for understanding and engineering bioactive natural product biosynthesis. Asperosaponin , a hederagenin-based saponin, accumulates at exceptionally high levels in Dipsacus asperoides roots and is by far the predominant triterpenoid saponin. Here, by integrating a chromosome-level genome assembly with comparative genomics, transcriptomics, metabolite profiling, and biochemical characterization, we reconstructed a major biosynthetic route to asperosaponin and identified diversification of triterpenoid-associated gene families. Functional analyses revealed an ordered glycosylation sequence in which DaUGT73GZ2 preferentially accepts C-3-glycosylated substrates retaining a free C-28 carboxyl group, thereby establishing a C-3-before-C-28 glycosylation order during asperosaponin biosynthesis. Phylogenetic and biochemical analyses further uncovered functional differentiation among UGT85CA enzymes involved in C-3 arabinosylation, while genomic and expression analyses revealed lineage-specific patterns of pathway gene duplication and transcriptional regulation. Together, these findings identify genomic, enzymatic, and transcriptional features associated with the distinctive, high-abundance triterpenoid saponin profile of D. asperoides roots and provide a framework for understanding and engineering triterpenoid saponin biosynthesis.

genomics↗