Differential DNA methylation in recovery from shift work disorder

Abstract

The human DNA methylome is responsive to our environment, but its dynamics remain underexplored. We investigated the temporal changes to DNA methylation (DNAme) in relation to recovery from a shift work disorder (SWD) by performing a paired epigenome-wide analysis in an occupational cohort of 32 shift workers (25 men, age = 43.8 ± 8.8 years, 21 SWD cases). We found that the effect of vacation on DNAme was more prominent in the SWD-group as compared to controls, with respect to the amount of significantly differentially methylated positions (DMPs; P_unadj < 0.05) 6.5 vs 3.7%, respectively. The vast majority (78%) of these DMPs were hypomethylated in SWD but not in controls (27%) during the work period. The Gene Ontology Cellular component "NMDA glutamate receptor" (P_FDR < 0.05) was identified in a pathway analysis of the top 30 genes in SWD. In-depth pathway analyses revealed that the Reactome pathway "CREB phosphorylation through the activation of CaMKII" might underlie the recovery. Furthermore, three DMPs from this pathway, corresponding to GRIN2C, CREB1, and CAMK2B, correlated with the degree of recovery (P_unadj < 0.05). Our findings provide evidence for the dynamic nature of DNAme in relation to the recovery process from a circadian disorder, with biological relevance of the emerging pathways.

Figure 1

Quantile–quantile plots for (a) SWD group, (b) control group, (c) either group, and (d) both groups. Dots represents individual CpG sites and the line identity.

Figure 2

Quantile–quantile plots for the epigenome-wide association in the 458 CpGs corresponding to 15 genes from the pathway “CREB phosphorylation through the activation of CaMKII”: (a) SWD group, (b) controls. Dots represent individual CpG sites and the lines identity. (c) Volcano plot for the Reactome 2016 pathway “CREB phosphorylation through the activation of CaMKII”. Colors of points correspond to: grey, CpGs with unadjusted P values > 0.05; green, DMPs for SWD group; black, DMPs for the controls.

Figure 3

Boxplots of the three discovered differentially methylated CpG in the Reactome 2016 pathway “CREB phosphorylation through the activation of CaMKII” for the groups with different degree of recovery. Y-axis represents the absolute change in the M-values from work to vacation. Colors of the dots correspond to the different groups: red, poorly recovered; blue, recovered; green, well-recovered. The horizontal line is median, box is 25 to 75%, the whiskers denote data, and the dots represent individual samples.

Figure 4

T-SNE mapping of the global DNA methylome profiles across the recovery groups of SWD group. Colors of the dots correspond to the different groups: red, poorly recovered; blue, recovered; green, well-recovered; grey, controls. Hollow markers represent samples collected during work and filled ones during vacation, dashed lines connecting the samples of each patient.