Parkinson's disease is associated with DNA methylation levels in human blood and saliva

Abstract

Background: Several articles suggest that DNA methylation levels in blood relate to Parkinson's disease (PD) but there is a need for a large-scale study that involves suitable population based controls. The purposes of the study were: (1) to study whether PD status is associated with DNA methylation levels in blood/saliva; (2) to study whether observed associations relate to blood cell types; and (3) to characterize genome-wide significant markers ("CpGs") and clusters of CpGs (co-methylation modules) in terms of biological pathways.

Methods: In a population-based case control study of PD, we studied blood samples from 335 PD cases and 237 controls and saliva samples from another 128 cases and 131 controls. DNA methylation data were generated from over 486,000 CpGs using the Illumina Infinium array. We identified modules of CpGs (clusters) using weighted correlation network analysis (WGCNA).

Results: Our cross-sectional analysis of blood identified 82 genome-wide significant CpGs (including cg02489202 in LARS2 p = 8.3 × 10^-11 and cg04772575 in ABCB9 p = 4.3 × 10^-10). Three out of six PD related co-methylation modules in blood were significantly enriched with immune system related genes. Our analysis of saliva identified five significant CpGs. PD-related CpGs are located near genes that relate to mitochondrial function, neuronal projection, cytoskeleton organization, systemic immune response, and iron handling.

Conclusions: This study demonstrates that: (1) PD status has a profound association with DNA methylation levels in blood and saliva; and (2) the most significant PD-related changes reflect changes in blood cell composition. Overall, this study highlights the role of the immune system in PD etiology but future research will need to address the causal structure of these relationships.

Keywords: Bioinformatics; Blood cell counts; Cytoskeleton; DNA methylation; Epigenomics; Immune system; Mitochondrial dysfunction; Parkinson’s disease; Saliva; WGCNA.

Fig. 1

Flowchart of analysis process. EWAS and WGCNA analyses in blood and saliva separately. ^aBonferroni, Benjamini corrected pvalues, and FDR were also provided. ^bNo CpG with EWAS pvalues <10^-7 was found; therefore, we relaxed the significance criteria

Fig. 2

EWAS results for PD and blood-based DNA methylation analyses without cell composition adjustment. Differential methylation associated with PD status in 508 PEG1 subjects of European ancestry adjusting for age and gender. a Manhattan plot of p values adjusted for age and gender (red line: p value threshold of 10^–7). b Distributions of CpGs relative to CpG island and gene regions for all 450,000 CpGs on the microarray and the 82 most significant coffee-associated CpGs listed in Table 1. c Distribution of DNA methylation levels for the top three most significant PD-associated CpGs by PD status (1 = PD)

Fig. 3

WGCNA results for PD and blood-based DNA methylation analyses without cell composition adjustment. Correlations of module eigengenes (ME) with PD status and other traits in 508 PEG1 individuals of European ancestry adjusting for age and gender. The rows represent ME and its color. The columns represent clinical traits. The Pearson’s correlation coefficients and the corresponding p values are shown for each cell. Red indicates positive correlations while color indicates negative correlations. a ME 1-27. b ME 28-54. c ME 55-80