Epigenome-wide association studies (EWAS) have identified distinctive patterns of DNA methylation levels associated with PD. However, none has utilized a prospective study design.

We included Nurses' Health Study participants who provided repeated blood samples collected up to a median of 19 years before PD onset. DNA methylation profiles (EPIC array) were obtained from 75 individuals who developed PD and 74 age-matched controls. We prospectively examined the association of epigenome-wide DNA methylation levels in blood with PD risk, age at PD onset, and time to PD onset. To further aid interpretation of results from differential methylation analysis, we conducted gene ontology and pathway enrichment analyses.

In probe-wise differential methylation analysis, at a significance threshold of nominal p-value< 5×10^-5, we identified 40 cytosine-phosphate-guanine sites (CpGs) in the first blood sample and 50 CpGs in the second blood sample that differed between PD cases and controls. In longitudinal analysis, we further observed significant changes in DNA methylation levels in 48 CpGs over 10 years (p-value < 5×10^-5). Differential methylation regions analysis revealed numerous novel genomic regions, with the five most statistically significant observed near genes ETV7, SCRIB, RUNX1, ANGPT2, and MCPH1. Gene ontology and KEGG pathway analyses highlighted nominally significant pathways related to dopaminergic synapses, cytochrome P450 metabolism, nicotine addiction, and gamma-aminobutyric acid transport.

Our study identified novel gene regions that might play a role in the prodromal phase of PD and provided insights into epigenetic pathways contributing to PD pathogenesis.