Detection of early Parkinson’s disease using 5-hydroxymethylcytosine episignatures in blood DNA

Background Parkinson’s disease (PD) is a common neurodegenerative disorder. However, alterations in the blood hydroxymethylome and the potential of 5-hydroxymethylcytosine episignatures as diagnostic biomarkers for PD remain unclear. Methods We employed APOBEC-coupled epigenetic sequencing (ACE-seq) in a two-phase study design. In the first step, we performed single-base resolution profiling of the hydroxymethylome in a small cohort of drug-naïve PD patients and matched controls. Differentially hydroxymethylated regions (DhmRs) were identified and selected for validation. In the second step, these regions were re-sequenced in a larger cohort to develop and evaluate a diagnostic model. Results Initial genome-wide screening identified 16 candidate DhmRs. Although models based solely on these regions yielded modest diagnostic performance, an alternative analysis focusing on differentially hydroxymethylated cytosines within the 16 regions led to a diagnostic panel with robust performance, particularly for early PD detection. Retrospective analyses further confirmed the panel’s ability to distinguish early PD patients from controls. Conclusions Our study provides the first evidence that blood-based hydroxymethylome profiles are promising biomarkers for the early diagnosis of PD.