# Mitoepigenetic Alterations in Early-Onset Parkinson’s Disease

## TL;DR

This study identifies unique mitochondrial DNA methylation patterns in early-onset Parkinson’s disease, which could serve as potential blood-based biomarkers.

## Contribution

The study provides the first comprehensive, single-base resolution analysis of mtDNA methylation and hydroxymethylation in early-onset Parkinson’s disease.

## Key findings

- Global mtDNA methylation was significantly higher in EOPD patients compared to controls in both CpG and non-CpG contexts.
- Hypomethylation at specific sites in the D-loop region of mtDNA was observed in EOPD patients.
- Results suggest that mtDNA (hydroxy)methylation could act as a blood-based biomarker for EOPD.

## Abstract

There is accumulating evidence that distinct mitochondrial DNA (mtDNA) methylation and hydroxymethylation patterns exist in Parkinson’s disease (PD). However, most studies have been limited to the investigation of specific target regions, rather than the entire mtDNA, and have been further hindered by other methodological discrepancies and the lack of non-CpG context investigation. Here, we provide a comprehensive profile of methylation and hydroxymethylation levels across the mitochondrial genome, at global and single-base resolution, in CpG and non-CpG (CHG, CHH) contexts in blood samples from early-onset PD (EOPD) patients (n = 39) and age- and sex-matched controls (n = 63). Bisulfite (BS) and oxidative-bisulfite (oxBS) conversions in parallel workflows followed by next-generation sequencing (NGS) using Illumina’s Novaseq 6000 sequencing system identified mitochondrial 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) in all contexts. Global mtDNA methylation was significantly higher in EOPD patients vs. matched controls in the CpG context (p = 5.63 × 10−3) in the BS status, and in all contexts [CpG (p = 2.67 × 10−4), CHG (p = 0.015), CHH (p = 0.012)] in the oxBS status, i.e., “true methylation”. At single-base resolution, the most statistically significant sites across the mitogenome, in the D-loop region, and CpG context, were primarily hypomethylated in EOPD patients compared to matched controls. Upon further validation, both global and base resolution mtDNA (hydroxy)methylation results could act as blood-based biomarkers for EOPD.