{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T09:58:00Z","timestamp":1771840680482,"version":"3.50.1"},"reference-count":49,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2026,2,21]],"date-time":"2026-02-21T00:00:00Z","timestamp":1771632000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000864","name":"Michael J. Fox Foundation","doi-asserted-by":"publisher","award":["15676"],"award-info":[{"award-number":["15676"]}],"id":[{"id":"10.13039\/100000864","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Telethon Cyprus","award":["33173178"],"award-info":[{"award-number":["33173178"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>There is accumulating evidence that distinct mitochondrial DNA (mtDNA) methylation and hydroxymethylation patterns exist in Parkinson\u2019s 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\u2019s 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 \u00d7 10\u22123) in the BS status, and in all contexts [CpG (p = 2.67 \u00d7 10\u22124), CHG (p = 0.015), CHH (p = 0.012)] in the oxBS status, i.e., \u201ctrue methylation\u201d. 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.<\/jats:p>","DOI":"10.3390\/ijms27042033","type":"journal-article","created":{"date-parts":[[2026,2,23]],"date-time":"2026-02-23T08:58:21Z","timestamp":1771837101000},"page":"2033","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Mitoepigenetic Alterations in Early-Onset Parkinson\u2019s Disease"],"prefix":"10.3390","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2501-1561","authenticated-orcid":false,"given":"Rana","family":"Abu Manneh","sequence":"first","affiliation":[{"name":"Neuroepidemiology Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"},{"name":"Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2660-0840","authenticated-orcid":false,"given":"Paraskevi P.","family":"Chairta","sequence":"additional","affiliation":[{"name":"Neuroepidemiology Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4503-7758","authenticated-orcid":false,"given":"Maria A.","family":"Loizidou","sequence":"additional","affiliation":[{"name":"Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0136-9921","authenticated-orcid":false,"given":"Maria","family":"Zanti","sequence":"additional","affiliation":[{"name":"Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4214-3678","authenticated-orcid":false,"given":"Andrea N.","family":"Georgiou","sequence":"additional","affiliation":[{"name":"Neuroepidemiology Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"},{"name":"Department of Psychology, University of Cyprus, Nicosia 1678, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7065-1237","authenticated-orcid":false,"given":"Kyriaki","family":"Michailidou","sequence":"additional","affiliation":[{"name":"Biostatistics Unit, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4002-2880","authenticated-orcid":false,"given":"Christiana","family":"Demetriou","sequence":"additional","affiliation":[{"name":"Neuroepidemiology Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2937-384X","authenticated-orcid":false,"given":"Marios","family":"Pantzaris","sequence":"additional","affiliation":[{"name":"Neuroimmunology Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eleni","family":"Zamba-Papanicolaou","sequence":"additional","affiliation":[{"name":"Neuroepidemiology Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5636-0799","authenticated-orcid":false,"given":"Andreas","family":"Hadjisavvas","sequence":"additional","affiliation":[{"name":"Cancer Genetics, Therapeutics & Ultrastructural Pathology Department, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1968","published-online":{"date-parts":[[2026,2,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e464","DOI":"10.1016\/S2666-7568(24)00094-1","article-title":"Temporal trends in the prevalence of Parkinson\u2019s disease from 1980 to 2023: A systematic review and meta-analysis","volume":"5","author":"Zhu","year":"2024","journal-title":"Lancet Healthy Longev."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1055\/s-0037-1601888","article-title":"Diagnosis and Management of Parkinson\u2019s Disease","volume":"37","author":"Tarakad","year":"2017","journal-title":"Semin. 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