{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:35:08Z","timestamp":1790728508123,"version":"4.1.0"},"reference-count":53,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2025,9,3]],"date-time":"2025-09-03T00:00:00Z","timestamp":1756857600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"ANZMES"},{"name":"the NZ ME\/CFS national advisory society and donations from ME\/CFS families"},{"name":"Massey University Research Fund"},{"name":"University of Otago (\u014ct\u0101kou Whakaihu Waka)"},{"name":"Sir Charles Hercus Fellowship (from the Health Research Council of New Zealand)"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["IJMS"],"abstract":"<jats:p>Post-exertional malaise (PEM) is a defining symptom of Myalgic Encephalomyelitis\/Chronic Fatigue Syndrome (ME\/CFS), yet its molecular underpinnings remain elusive. This study investigated the temporal\u2013longitudinal DNA methylation changes associated with PEM using a structured two-day maximum repeated effort cardiopulmonary exercise testing (CPET) protocol involving pre- and two post-exercise blood samplings from five ME\/CFS patients. Cardiopulmonary measurements revealed complex heterogeneous profiles among the patients compared to typical healthy controls, and VO2 peak indicated all patients had poor normative fitness. The switch to anaerobic metabolism occurred at a lower workload in some patients on Day Two of the test. Reduced Representation Bisulphite Sequencing followed by analysis with Differential Methylation Analysis Package-version 2 (DMAP2) identified differentially methylated fragments (DMFs) present in the DNA genomes of all five ME\/CFS patients through the exercise test compared with \u2018before exercise\u2019. With further filtering for &gt;10% methylation differences, there were early DMFs (0\u201324 h after first exercise test) and late DMFs between (24\u201348 h after the second exercise test), as well as DMFs that changed gradually (between 0 and 48 h). Of these, 98% were ME\/CFS-specific, compared with the two healthy controls accompanying the longitudinal study. Principal component analysis illustrated the three distinct clusters at the 0 h, 24 h, and 48 h timepoints, but with heterogeneity among the patients within the clusters, highlighting dynamic methylation responses to exertion in individual patients. There were 24 ME\/CFS-specific DMFs at gene promoter fragments that revealed distinct patterns of temporal methylation across the timepoints. Functional enrichment of ME-specific DMFs revealed pathways involved in endothelial function, morphogenesis, inflammation, and immune regulation. These findings uncovered temporally dynamic epigenetic changes in stress\/immune functions in ME\/CFS during PEM and suggest molecular signatures with potential for diagnosis and of mechanistic significance.<\/jats:p>","DOI":"10.3390\/ijms26178563","type":"journal-article","created":{"date-parts":[[2025,9,4]],"date-time":"2025-09-04T09:18:57Z","timestamp":1756977537000},"page":"8563","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["Precision Medicine Study of Post-Exertional Malaise Epigenetic Changes in Myalgic Encephalomyelitis\/Chronic Fatigue Patients During Exercise"],"prefix":"10.3390","volume":"26","author":[{"ORCID":"https:\/\/orcid.org\/0009-0005-9538-3415","authenticated-orcid":false,"given":"Sayan","family":"Sharma","sequence":"first","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7482-0499","authenticated-orcid":false,"given":"Lynette D.","family":"Hodges","sequence":"additional","affiliation":[{"name":"School of Sport, Exercise and Nutrition, College of Health, Massey University, Palmerston North 4410, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-6072-5926","authenticated-orcid":false,"given":"Katie","family":"Peppercorn","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jemma","family":"Davis","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christina D.","family":"Edgar","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9016, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9615-5896","authenticated-orcid":false,"given":"Euan J.","family":"Rodger","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7276-2248","authenticated-orcid":false,"given":"Aniruddha","family":"Chatterjee","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6971-7734","authenticated-orcid":false,"given":"Warren P.","family":"Tate","sequence":"additional","affiliation":[{"name":"Department of Pathology and Molecular Medicine, Dunedin School of Medicine, University of Otago, Dunedin 9016, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2025,9,3]]},"reference":[{"key":"ref_1","unstructured":"Shepherd, C. 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