Abstract
Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS) and Long COVID (LC) are chronic conditions with complex pathophysiology, affecting millions globally and thousands in New Zealand. Diagnosis is time consuming to exclude other conditions resulting in a lack of clinical management at a critical time of the disease. Development of a diagnostic test allowing early diagnosis would be a major step in enhancing the quality of life for those affected.
Epigenetic DNA methylation modifications play a critical role in the pathogenesis and progression of human diseases, and methylation changes have shown potential for diagnosis in the clinic. Our current study used reduced representation bisulphite sequencing (RRBS) on DNA from Peripheral Blood Mononuclear Cells (PBMCs) to analyse DNA methylomes from each of 5 ME/CFS and 5 LC age-sex matched patients and 5 healthy controls (HC). Results showed 73,239 methylated fragments were present in every participant, of which 3,363 were differentially methylated (p<0.05) between ME/CFS, LC and HC. A principal component analysis (PCA) separated the disease cohorts from the controls, with tight clustering within each cohort. In both ME/CFS and LC cohorts, 118 Differentially Methylated Fragments (DMFs) were identified compared with healthy controls (>10% methylation difference). Eighteen of these DMFs were associated with gene promoters and exons where ME/CFS and LC patients had similar changes in methylation compared to HC, however in certain cases ME/CFS and LC displayed opposite methylation changes as well. Functional Categories of the genes illustrated the physiological consequences of the differential methylation, identifying immune function, transcription, signal transduction and cytoskeleton as four categories common in both ME and LC cohorts, suggesting shared molecular mechanisms that may contribute to similar clinical features.
Encouraging for the development of an early diagnostic test is the identification of specific changes at important genomic sites in all patients. This suggests the technology can provide molecular signatures with high specificity and selectivity for a molecular diagnostic test.