Abstract
Mutations in either mitochondrial DNA (mtDNA) or nuclear genes that encode mitochondrial proteins may lead to dysfunctional mitochondria, giving rise to mitochondrial diseases. Some mitochondrial myopathies, however, present without a known underlying cause. Interestingly, methylation of mtDNA has been associated with various clinical pathologies. The present study set out to assess whether mtDNA methylation could explain impaired mitochondrial function in patients diagnosed with myopathy without known underlying genetic mutations. Enhanced mtDNA methylation was indicated by pyrosequencing for muscle biopsies of 14 myopathy patients compared to four healthy controls, at selected cytosines in the Cytochrome B (CYTB) gene, but not within the displacement loop (D-loop) region. The mtDNA methylation patterns of the four healthy muscle biopsies were highly consistent and showed intriguing tissue-specific differences at particular cytosines with control skin fibroblasts cultured in vitro. Within individual myopathy patients, the overall mtDNA methylation pattern correlated well between muscle and skin fibroblasts. Despite this correlation, a pilot analysis of four myopathy and five healthy fibroblast samples did not reveal a disease-associated difference in mtDNA methylation. We did, however, detect increased expression of solute carrier family 25A26 (SLC25A26), encoding the importer of S-adenosylmethionine, together with enhanced mtDNA copy numbers in myopathy fibroblasts compared to healthy controls. To confirm that pyrosequencing indeed reflected DNA methylation and not bisulfite accessibility, mass spectrometry was employed. Although no myopathy-related differences in total amount of methylated cytosines were detected at this stage, a significant contribution of contaminating nuclear DNA (nDNA) was revealed, and steps to improve enrichment for mtDNA are reported. In conclusion, in this explorative study we show that analyzing the mitochondrial genome beyond its sequence opens novel avenues to identify potential molecular biomarkers assisting in the diagnosis of unexplained myopathies.
Highlights
Mitochondrial myopathies are a group of mitochondrial diseases that develop due to mitochondrial dysfunction in muscle tissue, which results in impaired muscle function and weakness [1]
Mitochondrial diseases can be categorized in two groups: primary mitochondrial diseases, which occur due to inherited mutations in either mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) in genes encoding electron transport chain (ETC) proteins; and secondary mitochondrial dysfunction, which describes diseases that can be acquired secondary to environmental effects [8]
To set up the pyrosequencing readout for mtDNA methylation, we first explored whether treatment with S-adenosylmethionine (SAM) induced mtDNA methylation by treating human skeletal muscle cell line cells (HSkMCs) with increasing concentrations of SAM
Summary
Mitochondrial myopathies are a group of mitochondrial diseases that develop due to mitochondrial dysfunction in muscle tissue, which results in impaired muscle function and weakness [1]. Mitochondrial diseases can be categorized in two groups: primary mitochondrial diseases, which occur due to inherited mutations in either mtDNA or nDNA in genes encoding ETC proteins; and secondary mitochondrial dysfunction, which describes diseases that can be acquired secondary to environmental effects [8]. In both subgroups, mutations in mtDNA or nDNA are associated with mitochondrial disease. In a study addressing skeletal muscle myopathy, mitochondrial dysfunction and nDNA hypermethylation were observed in mice with hyperhomocysteinemia [14]
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