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The Mitochondrial Epigenome : An Unexplored Avenue to Explain Unexplained Myopathies?

Mposhi, Archibold ; Liang, Lin ; Mennega, Kevin P. ; Yildiz, Dilemin ; Kampert, Crista ; Hof, Ingrid H. ; Jellema, Pytrick G. ; de Koning, Tom J. LU ; Faber, Klaas Nico and Ruiters, Marcel H.J. , et al. (2022) In International Journal of Molecular Sciences 23(4).
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... (More)

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.

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organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Cytochrome B, Mitochondrial DNA methylation, Mitochondrial epigenome, Myopathies
in
International Journal of Molecular Sciences
volume
23
issue
4
article number
2197
publisher
MDPI AG
external identifiers
  • pmid:35216315
  • scopus:85124594868
ISSN
1661-6596
DOI
10.3390/ijms23042197
language
English
LU publication?
yes
additional info
Funding Information: This work was supported by the University Medical Center Groningen (a Talent grant to Archibold Mposhi) and funding to the Laboratory of Metabolic Diseases (Laboratory Medicine) UMCG. Lin Liang was supported by the China Scholarship Council (CSC). The authors also wish to acknowledge EU H2020 CM1406 (www.EpiChemBio.eu (accessed on 30 December 2021)) supported by COST (European Cooperation in Science and Technology). Publisher Copyright: © 2022 by the authors. Licensee MDPI, Basel, Switzerland.
id
8f584615-3d43-4507-b0a4-e5764172bd81
date added to LUP
2022-02-28 09:03:29
date last changed
2024-07-06 16:17:03
@article{8f584615-3d43-4507-b0a4-e5764172bd81,
  abstract     = {{<p>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.</p>}},
  author       = {{Mposhi, Archibold and Liang, Lin and Mennega, Kevin P. and Yildiz, Dilemin and Kampert, Crista and Hof, Ingrid H. and Jellema, Pytrick G. and de Koning, Tom J. and Faber, Klaas Nico and Ruiters, Marcel H.J. and Niezen-Koning, Klary E. and Rots, Marianne G.}},
  issn         = {{1661-6596}},
  keywords     = {{Cytochrome B; Mitochondrial DNA methylation; Mitochondrial epigenome; Myopathies}},
  language     = {{eng}},
  month        = {{02}},
  number       = {{4}},
  publisher    = {{MDPI AG}},
  series       = {{International Journal of Molecular Sciences}},
  title        = {{The Mitochondrial Epigenome : An Unexplored Avenue to Explain Unexplained Myopathies?}},
  url          = {{http://dx.doi.org/10.3390/ijms23042197}},
  doi          = {{10.3390/ijms23042197}},
  volume       = {{23}},
  year         = {{2022}},
}