Abstract
The transport of mitochondrial proteins, which are encoded by gDNA and synthesized by free ribosomes in the cytosol, to the organelle must be error-free for the proper functioning of mitochondria. It has been shown that abnormal mitochondrial morphology, decreased membrane potential, ATP production, and increased ROS affect mitochondrial protein import. Also, possible target genes of common miRNAs, which are involved in the regulation of secondary mitochondrial damage observed in rare neuromuscular diseases, have been found to be associated with mitochondrial protein import. For this purpose, the relationship between mitochondrial protein import mechanism and mitochondrial damage observed as a common and secondary finding in the etiopathogenesis of DMD, Megaconial CMD, and Ullrich CMD was investigated. As the first step, the pcDNA3/Mito-GFP plasmid containing a mitochondrial targeting signal sequence was transfected into primary myoblasts of the control and patient groups, and a significant decrease in MitoGFP-TOM20 co-localization was observed in all patients. When miR-382-5p, which we directly associate with secondary mitochondrial damage, was co-transfected with pcDNA3/mito-GFP into C2C12 cells, a significant reduction in MitoGFP-TOM20 co-localization was detected compared to the control. As the second step, proteomic analyses were performed by LC-MS/MS after isolation of mitochondria from primary myoblasts. Although the amount of SLC25A4, which acts as an ATP/ADP transporter, decreased in the mitochondrial fraction, it was determined that its expression at the RNA and protein level was preserved in total cells by qRT-PCR and Western Blot. Decreased localization of SLC25A4 in mitochondria in primary myoblasts of patients was confirmed by SLC25A4-TOM20 co-immunofluorescence staining. With this thesis, the potential role of the mitochondrial import mechanism in rare neuromuscular diseases in which secondary mitochondrial damage is seen in the pathogenesis has been elucidated, allowing the identification of common therapeutic targets for new and different disease groups to prevent/reverse organelle damage.
xmlui.mirage2.itemSummaryView.Collections
xmlui.dri2xhtml.METS-1.0.item-citation
1. Wiedemann N, Pfanner N. Mitochondrial Machineries for Protein Import and Assembly. Annu Rev Biochem. 2017;86:685-714.
2. Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J, et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research. 2018;47(D1):D607-D13.
3. Al Teneiji A, Siriwardena K, George K, Mital S, Mercimek-Mahmutoglu S. Progressive Cerebellar Atrophy and a Novel Homozygous Pathogenic <em>DNAJC19</em> Variant as a Cause of Dilated Cardiomyopathy Ataxia Syndrome. Pediatric Neurology. 2016;62:58-61.
4. Kang Y, Stroud DA, Baker MJ, De Souza DP, Frazier AE, Liem M, et al. Sengers Syndrome-Associated Mitochondrial Acylglycerol Kinase Is a Subunit of the Human TIM22 Protein Import Complex. Molecular Cell. 2017;67(3):457-70.e5.
5. Ojala T, Polinati P, Manninen T, Hiippala A, Rajantie J, Karikoski R, et al. New mutation of mitochondrial DNAJC19 causing dilated and noncompaction cardiomyopathy, anemia, ataxia, and male genital anomalies. Pediatric Research. 2012;72(4):432-7.
6. Roesch K, Curran SP, Tranebjaerg L, Koehler CM. Human deafness dystonia syndrome is caused by a defect in assembly of the DDP1/TIMM8a-TIMM13 complex. Hum Mol Genet. 2002;11(5):477-86.
7. Takakubo F, Cartwright P, Hoogenraad N, Thorburn DR, Collins F, Lithgow T, et al. An amino acid substitution in the pyruvate dehydrogenase E1 alpha gene, affecting mitochondrial import of the precursor protein. Am J Hum Genet. 1995;57(4):772-80.
8. Devi L, Prabhu BM, Galati DF, Avadhani NG, Anandatheerthavarada HK. Accumulation of Amyloid Precursor Protein in the Mitochondrial Import Channels of Human Alzheimer’s Disease Brain Is Associated with Mitochondrial Dysfunction. The Journal of Neuroscience. 2006;26(35):9057.
9. Di Maio R, Barrett PJ, Hoffman EK, Barrett CW, Zharikov A, Borah A, et al. alpha-Synuclein binds to TOM20 and inhibits mitochondrial protein import in Parkinson's disease. Sci Transl Med. 2016;8(342):342ra78.
10. Yano H, Baranov SV, Baranova OV, Kim J, Pan Y, Yablonska S, et al. Inhibition of mitochondrial protein import by mutant huntingtin. Nat Neurosci. 2014;17(6):822-31.
11. Altmann K, Westermann B. Role of Essential Genes in Mitochondrial Morphogenesis in Saccharomyces cerevisiae. Molecular Biology of the Cell. 2005;16(11):5410-7.
12. Dimmer KS, Fritz S, Fuchs F, Messerschmitt M, Weinbach N, Neupert W, et al. Genetic basis of mitochondrial function and morphology in Saccharomyces cerevisiae. Molecular Biology of the Cell. 2002;13(3):847-53.
13. Herlan M, Bornhövd C, Hell K, Neupert W, Reichert AS. Alternative topogenesis of Mgm1 and mitochondrial morphology depend on ATP and a functional import motor. Journal of Cell Biology. 2004;165(2):167-73.
14. Meisinger C, Rissler M, Chacinska A, Szklarz LKS, Milenkovic D, Kozjak V, et al. The Mitochondrial Morphology Protein Mdm10 Functions in Assembly of the Preprotein Translocase of the Outer Membrane. Developmental Cell. 2004;7(1):61-71.
15. Liu W, Duan X, Fang X, Shang W, Tong C. Mitochondrial protein import regulates cytosolic protein homeostasis and neuronal integrity. Autophagy. 2018;14(8):1293-309.
16. Mapa K, Sikor M, Kudryavtsev V, Waegemann K, Kalinin S, Seidel CA, et al. The conformational dynamics of the mitochondrial Hsp70 chaperone. Mol Cell. 2010;38(1):89-100.
17. Wachter C, Schatz G, Glick BS. Protein import into mitochondria: the requirement for external ATP is precursor-specific whereas intramitochondrial ATP is universally needed for translocation into the matrix. Molecular biology of the cell. 1994;5(4):465-74.
18. Martin J, Mahlke K, Pfanner N. Role of an energized inner membrane in mitochondrial protein import. Delta psi drives the movement of presequences. J Biol Chem. 1991;266(27):18051-7.
19. Kovermann P, Truscott KN, Guiard B, Rehling P, Sepuri NB, Müller H, et al. Tim22, the Essential Core of the Mitochondrial Protein Insertion Complex, Forms a Voltage-Activated and Signal-Gated Channel. Molecular Cell. 2002;9(2):363-73.
20. Truscott KN, Kovermann P, Geissler A, Merlin A, Meijer M, Driessen AJ, et al. A presequence- and voltage-sensitive channel of the mitochondrial preprotein translocase formed by Tim23. Nat Struct Biol. 2001;8(12):1074-82.
21. Castro-Gago M, Dacruz-Alvarez D, Pintos-Martínez E, Beiras-Iglesias A, Arenas J, Martín MÁ, et al. Congenital neurogenic muscular atrophy in megaconial myopathy due to a mutation in CHKB gene. Brain and Development. 2016;38(1):167-72.
22. Gutierrez Rios P, Kalra AA, Wilson JD, Tanji K, Akman HO, Area Gomez E, et al. Congenital megaconial myopathy due to a novel defect in the choline kinase Beta gene. Arch Neurol. 2012;69(5):657-61.
23. Irwin WA, Bergamin N, Sabatelli P, Reggiani C, Megighian A, Merlini L, et al. Mitochondrial dysfunction and apoptosis in myopathic mice with collagen VI deficiency. Nat Genet. 2003;35(4):367-71.
24. Mitsuhashi S, Hatakeyama H, Karahashi M, Koumura T, Nonaka I, Hayashi YK, et al. Muscle choline kinase beta defect causes mitochondrial dysfunction and increased mitophagy. Human Molecular Genetics. 2011;20(19):3841-51.
25. Rybalka E, Timpani CA, Cooke MB, Williams AD, Hayes A. Defects in Mitochondrial ATP Synthesis in Dystrophin-Deficient Mdx Skeletal Muscles May Be Caused by Complex I Insufficiency. PLoS One. 2014;9(12):e115763.
26. Shkryl VM, Martins AS, Ullrich ND, Nowycky MC, Niggli E, Shirokova N. Reciprocal amplification of ROS and Ca2+ signals in stressed mdx dystrophic skeletal muscle fibers. Pflügers Archiv - European Journal of Physiology. 2009;458(5):915-28.
27. Tagliavini F, Sardone F, Squarzoni S, Maraldi NM, Merlini L, Faldini C, et al. Ultrastructural changes in muscle cells of patients with collagen VI-related myopathies. Muscles Ligaments Tendons J. 2013;3(4):281-6.
28. Vila MC, Rayavarapu S, Hogarth MW, Van der Meulen JH, Horn A, Defour A, et al. Mitochondria mediate cell membrane repair and contribute to Duchenne muscular dystrophy. Cell Death & Differentiation. 2017;24(2):330-42.
29. Aksu-Menges E, Akkaya-Ulum YZ, Dayangac-Erden D, Balci-Peynircioglu B, Yuzbasioglu A, Topaloglu H, et al. The Common miRNA Signatures Associated with Mitochondrial Dysfunction in Different Muscular Dystrophies. Am J Pathol. 2020;190(10):2136-45.
30. Aksu E, Talim B, Balci-Hayta B. Impaired balance of mitochondrial fission and fusion in an invitro model of mitochondrial unfolded protein response. The European Human Genetics Conference; 27-30 May 2017; Copenhagen-Denmark2017.
31. Gebert N, Ryan MT, Pfanner N, Wiedemann N, Stojanovski D. Mitochondrial protein import machineries and lipids: A functional connection. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2011;1808(3):1002-11.
32. Schuler M-H, Di Bartolomeo F, Martensson CU, Daum G, Becker T. Phosphatidylcholine Affects Inner Membrane Protein Translocases of Mitochondria. Journal of Biological Chemistry. 2016.
33. Schuler MH, Di Bartolomeo F, Bottinger L, Horvath SE, Wenz LS, Daum G, et al. Phosphatidylcholine affects the role of the sorting and assembly machinery in the biogenesis of mitochondrial beta-barrel proteins. J Biol Chem. 2015;290(44):26523-32.
34. Benz R. Biophysical properties of porin pores from mitochondrial outer membrane of eukaryotic cells. Experientia. 1990;46:131-7.
35. Jaworska A, Malek K, Kudelski A. Intracellular pH – Advantages and pitfalls of surface-enhanced Raman scattering and fluorescence microscopy – A review. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy. 2021;251:119410.
36. Xian H, Liou Y-C. Functions of outer mitochondrial membrane proteins: mediating the crosstalk between mitochondrial dynamics and mitophagy. Cell Death & Differentiation. 2021;28(3):827-42.
37. Moyes CD, Le Moine CMR. TISSUE RESPIRATION | Specializations in Mitochondrial Respiration of Fish. In: Farrell AP, editor. Encyclopedia of Fish Physiology. San Diego: Academic Press; 2011. p. 966-72.
38. Lemasters JJ. Modulation of mitochondrial membrane permeability in pathogenesis, autophagy and control of metabolism. J Gastroenterol Hepatol. 2007;22 Suppl 1:S31-7.
39. Cooper GM. The Cell: A Molecular Approach. 2nd edition. 2 ed: Sinauer Associates; 2000.
40. Saraste M. Oxidative phosphorylation at the fin de siècle. Science. 1999;283(5407):1488-93.
41. Kühlbrandt W. Structure and function of mitochondrial membrane protein complexes. BMC Biology. 2015;13(1):89.
42. Nunnari J, Suomalainen A. Mitochondria: in sickness and in health. Cell. 2012;148(6):1145-59.
43. Bartlett K, Eaton S. Mitochondrial beta-oxidation. Eur J Biochem. 2004;271(3):462-9.
44. Duchen MR. Mitochondria and calcium: from cell signalling to cell death. J Physiol. 2000;529 Pt 1(Pt 1):57-68.
45. Hogeboom GH, Schneider WC, Pallade GE. Cytochemical studies of mammalian tissues; isolation of intact mitochondria from rat liver; some biochemical properties of mitochondria and submicroscopic particulate material. J Biol Chem. 1948;172(2):619-35.
46. Kennedy EP, Lehninger AL. Oxidation of fatty acids and tricarboxylic acid cycle intermediates by isolated rat liver mitochondria. J Biol Chem. 1949;179(2):957-72.
47. Lehninger AL. ESTERIFICATION OF INORGANIC PHOSPHATE COUPLED TO ELECTRON TRANSPORT BETWEEN DIHYDRODIPHOSPHOPYRIDINE NUCLEOTIDE AND OXYGEN. II. Journal of Biological Chemistry. 1949;178(2):625-44.
48. Lill R, Diekert K, Kaut A, Lange H, Pelzer W, Prohl C, et al. The essential role of mitochondria in the biogenesis of cellular iron-sulfur proteins. Biol Chem. 1999;380(10):1157-66.
49. Susin SA, Lorenzo HK, Zamzami N, Marzo I, Snow BE, Brothers GM, et al. Molecular characterization of mitochondrial apoptosis-inducing factor. Nature. 1999;397(6718):441-6.
50. Tait SW, Green DR. Mitochondria and cell signalling. J Cell Sci. 2012;125(Pt 4):807-15.
51. Wallace DC, Chalkia D. Mitochondrial DNA genetics and the heteroplasmy conundrum in evolution and disease. Cold Spring Harb Perspect Biol. 2013;5(11):a021220.
52. Rygiel KA, Picard M, Turnbull DM. The ageing neuromuscular system and sarcopenia: a mitochondrial perspective. J Physiol. 2016;594(16):4499-512.
53. Sebastián D, Palacín M, Zorzano A. Mitochondrial Dynamics: Coupling Mitochondrial Fitness with Healthy Aging. Trends Mol Med. 2017;23(3):201-15.
54. Wai T, Langer T. Mitochondrial Dynamics and Metabolic Regulation. Trends Endocrinol Metab. 2016;27(2):105-17.
55. Archer SL. Mitochondrial Dynamics — Mitochondrial Fission and Fusion in Human Diseases. New England Journal of Medicine. 2013;369(23):2236-51.
56. Jheng HF, Tsai PJ, Guo SM, Kuo LH, Chang CS, Su IJ, et al. Mitochondrial fission contributes to mitochondrial dysfunction and insulin resistance in skeletal muscle. Mol Cell Biol. 2012;32(2):309-19.
57. Gomes LC, Benedetto GD, Scorrano L. During autophagy mitochondria elongate, are spared from degradation and sustain cell viability. Nature Cell Biology. 2011;13(5):589-98.
58. Rambold AS, Kostelecky B, Elia N, Lippincott-Schwartz J. Tubular network formation protects mitochondria from autophagosomal degradation during nutrient starvation. Proc Natl Acad Sci U S A. 2011;108(25):10190-5.
59. Song M, Mihara K, Chen Y, Scorrano L, Dorn GW, 2nd. Mitochondrial fission and fusion factors reciprocally orchestrate mitophagic culling in mouse hearts and cultured fibroblasts. Cell Metab. 2015;21(2):273-86.
60. Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong SE, et al. A mitochondrial protein compendium elucidates complex I disease biology. Cell. 2008;134(1):112-23.
61. Aviram N, Schuldiner M. Targeting and translocation of proteins to the endoplasmic reticulum at a glance. J Cell Sci. 2017;130(24):4079-85.
62. Chacinska A, Koehler CM, Milenkovic D, Lithgow T, Pfanner N. Importing mitochondrial proteins: machineries and mechanisms. Cell. 2009;138(4):628-44.
63. Schmidt O, Pfanner N, Meisinger C. Mitochondrial protein import: from proteomics to functional mechanisms. Nat Rev Mol Cell Biol. 2010;11(9):655-67.
64. Cichocki BA, Krumpe K, Vitali DG, Rapaport D. Pex19 is involved in importing dually targeted tail-anchored proteins to both mitochondria and peroxisomes. Traffic. 2018;19(10):770-85.
65. Jores T, Lawatscheck J, Beke V, Franz-Wachtel M, Yunoki K, Fitzgerald JC, et al. Cytosolic Hsp70 and Hsp40 chaperones enable the biogenesis of mitochondrial β-barrel proteins. J Cell Biol. 2018;217(9):3091-108.
66. Young JC, Hoogenraad NJ, Hartl FU. Molecular chaperones Hsp90 and Hsp70 deliver preproteins to the mitochondrial import receptor Tom70. Cell. 2003;112(1):41-50.
67. Bausewein T, Mills DJ, Langer JD, Nitschke B, Nussberger S, Kühlbrandt W. Cryo-EM Structure of the TOM Core Complex from Neurospora crassa. Cell. 2017;170(4):693-700.e7.
68. Vögtle FN, Wortelkamp S, Zahedi RP, Becker D, Leidhold C, Gevaert K, et al. Global analysis of the mitochondrial N-proteome identifies a processing peptidase critical for protein stability. Cell. 2009;139(2):428-39.
69. Doyle SR, Kasinadhuni NR, Chan CK, Grant WN. Evidence of evolutionary constraints that influences the sequence composition and diversity of mitochondrial matrix targeting signals. PLoS One. 2013;8(6):e67938.
70. Geissler A, Krimmer T, Bömer U, Guiard B, Rassow J, Pfanner N. Membrane potential-driven protein import into mitochondria. The sorting sequence of cytochrome b(2) modulates the deltapsi-dependence of translocation of the matrix-targeting sequence. Mol Biol Cell. 2000;11(11):3977-91.
71. Huang S, Taylor NL, Whelan J, Millar AH. Refining the definition of plant mitochondrial presequences through analysis of sorting signals, N-terminal modifications, and cleavage motifs. Plant Physiol. 2009;150(3):1272-85.
72. Sinzel M, Tan T, Wendling P, Kalbacher H, Özbalci C, Chelius X, et al. Mcp3 is a novel mitochondrial outer membrane protein that follows a unique IMP-dependent biogenesis pathway. EMBO Rep. 2016;17(7):965-81.
73. Wiedemann N, Pfanner N, Ryan MT. The three modules of ADP/ATP carrier cooperate in receptor recruitment and translocation into mitochondria. Embo J. 2001;20(5):951-60.
74. Milenkovic D, Ramming T, Müller JM, Wenz LS, Gebert N, Schulze-Specking A, et al. Identification of the signal directing Tim9 and Tim10 into the intermembrane space of mitochondria. Mol Biol Cell. 2009;20(10):2530-9.
75. Sideris DP, Petrakis N, Katrakili N, Mikropoulou D, Gallo A, Ciofi-Baffoni S, et al. A novel intermembrane space-targeting signal docks cysteines onto Mia40 during mitochondrial oxidative folding. J Cell Biol. 2009;187(7):1007-22.
76. Caplan AJ, Cyr DM, Douglas MG. YDJ1p facilitates polypeptide translocation across different intracellular membranes by a conserved mechanism. Cell. 1992;71(7):1143-55.
77. Gold VA, Chroscicki P, Bragoszewski P, Chacinska A. Visualization of cytosolic ribosomes on the surface of mitochondria by electron cryo-tomography. EMBO Rep. 2017;18(10):1786-800.
78. Wienhues U, Becker K, Schleyer M, Guiard B, Tropschug M, Horwich AL, et al. Protein folding causes an arrest of preprotein translocation into mitochondria in vivo. Journal of Cell Biology. 1991;115(6):1601-9.
79. Papić D, Elbaz-Alon Y, Koerdt SN, Leopold K, Worm D, Jung M, et al. The role of Djp1 in import of the mitochondrial protein Mim1 demonstrates specificity between a cochaperone and its substrate protein. Mol Cell Biol. 2013;33(20):4083-94.
80. Chacinska A, Lind M, Frazier AE, Dudek J, Meisinger C, Geissler A, et al. Mitochondrial presequence translocase: switching between TOM tethering and motor recruitment involves Tim21 and Tim17. Cell. 2005;120(6):817-29.
81. Kiebler M, Pfaller R, Sollner T, Griffiths G, Horstmann H, Pfanner N, et al. Identification of a mitochondrial receptor complex required for recognition and membrane insertion of precursor proteins. Nature. 1990;348(6302):610-6.
82. Stojanovski D, Rissler M, Pfanner N, Meisinger C. Mitochondrial morphology and protein import—A tight connection? Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 2006;1763(5):414-21.
83. Hawlitschek G, Schneider H, Schmidt B, Tropschug M, Hartl FU, Neupert W. Mitochondrial protein import: identification of processing peptidase and of PEP, a processing enhancing protein. Cell. 1988;53(5):795-806.
84. Joseph A-M, Ljubicic V, Adhihetty PJ, Hood DA. Biogenesis of the mitochondrial Tom40 channel in skeletal muscle from aged animals and its adaptability to chronic contractile activity. American Journal of Physiology-Cell Physiology. 2010;298(6):C1308-C14.
85. Sirrenberg C, Bauer MF, Guiard B, Neupert W, Brunner M. Import of carrier proteins into the mitochondrial inner membrane mediated by Tim22. Nature. 1996;384(6609):582-5.
86. Sirrenberg C, Endres M, Folsch H, Stuart RA, Neupert W, Brunner M. Carrier protein import into mitochondria mediated by the intermembrane proteins Tim10/Mrs11 and Tim12/Mrs5. Nature. 1998;391(6670):912-5.
87. Wiedemann N, Kozjak V, Chacinska A, Schonfisch B, Rospert S, Ryan MT, et al. Machinery for protein sorting and assembly in the mitochondrial outer membrane. Nature. 2003;424(6948):565-71.
88. Becker T, Pfannschmidt S, Guiard B, Stojanovski D, Milenkovic D, Kutik S, et al. Biogenesis of the mitochondrial TOM complex - Mim1 promotes insertion and assembly of signal-anchored receptors. Journal of Biological Chemistry. 2008;283(1):120-7.
89. Hulett JM, Lueder F, Chan NC, Perry AJ, Wolynec P, Likic VA, et al. The transmembrane segment of Tom20 is recognized by Mim1 for docking to the mitochondrial TOM complex. J Mol Biol. 2008;376(3):694-704.
90. Popov-Celeketic J, Waizenegger T, Rapaport D. Mim1 functions in an oligomeric form to facilitate the integration of Tom20 into the mitochondrial outer membrane. J Mol Biol. 2008;376(3):671-80.
91. Chacinska A, Pfannschmidt S, Wiedemann N, Kozjak V, Szklarz LKS, Schulze-Specking A, et al. Essential role of Mia40 in import and assembly of mitochondrial intermembrane space proteins. Embo J. 2004;23(19):3735-46.
92. Naoe M, Ohwa Y, Ishikawa D, Ohshima C, Nishikawa S, Yamamoto H, et al. Identification of Tim40 that mediates protein sorting to the mitochondrial intermembrane space. Journal of Biological Chemistry. 2004;279(46):47815-21.
93. Stiller SB, Hopker J, Oeljeklaus S, Schutze C, Schrempp SG, Vent-Schmidt J, et al. Mitochondrial OXA Translocase Plays a Major Role in Biogenesis of Inner-Membrane Proteins. Cell Metab. 2016;23(5):901-8.
94. Yano H, Baranov SV, Baranova OV, Kim J, Pan Y, Yablonska S, et al. Inhibition of mitochondrial protein import by mutant huntingtin. Nature Neuroscience. 2014;17(6):822-31.
95. Rahman J, Rahman S. Mitochondrial medicine in the omics era. The Lancet. 2018;391(10139):2560-74.
96. Gorman GS, Chinnery PF, DiMauro S, Hirano M, Koga Y, McFarland R, et al. Mitochondrial diseases. Nat Rev Dis Primers. 2016;2:16080.
97. Rahman S. Mitochondrial disease in children. J Intern Med. 2020;287(6):609-33.
98. Niyazov DM, Kahler SG, Frye RE. Primary Mitochondrial Disease and Secondary Mitochondrial Dysfunction: Importance of Distinction for Diagnosis and Treatment. Mol Syndromol. 2016;7(3):122-37.
99. Mavraki E, Labrum R, Sergeant K, Alston CL, Woodward C, Smith C, et al. Genetic testing for mitochondrial disease: the United Kingdom best practice guidelines. European Journal of Human Genetics. 2023;31(2):148-63.
100. Hoffman EP, Fischbeck KH, Brown RH, Johnson M, Medori R, Loike JD, et al. Characterization of dystrophin in muscle-biopsy specimens from patients with Duchenne's or Becker's muscular dystrophy. N Engl J Med. 1988;318(21):1363-8.
101. Kieny P, Chollet S, Delalande P, Le Fort M, Magot A, Pereon Y, et al. Evolution of life expectancy of patients with Duchenne muscular dystrophy at AFM Yolaine de Kepper centre between 1981 and 2011. Ann Phys Rehabil Med. 2013;56(6):443-54.
102. McDonald CM, Henricson EK, Abresch RT, Han JJ, Escolar DM, Florence JM, et al. The cooperative international neuromuscular research group Duchenne natural history study--a longitudinal investigation in the era of glucocorticoid therapy: design of protocol and the methods used. Muscle Nerve. 2013;48(1):32-54.
103. Koenig M, Beggs AH, Moyer M, Scherpf S, Heindrich K, Bettecken T, et al. The molecular basis for Duchenne versus Becker muscular dystrophy: correlation of severity with type of deletion. Am J Hum Genet. 1989;45(4):498-506.
104. Onopiuk M, Brutkowski W, Wierzbicka K, Wojciechowska S, Szczepanowska J, Fronk J, et al. Mutation in dystrophin-encoding gene affects energy metabolism in mouse myoblasts. Biochem Biophys Res Commun. 2009;386(3):463-6.
105. Percival JM, Siegel MP, Knowels G, Marcinek DJ. Defects in mitochondrial localization and ATP synthesis in the mdx mouse model of Duchenne muscular dystrophy are not alleviated by PDE5 inhibition. Hum Mol Genet. 2013;22(1):153-67.
106. Schuh RA, Jackson KC, Khairallah RJ, Ward CW, Spangenburg EE. Measuring mitochondrial respiration in intact single muscle fibers. Am J Physiol Regul Integr Comp Physiol. 2012;302(6):R712-9.
107. Moore TM, Lin AJ, Strumwasser AR, Cory K, Whitney K, Ho T, et al. Mitochondrial Dysfunction Is an Early Consequence of Partial or Complete Dystrophin Loss in mdx Mice. Front Physiol. 2020;11:690.
108. Yao S, Chen Z, Yu Y, Zhang N, Jiang H, Zhang G, et al. Current Pharmacological Strategies for Duchenne Muscular Dystrophy. Front Cell Dev Biol. 2021;9:689533.
109. Buyse GM, Van der Mieren G, Erb M, D'Hooge J, Herijgers P, Verbeken E, et al. Long-term blinded placebo-controlled study of SNT-MC17/idebenone in the dystrophin deficient mdx mouse: cardiac protection and improved exercise performance. Eur Heart J. 2009;30(1):116-24.
110. McKenna MJ, Medved I, Goodman CA, Brown MJ, Bjorksten AR, Murphy KT, et al. N-acetylcysteine attenuates the decline in muscle Na+,K+-pump activity and delays fatigue during prolonged exercise in humans. J Physiol. 2006;576(Pt 1):279-88.
111. Spurney CF, Rocha CT, Henricson E, Florence J, Mayhew J, Gorni K, et al. CINRG pilot trial of coenzyme Q10 in steroid-treated Duchenne muscular dystrophy. Muscle Nerve. 2011;44(2):174-8.
112. Mitsuhashi S, Ohkuma A, Talim B, Karahashi M, Koumura T, Aoyama C, et al. A congenital muscular dystrophy with mitochondrial structural abnormalities caused by defective de novo phosphatidylcholine biosynthesis. Am J Hum Genet. 2011;88(6):845-51.
113. Nishino I, Kobayashi O, Goto Y, Kurihara M, Kumagai K, Fujita T, et al. A new congenital muscular dystrophy with mitochondrial structural abnormalities. Muscle Nerve. 1998;21(1):40-7.
114. Shy GM, Gonatas NK, Perez M. Two childhood myopathies with abnormal mitochondria. I. Megaconial myopathy. II. Pleoconial myopathy. Brain. 1966;89(1):133-58.
115. Bardhan M, Polavarapu K, Bevinahalli NN, Veeramani PK, Anjanappa RM, Arunachal G, et al. Megaconial congenital muscular dystrophy secondary to novel CHKB mutations resemble atypical Rett syndrome. J Hum Genet. 2021;66(8):813-23.
116. Haliloglu G, Talim B, Sel CG, Topaloglu H. Clinical characteristics of megaconial congenital muscular dystrophy due to choline kinase beta gene defects in a series of 15 patients. J Inherit Metab Dis. 2015;38(6):1099-108.
117. Mitsuhashi S, Nishino I. Phospholipid synthetic defect and mitophagy in muscle disease. Autophagy. 2011;7(12):1559-61.
118. Quinlivan R, Mitsuahashi S, Sewry C, Cirak S, Aoyama C, Mooore D, et al. Muscular dystrophy with large mitochondria associated with mutations in the CHKB gene in three British patients: extending the clinical and pathological phenotype. Neuromuscul Disord. 2013;23(7):549-56.
119. Ríos PG, Kalra AA, Wilson JD, Tanji K, Akman HO, Gómez EA, et al. Congenital Megaconial Myopathy Due to a Novel Defect in the Choline Kinase Beta Gene. Archives of Neurology. 2012;69(5):657-61.
120. Aksu-Menges E, Eylem CC, Nemutlu E, Gizer M, Korkusuz P, Topaloglu H, et al. Reduced mitochondrial fission and impaired energy metabolism in human primary skeletal muscle cells of Megaconial Congenital Muscular Dystrophy. Sci Rep. 2021;11(1):18161.
121. Sayed-Zahid AA, Sher RB, Sukoff Rizzo SJ, Anderson LC, Patenaude KE, Cox GA. Functional rescue in a mouse model of congenital muscular dystrophy with megaconial myopathy. Hum Mol Genet. 2019;28(16):2635-47.
122. Tavasoli M, Lahire S, Sokolenko S, Novorolsky R, Reid SA, Lefsay A, et al. Mechanism of action and therapeutic route for a muscular dystrophy caused by a genetic defect in lipid metabolism. Nat Commun. 2022;13(1):1559.
123. Baker NL, Mörgelin M, Peat R, Goemans N, North KN, Bateman JF, et al. Dominant collagen VI mutations are a common cause of Ullrich congenital muscular dystrophy. Human Molecular Genetics. 2005;14(2):279-93.
124. Hicks D, Lampe AK, Barresi R, Charlton R, Fiorillo C, Bonnemann CG, et al. A refined diagnostic algorithm for Bethlem myopathy. Neurology. 2008;70(14):1192.
125. Okada M, Kawahara G, Noguchi S, Sugie K, Murayama K, Nonaka I, et al. Primary collagen VI deficiency is the second most common congenital muscular dystrophy in Japan. Neurology. 2007;69(10):1035.
126. Pace RA, Peat RA, Baker NL, Zamurs L, Mörgelin M, Irving M, et al. Collagen VI glycine mutations: Perturbed assembly and a spectrum of clinical severity. Annals of Neurology. 2008;64(3):294-303.
127. Castagnaro S, Pellegrini C, Pellegrini M, Chrisam M, Sabatelli P, Toni S, et al. Autophagy activation in COL6 myopathic patients by a low-protein-diet pilot trial. Autophagy. 2016;12(12):2484-95.
128. Merlini L, Angelin A, Tiepolo T, Braghetta P, Sabatelli P, Zamparelli A, et al. Cyclosporin A corrects mitochondrial dysfunction and muscle apoptosis in patients with collagen VI myopathies. Proc Natl Acad Sci U S A. 2008;105(13):5225-9.
129. Merlini L, Sabatelli P, Armaroli A, Gnudi S, Angelin A, Grumati P, et al. Cyclosporine A in Ullrich congenital muscular dystrophy: long-term results. Oxid Med Cell Longev. 2011;2011:139194.
130. Duarte FV, Palmeira CM, Rolo AP. The Role of microRNAs in Mitochondria: Small Players Acting Wide. Genes (Basel). 2014;5(4):865-86.
131. Schneider HC, Berthold J, Bauer MF, Dietmeier K, Guiard B, Brunner M, et al. Mitochondrial Hsp70/MIM44 complex facilitates protein import. Nature. 1994;371(6500):768-74.
132. van der Laan M, Wiedemann N, Mick DU, Guiard B, Rehling P, Pfanner N. A role for Tim21 in membrane-potential-dependent preprotein sorting in mitochondria. Curr Biol. 2006;16(22):2271-6.
133. Barth PG, Scholte HR, Berden JA, Van der Klei-Van Moorsel JM, Luyt-Houwen IE, Van 't Veer-Korthof ET, et al. An X-linked mitochondrial disease affecting cardiac muscle, skeletal muscle and neutrophil leucocytes. J Neurol Sci. 1983;62(1-3):327-55.
134. Gebert N, Joshi AS, Kutik S, Becker T, McKenzie M, Guan XL, et al. Mitochondrial Cardiolipin Involved in Outer-Membrane Protein Biogenesis: Implications for Barth Syndrome. Current Biology. 2009;19(24):2133-9.
135. Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, et al. Fiji: an open-source platform for biological-image analysis. Nature Methods. 2012;9(7):676-82.
136. Panov AV. Practical Mitochondriology: Pitfalls and Problems in Studies of Mitochondria: CreateSpace Independent Publishing Platform: CreateSpace Independent Publishing Platform; 2013.
137. Coudert E, Gehant S, de Castro E, Pozzato M, Baratin D, Neto T, et al. Annotation of biologically relevant ligands in UniProtKB using ChEBI. Bioinformatics. 2023;39(1).
138. Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;14:128.
139. Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, et al. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Res. 2016;44(W1):W90-7.
140. Xie Z, Bailey A, Kuleshov MV, Clarke DJB, Evangelista JE, Jenkins SL, et al. Gene Set Knowledge Discovery with Enrichr. Current Protocols. 2021;1(3):e90.
141. Dodds E, Dunckley MG, Naujoks K, Michaelis U, Dickson G. Lipofection of cultured mouse muscle cells: a direct comparison of Lipofectamine and DOSPER. Gene Ther. 1998;5(4):542-51.
142. Trivedi RA, Dickson G. Liposome-mediated gene transfer into normal and dystrophin-deficient mouse myoblasts. J Neurochem. 1995;64(5):2230-8.
143. Yamano S, Dai J, Moursi AM. Comparison of transfection efficiency of nonviral gene transfer reagents. Mol Biotechnol. 2010;46(3):287-300.
144. Quenneville SP, Chapdelaine P, Rousseau J, Beaulieu J, Caron NJ, Skuk D, et al. Nucleofection of muscle-derived stem cells and myoblasts with ϕC31 integrase: stable expression of a full-length-dystrophin fusion gene by human myoblasts. Molecular Therapy. 2004;10(4):679-87.
145. Franco-Iborra S, Cuadros T, Parent A, Romero-Gimenez J, Vila M, Perier C. Defective mitochondrial protein import contributes to complex I-induced mitochondrial dysfunction and neurodegeneration in Parkinson’s disease. Cell Death & Disease. 2018;9(11):1122.
146. Sekar D, Johnson J, Biruntha M, Lakhmanan G, Gurunathan D, Ross K. Biological and Clinical Relevance of microRNAs in Mitochondrial Diseases/Dysfunctions. DNA Cell Biol. 2020;39(8):1379-84.
147. Zhang S, Cheng Z, Wang Y, Han T. The Risks of miRNA Therapeutics: In a Drug Target Perspective. Drug Des Devel Ther. 2021;15:721-33.
148. Catanesi M, d'Angelo M, Tupone MG, Benedetti E, Giordano A, Castelli V, et al. MicroRNAs Dysregulation and Mitochondrial Dysfunction in Neurodegenerative Diseases. Int J Mol Sci. 2020;21(17).
149. Paramasivam A, Vijayashree Priyadharsini J. MitomiRs: new emerging microRNAs in mitochondrial dysfunction and cardiovascular disease. Hypertens Res. 2020;43(8):851-3.
150. Dahlmans D, Houzelle A, Andreux P, Wang X, Jorgensen JA, Moullan N, et al. MicroRNA-382 silencing induces a mitonuclear protein imbalance and activates the mitochondrial unfolded protein response in muscle cells. J Cell Physiol. 2019;234(5):6601-10.
151. Zhou H, Gan M, Jin X, Dai M, Wang Y, Lei Y, et al. miR‑382 inhibits breast cancer progression and metastasis by affecting the M2 polarization of tumor‑associated macrophages by targeting PGC‑1α. Int J Oncol. 2022;61(4).
152. Chakraborty C, Sharma AR, Sharma G, Lee SS. Therapeutic advances of miRNAs: A preclinical and clinical update. J Adv Res. 2021;28:127-38.
153. Dimauro I, Pearson T, Caporossi D, Jackson MJ. A simple protocol for the subcellular fractionation of skeletal muscle cells and tissue. BMC Research Notes. 2012;5(1):513.
154. Dixit B, Vanhoozer S, Anti NA, O'Connor MS, Boominathan A. Rapid enrichment of mitochondria from mammalian cell cultures using digitonin. MethodsX. 2021;8:101197.
155. Djafarzadeh S, Jakob SM. Isolation of Intact Mitochondria from Skeletal Muscle by Differential Centrifugation for High-resolution Respirometry Measurements. J Vis Exp. 2017(121).
156. Sims NR, Anderson MF. Isolation of mitochondria from rat brain using Percoll density gradient centrifugation. Nat Protoc. 2008;3(7):1228-39.
157. Younis AZ, Lavery GG, Christian M, Doig CL. Rapid isolation of respiring skeletal muscle mitochondria using nitrogen cavitation. Frontiers in Physiology. 2023;14.
158. Clayton DA, Shadel GS. Isolation of mitochondria from tissue culture cells. Cold Spring Harb Protoc. 2014;2014(10):pdb.prot080002.
159. Liao PC, Bergamini C, Fato R, Pon LA, Pallotti F. Isolation of mitochondria from cells and tissues. Methods Cell Biol. 2020;155:3-31.
160. Caldeira DAF, de Oliveira DF, Cavalcanti-de-Albuquerque JP, Nascimento JHM, Zin WA, Maciel L. Isolation of Mitochondria From Fresh Mice Lung Tissue. Front Physiol. 2021;12:748261.
161. Frezza C, Cipolat S, Scorrano L. Organelle isolation: functional mitochondria from mouse liver, muscle and cultured filroblasts. Nature Protocols. 2007;2(2):287-95.
162. Corcelli A, Saponetti MS, Zaccagnino P, Lopalco P, Mastrodonato M, Liquori GE, et al. Mitochondria isolated in nearly isotonic KCl buffer: Focus on cardiolipin and organelle morphology. Biochimica et Biophysica Acta (BBA) - Biomembranes. 2010;1798(3):681-7.
163. Ishii M, Beeson G, Beeson C, Rohrer B. An improved method for isolation of mitochondria from cell lines that enables reconstitution of calcium-dependent processes. Anal Biochem. 2019;577:52-8.
164. Goldstein AH, Anderson JO, McDaniel RG. Effects of protectants on the activity of wheat mitochondria. Prep Biochem. 1981;11(1):33-47.
165. Korge P, Honda HM, Weiss JN. Effects of fatty acids in isolated mitochondria: implications for ischemic injury and cardioprotection. Am J Physiol Heart Circ Physiol. 2003;285(1):H259-69.
166. Ngo J, Benador IY, Brownstein AJ, Vergnes L, Veliova M, Shum M, et al. Isolation and functional analysis of peridroplet mitochondria from murine brown adipose tissue. STAR Protoc. 2021;2(1):100243.
167. Sacktor B, O'Neill JJ, Cochran DG. The requirement for serum albumin in oxidative phosphorylation of flight muscle mitochondria. J Biol Chem. 1958;233(5):1233-5.
168. Weinbach EC, Garbus J. The rapid restoration of respiratory control to uncoupled mitochondria. J Biol Chem. 1966;241(16):3708-13.
169. Blanco-Fernandez J, Jourdain AA. Two-Step Tag-Free Isolation of Mitochondria for Improved Protein Discovery and Quantification. J Vis Exp. 2023(196).
170. Kruse R, Sahebekhtiari N, Højlund K. The Mitochondrial Proteomic Signatures of Human Skeletal Muscle Linked to Insulin Resistance. Int J Mol Sci. 2020;21(15).
171. Schaffer LV, Rensvold JW, Shortreed MR, Cesnik AJ, Jochem A, Scalf M, et al. Identification and Quantification of Murine Mitochondrial Proteoforms Using an Integrated Top-Down and Intact-Mass Strategy. J Proteome Res. 2018;17(10):3526-36.
172. Poulaki A, Giannouli S. Mitochondrial Lipids: From Membrane Organization to Apoptotic Facilitation. Int J Mol Sci. 2022;23(7).
173. Buono MJ, Kolkhorst FW. Estimating ATP resynthesis during a marathon run: a method to introduce metabolism. AMER PHYSIOLOGICAL SOC 9650 ROCKVILLE PIKE, BETHESDA, MD 20814 USA; 2001. p. 70-1.
174. Garrett RH. Biochemistry: Cengage Learning Canada Inc; 2015.
175. Stepien G, Torroni A, Chung AB, Hodge JA, Wallace DC. Differential expression of adenine nucleotide translocator isoforms in mammalian tissues and during muscle cell differentiation. J Biol Chem. 1992;267(21):14592-7.
176. Thompson K, Majd H, Dallabona C, Reinson K, King MS, Alston CL, et al. Recurrent De Novo Dominant Mutations in SLC25A4 Cause Severe Early-Onset Mitochondrial Disease and Loss of Mitochondrial DNA Copy Number. Am J Hum Genet. 2016;99(4):860-76.
177. Claypool SM, Oktay Y, Boontheung P, Loo JA, Koehler CM. Cardiolipin defines the interactome of the major ADP/ATP carrier protein of the mitochondrial inner membrane. J Cell Biol. 2008;182(5):937-50.
178. Agostino A, Valletta L, Chinnery PF, Ferrari G, Carrara F, Taylor RW, et al. Mutations of ANT1, Twinkle, and POLG1 in sporadic progressive external ophthalmoplegia (PEO). Neurology. 2003;60(8):1354-6.
179. Echaniz-Laguna A, Chassagne M, Ceresuela J, Rouvet I, Padet S, Acquaviva C, et al. Complete loss of expression of the ANT1 gene causing cardiomyopathy and myopathy. J Med Genet. 2012;49(2):146-50.
180. Komaki H, Fukazawa T, Houzen H, Yoshida K, Nonaka I, Goto Y. A novel D104G mutation in the adenine nucleotide translocator 1 gene in autosomal dominant progressive external ophthalmoplegia patients with mitochondrial DNA with multiple deletions. Ann Neurol. 2002;51(5):645-8.
181. Palmieri L, Alberio S, Pisano I, Lodi T, Meznaric-Petrusa M, Zidar J, et al. Complete loss-of-function of the heart/muscle-specific adenine nucleotide translocator is associated with mitochondrial myopathy and cardiomyopathy. Hum Mol Genet. 2005;14(20):3079-88.
182. Strauss KA, DuBiner L, Simon M, Zaragoza M, Sengupta PP, Li P, et al. Severity of cardiomyopathy associated with adenine nucleotide translocator-1 deficiency correlates with mtDNA haplogroup. Proc Natl Acad Sci U S A. 2013;110(9):3453-8.
183. Invitae. Invitae Comprehensive Neuromuscular Disorders Panel USA: Invitae Corporation; 2023 [Available from: https://www.invitae.com/us/providers/test-catalog/test-03280.
184. Mikrogenlab. Cardiomyopathy Panel (110 Genes) Ankara, Turkey: Mikrogenlab; 2023 [Available from: https://en.mikrogenlab.com/test/cardiomyopathy-panel-110-genes/.
185. Services WUP. Cardiomyopathy panel | NGS St. Louis, USA: Washington University in St. Louis; 2023 [Available from: https://pathologyservices.wustl.edu/items/cardiomyopathy-gene-set-ngs/.
186. Capitanio D, Moriggi M, Torretta E, Barbacini P, De Palma S, Viganò A, et al. Comparative proteomic analyses of Duchenne muscular dystrophy and Becker muscular dystrophy muscles: changes contributing to preserve muscle function in Becker muscular dystrophy patients. J Cachexia Sarcopenia Muscle. 2020;11(2):547-63.