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Zhang M, Luo X, Zhang B, Luo D, Huang L, Long Q. Unveiling OSCP as the potential therapeutic target for mitochondrial dysfunction-related diseases. Life Sci 2024; 336:122293. [PMID: 38030056 DOI: 10.1016/j.lfs.2023.122293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 11/06/2023] [Accepted: 11/21/2023] [Indexed: 12/01/2023]
Abstract
Mitochondria are important organelles in cells responsible for energy production and regulation. Mitochondrial dysfunction has been implicated in the pathogenesis of many diseases. Oligomycin sensitivity-conferring protein (OSCP), a component of the inner mitochondrial membrane, has been studied for a long time. OSCP is a component of the F1Fo-ATP synthase in mitochondria and is closely related to the regulation of the mitochondrial permeability transition pore (mPTP). Studies have shown that OSCP plays an important role in cardiovascular disease, neurological disorders, and tumor development. This review summarizes the localization, structure, function, and regulatory mechanisms of OSCP and outlines its role in cardiovascular disease, neurological disease, and tumor development. In addition, this article reviews the research on the interaction between OSCP and mPTP. Finally, the article suggests future research directions, including further exploration of the mechanism of action of OSCP, the interaction between OSCP and other proteins and signaling pathways, and the development of new treatment strategies for mitochondrial dysfunction. In conclusion, in-depth research on OSCP will help to elucidate its importance in cell function and disease and provide new ideas for the treatment and prevention of related diseases.
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Affiliation(s)
- Mingyue Zhang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine (Institute of Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Chinese Medicine for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Xia Luo
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine (Institute of Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Chinese Medicine for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Binzhi Zhang
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine (Institute of Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Chinese Medicine for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Duosheng Luo
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine (Institute of Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Chinese Medicine for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China.
| | - Lizhen Huang
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou 510006, China
| | - Qinqiang Long
- Guangdong Metabolic Diseases Research Center of Integrated Chinese and Western Medicine (Institute of Chinese Medicine), Guangdong Pharmaceutical University, Guangzhou 510006, China; Key Laboratory of Glucolipid Metabolic Disorder, Ministry of Education, Guangdong Pharmaceutical University, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Chinese Medicine for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou 510006, China.
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2
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Gao Y, Guo L, Wang F, Wang Y, Li P, Zhang D. Development of mitochondrial gene-editing strategies and their potential applications in mitochondrial hereditary diseases: a review. Cytotherapy 2024; 26:11-24. [PMID: 37930294 DOI: 10.1016/j.jcyt.2023.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
Mitochondrial DNA (mtDNA) is a critical genome contained within the mitochondria of eukaryotic cells, with many copies present in each mitochondrion. Mutations in mtDNA often are inherited and can lead to severe health problems, including various inherited diseases and premature aging. The lack of efficient repair mechanisms and the susceptibility of mtDNA to damage exacerbate the threat to human health. Heteroplasmy, the presence of different mtDNA genotypes within a single cell, increases the complexity of these diseases and requires an effective editing method for correction. Recently, gene-editing techniques, including programmable nucleases such as restriction endonuclease, zinc finger nuclease, transcription activator-like effector nuclease, clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated 9 and base editors, have provided new tools for editing mtDNA in mammalian cells. Base editors are particularly promising because of their high efficiency and precision in correcting mtDNA mutations. In this review, we discuss the application of these techniques in mitochondrial gene editing and their limitations. We also explore the potential of base editors for mtDNA modification and discuss the opportunities and challenges associated with their application in mitochondrial gene editing. In conclusion, this review highlights the advancements, limitations and opportunities in current mitochondrial gene-editing technologies and approaches. Our insights aim to stimulate the development of new editing strategies that can ultimately alleviate the adverse effects of mitochondrial hereditary diseases.
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Affiliation(s)
- Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Linlin Guo
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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3
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Hanssen JNS, Dhiman S. Impact of subtle intermolecular interactions on the structure and dynamics of multicomponent supramolecular polymers. Chem Commun (Camb) 2023; 59:13466-13469. [PMID: 37877229 DOI: 10.1039/d3cc04567f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Multicomponent supramolecular polymers offer versatile dynamic and functional properties; however, the influence of the monomer chemical structures on their structure-dynamics-function relationship remains unclear. In this study, we investigated the subtle variations in monomer interactions using one monomer and its two dopant derivatives, with functionalization away from the self-assembling core. We systematically investigated their multicomponent supramolecular polymers using a combination of spectroscopy and super-resolution microscopy. Our results highlight the significant impact of the supplementary intermolecular interactions, resulting from the functional motifs located away from the core and present in small quantities, on the microstructure and dynamics. Thus, a comprehensive approach, combining spectroscopy, microscopy, and well-designed experiments, is essential for assessing multicomponent supramolecular polymers. These findings have implications for the rational design of functional multicomponent supramolecular materials.
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Affiliation(s)
- Job N S Hanssen
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, D-55128, Mainz, Germany.
| | - Shikha Dhiman
- Department of Chemistry, Johannes Gutenberg University Mainz, Duesbergweg 10-14, D-55128, Mainz, Germany.
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4
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DeFoor N, Paul S, Li S, Basso EKG, Stevenson V, Browning JL, Prater AK, Brindley S, Tao G, Pickrell AM. Remdesivir increases mtDNA copy number causing mild alterations to oxidative phosphorylation. Sci Rep 2023; 13:15339. [PMID: 37714940 PMCID: PMC10504289 DOI: 10.1038/s41598-023-42704-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/13/2023] [Indexed: 09/17/2023] Open
Abstract
SARS-CoV-2 causes the severe respiratory disease COVID-19. Remdesivir (RDV) was the first fast-tracked FDA approved treatment drug for COVID-19. RDV acts as an antiviral ribonucleoside (adenosine) analogue that becomes active once it accumulates intracellularly. It then diffuses into the host cell and terminates viral RNA transcription. Previous studies have shown that certain nucleoside analogues unintentionally inhibit mitochondrial RNA or DNA polymerases or cause mutational changes to mitochondrial DNA (mtDNA). These past findings on the mitochondrial toxicity of ribonucleoside analogues motivated us to investigate what effects RDV may have on mitochondrial function. Using in vitro and in vivo rodent models treated with RDV, we observed increases in mtDNA copy number in Mv1Lu cells (35.26% increase ± 11.33%) and liver (100.27% increase ± 32.73%) upon treatment. However, these increases only resulted in mild changes to mitochondrial function. Surprisingly, skeletal muscle and heart were extremely resistant to RDV treatment, tissues that have preferentially been affected by other nucleoside analogues. Although our data suggest that RDV does not greatly impact mitochondrial function, these data are insightful for the treatment of RDV for individuals with mitochondrial disease.
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Affiliation(s)
- Nicole DeFoor
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA
| | - Swagatika Paul
- Graduate Program in Biomedical and Veterinary Sciences, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24061, USA
| | - Shuang Li
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Erwin K Gudenschwager Basso
- Department of Biomedical Sciences and Pathobiology, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24061, USA
| | - Valentina Stevenson
- Virginia Tech Animal Laboratory Services, Virginia-Maryland College of Veterinary Medicine, Blacksburg, VA, 24061, USA
| | - Jack L Browning
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA
| | - Anna K Prater
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA
| | - Samantha Brindley
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA
| | - Ge Tao
- Department of Regenerative Medicine and Cell Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Alicia M Pickrell
- School of Neuroscience, Virginia Tech, Life Science I Room 217, 970 Washington Street SW, Blacksburg, VA, 24061, USA.
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Yasmin S, Kumar S, Azad GK. A computational study on mitogenome-encoded proteins of Pavo cristatus and Pavo muticus identifies key genetic variations with functional implications. J Genet Eng Biotechnol 2023; 21:80. [PMID: 37544976 PMCID: PMC10404576 DOI: 10.1186/s43141-023-00534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023]
Abstract
BACKGROUND The Pavo cristatus population, native to the Indian subcontinent, is thriving well in India. However, the Pavo muticus population, native to the tropical forests of Southeast Asia, has reduced drastically and has been categorised as an endangered group. To understand the probable genetic factors associated with the decline of P. muticus, we compared the mitogenome-encoded proteins (13 proteins) between these two species. RESULTS Our data revealed that the most frequent variant between these two species was mtND1, which had an alteration in 9.57% residues, followed by mtND5 and mtATP6. We extended our study on the rest of the proteins and observed that cytochrome c oxidase subunits 1, 2, and 3 do not have any change. The 3-dimensional structure of all 13 proteins was modeled using the Phyre2 programme. Our data show that most of the proteins are alpha helical, and the variations observed in P. muticus reside on the surface of the respective proteins. The effect of variation on protein function was also predicted, and our results show that amino acid substitution in mtND1 at 14 sites could be deleterious. Similarly, destabilising changes were observed in mtND1, 2, 3, 4, 5, and 6 and mtATP6-8 due to amino acid substitution in P. muticus. Furthermore, protein disorder scores were considerably altered in mtND1, 2, and 5 of P. muticus. CONCLUSIONS The results presented here strongly suggest that variations in mitogenome-encoded proteins of P. cristatus and P. muticus may alter their structure and functions. Subsequently, these variations could alter energy production and may correlate with the decline in the population of P. muticus.
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Affiliation(s)
- Shahla Yasmin
- Department of Zoology, Patna University, Patna, Bihar, India
| | - Sushant Kumar
- Molecular Biology Laboratory, Department of Zoology, Patna University, Patna, 800005, Bihar, India
| | - Gajendra Kumar Azad
- Molecular Biology Laboratory, Department of Zoology, Patna University, Patna, 800005, Bihar, India.
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Schniertshauer D, Wespel S, Bergemann J. Natural Mitochondria Targeting Substances and Their Effect on Cellular Antioxidant System as a Potential Benefit in Mitochondrial Medicine for Prevention and Remediation of Mitochondrial Dysfunctions. Curr Issues Mol Biol 2023; 45:3911-3932. [PMID: 37232719 DOI: 10.3390/cimb45050250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/27/2023] Open
Abstract
Based on the knowledge that many diseases are caused by defects in the metabolism of the cells and, in particular, in defects of the mitochondria, mitochondrial medicine starts precisely at this point. This new form of therapy is used in numerous fields of human medicine and has become a central focus within the field of medicine in recent years. With this form of therapy, the disturbed cellular energy metabolism and an out-of-balance antioxidant system of the patient are to be influenced to a greater extent. The most important tool here is mitotropic substances, with the help of which attempts are made to compensate for existing dysfunction. In this article, both mitotropic substances and accompanying studies showing their efficacy are summarized. It appears that the action of many mitotropic substances is based on two important properties. First, on the property of acting antioxidantly, both directly as antioxidants and via activation of downstream enzymes and signaling pathways of the antioxidant system, and second, via enhanced transport of electrons and protons in the mitochondrial respiratory chain.
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Affiliation(s)
- Daniel Schniertshauer
- Department of Life Sciences, Albstadt-Sigmaringen University of Applied Sciences, Anton-Günther-Str. 51, 72488 Sigmaringen, Germany
| | - Susanne Wespel
- Department of Life Sciences, Albstadt-Sigmaringen University of Applied Sciences, Anton-Günther-Str. 51, 72488 Sigmaringen, Germany
| | - Jörg Bergemann
- Department of Life Sciences, Albstadt-Sigmaringen University of Applied Sciences, Anton-Günther-Str. 51, 72488 Sigmaringen, Germany
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Monge-Ochoa B, Montoro L, Montoya J, Ruiz-Pesini E, López-Pérez MJ, de Castro F, Díez-Sánchez C. m.4216 T > C polymorphism in JT cluster determines a lower pregnancy rate in response to controlled ovarian stimulation treatment. J Assist Reprod Genet 2023; 40:671-682. [PMID: 36701026 PMCID: PMC10033795 DOI: 10.1007/s10815-023-02721-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 01/10/2023] [Indexed: 01/27/2023] Open
Abstract
PURPOSE To analyze the influence of Caucasian mitochondrial haplogroups on controlled ovarian stimulation outcome (COS), embryo (E), and pregnancy success. METHODS In a Caucasian population (n = 517) undergoing COS, mitochondrial haplogroups and physiological parameters were determined. Patients were classified, according to Bologna criteria, as good (>3)/poor ≤3) responder, on dependence of recruited oocytes (RO), and in pregnancy/non-pregnancy groups. Haplogroups were determined by sequencing mitochondrial hypervariable sequence I and confirmed by polymerase chain reaction (PCR), followed by restriction fragment length polymorphisms (RFLP). RESULTS The rank of total dose of FSH (TD FSH) was similar in all clusters/haplogroups, except in JT, which is narrower (950-3,650 IU), particularly in T (1,350-3,650 IU). The statistical analysis showed higher RO and E in JT when compared to U, although it was only Uk which accumulated significantly in pregnancy respect to JT. Pearson's correlations between TD FSH and RO showed negative statistical significance in all population (P = 0.001), H (P = 0.03), JT (P = 0.01), and T (P = 0.03). The percentage of contribution of TD FSH on RO was almost nine times in the JT cluster as compared to all population one. CONCLUSIONS JT cluster shows a different influence of TD FSH on RO. JT cluster shows higher RO and E than U, but it is Uk which exhibits a significant higher pregnancy rate than JT. The negative influence of the JT cluster on pregnancy success strongly suggests that the m.4216 T > C polymorphism could be responsible.
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Affiliation(s)
- Belén Monge-Ochoa
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - Luis Montoro
- Unidad de Reproducción Asistida, Hospital Universitario Príncipe de Asturias, Universidad Complutense de Madrid, Alcalá de Henares, Madrid, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria (IIS) de Aragón, Zaragoza, Spain
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
- Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria (IIS) de Aragón, Zaragoza, Spain
| | - Manuel J López-Pérez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain
| | - Francisco de Castro
- Unidad de Reproducción Asistida, Hospital Universitario Príncipe de Asturias, Universidad Complutense de Madrid, Alcalá de Henares, Madrid, Spain
| | - Carmen Díez-Sánchez
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, Zaragoza, Spain.
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Giannese D, Montano V, Lopriore P, Nesti C, LoGerfo A, Caligo MA, Dal Canto F, Pasquinelli G, Bonadio AG, Moriconi D, Siciliano G, Mancuso M. A Multisystem Mitochondrial Disease Caused by a Novel MT-TL1 mtDNA Variant: A Case Report. J Neuromuscul Dis 2023; 10:119-123. [PMID: 36404555 PMCID: PMC9881017 DOI: 10.3233/jnd-221526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
BACKGROUND Mitochondrial tRNA (MTT) genes are hotspot for mitochondrial DNA mutation and are responsible of half mitochondrial disease. MTT mutations are associated with a broad spectrum of phenotype often with complex multisystem involvement and complex genotype-phenotype correlations. MT-TL1 mutations, among which the m.3243A>G mutation is the most frequent, are associated with myopathy, maternal inherited diabetes and deafness, MELAS, cardiomyopathy, and focal segmental glomerulosclerosis. CASE STUDY Here we report the case of an Italian 49-years old female presenting with encephalomyopathy, chronic proteinuric kidney disease and a new heteroplasmic m.3274_3275delAC MT-TL1 gene mutation. CONCLUSIONS Our case demonstrates a systemic mitochondrial disease caused by the heteroplasmic m.3274_3275delAC MT-TL1 gene mutation, not yet described in the literature. A mitochondrial disease should be suspected in case of complex multisystem phenotypes, including steroid-resistant nephrotic syndrome with multisystemic involvement.
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Affiliation(s)
- Domenico Giannese
- Department of Clinical and Experimental Medicine, Nephrology, Transplant and Dialysis Division, University Hospital of Pisa, Pisa, Italy
| | - Vincenzo Montano
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Piervito Lopriore
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Claudia Nesti
- Molecular Medicine, IRCCS Fondazione Stella Maris, Pisa, Italy
| | - Annalisa LoGerfo
- Laboratory of Molecular Genetics, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | - Maria Adelaide Caligo
- Laboratory of Molecular Genetics, Azienda Ospedaliero-Universitaria Pisana, Pisa, Italy
| | | | - Gianandrea Pasquinelli
- Department of Experimental, Biotechnology and Methods in Laboratory Medicine, Diagnostic and Specialty Medicine (DIMES), University of Bologna, Bologna, Italy,Subcellular Nephro-Vascular Diagnostic Program, Pathology Unit, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Angelo Giovanni Bonadio
- Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Diego Moriconi
- Department of Surgical, Medical, Molecular and Critical Area Pathology, University of Pisa, Pisa, Italy
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy
| | - Michelangelo Mancuso
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Pisa, Italy,Correspondence to: Michelangelo Mancuso, MD, PhD, Department of Clinical and Experimental Medicine, Neurological Institute, University of Pisa, Pisa, Italy. E-mail:
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9
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Chen K, Lu P, Beeraka NM, Sukocheva OA, Madhunapantula SV, Liu J, Sinelnikov MY, Nikolenko VN, Bulygin KV, Mikhaleva LM, Reshetov IV, Gu Y, Zhang J, Cao Y, Somasundaram SG, Kirkland CE, Fan R, Aliev G. Mitochondrial mutations and mitoepigenetics: Focus on regulation of oxidative stress-induced responses in breast cancers. Semin Cancer Biol 2022; 83:556-569. [PMID: 33035656 DOI: 10.1016/j.semcancer.2020.09.012] [Citation(s) in RCA: 113] [Impact Index Per Article: 56.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 09/28/2020] [Accepted: 09/28/2020] [Indexed: 02/08/2023]
Abstract
Epigenetic regulation of mitochondrial DNA (mtDNA) is an emerging and fast-developing field of research. Compared to regulation of nucler DNA, mechanisms of mtDNA epigenetic regulation (mitoepigenetics) remain less investigated. However, mitochondrial signaling directs various vital intracellular processes including aerobic respiration, apoptosis, cell proliferation and survival, nucleic acid synthesis, and oxidative stress. The later process and associated mismanagement of reactive oxygen species (ROS) cascade were associated with cancer progression. It has been demonstrated that cancer cells contain ROS/oxidative stress-mediated defects in mtDNA repair system and mitochondrial nucleoid protection. Furthermore, mtDNA is vulnerable to damage caused by somatic mutations, resulting in the dysfunction of the mitochondrial respiratory chain and energy production, which fosters further generation of ROS and promotes oncogenicity. Mitochondrial proteins are encoded by the collective mitochondrial genome that comprises both nuclear and mitochondrial genomes coupled by crosstalk. Recent reports determined the defects in the collective mitochondrial genome that are conducive to breast cancer initiation and progression. Mutational damage to mtDNA, as well as its overproliferation and deletions, were reported to alter the nuclear epigenetic landscape. Unbalanced mitoepigenetics and adverse regulation of oxidative phosphorylation (OXPHOS) can efficiently facilitate cancer cell survival. Accordingly, several mitochondria-targeting therapeutic agents (biguanides, OXPHOS inhibitors, vitamin-E analogues, and antibiotic bedaquiline) were suggested for future clinical trials in breast cancer patients. However, crosstalk mechanisms between altered mitoepigenetics and cancer-associated mtDNA mutations remain largely unclear. Hence, mtDNA mutations and epigenetic modifications could be considered as potential molecular markers for early diagnosis and targeted therapy of breast cancer. This review discusses the role of mitoepigenetic regulation in cancer cells and potential employment of mtDNA modifications as novel anti-cancer targets.
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Affiliation(s)
- Kuo Chen
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China; Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Pengwei Lu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Narasimha M Beeraka
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Olga A Sukocheva
- Discipline of Health Sciences, College of Nursing and Health Sciences, Flinders University, Bedford Park, South Australia, 5042, Australia
| | - SubbaRao V Madhunapantula
- Center of Excellence in Regenerative Medicine and Molecular Biology (CEMR), Department of Biochemistry, JSS Academy of Higher Education and Research (JSS AHER), Mysuru, Karnataka, India
| | - Junqi Liu
- Cancer Center, The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Str., Zhengzhou, 450052, China
| | - Mikhail Y Sinelnikov
- Institue for Regenerative Medicine, I.M. Sechenov First Moscow State Medical University (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Vladimir N Nikolenko
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Kirill V Bulygin
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Department of Normal and Topographic Anatomy, Faculty of Fundamental Medicine, M.V. Lomonosov Moscow State University (MSU), 31-5 Lomonosovsky Prospect, 117192, Moscow, Russia
| | - Liudmila M Mikhaleva
- Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation
| | - Igor V Reshetov
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yuanting Gu
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China
| | - Jin Zhang
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Yu Cao
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia
| | - Siva G Somasundaram
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Cecil E Kirkland
- Department of Biological Sciences, Salem University, 223 West Main Street Salem, WV, 26426, USA
| | - Ruitai Fan
- The First Affiliated Hospital of Zhengzhou University, 1 Jianshedong Street, Zhengzhou, 450052, China.
| | - Gjumrakch Aliev
- I.M. Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), 8/2 Trubetskaya Street, Moscow, 119991, Russia; Research Institute of Human Morphology, 3 Tsyurupy Street, Moscow, 117418, Russian Federation; Institute of Physiologically Active Compounds of Russian Academy of Sciences, Severny pr. 1, Chernogolovka, Moscow Region, 142432, Russia; GALLY International Research Institute, 7733 Louis Pasteur Drive, #330, San Antonio, TX, 78229, USA
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10
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The SNPs of mitochondrial DNA displacement loop region and mitochondrial DNA copy number associated with risk of polymyositis and dermatomyositis. Sci Rep 2022; 12:5903. [PMID: 35393495 PMCID: PMC8990067 DOI: 10.1038/s41598-022-09943-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Accepted: 03/30/2022] [Indexed: 12/24/2022] Open
Abstract
Oxidative damage-induced mitochondrial dysfunction may activate muscle catabolism and autophagy pathways to initiate muscle weakening in idiopathic inflammatory myopathies (IIMs). In this study, Single nucleotide polymorphisms (SNPs) in the mitochondrial displacement loop (D-loop) and mitochondrial DNA (mtDNA) copy number were assessed and their association with the risk of polymyositis and dermatomyositis (PM/DM) was evaluated. Excessive D-loop SNPs (8.779 ± 1.912 vs. 7.972 ± 1.903, p = 0.004) correlated positively with mtDNA copy number (0.602 ± 0.457 vs. 0.300 ± 0.118, p < 0.001). Compared with that of the controls, the mtDNA of PM/DM patients showed D-loop SNP accumulation. In addition, the distribution frequencies of 16304C (p = 0.047) and 16519C (p = 0.043) were significantly higher in the patients with PM/DM. Subsequent analysis showed that reactive oxygen species (ROS) generation was increased in PM/DM patients compared with that in the controls (18,477.756 ± 13,574.916 vs. 14,484.191 ± 5703.097, p = 0.012). Further analysis showed that the PM/DM risk-related allele 16304C was significantly associated with lower IL-4 levels (p = 0.021), while 16519C had a trend to be associated with higher IL-2 expression (p = 0.064). The allele 16519C was associated with a positive antinuclear antibody (ANA) status in PM/DM patients (p = 0.011). Our findings suggest that mitochondrial D-loop SNPs could be potential biomarkers for PM/DM risk and these SNPs associated with cytokine expression may be involved in the development of PM/DM. Further, mtDNA copy number-mediated mitochondrial dysfunction may precede the onset of PM/DM.
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11
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Manini A, Abati E, Comi GP, Corti S, Ronchi D. Mitochondrial DNA homeostasis impairment and dopaminergic dysfunction: A trembling balance. Ageing Res Rev 2022; 76:101578. [PMID: 35114397 DOI: 10.1016/j.arr.2022.101578] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 12/26/2021] [Accepted: 01/28/2022] [Indexed: 02/07/2023]
Abstract
Maintenance of mitochondrial DNA (mtDNA) homeostasis includes a variety of processes, such as mtDNA replication, repair, and nucleotides synthesis, aimed at preserving the structural and functional integrity of mtDNA molecules. Mutations in several nuclear genes (i.e., POLG, POLG2, TWNK, OPA1, DGUOK, MPV17, TYMP) impair mtDNA maintenance, leading to clinical syndromes characterized by mtDNA depletion and/or deletions in affected tissues. In the past decades, studies have demonstrated a progressive accumulation of multiple mtDNA deletions in dopaminergic neurons of the substantia nigra in elderly population and, to a greater extent, in Parkinson's disease patients. Moreover, parkinsonism has been frequently described as a prominent clinical feature in mtDNA instability syndromes. Among Parkinson's disease-related genes with a significant role in mitochondrial biology, PARK2 and LRRK2 specifically take part in mtDNA maintenance. Moreover, a variety of murine models (i.e., "Mutator", "MitoPark", "PD-mitoPstI", "Deletor", "Twinkle-dup" and "TwinkPark") provided in vivo evidence that mtDNA stability is required to preserve nigrostriatal integrity. Here, we review and discuss the clinical, genetic, and pathological background underlining the link between impaired mtDNA homeostasis and dopaminergic degeneration.
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12
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Fu H, Sun J, Xu X. The mitochondrial tRNAAsp T7561C, tRNAHis C12153T and A12172G mutations may be associated with essential hypertension in a Han Chinese pedigree. Hum Hered 2022; 87:000524163. [PMID: 35344953 DOI: 10.1159/000524163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 02/28/2022] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Mutations in mitochondrial tRNA (mt-tRNA) are the important causes for maternally inherited hypertension, however, the pathophysiology of mt-tRNA mutations in clinical expression of hypertension remains poorly understood. MATERIAL AND METHODS In this study, we report the molecular features of a Han Chinese pedigree with maternally transmitted essential hypertension. The entire mitochondrial genomes are PCR amplified and sequenced, Moreover, phylogenetic analysis, haplogroup analysis, as well as pathogenicity scoring system are used to assess the potential roles for mtDNA mutations. RESULTS Strikingly, among ten matrilineal relatives, three of them suffer from variable degree of hypertension at different age at onset. Sequence analysis of the complete mitochondrial genomes suggests the presence of three possible pathogenic mtDNA mutations: tRNAAsp T7561C, tRNAHis C12153T and A12172G, together with a set of variants belonging to East Asian mitochondrial haplogroup M7a. Interestingly, the T7561C mutation occurs at position 44 in the variable region of tRNAAsp, while the C12153T and A12172G mutations are localized at extremely conserved nucleotides in the D-arm and anticodon stem of tRNAHis gene, respectively, which are critical for tRNA steady-state level and function. CONCLUSIONS Mitochondrial T7561C, C12153T and A12172G mutations may lead to the failure in tRNAs metabolism, and cause mitochondrial dysfunction that is responsible for hypertension. However, the homoplasmy form of mt-tRNA mutations, incomplete penetrance of hypertension suggest that T7561C, C12153T and A12172G mutations are insufficient to produce the clinical phenotype, hence, other risk factors such as environmental factors, nuclear genes and epigenetic modifications may contribute to the phenotypic manifestation of maternally inherited hypertension in this Chinese pedigree.
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Use of Next-Generation Sequencing for Identifying Mitochondrial Disorders. Curr Issues Mol Biol 2022; 44:1127-1148. [PMID: 35723297 PMCID: PMC8947152 DOI: 10.3390/cimb44030074] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 02/18/2022] [Accepted: 02/24/2022] [Indexed: 12/06/2022] Open
Abstract
Mitochondria are major contributors to ATP synthesis, generating more than 90% of the total cellular energy production through oxidative phosphorylation (OXPHOS): metabolite oxidation, such as the β-oxidation of fatty acids, and the Krebs’s cycle. OXPHOS inadequacy due to large genetic lesions in mitochondrial as well as nuclear genes and homo- or heteroplasmic point mutations in mitochondrially encoded genes is a characteristic of heterogeneous, maternally inherited genetic disorders known as mitochondrial disorders that affect multisystemic tissues and organs with high energy requirements, resulting in various signs and symptoms. Several traditional diagnostic approaches, including magnetic resonance imaging of the brain, cardiac testing, biochemical screening, variable heteroplasmy genetic testing, identifying clinical features, and skeletal muscle biopsies, are associated with increased risks, high costs, a high degree of false-positive or false-negative results, or a lack of precision, which limits their diagnostic abilities for mitochondrial disorders. Variable heteroplasmy levels, mtDNA depletion, and the identification of pathogenic variants can be detected through genetic sequencing, including the gold standard Sanger sequencing. However, sequencing can be time consuming, and Sanger sequencing can result in the missed recognition of larger structural variations such as CNVs or copy-number variations. Although each sequencing method has its own limitations, genetic sequencing can be an alternative to traditional diagnostic methods. The ever-growing roster of possible mutations has led to the development of next-generation sequencing (NGS). The enhancement of NGS methods can offer a precise diagnosis of the mitochondrial disorder within a short period at a reasonable expense for both research and clinical applications.
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14
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Mitochondrial calcium uniporter is essential for hearing and hair cell preservation in congenic FVB/NJ mice. Sci Rep 2021; 11:9660. [PMID: 33958614 PMCID: PMC8102556 DOI: 10.1038/s41598-021-88841-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/13/2021] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial Ca2+ regulates a wide range of cell processes, including morphogenesis, metabolism, excitotoxicity, and survival. In cochlear hair cells, the activation of mechano-electrical transduction and voltage-gated Ca2+ channels result in a large influx of Ca2+. The intracellular rise in Ca2+ is partly balanced by the mitochondria which rapidly uptakes Ca2+ via a highly selective channel comprised of the main pore-forming subunit, the mitochondrial Ca2+ uniporter (MCU), and associated regulatory proteins. MCU thus contributes to Ca2+ buffering, ensuring cytosolic homeostasis, and is posited to have a critical role in hair cell function and hearing. To test this hypothesis, Ca2+ homeostasis in hair cells and cochlear function were investigated in FVB/NJ mice carrying the knockout allele of Mcu (Mcu+/− or Mcu−/−). The Mcu knockout allele, which originated in C57BL/6 strain cosegregated along with Cdh23ahl allele to the FVB/NJ strain, due to the close proximity of these genes. Neither Mcu+/− nor Mcu−/− genotypes affected cochlear development, morphology, or Ca2+ homeostasis of auditory hair cells in the first two postnatal weeks. However, Mcu−/− mice displayed high-frequency hearing impairment as early as 3 weeks postnatal, which then progressed to profound hearing loss at all frequencies in about 6 months. In Mcu+/− mice, significantly elevated ABR thresholds were observed at 6 months and 9 months of age only at 32 kHz frequency. In three-month-old Mcu−/− mice, up to 18% of the outer hair cells and occasionally some inner hair cells were missing in the mid-cochlear region. In conclusion, mitochondrial Ca2+ uniporter is not required for the development of cochlea in mice, but is essential for hearing and hair cell preservation in congenic FVB/NJ mice.
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15
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Oishi N, Kubota D, Nakamoto K, Takeda Y, Hayashi M, Gocho K, Yamaki K, Igarashi T, Takahashi H, Kameya S. Multimodal imaging analysis of macular dystrophy in patient with maternally inherited diabetes and deafness (MIDD) with m.3243A>G mutation. Ophthalmic Genet 2021; 42:304-311. [PMID: 33541179 DOI: 10.1080/13816810.2021.1881978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Purpose: Maternally inherited diabetes and deafness (MIDD) is caused by a heteroplasmic m.3243A>G mutation in the mitochondrial DNA. The main ocular feature in MIDD is macular dystrophy. The purpose of this study was to identify the phenotypical characteristics of a patient with MIDD by multimodal high-resolution imaging analyses.Methods: A detailed history and ophthalmic examination were performed on a 39-year-old patient with MIDD. Multi-modal imaging included fundus photography, fundus autofluorescence imaging, fluorescein angiography, spectral-domain optical coherence tomography, OCT-angiography, and adaptive optics imaging. The PCR-invader and whole exome sequencing (WES) methods were performed on the DNA of the patient.Results: A 39-year-old woman with sensorineural hearing loss, diabetes mellitus presented with atrophic perifoveal changes and MIDD was suspected. The PCR-invader and WES methods showed that the patient had a m.3243A>G mutation in the mitochondrial DNA with 29% and 16.7% of the heteroplasmy in the peripheral blood, respectively. Morphological analyses revealed that the areas of photoreceptor degeneration and chorioretinal atrophy were present mainly in the perifoveal region. Multifocal ERGs showed that the perifoveal responses were reduced. Goldmann visual field was significant for a cecocentral scotoma in the right eye and an enlarged blind spot in the left eye. The central isopter was constricted bilaterally. The results of high-resolution retinal imaging by AO revealed that the densities of the cone photoreceptor were significantly reduced in the fovea where no obvious atrophy of the RPE and choroid was observed.Conclusions: Our findings indicate that WES analysis can be used to detect the m.3243A>G mutation in the mtDNA. The results of multimodal imaging analyses indicated that the primary dysfunction of the photoreceptors in the fovea might precede the dysfunction of the RPE in patient with MIDD.
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Affiliation(s)
- Noriko Oishi
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, Inzai, Chiba, Japan
| | - Daiki Kubota
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, Inzai, Chiba, Japan
| | - Kenji Nakamoto
- Department of Ophthalmology, Nippon Medical School, Tokyo, Japan
| | - Yukito Takeda
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, Inzai, Chiba, Japan
| | - Mika Hayashi
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, Inzai, Chiba, Japan
| | - Kiyoko Gocho
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, Inzai, Chiba, Japan.,Clinical Investigation Center 1423, Inserm and Quinze-Vingts National Ophthalmology Hospital, Paris, France
| | - Kunihiko Yamaki
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, Inzai, Chiba, Japan
| | - Tsutomu Igarashi
- Department of Ophthalmology, Nippon Medical School, Tokyo, Japan
| | | | - Shuhei Kameya
- Department of Ophthalmology, Nippon Medical School Chiba Hokusoh Hospital, Inzai, Chiba, Japan
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16
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Montano V, Gruosso F, Simoncini C, Siciliano G, Mancuso M. Clinical features of mtDNA-related syndromes in adulthood. Arch Biochem Biophys 2020; 697:108689. [PMID: 33227288 DOI: 10.1016/j.abb.2020.108689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 11/06/2020] [Accepted: 11/15/2020] [Indexed: 01/26/2023]
Abstract
Mitochondrial diseases are the most common inheritable metabolic diseases, due to defects in oxidative phosphorylation. They are caused by mutations of nuclear or mitochondrial DNA in genes involved in mitochondrial function. The peculiarity of "mitochondrial DNA genetics rules" in part explains the marked phenotypic variability, the complexity of genotype-phenotype correlations and the challenge of genetic counseling. The new massive genetic sequencing technologies have changed the diagnostic approach, enhancing mitochondrial DNA-related syndromes diagnosis and often avoiding the need of a tissue biopsy. Here we present the most common phenotypes associated with a mitochondrial DNA mutation with the recent advances in diagnosis and in therapeutic perspectives.
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Affiliation(s)
- V Montano
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Italy
| | - F Gruosso
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Italy
| | - C Simoncini
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Italy
| | - G Siciliano
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Italy
| | - M Mancuso
- Department of Clinical and Experimental Medicine, Neurological Clinic, University of Pisa, Italy.
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17
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Jaberi E, Tresse E, Grønbæk K, Weischenfeldt J, Issazadeh-Navikas S. Identification of unique and shared mitochondrial DNA mutations in neurodegeneration and cancer by single-cell mitochondrial DNA structural variation sequencing (MitoSV-seq). EBioMedicine 2020; 57:102868. [PMID: 32629384 PMCID: PMC7334819 DOI: 10.1016/j.ebiom.2020.102868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023] Open
Abstract
Background Point mutations and structural variations (SVs) in mitochondrial DNA (mtDNA) contribute to many neurodegenerative diseases. Technical limitations and heteroplasmy, however, have impeded their identification, preventing these changes from being examined in neurons in healthy and disease states. Methods We have developed a high-resolution technique—Mitochondrial DNA Structural Variation Sequencing (MitoSV-seq)—that identifies all types of mtDNA SVs and single-nucleotide variations (SNVs) in single neurons and novel variations that have been undetectable with conventional techniques. Findings Using MitoSV-seq, we discovered SVs/SNVs in dopaminergic neurons in the Ifnar1−/− murine model of Parkinson disease. Further, MitoSV-seq was found to have broad applicability, delivering high-quality, full-length mtDNA sequences in a species-independent manner from human PBMCs, haematological cancers, and tumour cell lines, regardless of heteroplasmy. We characterised several common SVs in haematological cancers (AML and MDS) that were linked to the same mtDNA region, MT-ND5, using only 10 cells, indicating the power of MitoSV-seq in determining single-cancer-cell ontologies. Notably, the MT-ND5 hotspot, shared between all examined cancers and Ifnar1−/− dopaminergic neurons, suggests that its mutations have clinical value as disease biomarkers. Interpretation MitoSV-seq identifies disease-relevant mtDNA mutations in single cells with high resolution, rendering it a potential drug screening platform in neurodegenerative diseases and cancers. Funding The Lundbeck Foundation, Danish Council for Independent Research-Medicine, and European Union Horizon 2020 Research and Innovation Programme.
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Affiliation(s)
- Elham Jaberi
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Emilie Tresse
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Kirsten Grønbæk
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; Department of Hematology, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, DK-2200 Copenhagen, Denmark
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Shohreh Issazadeh-Navikas
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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18
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Zereg E, Chaussenot A, Morel G, Bannwarth S, Sacconi S, Soriani MH, Attarian S, Cano A, Pouget J, Bellance R, Tranchant C, Lannes B, de Paula AM, Saadi Ait-El-Mkadem S, Chafino B, Berthet M, Fragaki K, Paquis-Flucklinger V, Rouzier C. Single-fiber studies for assigning pathogenicity of eight mitochondrial DNA variants associated with mitochondrial diseases. Hum Mutat 2020; 41:1394-1406. [PMID: 32419253 DOI: 10.1002/humu.24037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/29/2020] [Accepted: 04/19/2020] [Indexed: 12/21/2022]
Abstract
Whole mitochondrial DNA (mtDNA) sequencing is now systematically used in clinical laboratories to screen patients with a phenotype suggestive of mitochondrial disease. Next Generation Sequencing (NGS) has significantly increased the number of identified pathogenic mtDNA variants. Simultaneously, the number of variants of unknown significance (VUS) has increased even more, thus challenging their interpretation. Correct classification of the variants' pathogenicity is essential for optimal patient management, including treatment and genetic counseling. Here, we used single muscle fiber studies to characterize eight heteroplasmic mtDNA variants, among which were three novel variants. By applying the pathogenicity scoring system, we classified four variants as "definitely pathogenic" (m.590A>G, m.9166T>C, m.12293G>A, and m.15958A>T). Two variants remain "possibly pathogenic" (m.4327T>C and m.5672T>C) but should these be reported in a different family, they would be reclassified as "definitely pathogenic." We also illustrate the contribution of single-fiber studies to the diagnostic approach in patients harboring pathogenic variants with low level heteroplasmy.
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Affiliation(s)
- Elamine Zereg
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France
| | - Annabelle Chaussenot
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Godelieve Morel
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France
| | - Sylvie Bannwarth
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Sabrina Sacconi
- Department of Clinical Neurosciences, Neuromuscular Diseases Centre, Nice Teaching Hospital, Nice, France
| | - Marie-Hélène Soriani
- Department of Clinical Neurosciences, Neuromuscular Diseases Centre, Nice Teaching Hospital, Nice, France
| | - Shahram Attarian
- Neurology Department, Referral Center for ALS and Neuromuscular Diseases, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Aline Cano
- Pediatric Neurology Department, Reference Center for Inherited Metabolic Diseases, Timone Hospital, Marseille, France
| | - Jean Pouget
- Neurology Department, Referral Center for ALS and Neuromuscular Diseases, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Rémi Bellance
- Neuromyology Department, Neuromuscular Reference Center, Fort-de-France Teaching Hospital, Fort-de-France, France
| | - Christine Tranchant
- Department of Movement Pathology, Strasbourg Teaching Hospital, Strasbourg, France
| | - Béatrice Lannes
- Pathology Department, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - André Maues de Paula
- Pathology Department, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Samira Saadi Ait-El-Mkadem
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Bernadette Chafino
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France
| | - Mathieu Berthet
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France
| | - Konstantina Fragaki
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Véronique Paquis-Flucklinger
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Cécile Rouzier
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
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Abstract
Modern broilers show dramatic growth over a short interval and contribute directly to the success of the poultry meat industry. The growth performance of commercial broilers is a result of genetic selection for "performance traits", such as body size, meat yield, and feed conversion rate. However, due to the rapid growth rate of modern commercial broilers, several growth-related conditions have arisen, increasing economic losses and consumer concerns. Among the most economically consequential is the muscle disorder called wooden breast. Together with associated myopathies such as white striping and spaghetti meat, wooden breast is causing losses of $200 million a year in the U.S. alone and occurs worldwide. No causative factors are known for wooden breast to date. Wooden breast can affect over 80% of broilers in a flock, yet no methods of amelioration are currently available. Overall, the evidence suggests that wooden breast is a genetic, age-dependent condition associated with fast growth rate. The primary features of wooden breast are muscle degeneration and fibrosis, high levels of oxidative stress, hypoxia, and altered energy metabolism. Recent work has also implicated reduced pectoral vessel density in the pathogenesis of wooden breast. This review examines the history of myopathies in commercial broilers and the relationship of myopathies to metabolism and oxidative performance. This review summarizes the foundational knowledge of wooden breast and provides a platform for further investigation of wooden breast.
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20
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Çağdaş D, Sürücü N, Tan Ç, Kayaoğlu B, Özgül RK, Akkaya-Ulum YZ, Aydınoğlu AT, Aytaç S, Gümrük F, Balci-Hayta B, Balci-Peynircioğlu B, Özen S, Gürsel M, Tezcan İ. Autoinflammation in addition to combined immunodeficiency: SLC29A3 gene defect. Mol Immunol 2020; 121:28-37. [PMID: 32151906 DOI: 10.1016/j.molimm.2020.02.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/08/2020] [Accepted: 02/20/2020] [Indexed: 01/01/2023]
Abstract
INTRODUCTION H Syndrome is an autosomal recessive (AR) disease caused by defects in SLCA29A3 gene. This gene encodes the equilibrative nucleoside transporter, the protein which is highly expressed in spleen, lymph node and bone marrow. Autoinflammation and autoimmunity accompanies H Syndrome (HS). AIM The aim was to further elucidate the mechanisms of disease by molecular studies in a patient with SLC29A3 gene defect. PATIENT AND METHODS Mitochondrial dysfunction, lysosomal integrity, cytokine response in response to stimulation with different pattern recognition receptor ligands, and circulating cell-free mitochondrial-DNA(ccf-mtDNA) level in plasma were analyzed compared to controls to understand the cellular triggers of autoinflammation. RNA sequencing (RS) analyses were also performed in monocytes before/after culture with lipopolysaccharide. RESULTS Patient had progressive destructive arthropathy in addition to clinical findings due to combined immunodeficiency. Pure red cell aplasia (PRCA), vitiligo, diabetes, multiple autoantibody positivity, lymphopenia, increased acute phase reactants were present. Recent thymic emigrants (RTE), naïve T cells were decreased, effector memory CD4 + T cells, nonclassical inflammatory monocytes were increased. Patient's peripheral blood mononuclear cells secreted more IL-1β and IL-6, showed lysosomal disruption and significant mitochondrial dysfunction compared to healthy controls. Plasma ccf-mtDNA level was significantly elevated compared to age-matched controls (p < 0.05). RNA sequencing studies revealed decreased expression of NLR Family Caspase Recrument-Domain Containing 4(NLRC4), 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 4(PFKFB4), serine dehydratase(SDS), heparan sulfate(Glucosamine) 3-O-sulfotransferase 1(HS3ST1), neutral cholesterol ester hydrolase 1 (NCEH1), and interleukin-8 (IL-8) in patient's monocytes compared to controls. Longstanding PRCA, which is possibly autoimmune, resolved after initiating monthly intravenous immunoglobulins (IVIG) and low dose steroids to the patient. CONCLUSION Although autoinflammation and autoimmunity are reported in HS, by functional analyses we here show in the present patient that over-active inflammasome pathway in HS might be related with mitochondrial and lysosomal dysfunction. Increased plasma ccf-mtDNA may be used as a biomarker of inflammasomopathy in HS. HS should be included in the classification of primary immunodeficiency diseases.
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Affiliation(s)
- Deniz Çağdaş
- Department of Pediatric Immunology, Hacettepe University Medical Faculty, Ankara, Turkey.
| | - Naz Sürücü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Çağman Tan
- Institute of Child Health, Hacettepe University Medical Faculty, Ankara, Turkey
| | - Başak Kayaoğlu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Rıza Köksal Özgül
- Department of Pediatric Metabolism, Hacettepe University Medical Faculty, Ankara, Turkey
| | - Yeliz Z Akkaya-Ulum
- Department of Medical Biology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Ayşe Tülay Aydınoğlu
- Department of Medical Biology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | - Selin Aytaç
- Department of Pediatric Hematology, Hacettepe University Medical Faculty, Ankara, Turkey
| | - Fatma Gümrük
- Department of Pediatric Hematology, Hacettepe University Medical Faculty, Ankara, Turkey
| | - Burcu Balci-Hayta
- Department of Medical Biology, Hacettepe University Faculty of Medicine, Ankara, Turkey
| | | | - Seza Özen
- Department of Pediatric Rheumatology, Hacettepe University Medical Faculty, Ankara, Turkey
| | - Mayda Gürsel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İlhan Tezcan
- Department of Pediatric Immunology, Hacettepe University Medical Faculty, Ankara, Turkey
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21
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Vitale O, Preste R, Palmisano D, Attimonelli M. A data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information. Mol Genet Genomic Med 2019; 8:e1085. [PMID: 31821723 PMCID: PMC7005629 DOI: 10.1002/mgg3.1085] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/24/2019] [Accepted: 10/30/2019] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Human mitochondrial DNA has an important role in the cellular energy production through oxidative phosphorylation. Therefore, this process may be the cause and have an effect on mitochondrial DNA mutability, functional alteration, and disease onset related to a wide range of different clinical expressions and phenotypes. Although a large part of the observed variations is fixed in a population and hence expected to be benign, the estimation of the degree of the pathogenicity of any possible human mitochondrial DNA variant is clinically pivotal. METHODS In this scenario, the establishment of standard criteria based on functional studies is required. In this context, a "data and text mining" pipeline is proposed here, developed using the programming language R, capable of extracting information regarding mitochondrial DNA functional studies and related clinical assessments from the literature, thus improving the annotation of human mitochondrial variants reported in the HmtVar database. RESULTS The data mining pipeline has produced a list of 1,073 Pubmed IDs (PMIDs) from which the text mining pipeline has retrieved information on 932 human mitochondrial variants regarding experimental validation and clinical features. CONCLUSIONS The application of the pipeline will contribute to supporting the interpretation of pathogenicity of human mitochondrial variants by facilitating diagnosis to clinicians and researchers faced with this task.
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Affiliation(s)
- Ornella Vitale
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Roberto Preste
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Donato Palmisano
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
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Abstract
The maternally inherited mitochondrial DNA (mtDNA) is a circular 16,569bp double stranded DNA that encodes 37 genes, 24 of which (2 rRNAs and 22 tRNAs) are necessary for transcription and translation of 13 polypeptides that are all subunits of respiratory chain. Pathogenic mutations in mtDNA cause respiratory chain dysfunction, and are the underlying defect in an ever-increasing number of mtDNA-related encephalomyopathies with distinct phenotypes. In this chapter, we present an overview of mtDNA mutations and describe the molecular techniques currently employed in our laboratory to detect two types of mtDNA mutations: single-large-scale rearrangements and point mutations.
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23
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Yao Y, Nishimura M, Murayama K, Kuranobu N, Tojo S, Beppu M, Ishige T, Itoga S, Tsuchida S, Mori M, Takayanagi M, Yokoyama M, Yamagata K, Kishita Y, Okazaki Y, Nomura F, Matsushita K, Tanaka T. A simple method for sequencing the whole human mitochondrial genome directly from samples and its application to genetic testing. Sci Rep 2019; 9:17411. [PMID: 31757988 PMCID: PMC6874554 DOI: 10.1038/s41598-019-53449-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 10/31/2019] [Indexed: 12/23/2022] Open
Abstract
Next-generation sequencing (NGS) is a revolutionary sequencing technology for analyzing genomes. However, preprocessing methods for mitochondrial DNA (mtDNA) sequencing remain complex, and it is required to develop an authenticated preprocessing method. Here, we developed a simple and easy preprocessing method based on isothermal rolling circle mtDNA amplification using commercially available reagents. Isothermal amplification of mtDNA was successfully performed using both nanoliter quantities of plasma directly and 25 ng of total DNA extracted from blood or tissue samples. Prior to mtDNA amplification, it was necessary to treat the extracted total DNA with Exonuclease V, but it was not required to treat plasma. The NGS libraries generated from the amplified mtDNA provided sequencing coverage of the entire human mitochondrial genome. Furthermore, the sequencing results successfully detected heteroplasmy in patient samples, with called mutations and variants matching those from previous, independent, Sanger sequencing analysis. Additionally, a novel single nucleotide variant was detected in a healthy volunteer. The successful analysis of mtDNA using very small samples from patients is likely to be valuable in clinical medicine, as it could reduce patient discomfort by reducing sampling-associated damage to tissues. Overall, the simple and convenient preprocessing method described herein may facilitate the future development of NGS-based clinical and forensic mtDNA tests.
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Affiliation(s)
- Yue Yao
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Motoi Nishimura
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kei Murayama
- Division of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Naomi Kuranobu
- Division of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Satomi Tojo
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Minako Beppu
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Sakae Itoga
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Sachio Tsuchida
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Masato Mori
- Department of Pediatrics, Matsudo City Hospital, Matsudo, 270-2296, Japan
| | - Masaki Takayanagi
- Division of Metabolism, Chiba Children's Hospital, Chiba, 266-0007, Japan
| | - Masataka Yokoyama
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kazuyuki Yamagata
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Yoshihito Kishita
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Yasushi Okazaki
- Diagnostics and Therapeutics of Intractable Diseases, Intractable Disease Research Center, Graduate School of Medicine, Juntendo University, Hongo 2-1-1, Bunkyo-ku, Tokyo, 113-8421, Japan
| | - Fumio Nomura
- Division of Clinical Mass Spectrometry, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Clinical Genetics and Proteomics, Chiba University Hospital, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan
| | - Tomoaki Tanaka
- Department of Molecular Diagnosis, Graduate School of Medicine, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba, 260-8670, Japan.
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24
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Al Khatib I, Shutt TE. Advances Towards Therapeutic Approaches for mtDNA Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:217-246. [PMID: 31452143 DOI: 10.1007/978-981-13-8367-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondria maintain and express their own genome, referred to as mtDNA, which is required for proper mitochondrial function. While mutations in mtDNA can cause a heterogeneous array of disease phenotypes, there is currently no cure for this collection of diseases. Here, we will cover characteristics of the mitochondrial genome important for understanding the pathology associated with mtDNA mutations, and review recent approaches that are being developed to treat and prevent mtDNA disease. First, we will discuss mitochondrial replacement therapy (MRT), where mitochondria from a healthy donor replace maternal mitochondria harbouring mutant mtDNA. In addition to ethical concerns surrounding this procedure, MRT is only applicable in cases where the mother is known or suspected to carry mtDNA mutations. Thus, there remains a need for other strategies to treat patients with mtDNA disease. To this end, we will also discuss several alternative means to reduce the amount of mutant mtDNA present in cells. Such methods, referred to as heteroplasmy shifting, have proven successful in animal models. In particular, we will focus on the approach of targeting engineered endonucleases to specifically cleave mutant mtDNA. Together, these approaches offer hope to prevent the transmission of mtDNA disease and potentially reduce the impact of mtDNA mutations.
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Affiliation(s)
- Iman Al Khatib
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Timothy E Shutt
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.
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25
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Boggan RM, Lim A, Taylor RW, McFarland R, Pickett SJ. Resolving complexity in mitochondrial disease: Towards precision medicine. Mol Genet Metab 2019; 128:19-29. [PMID: 31648942 DOI: 10.1016/j.ymgme.2019.09.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 12/12/2022]
Abstract
Mitochondrial diseases, caused by mutations in either the nuclear or mitochondrial genomes (mtDNA), are the most common form of inherited neurometabolic disorders. They are remarkably heterogeneous, both in their clinical presentation and genetic etiology, presenting challenges for diagnosis, clinical management and elucidation of molecular mechanism. The multifaceted nature of these diseases, compounded by the unique characteristics of mitochondrial genetics, cement their space in the field of complex disease. In this review we examine the m.3243A>G variant, one of the most prevalent mitochondrial DNA mutations, using it as an exemplar to demonstrate the challenges presented by these complex disorders. Disease caused by m.3243A>G is one of the most phenotypically diverse of all mitochondrial diseases; we outline known causes of this heterogeneity including mtDNA heteroplasmy, mtDNA copy number and nuclear genetic factors. We consider the impact that this has in the clinic, discussing the personalized management of common manifestations attributed to this pathogenic mtDNA variant, including hearing impairment, diabetes mellitus, myopathy, cardiac disease, stroke-like episodes and gastrointestinal disturbances. Future research into this complex disorder must account for this heterogeneity, benefitting from the use of large patient cohorts to build upon current clinical expertise. Through multi-disciplinary collaboration, the complexities of this mitochondrial disease can be addressed with the variety of diagnostic, prognostic, and treatment approaches that are moulded to best fit the needs of each individual patient.
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Affiliation(s)
- Róisín M Boggan
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Albert Lim
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK.
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research, Institute of Neuroscience, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
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26
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Affiliation(s)
- Marcelo Matiello
- From the Departments of Neurology (M.M., M.B.) and Pediatrics (A.K.), Massachusetts General Hospital, the Departments of Neurology (M.M., M.B.), Radiology (A.F.J.), and Pediatrics (A.K.), Harvard Medical School, and the Department of Radiology, Massachusetts Eye and Ear Infirmary (A.F.J.) - all in Boston
| | - Amy F Juliano
- From the Departments of Neurology (M.M., M.B.) and Pediatrics (A.K.), Massachusetts General Hospital, the Departments of Neurology (M.M., M.B.), Radiology (A.F.J.), and Pediatrics (A.K.), Harvard Medical School, and the Department of Radiology, Massachusetts Eye and Ear Infirmary (A.F.J.) - all in Boston
| | - Michael Bowley
- From the Departments of Neurology (M.M., M.B.) and Pediatrics (A.K.), Massachusetts General Hospital, the Departments of Neurology (M.M., M.B.), Radiology (A.F.J.), and Pediatrics (A.K.), Harvard Medical School, and the Department of Radiology, Massachusetts Eye and Ear Infirmary (A.F.J.) - all in Boston
| | - Amel Karaa
- From the Departments of Neurology (M.M., M.B.) and Pediatrics (A.K.), Massachusetts General Hospital, the Departments of Neurology (M.M., M.B.), Radiology (A.F.J.), and Pediatrics (A.K.), Harvard Medical School, and the Department of Radiology, Massachusetts Eye and Ear Infirmary (A.F.J.) - all in Boston
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27
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Fujimoto C, Yamasoba T. Mitochondria-Targeted Antioxidants for Treatment of Hearing Loss: A Systematic Review. Antioxidants (Basel) 2019; 8:E109. [PMID: 31022870 PMCID: PMC6523236 DOI: 10.3390/antiox8040109] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 04/22/2019] [Accepted: 04/23/2019] [Indexed: 01/22/2023] Open
Abstract
Mitochondrial dysfunction is associated with the etiologies of sensorineural hearing loss, such as age-related hearing loss, noise- and ototoxic drug-induced hearing loss, as well as hearing loss due to mitochondrial gene mutation. Mitochondria are the main sources of reactive oxygen species (ROS) and ROS-induced oxidative stress is involved in cochlear damage. Moreover, the release of ROS causes further damage to mitochondrial components. Antioxidants are thought to counteract the deleterious effects of ROS and thus, may be effective for the treatment of oxidative stress-related diseases. The administration of mitochondria-targeted antioxidants is one of the drug delivery systems targeted to mitochondria. Mitochondria-targeted antioxidants are expected to help in the prevention and/or treatment of diseases associated with mitochondrial dysfunction. Of the various mitochondria-targeted antioxidants, the protective effects of MitoQ and SkQR1 against ototoxicity have been previously evaluated in animal models and/or mouse auditory cell lines. MitoQ protects against both gentamicin- and cisplatin-induced ototoxicity. SkQR1 also provides auditory protective effects against gentamicin-induced ototoxicity. On the other hand, decreasing effect of MitoQ on gentamicin-induced cell apoptosis in auditory cell lines has been controversial. No clinical studies have been reported for otoprotection using mitochondrial-targeted antioxidants. High-quality clinical trials are required to reveal the therapeutic effect of mitochondria-targeted antioxidants in terms of otoprotection in patients.
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Affiliation(s)
- Chisato Fujimoto
- Department of Otolaryngology and Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
- Department of Otolaryngology, Tokyo Teishin Hospital, 2-14-23, Fujimi, Chiyoda-ku, Tokyo 102-8798, Japan.
| | - Tatsuya Yamasoba
- Department of Otolaryngology and Head and Neck Surgery, Graduate School of Medicine, The University of Tokyo 7-3-1, Hongo, Bunkyo-ku, Tokyo 113-8655, Japan.
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28
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Schoonen M, Smuts I, Louw R, Elson JL, van Dyk E, Jonck LM, Rodenburg RJT, van der Westhuizen FH. Panel-Based Nuclear and Mitochondrial Next-Generation Sequencing Outcomes of an Ethnically Diverse Pediatric Patient Cohort with Mitochondrial Disease. J Mol Diagn 2019; 21:503-513. [PMID: 30872186 DOI: 10.1016/j.jmoldx.2019.02.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 01/08/2019] [Accepted: 02/06/2019] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial disease (MD) is a group of rare inherited disorders with clinical heterogeneous phenotypes. Recent advances in next-generation sequencing (NGS) allow for rapid genetic diagnostics in patients who experience MD, resulting in significant strides in determining its etiology. This, however, has not been the case in many patient populations. We report on a molecular diagnostic study using mitochondrial DNA and targeted nuclear DNA (nDNA) NGS of an extensive cohort of predominantly sub-Saharan African pediatric patients with clinical and biochemically defined MD. Patients in this novel cohort presented mostly with muscle involvement (73%). Of the original 212 patients, a muscle respiratory chain deficiency was identified in 127 cases. Genetic analyses were conducted for these 127 cases based on biochemical deficiencies, for both mitochondrial (n = 123) and nDNA using panel-based NGS (n = 86). As a pilot investigation, whole-exome sequencing was performed in a subset of African patients (n = 8). These analyses resulted in the identification of a previously reported pathogenic mitochondrial DNA variant and seven pathogenic or likely pathogenic nDNA variants (ETFDH, SURF1, COQ6, RYR1, STAC3, ALAS2, and TRIOBP), most of which were identified via whole-exome sequencing. This study contributes to knowledge of MD etiology in an understudied, ethnically diverse population; highlights inconsistencies in genotype-phenotype correlations; and proposes future directions for diagnostic approaches in such patient populations.
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Affiliation(s)
- Maryke Schoonen
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Izelle Smuts
- Department of Paediatrics and Child Health, Steve Biko Academic Hospital, University of Pretoria, Pretoria, South Africa
| | - Roan Louw
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Joanna L Elson
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa; Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Etresia van Dyk
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Lindi-Maryn Jonck
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa
| | - Richard J T Rodenburg
- Department of Pediatrics, Radboudumc Amalia Childrens Hospital, Radboud Center for Mitochondrial Medicine, Nijmegen, the Netherlands
| | - Francois H van der Westhuizen
- Human Metabolomics, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom, South Africa.
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29
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Schlapakow E, Peeva V, Zsurka G, Jeub M, Wabbels B, Kornblum C, Kunz WS. Distinct segregation of the pathogenic m.5667G>A mitochondrial tRNA Asn mutation in extraocular and skeletal muscle in chronic progressive external ophthalmoplegia. Neuromuscul Disord 2019; 29:358-367. [PMID: 30962064 DOI: 10.1016/j.nmd.2019.02.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 01/08/2019] [Accepted: 02/19/2019] [Indexed: 12/13/2022]
Abstract
Chronic progressive external ophthalmoplegia (CPEO) is a frequent clinical manifestation of disorders caused by pathogenic mitochondrial DNA mutations. However, for diagnostic purposes skeletal muscle tissue is used, since extraocular muscle tissue is usually not available for work-up. In the present study we aimed to identify causative factors that are responsible for extraocular muscle to be primarily affected in CPEO. We performed comparative histochemical and molecular genetic analyses of extraocular muscle and skeletal muscle single fibers in a case of isolated CPEO caused by the heteroplasmic m.5667G>A mutation in the mitochondrial tRNAAsn gene (MT-TN). Histochemical analyses revealed higher proportion of cytochrome c oxidase deficient fibers in extraocular muscle (41%) compared to skeletal muscle (10%). However, genetic analyses of single fibers revealed no significant difference either in the mutation loads between extraocular muscle and skeletal muscle cytochrome c oxidase deficient single fibers (extraocular muscle 86% ± 4.6%; skeletal muscle 87.8 %± 5.7%, p = 0.246) nor in the mutation threshold (extraocular muscle 74% ± 3%; skeletal muscle 74% ± 4%). We hypothesize that higher proportion of cytochrome c oxidase deficient fibers in extraocular muscle compared to skeletal muscle might be due to facilitated segregation of the m.5667G>A mutation into extraocular muscle, which may explain the preferential ocular manifestation and clinically isolated CPEO.
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Affiliation(s)
- Elena Schlapakow
- Department of Neurology, University Hospital of Bonn, Germany; Center for Rare Diseases, University Hospital of Bonn, Germany
| | - Viktoriya Peeva
- Division of Neurochemistry, Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany
| | - Gábor Zsurka
- Division of Neurochemistry, Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany; Department of Epileptology, University of Bonn, Germany
| | - Monika Jeub
- Department of Neurology, University Hospital of Bonn, Germany
| | | | - Cornelia Kornblum
- Department of Neurology, University Hospital of Bonn, Germany; Center for Rare Diseases, University Hospital of Bonn, Germany
| | - Wolfram S Kunz
- Division of Neurochemistry, Institute of Experimental Epileptology and Cognition Research, University of Bonn, Sigmund-Freud-Str. 25, D-53105 Bonn, Germany; Department of Epileptology, University of Bonn, Germany.
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30
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Borghini A, Vecoli C, Piccaluga E, Guagliumi G, Picano E, Andreassi MG. Increased mitochondrial DNA4977-bp deletion in catheterization laboratory workers with long-term low-dose exposure to ionizing radiation. Eur J Prev Cardiol 2019; 26:976-984. [PMID: 30782005 DOI: 10.1177/2047487319831495] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
AIMS Ionizing radiation may lead to mitochondrial DNA (mtDNA) mutations and changes in mtDNA content in cells, major driving mechanisms for carcinogenesis, vascular aging and neurodegeneration. The aim of this study was to investigate the possible induction of common mitochondrial deletion (mtDNA4977) and mtDNA copy number (mtDNA-CN) changes in peripheral blood of personnel working in high-volume cardiac catheterization laboratories (Cath Labs). METHODS A group of 147 Cath Lab workers (median individual effective dose = 16.8 mSv, for the 41 with lifetime dosimetric record) and 74 unexposed individuals were evaluated. The occupational radiological risk score was computed for each subject on the basis of the length of employment, individual caseload and proximity to the radiation source. mtDNA4977 deletion and mtDNA-CN were assessed by using quantitative real-time polymerase chain reaction. RESULTS Increased levels of mtDNA4977 deletion were observed in high-exposure Cath Lab workers compared with unexposed individuals ( p < 0.0001). Conversely, mtDNA-CN was significantly greater in the low-exposure workers ( p = 0.003). Occupational radiological risk score was positively correlated with mtDNA4977 deletion (Spearman's r = 0.172, p = 0.03) and inversely correlated with mtDNA-CN (Spearman's r = -0.202, p = 0.01). In multiple regression model, occupational radiological risk score emerged as significant predictor of high levels of mtDNA4977 deletion (ß coefficient = 0.236, p = 0.04). CONCLUSION mtDNA4977 deletion is significantly high in Cath Lab personnel. Beyond the well-recognized nuclear DNA, mtDNA damage might deserve attention as a pathogenetic molecular pathway and a potential therapeutic target of ionizing radiation damage.
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Affiliation(s)
| | | | | | - Giulio Guagliumi
- 3 Ospedale Papa Giovanni XXIII, Cardiovascular Department, Bergamo, Italy
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31
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Proximal Myopathy due to m.5835G>A Mutation in Mitochondrial MT-TY Gene. Case Rep Neurol Med 2019; 2018:8406712. [PMID: 30643656 PMCID: PMC6311237 DOI: 10.1155/2018/8406712] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 10/31/2018] [Accepted: 12/02/2018] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial (mt) tRNA (MTT) gene mutations are an important cause of mitochondrial diseases and are associated with a wide range of clinical presentations. Most mutations fall into three mitochondrial tRNAs (tRNAIle, tRNALeu (UUR), and tRNALys) and are responsible for half of the mitochondrial diseasees associated with tRNA mutation, with MERRF, MELAS, mitochondrial myopathy, and Leigh syndrome being the most frequent phenotypes. More than 100 tRNA pathogenetic mutations are described, showing little correlation between the observed clinical phenotype and a specific mitochondrial tRNA mutation. Furthermore different mutation can manifest with similar clinical phenotypes, making the genotype-phenotype correlation difficult. Here we report the case of an Italian 53-year-old woman presenting with a proximal myopathy and the m.5835G>A mutation in MT-TY gene coding for the mitochondrial tRNA Tyrosine gene.
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32
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Luo Z, Fan P, Zhang S, Li Z. Single nucleotide polymorphisms in the D-loop region predicts earlyage-at-onset of malignant fibrous histiocytoma. MITOCHONDRIAL DNA PART B 2019. [DOI: 10.1080/23802359.2019.1619492] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Zucheng Luo
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Zhejiang Provincial Key Laboratory of Orthopaedics, Wenzhou, Zhejiang, P.R. China
- The Second School of Medicine, WenZhou Medical University, Wenzhou, Zhejiang, P.R. China
| | - Pei Fan
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Zhejiang Provincial Key Laboratory of Orthopaedics, Wenzhou, Zhejiang, P.R. China
| | - Shisi Zhang
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Zhejiang Provincial Key Laboratory of Orthopaedics, Wenzhou, Zhejiang, P.R. China
| | - Zhenxing Li
- Department of Orthopaedics, The Second Affiliated Hospital and Yuying Children’s Hospital of Wenzhou Medical University, Wenzhou, Zhejiang, P.R. China
- Zhejiang Provincial Key Laboratory of Orthopaedics, Wenzhou, Zhejiang, P.R. China
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33
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Jou MJ, Peng TI, Reiter RJ. Protective stabilization of mitochondrial permeability transition and mitochondrial oxidation during mitochondrial Ca 2+ stress by melatonin's cascade metabolites C3-OHM and AFMK in RBA1 astrocytes. J Pineal Res 2019; 66:e12538. [PMID: 30415481 DOI: 10.1111/jpi.12538] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/29/2018] [Accepted: 11/02/2018] [Indexed: 01/02/2023]
Abstract
Cyclic 3-hydroxymelatonin (C3-OHM) and N1-acetyl-N2-formyl-5-methoxykynuramine (AFMK) are two major cascade metabolites of melatonin. We previously showed melatonin provides multiple levels of mitochondria-targeted protection beyond as a mitochondrial antioxidant during ionomycin-induced mitochondrial Ca2+ (mCa2+ ) stress in RBA1 astrocytes. Using noninvasive laser scanning fluorescence coupled time-lapse digital imaging microscopy, this study investigated whether C3-OHM and AFMK also provide mitochondrial levels of protection during ionomycin-induced mCa2+ stress in RBA1 astrocytes. Interestingly, precise temporal and spatial dynamic live mitochondrial images revealed that C3-OHM and AFMK prevented specifically mCa2+ -mediated mitochondrial reactive oxygen species (mROS) formation and hence mROS-mediated depolarization of mitochondrial membrane potential (△Ψm ) and permanent lethal opening of the MPT (p-MPT). The antioxidative effects of AFMK, however, were less potent than that of C3-OHM. Whether C3-OHM and AFMK targeted directly the MPT was investigated under a condition of "oxidation free-Ca2+ stress" using a classic antioxidant vitamin E to remove mCa2+ -mediated mROS stress and the potential antioxidative effects of C3-OHM and AFMK. Intriguingly, two compounds still effectively postponed "oxidation free-Ca2+ stress"-mediated depolarization of △Ψm and p-MPT. Measurements using a MPT pore-specific indicator Calcein further identified that C3-OHM and AFMK, rather than inhibiting, stabilized the MPT in its transient protective opening mode (t-MPT), a critical mechanism to reduce overloaded mROS and mCa2+ . These multiple layers of mitochondrial protection provided by C3-OHM and AFMK thus crucially allow melatonin to extend its metabolic cascades of mitochondrial protection during mROS- and mCa2+ -mediated MPT-associated apoptotic stresses and may provide therapeutic benefits against astrocyte-mediated neurodegeneration in the CNS.
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Affiliation(s)
- Mei-Jie Jou
- Department of Physiology and Pharmacology, College of Medicine, Chang Gung University, Tao-Yuan, Taiwan
- Department of Neurology, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan
| | - Tsung-I Peng
- Department of Neurology, Chang Gung Memorial Hospital, Keelung Branch, Keelung, Taiwan
- Department of Medicine, Chang Gung University, Tao-Yuan, Taiwan
| | - Russel J Reiter
- Department of Cellular and Structural Biology, University of Texas Health Science Center, San Antonio, Texas
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The Mitochondrial tRNA Gly T10003C Mutation may not be Associated with Diabetes Mellitus. Balkan J Med Genet 2018; 21:53-57. [PMID: 30425911 PMCID: PMC6231318 DOI: 10.2478/bjmg-2018-0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations have long been proposed to play important roles in the pathogenesis of diabetes mellitus (DM). A large proportion of these mutations are localized at the mt-tRNA genes. Owing to its high mutation rate, a growing number of mt-tRNA mutations have been reported; however some of them are neutral genetic polymorphisms and will not result in the alteration of the mitochondrial function responsible for DM. In this study, we reassessed a recent reported "pathogenic" mutation, tRNAGly T10003C, in a clinical manifestation of DM. We first performed the conservation assessment of this mutation between different species. Moreover, the bioinformatics analysis was used to predict the secondary structure of mt-tRNAGly in wild type version and the mutant carrying the T10003C mutation. We also screened the presence of the T10003C mutation in 500 unrelated DM patients and 300 healthy controls. We noticed that the T10003C mutation was not very conserved and did not cause the secondary structure change of mt-tRNAGly. Moreover, this mutation was absent in the 500 unrelated DM patients and controls, suggesting that this mutation may be a rare event in the human population. In conclusion, the current study showed no association between the T10003C mutation and DM in humans.
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Tyagi A, Pramanik R, Vishnubhatla S, Ali S, Bakhshi R, Chopra A, Singh A, Bakhshi S. Pattern of mitochondrial D-loop variations and their relation with mitochondrial encoded genes in pediatric acute myeloid leukemia. Mutat Res 2018; 810:13-18. [PMID: 29883862 DOI: 10.1016/j.mrfmmm.2018.05.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 05/08/2018] [Accepted: 05/24/2018] [Indexed: 06/08/2023]
Abstract
Role of mitochondrial DNA variations, particularly in D loop region, remains investigational in acute myeloid leukaemia (AML). Consecutive 151 pediatric AML patients were prospectively enrolled from June 2013 to August 2016, for evaluating pattern of variations in mitochondrial D-loop region and to determine their association, if any, with expression of mitochondrial-encoded genes. For each patient, D-loop region was sequenced on baseline bone marrow, buccal swab and mother's blood sample. Real time PCR was used for relative gene expression of four mitochondrial DNA encoded genes viz. Nicotinamide-adenine-dineucleotide-dehydrogenase subunit 3 (ND3), Cytochrome-B (Cyt-B), Cytochrome c oxidase-I (COX1) and ATP-synthetase F0 subunit-6 (ATP6). Total 1490 variations were found at 237 positions in D-Loop; 1206 (80.9%) were germline and 284 (19.1%) were somatic. Positions 73-263 were identified as a probable hotspot region. G bases appeared to be most stable nucleotide (least number of single base substitutions) whereas T appeared to be most susceptible to variations with germline T-C being the commonest. Gene expression of Cyt-B was found to be significantly higher for any variation (somatic or germline) at positions 16,192 and 16,327 while it was significantly lower for variations at positions 16,051 and 207. Any variation at positions 152, 207 and 513 significantly decreased COX1 expression while those at positions 16,051 and 152 attenuated ATP6 expression. This first study evaluated type and overall pattern of D-loop variations in AML, and also showed that some of these variations in D loop region might have an effect on the mitochondrial-encoded genes which is new and valuable information in AML genomics.
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Affiliation(s)
- Anudishi Tyagi
- Department of Medical Oncology; Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India
| | - Raja Pramanik
- Department of Medical Oncology; Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India
| | | | - Safdar Ali
- Shaheed Rajguru College of Applied Sciences, India; University of Delhi , New Delhi
| | - Radhika Bakhshi
- Shaheed Rajguru College of Applied Sciences, India; University of Delhi , New Delhi
| | - Anita Chopra
- Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India; Department of Lab oncology
| | - Archna Singh
- All India Institute of Medical Sciences, New Delhi, India; Department of Biochemistry
| | - Sameer Bakhshi
- Department of Medical Oncology; Dr. B. R. A. Institute Rotary Cancer Hospital; All India Institute of Medical Sciences, New Delhi, India.
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36
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Meseguer S, Panadero J, Navarro-González C, Villarroya M, Boutoual R, Comi GP, Armengod ME. The MELAS mutation m.3243A>G promotes reactivation of fetal cardiac genes and an epithelial-mesenchymal transition-like program via dysregulation of miRNAs. Biochim Biophys Acta Mol Basis Dis 2018; 1864:3022-3037. [PMID: 29928977 DOI: 10.1016/j.bbadis.2018.06.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 05/25/2018] [Accepted: 06/13/2018] [Indexed: 12/25/2022]
Abstract
The pathomechanisms underlying oxidative phosphorylation (OXPHOS) diseases are not well-understood, but they involve maladaptive changes in mitochondria-nucleus communication. Many studies on the mitochondria-nucleus cross-talk triggered by mitochondrial dysfunction have focused on the role played by regulatory proteins, while the participation of miRNAs remains poorly explored. MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) is mostly caused by mutation m.3243A>G in mitochondrial tRNALeu(UUR) gene. Adverse cardiac and neurological events are the commonest causes of early death in m.3243A>G patients. Notably, the incidence of major clinical features associated with this mutation has been correlated to the level of m.3243A>G mutant mitochondrial DNA (heteroplasmy) in skeletal muscle. In this work, we used a transmitochondrial cybrid model of MELAS (100% m.3243A>G mutant mitochondrial DNA) to investigate the participation of miRNAs in the mitochondria-nucleus cross-talk associated with OXPHOS dysfunction. High-throughput analysis of small-RNA-Seq data indicated that expression of 246 miRNAs was significantly altered in MELAS cybrids. Validation of selected miRNAs, including miR-4775 and miR-218-5p, in patient muscle samples revealed miRNAs whose expression declined with high levels of mutant heteroplasmy. We show that miR-218-5p and miR-4775 are direct regulators of fetal cardiac genes such as NODAL, RHOA, ISL1 and RXRB, which are up-regulated in MELAS cybrids and in patient muscle samples with heteroplasmy above 60%. Our data clearly indicate that TGF-β superfamily signaling and an epithelial-mesenchymal transition-like program are activated in MELAS cybrids, and suggest that down-regulation of miRNAs regulating fetal cardiac genes is a risk marker of heart failure in patients with OXPHOS diseases.
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Affiliation(s)
- Salvador Meseguer
- RNA Modification and Mitochondrial Diseases Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Carrer d'Eduardo Primo Yúfera 3, Valencia 46012, Spain.
| | - Joaquin Panadero
- Unidad de Genómica, Instituto de Investigación Sanitaria La Fe, Avenida Fernando Abril Martorell, 106 Torre A 7ª planta, Valencia 46026, Spain.
| | - Carmen Navarro-González
- RNA Modification and Mitochondrial Diseases Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Carrer d'Eduardo Primo Yúfera 3, Valencia 46012, Spain.
| | - Magda Villarroya
- RNA Modification and Mitochondrial Diseases Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Carrer d'Eduardo Primo Yúfera 3, Valencia 46012, Spain.
| | - Rachid Boutoual
- RNA Modification and Mitochondrial Diseases Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Carrer d'Eduardo Primo Yúfera 3, Valencia 46012, Spain.
| | - Giacomo Pietro Comi
- Dino Ferrari Centre, Department of Pathophysiology and Transplantation (DEPT), University of Milan, I.R.C.C.S. Foundation Ca' Granda, Ospedale Maggiore Policlinico, via F. Sforza 35, 20122 Milan, Italy.
| | - M-Eugenia Armengod
- RNA Modification and Mitochondrial Diseases Laboratory, Centro de Investigación Príncipe Felipe (CIPF), Carrer d'Eduardo Primo Yúfera 3, Valencia 46012, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER) node 721, Madrid 28029, Spain.
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37
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Cuperfain AB, Zhang ZL, Kennedy JL, Gonçalves VF. The Complex Interaction of Mitochondrial Genetics and Mitochondrial Pathways in Psychiatric Disease. MOLECULAR NEUROPSYCHIATRY 2018; 4:52-69. [PMID: 29998118 DOI: 10.1159/000488031] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 02/27/2018] [Indexed: 12/18/2022]
Abstract
While accounting for only 2% of the body's weight, the brain utilizes up to 20% of the body's total energy. Not surprisingly, metabolic dysfunction and energy supply-and-demand mismatch have been implicated in a variety of neurological and psychiatric disorders. Mitochondria are responsible for providing the brain with most of its energetic demands, and the brain uses glucose as its exclusive energy source. Exploring the role of mitochondrial dysfunction in the etiology of psychiatric disease is a promising avenue to investigate further. Genetic analysis of mitochondrial activity is a cornerstone in understanding disease pathogenesis related to metabolic dysfunction. In concert with neuroimaging and pathological study, genetics provides an important bridge between biochemical findings and clinical correlates in psychiatric disease. Mitochondrial genetics has several unique aspects to its analysis, and corresponding special considerations. Here, we review the components of mitochondrial genetic analysis - nuclear DNA, mitochon-drial DNA, mitochondrial pathways, pseudogenes, nuclear-mitochondrial mismatch, and microRNAs - that could contribute to an observable clinical phenotype. Throughout, we highlight psychiatric diseases that can arise due to dysfunction in these processes, with a focus on schizophrenia and bipolar disorder.
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Affiliation(s)
- Ari B Cuperfain
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Neuroscience Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Zhi Lun Zhang
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Neuroscience Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - James L Kennedy
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Neuroscience Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
| | - Vanessa F Gonçalves
- Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.,Neuroscience Section, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
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38
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Sharbrough J, Cruise JL, Beetch M, Enright NM, Neiman M. Genetic Variation for Mitochondrial Function in the New Zealand Freshwater Snail Potamopyrgus antipodarum. J Hered 2018; 108:759-768. [PMID: 28460111 DOI: 10.1093/jhered/esx041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2016] [Accepted: 04/26/2017] [Indexed: 02/04/2023] Open
Abstract
The proteins responsible for mitochondrial function are encoded by 2 different genomes with distinct inheritance regimes, rendering rigorous inference of genotype-phenotype connections intractable for all but a few model systems. Asexual organisms provide a powerful means to address these challenges because offspring produced without recombination inherit both nuclear and mitochondrial genomes from a single parent. As such, these offspring inherit mitonuclear genotypes that are identical to the mitonuclear genotypes of their parents and siblings but different from those of other asexual lineages. Here, we compared mitochondrial function across distinct asexual lineages of Potamopyrgus antipodarum, a New Zealand freshwater snail model for understanding the evolutionary consequences of asexuality. Our analyses revealed substantial phenotypic variation across asexual lineages at 3 levels of biological organization: mitogenomic, organellar, and organismal. These data demonstrate that different asexual lineages have different mitochondrial function phenotypes, likely reflecting heritable variation (i.e., the raw material for evolution) for mitochondrial function in P. antipodarum. The discovery of this variation combined with the methods developed here sets the stage to use P. antipodarum to study central evolutionary questions involving mitochondrial function, including whether mitochondrial mutation accumulation influences the maintenance of sexual reproduction in natural populations.
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Affiliation(s)
- Joel Sharbrough
- Department of Biology, University of Iowa, Iowa City, IA.,Department of Biology, Colorado State University, Fort Collins, CO
| | | | - Megan Beetch
- Department of Biology, University of Iowa, Iowa City, IA.,Department of Biology, University of St. Thomas, Saint Paul, MN
| | | | - Maurine Neiman
- Department of Biology, University of Iowa, Iowa City, IA
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39
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Burr SP, Pezet M, Chinnery PF. Mitochondrial DNA Heteroplasmy and Purifying Selection in the Mammalian Female Germ Line. Dev Growth Differ 2018; 60:21-32. [PMID: 29363102 DOI: 10.1111/dgd.12420] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 12/08/2017] [Indexed: 01/19/2023]
Abstract
Inherited mutations in the mitochondrial (mt)DNA are a major cause of human disease, with approximately 1 in 5000 people affected by one of the hundreds of identified pathogenic mtDNA point mutations or deletions. Due to the severe, and often untreatable, symptoms of many mitochondrial diseases, identifying how these mutations are inherited from one generation to the next has been an area of intense research in recent years. Despite large advances in our understanding of this complex process, many questions remain unanswered, with one of the most hotly debated being whether or not purifying selection acts against pathogenic mutations during germline development.
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Affiliation(s)
- Stephen P Burr
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mikael Pezet
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Patrick F Chinnery
- MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
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40
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N Zekri AR, Salama H, Medhat E, Hamdy S, Hassan ZK, Bakr YM, Youssef ASED, Saleh D, Saeed R, Omran D. Potential Diagnostic and Prognostic Value of Lymphocytic Mitochondrial DNA Deletion in Relation to Folic Acid Status in HCV-Related Hepatocellular Carcinoma. ASIAN PACIFIC JOURNAL OF CANCER PREVENTION : APJCP 2017; 18:2451-2457. [PMID: 28952275 PMCID: PMC5720650 DOI: 10.22034/apjcp.2017.18.9.2451] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Objective: We assessed the possibility of using mitochondrial (mt) DNA deletion as a molecular biomarker for disease progression in HCV-related hepatocellular carcinoma (HCC) and to identify its association with folic acid status. Methods: Serum folic acid and lymphocytic mtDNA deletions were assessed in 90 patients; 50 with HCC, 20 with liver cirrhosis (LC), and 20 with chronic hepatitis C (CHC) compared to 10 healthy control subjects. The diagnostic accuracy of mtDNA deletions frequency was evaluated using receiver-operating characteristic (ROC) curve analysis Survival analysis was performed using the Kaplan-Meier method. Differences in the survival rates were compared using log-rank test. Result: Our data revealed a significant elevation of mtDNA deletions frequency in the HCC group compared to the other groups (P-value <0.01). Also, our data showed a significant correlation between folate deficiency and high frequency of mtDNA deletions in patients with HCV-related HCC when compared to the other groups (r= -0.094 and P-value <0.05). Moreover, the size of the hepatic focal lesion in the HCC patients was positively correlated with mtDNA deletions (r= 0.09 and P-value <0.01). The median survival time for the HCC patients with high frequency of mtDNA deletions (∆Ct ≥3.9; 5.7+ 0.6 months) was significantly shorter than those with low mtDNA deletions frequency (∆Ct < 3.9; 11.9+ 0.04 months, P-value <0.01). Conclusion: Our data provided an evidence that lymphocytic mtDNA deletion could be used as non-invasive biomarker for disease progression and patients’ survival in HCV-related HCC. Also, our findings implied a causal relationship between the folate deficiency and the high mtDNA deletions frequency among Egyptian patients with HCV related HCC.
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Affiliation(s)
- Abdel Rahman N Zekri
- Virology and Immunology Unit, Cancer Biology Department, National Cancer Institute, Cairo University, Cairo, Egypt.
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41
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Venter M, van der Westhuizen FH, Elson JL. The aetiology of cardiovascular disease: a role for mitochondrial DNA? Cardiovasc J Afr 2017; 29:122-132. [PMID: 28906532 PMCID: PMC6009096 DOI: 10.5830/cvja-2017-037] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 07/17/2017] [Indexed: 01/03/2023] Open
Abstract
Cardiovascular disease (CVD) is a world-wide cause of mortality in humans and its incidence is on the rise in Africa. In this review, we discuss the putative role of mitochondrial dysfunction in the aetiology of CVD and consequently identify mitochondrial DNA (mtDNA) variation as a viable genetic risk factor to be considered. We then describe the contribution and pitfalls of several current approaches used when investigating mtDNA in relation to complex disease. We also propose an alternative approach, the adjusted mutational load hypothesis, which would have greater statistical power with cohorts of moderate size, and is less likely to be affected by population stratification. We therefore address some of the shortcomings of the current haplogroup association approach. Finally, we discuss the unique challenges faced by studies done on African populations, and recommend the most viable methods to use when investigating mtDNA variation in CVD and other common complex disease.
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Affiliation(s)
- Marianne Venter
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
| | | | - Joanna L Elson
- Human Metabolomics, North-West University, Potchefstroom, South Africa; Institute of Genetic Medicine, Newcastle University, United Kingdom
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42
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Mitochondrial DNA copy number in peripheral blood cell and hypertension risk among mining workers: a case–control study in Chinese coal miners. J Hum Hypertens 2017; 31:585-590. [DOI: 10.1038/jhh.2017.30] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Revised: 02/28/2017] [Accepted: 03/17/2017] [Indexed: 12/20/2022]
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Martín-Navarro A, Gaudioso-Simón A, Álvarez-Jarreta J, Montoya J, Mayordomo E, Ruiz-Pesini E. Machine learning classifier for identification of damaging missense mutations exclusive to human mitochondrial DNA-encoded polypeptides. BMC Bioinformatics 2017; 18:158. [PMID: 28270093 PMCID: PMC5341421 DOI: 10.1186/s12859-017-1562-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Accepted: 02/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several methods have been developed to predict the pathogenicity of missense mutations but none has been specifically designed for classification of variants in mtDNA-encoded polypeptides. Moreover, there is not available curated dataset of neutral and damaging mtDNA missense variants to test the accuracy of predictors. Because mtDNA sequencing of patients suffering mitochondrial diseases is revealing many missense mutations, it is needed to prioritize candidate substitutions for further confirmation. Predictors can be useful as screening tools but their performance must be improved. RESULTS We have developed a SVM classifier (Mitoclass.1) specific for mtDNA missense variants. Training and validation of the model was executed with 2,835 mtDNA damaging and neutral amino acid substitutions, previously curated by a set of rigorous pathogenicity criteria with high specificity. Each instance is described by a set of three attributes based on evolutionary conservation in Eukaryota of wildtype and mutant amino acids as well as coevolution and a novel evolutionary analysis of specific substitutions belonging to the same domain of mitochondrial polypeptides. Our classifier has performed better than other web-available tested predictors. We checked performance of three broadly used predictors with the total mutations of our curated dataset. PolyPhen-2 showed the best results for a screening proposal with a good sensitivity. Nevertheless, the number of false positive predictions was too high. Our method has an improved sensitivity and better specificity in relation to PolyPhen-2. We also publish predictions for the complete set of 24,201 possible missense variants in the 13 human mtDNA-encoded polypeptides. CONCLUSIONS Mitoclass.1 allows a better selection of candidate damaging missense variants from mtDNA. A careful search of discriminatory attributes and a training step based on a curated dataset of amino acid substitutions belonging exclusively to human mtDNA genes allows an improved performance. Mitoclass.1 accuracy could be improved in the future when more mtDNA missense substitutions will be available for updating the attributes and retraining the model.
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Affiliation(s)
- Antonio Martín-Navarro
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain.,Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain
| | - Andrés Gaudioso-Simón
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain
| | - Jorge Álvarez-Jarreta
- Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain.,Instituto de Investigación en Ingeniería de Aragón (I3A), Universidad de Zaragoza, Zaragoza, Spain
| | - Julio Montoya
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain.,Instituto de Investigación Sanitaria de Aragón (IISA), Universidad de Zaragoza, Zaragoza, Spain.,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Universidad de Zaragoza, Zaragoza, Spain
| | - Elvira Mayordomo
- Departamento de Informática e Ingeniería de Sistemas, Universidad de Zaragoza, C/ María de Luna 1, Zaragoza, 50018, Spain. .,Instituto de Investigación en Ingeniería de Aragón (I3A), Universidad de Zaragoza, Zaragoza, Spain.
| | - Eduardo Ruiz-Pesini
- Departamento de Bioquímica, Biología Molecular y Celular, Universidad de Zaragoza, C/ Miguel Servet 177, Zaragoza, 50013, Spain. .,Instituto de Investigación Sanitaria de Aragón (IISA), Universidad de Zaragoza, Zaragoza, Spain. .,Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Universidad de Zaragoza, Zaragoza, Spain. .,Fundación ARAID, Universidad de Zaragoza, Zaragoza, Spain.
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Garcia I, Jones E, Ramos M, Innis-Whitehouse W, Gilkerson R. The little big genome: the organization of mitochondrial DNA. Front Biosci (Landmark Ed) 2017; 22:710-721. [PMID: 27814641 DOI: 10.2741/4511] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The small (16,569 base pair) human mitochondrial genome plays a significant role in cell metabolism and homeostasis. Mitochondrial DNA (mtDNA) contributes to the generation of complexes which are essential to oxidative phosphorylation (OXPHOS). As such, mtDNA is directly integrated into mitochondrial biogenesis and signaling and regulates mitochondrial metabolism in concert with nuclear-encoded mitochondrial factors. Mitochondria are a highly dynamic, pleiomorphic network that undergoes fission and fusion events. Within this network, mtDNAs are packaged into structures called nucleoids which are actively distributed in discrete foci within the network. This sensitive organelle is frequently disrupted by insults such as oxidants and inflammatory cytokines, and undergoes genomic damage with double- and single-strand breaks that impair its function. Collectively, mtDNA is emerging as a highly sensitive indicator of cellular stress, which is directly integrated into the mitochondrial network as a contributor of a wide range of critical signaling pathways.
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Affiliation(s)
| | | | - Manuel Ramos
- Department of Biology, The University of Texas Rio Grande Valley, Edinburg, TX 78539 USA
| | - Wendy Innis-Whitehouse
- Department of Biomedical Sciences, The University of Texas Rio Grande Valley, Edinburg, TX 78539 USA
| | - Robert Gilkerson
- Departments of Biology and Clinical Laboratory Sciences, The University of Texas Rio Grande Valley, 1201 West University Drive, Edinburg, TX 78539-2999,
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Bahreini F, Houshmand M, Modaresi MH, Tonekaboni H, Nafissi S, Nazari F, Akrami SM. Mitochondrial Copy Number and D-Loop Variants in Pompe Patients. CELL JOURNAL 2016; 18:405-15. [PMID: 27602323 PMCID: PMC5011329 DOI: 10.22074/cellj.2016.4569] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 01/24/2016] [Indexed: 02/06/2023]
Abstract
Objective Pompe disease is a rare neuromuscular genetic disorder and is classified
into two forms of early and late-onset. Over the past two decades, mitochondrial abnor-
malities have been recognized as an important contributor to an array of neuromuscular
diseases. We therefore aimed to compare mitochondrial copy number and mitochondrial
displacement-loop sequence variation in infantile and adult Pompe patients.
Materials and Methods In this retrospective study, the mitochondrial D-loop sequence
was analyzed by polymerase chain reaction (PCR) and direct sequencing to detect pos-
sible variation in 28 Pompe patients (17 infants and 11 adults). Results were compared
with 100 healthy controls and sequences of all individuals were compared with the Cam-
bridge reference sequence. Real-time PCR was used to quantify mitochondrial DNA copy
number.
Results Among 59 variants identified, 37(62.71%) were present in the infant group,
14(23.333%) in the adult group and 8(13.333%) in both groups. Mitochondrial copy
number in infant patients was lower than adults (P<0.05). A significant frequency differ-
ence was seen between the two groups for 12 single nucleotide polymorphism (SNP).
A novel insertion (317-318 ins CCC) was observed in patients and six SNPs were iden-
tified as neutral variants in controls. There was an inverse association between mito-
chondrial copy number and D-loop variant number (r=0.54).
Conclusion The 317-318 ins CCC was detected as a new mitochondrial variant in
Pompe patients.
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Affiliation(s)
- Fatemeh Bahreini
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Massoud Houshmand
- Department of Medical Genetic, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Mohammad Hossein Modaresi
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Hassan Tonekaboni
- Department of Pediatric Neurology, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Shahriar Nafissi
- Iranian Center for Neurological Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Ferdoss Nazari
- Iranian Center for Neurological Research, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammad Akrami
- Department of Medical Genetics, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
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46
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Marsit CJ, Brummel SS, Kacanek D, Seage GR, Spector SA, Armstrong DA, Lester BM, Rich K. Infant peripheral blood repetitive element hypomethylation associated with antiretroviral therapy in utero. Epigenetics 2016; 10:708-16. [PMID: 26067216 DOI: 10.1080/15592294.2015.1060389] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
The use of combination antiretroviral therapy (cART) to prevent HIV mother-to-child transmission during pregnancy and delivery is generally considered safe. However, vigilant assessment of potential risks of these agents remains warranted. Epigenetic changes including DNA methylation are considered potential mechanisms linking the in utero environment with long-term health outcomes. Few studies have examined the epigenetic effects of prenatal exposure to pharmaceutical agents, including antiretroviral therapies, on children. In this study, we examined the methylation status of the LINE-1 and ALU-Yb8 repetitive elements as markers of global DNA methylation alteration in peripheral blood mononuclear cells obtained from newborns participating in the Pediatric HIV/AIDS Cohort Study SMARTT cohort of HIV-exposed, cART-exposed uninfected infants compared to a historical cohort of HIV-exposed, antiretroviral-unexposed infants from the Women and Infants Transmission Study Cohort. In linear regression models controlling for potential confounders, we found the adjusted mean difference of AluYb8 methylation of the cART-exposed compared to the -unexposed was -0.568 (95% CI: -1.023, -0.149) and for LINE-1 methylation was -1.359 (95% CI: -1.860, -0.857). Among those exposed to cART, subjects treated with atazanavir (ATV), compared to those on other treatments, had less AluYb8 methylation (-0.524, 95% CI: -0.025, -1.024). Overall, these results suggest a small but statistically significant reduction in the methylation of these repetitive elements in an HIV-exposed, cART-exposed cohort compared to an HIV-exposed, cART-unexposed historic cohort. The potential long-term implications of these differences are worthy of further examination.
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Affiliation(s)
- Carmen J Marsit
- a Departments of Pharmacology and Toxicology and of Epidemiology; Geisel School of Medicine at Dartmouth ; Hanover , NH USA
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47
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Refinetti P, Morgenthaler S, Ekstrøm PO. Cycling temperature capillary electrophoresis: A quantitative, fast and inexpensive method to detect mutations in mixed populations of human mitochondrial DNA. Mitochondrion 2016; 29:65-74. [PMID: 27166160 DOI: 10.1016/j.mito.2016.04.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 03/30/2016] [Accepted: 04/29/2016] [Indexed: 11/26/2022]
Abstract
Cycling temperature capillary electrophoresis has been optimised for mutation detection in 76% of the mitochondrial genome. The method was tested on a mixed sample and compared to mutation detection by next generation sequencing. Out of 152 fragments 90 were concordant, 51 discordant and in 11 were semi-concordant. Dilution experiments show that cycling capillary electrophoresis has a detection limit of 1-3%. The detection limit of routine next generation sequencing was in the ranges of 15 to 30%. Cycling temperature capillary electrophoresis detect and accurate quantify mutations at a fraction of the cost and time required to perform a next generation sequencing analysis.
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Affiliation(s)
- Paulo Refinetti
- École Polytechnique Fédérale de Lausanne, EPFL - FSB - STAP, Station 8, Lausanne, Switzerland.
| | - Stephan Morgenthaler
- École Polytechnique Fédérale de Lausanne, EPFL - FSB - STAP, Station 8, Lausanne, Switzerland
| | - Per O Ekstrøm
- Department of Tumor Biology, Norwegian Radiumhospital, Oslo, Norway
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48
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Nardi F, Frati F, Liò P. Animal inference on human mitochondrial diseases. Comput Biol Chem 2016; 62:17-28. [PMID: 27023046 DOI: 10.1016/j.compbiolchem.2016.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 02/02/2016] [Indexed: 11/17/2022]
Abstract
Several pathological mutations in the human mitochondrial genome have been characterized based on medical, genetic and biochemical evidence. The observation that the structure and core functions of the mitochondrial genome are conserved from animals to man suggests that the analysis of animal variation may be informative to further characterize, and possibly predict, human pathological variants. We studied the distribution of sequence site-wise diversity and structural heterogeneity (based on several scales of hydrophobicity and supercomplex classification of mitochondrial genes) at different taxonomic levels in ∼15,000 human and animal genomes. We found that human pathological mutations tend to lay in regions of low diversity and that states that are pathological in humans appear to be extremely rare in animals, with two noticeable exceptions (T10663C and C14568T). Focusing on hydrophobicity, as possibly the most general site-wise functional parameter of a protein, we deploy the observed range of hydrophobicity in mammals as a proxy for the range of permissible states compatible with an efficient functioning of the mitochondrial machinery. We show that, while non pathological human variants tend to fall within the hypothesized range, pathological mutations generally fall outside this range. We further analyzed this distribution quantitatively to show that the estimated probability of observed states can indeed be used to predict the pathogenicity of a mutation in humans. This study provides a proof of principle that animal data can indeed be informative to predict the pathogenicity of a human mutation alongside, or in the absence of, additional evidence.
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Affiliation(s)
| | | | - Pietro Liò
- Computer Laboratory, University of Cambridge, Cambridge, UK.
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49
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Rodrigues GS, Godinho RO, Kiyomoto BH, Gamba J, Oliveira ASB, Schmidt B, Tengan CH. Integrated analysis of the involvement of nitric oxide synthesis in mitochondrial proliferation, mitochondrial deficiency and apoptosis in skeletal muscle fibres. Sci Rep 2016; 6:20780. [PMID: 26856437 PMCID: PMC4746761 DOI: 10.1038/srep20780] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/12/2016] [Indexed: 12/18/2022] Open
Abstract
Nitric oxide (NO) is an important signaling messenger involved in different mitochondrial processes but only few studies explored the participation of NO in mitochondrial abnormalities found in patients with genetic mitochondrial deficiencies. In this study we verified whether NO synthase (NOS) activity was altered in different types of mitochondrial abnormalities and whether changes in mitochondrial function and NOS activity could be associated with the induction of apoptosis. We performed a quantitative and integrated analysis of NOS activity in individual muscle fibres of patients with mitochondrial diseases, considering mitochondrial function (cytochrome-c-oxidase activity), mitochondrial content, mitochondrial DNA mutation and presence of apoptotic nuclei. Our results indicated that sarcolemmal NOS activity was increased in muscle fibres with mitochondrial proliferation, supporting the relevance of neuronal NOS in the mitochondrial biogenesis process. Sarcoplasmic NOS activity was reduced in cytochrome-c-oxidase deficient fibres, probably as a consequence of the involvement of NO in the regulation of the respiratory chain. Alterations in NOS activity or mitochondrial abnormalities were not predisposing factors to apoptotic nuclei. Taken together, our results show that NO can be considered a potential molecular target for strategies to increase mitochondrial content and indicate that this approach may not be associated with increased apoptotic events.
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Affiliation(s)
- Gabriela Silva Rodrigues
- Department of Neurology &Neurosurgery, Escola Paulista de Medicina, Universidade Federal de São Paulo;São Paulo, Brazil
| | - Rosely Oliveira Godinho
- Division of Cellular Pharmacology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Beatriz Hitomi Kiyomoto
- Department of Neurology &Neurosurgery, Escola Paulista de Medicina, Universidade Federal de São Paulo;São Paulo, Brazil
| | - Juliana Gamba
- Department of Neurology &Neurosurgery, Escola Paulista de Medicina, Universidade Federal de São Paulo;São Paulo, Brazil
| | - Acary Souza Bulle Oliveira
- Department of Neurology &Neurosurgery, Escola Paulista de Medicina, Universidade Federal de São Paulo;São Paulo, Brazil
| | - Beny Schmidt
- Department of Pathology, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Célia Harumi Tengan
- Department of Neurology &Neurosurgery, Escola Paulista de Medicina, Universidade Federal de São Paulo;São Paulo, Brazil
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50
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Niroula A, Vihinen M. PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations. Nucleic Acids Res 2016; 44:2020-7. [PMID: 26843426 PMCID: PMC4797295 DOI: 10.1093/nar/gkw046] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/14/2016] [Indexed: 12/19/2022] Open
Abstract
Transfer RNAs (tRNAs) are essential for encoding the transcribed genetic information from DNA into proteins. Variations in the human tRNAs are involved in diverse clinical phenotypes. Interestingly, all pathogenic variations in tRNAs are located in mitochondrial tRNAs (mt-tRNAs). Therefore, it is crucial to identify pathogenic variations in mt-tRNAs for disease diagnosis and proper treatment. We collected mt-tRNA variations using a classification based on evidence from several sources and used the data to develop a multifactorial probability-based prediction method, PON-mt-tRNA, for classification of mt-tRNA single nucleotide substitutions. We integrated a machine learning-based predictor and an evidence-based likelihood ratio for pathogenicity using evidence of segregation, biochemistry and histochemistry to predict the posterior probability of pathogenicity of variants. The accuracy and Matthews correlation coefficient (MCC) of PON-mt-tRNA are 1.00 and 0.99, respectively. In the absence of evidence from segregation, biochemistry and histochemistry, PON-mt-tRNA classifies variations based on the machine learning method with an accuracy and MCC of 0.69 and 0.39, respectively. We classified all possible single nucleotide substitutions in all human mt-tRNAs using PON-mt-tRNA. The variations in the loops are more often tolerated compared to the variations in stems. The anticodon loop contains comparatively more predicted pathogenic variations than the other loops. PON-mt-tRNA is available at http://structure.bmc.lu.se/PON-mt-tRNA/.
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Affiliation(s)
- Abhishek Niroula
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184 Lund, Sweden
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, BMC B13, SE-22184 Lund, Sweden
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