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Vila-Sanjurjo A, Smith PM, Elson JL. Heterologous Inferential Analysis (HIA) and Other Emerging Concepts: In Understanding Mitochondrial Variation In Pathogenesis: There is no More Low-Hanging Fruit. Methods Mol Biol 2021; 2277:203-245. [PMID: 34080154 DOI: 10.1007/978-1-0716-1270-5_14] [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] [Indexed: 06/12/2023]
Abstract
Here we summarize our latest efforts to elucidate the role of mtDNA variants affecting the mitochondrial translation machinery, namely variants mapping to the mt-rRNA and mt-tRNA genes. Evidence is accumulating to suggest that the cellular response to interference with mitochondrial translation is different from that occurring as a result of mutations in genes encoding OXPHOS proteins. As a result, it appears safe to state that a complete view of mitochondrial disease will not be obtained until we understand the effect of mt-rRNA and mt-tRNA variants on mitochondrial protein synthesis. Despite the identification of a large number of potentially pathogenic variants in the mitochondrially encoded rRNA (mt-rRNA) genes, we lack direct methods to firmly establish their pathogenicity. In the absence of such methods, we have devised an indirect approach named heterologous inferential analysis (HIA ) that can be used to make predictions concerning the disruptive potential of a large subset of mt-rRNA variants. We have used HIA to explore the mutational landscape of 12S and 16S mt-rRNA genes. Our HIA studies include a thorough classification of all rare variants reported in the literature as well as others obtained from studies performed in collaboration with physicians. HIA has also been used with non-mammalian mt-rRNA genes to elucidate how mitotypes influence the interaction of the individual and the environment. Regarding mt-tRNA variations, rapidly growing evidence shows that the spectrum of mutations causing mitochondrial disease might differ between the different mitochondrial haplogroups seen in human populations.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Departamento de Bioloxía, Facultade de Ciencias, Centro de Investigacións en Ciencias Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain.
| | - Paul M Smith
- Department of Paediatrics, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - Joanna L Elson
- Biosciences Institute Newcastle, Newcastle University, Newcastle upon Tyne, UK.
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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Sun D, Wei Y, Zheng HX, Jin L, Wang J. Contribution of Mitochondrial DNA Variation to Chronic Disease in East Asian Populations. Front Mol Biosci 2019; 6:128. [PMID: 31803756 PMCID: PMC6873657 DOI: 10.3389/fmolb.2019.00128] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/29/2019] [Indexed: 12/17/2022] Open
Abstract
Mitochondria are the main producers of energy in eukaryotic cells. Mitochondrial dysfunction is associated with specific mitochondrial DNA (mtDNA) variations (haplogroups), and these variations can contribute to human disease. East Asian populations show enrichment of many mitochondrial haplogroups, including A, B, D, G, M7, M8, M9, N9, R9, and exhibit half of the known haplogroups of worldwide. In this review, we summarize the current research in the field of mtDNA variation and associated disease in East Asian populations and discuss the physiological and pathological relevance of mitochondrial biology. mtDNA haplogroups are associated with various metabolic disorders ascribed to altered oxidative phosphorylation. The same mitochondrial haplogroup can show either a negative or positive association with different diseases. Mitochondrial dynamics, mitophagy, and mitochondrial oxidative stress, ultimately influence susceptibility to various diseases. In addition, mitochondrial retrograde signaling pathways may have profound effects on nuclear-mitochondrial interactions, affecting cellular morphology, and function. Other complex networks including proteostasis, mitochondrial unfolded protein response and reactive oxygen species signaling may also play pivotal roles in metabolic performance.
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Affiliation(s)
- Dayan Sun
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yang Wei
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Hong-Xiang Zheng
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
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Rodrigues-Antunes S, Borges BN. Alterations in mtDNA, gastric carcinogenesis and early diagnosis. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 30:226-233. [DOI: 10.1080/24701394.2018.1475478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- S. Rodrigues-Antunes
- Laboratório de Biologia Molecular “Francisco Mauro Salzano”, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
| | - B. N. Borges
- Laboratório de Biologia Molecular “Francisco Mauro Salzano”, Instituto de Ciências Biológicas, Universidade Federal do Pará, Belém, Brazil
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Soon BH, Abdul Murad NA, Then SM, Abu Bakar A, Fadzil F, Thanabalan J, Mohd Haspani MS, Toh CJ, Mohd Tamil A, Harun R, Wan Ngah WZ, Jamal R. Mitochondrial DNA Mutations in Grade II and III Glioma Cell Lines Are Associated with Significant Mitochondrial Dysfunction and Higher Oxidative Stress. Front Physiol 2017; 8:231. [PMID: 28484394 PMCID: PMC5399085 DOI: 10.3389/fphys.2017.00231] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 03/31/2017] [Indexed: 01/13/2023] Open
Abstract
The role of mitochondria in tumorigenesis has regained much attention as it could dysregulate cellular energetics, oxidative stress and apoptosis. However, the role of mitochondria in different grade gliomasis still unknown. This study aimed to identify mitochondrial DNA (mtDNA) sequence variations that could possibly affect the mitochondrial functions and also the oxidative stress status. Three different grades of human glioma cell lines and a normal human astrocyte cell line were cultured in-vitro and tested for oxidative stress biomarkers. Relative oxidative stress level, mitochondria activity, and mitochondrial mass were determined by live cell imaging with confocal laser scanning microscope using CM-H2DCFDA, MitoTracker Green, and MitoTracker Orange stains. The entire mitochondrial genome was sequenced using the AffymetrixGeneChip Human Mitochondrial Resequencing Array 2.0. The mitochondrial sequence variations were subjected to phylogenetic haplogroup assessment and pathogenicity of the mutations were predicted using pMUT and PolyPhen2. The Grade II astrocytoma cells showed increased oxidative stress wherea high level of 8-OHdG and oxidative stress indicator were observed. Simultaneously, Grade II and III glioma cells showed relatively poor mitochondria functions and increased number of mutations in the coding region of the mtDNA which could be due to high levels of oxidative stress in these cells. These non-synonymous mtDNA sequence variations were predicted to be pathogenic and could possibly lead to protein dysfunction, leading to oxidative phosphorylation (OXPHOS) impairment, mitochondria dysfunction and could create a vicious cycle of oxidative stress. The Grade IV cells had no missense mutation but preserved intact mitochondria and excellent antioxidant defense mechanisms thus ensuring better survival. In conclusion, Grade II and III glioma cells demonstrated coding region mtDNA mutations, leading to mitochondrial dysfunction and higher oxidative stress.
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Affiliation(s)
- Bee Hong Soon
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia.,Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Nor Azian Abdul Murad
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Sue-Mian Then
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia.,The University of Nottingham Malaysia CampusSemenyih, Malaysia
| | - Azizi Abu Bakar
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Farizal Fadzil
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Jegan Thanabalan
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | | | - Charng Jeng Toh
- Division of Neurosurgery, Department of Surgery, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Azmi Mohd Tamil
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Roslan Harun
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Wan Z Wan Ngah
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute, Universiti Kebangsaan MalaysiaKuala Lumpur, Malaysia
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Li H, Bi R, Fan Y, Wu Y, Tang Y, Li Z, He Y, Zhou J, Tang J, Chen X, Yao YG. mtDNA Heteroplasmy in Monozygotic Twins Discordant for Schizophrenia. Mol Neurobiol 2016; 54:4343-4352. [DOI: 10.1007/s12035-016-9996-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 06/14/2016] [Indexed: 12/30/2022]
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Gastric cancer and gene copy number variation: emerging cancer drivers for targeted therapy. Oncogene 2015; 35:1475-82. [PMID: 26073079 DOI: 10.1038/onc.2015.209] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Revised: 05/12/2015] [Accepted: 05/13/2015] [Indexed: 12/15/2022]
Abstract
Gastric cancer (GC) is among the most common malignancy in the world with poor prognosis and limited treatment options. It has been established that gastric carcinogenesis is caused by a complex interaction between host and environmental factors. Copy number variation (CNV) refers to a form of genomic structural variation that results in abnormal gene copy numbers, including gene amplification, gain, loss and deletion. DNA CNV is an important influential factor for the expression of both protein-coding and non-coding genes, affecting the activity of various signaling pathways. CNV arises as a result of preferential selection that favors cancer development, and thus, targeting the amplified 'driver genes' in GC may provide novel opportunities for personalized therapy. The detection of CNVs in chromosomal or mitochondrial DNA from tissue or blood samples may assist the diagnosis, prognosis and targeted therapy of GC. In this review, we discuss the recent CNV discoveries that shed light on the molecular pathogenesis of GC, with a specific emphasis on CNVs that display diagnostic, prognostic or therapeutic significances in GC.
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Kamiński MM, Röth D, Krammer PH, Gülow K. Mitochondria as oxidative signaling organelles in T-cell activation: physiological role and pathological implications. Arch Immunol Ther Exp (Warsz) 2013; 61:367-84. [PMID: 23749029 DOI: 10.1007/s00005-013-0235-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Accepted: 05/13/2013] [Indexed: 12/22/2022]
Abstract
Early scientific reports limited the cell biological role of reactive oxygen species (ROS) to the cause of pathological damage. However, extensive research performed over the last decade led to a wide recognition of intracellular oxidative/redox signaling as a crucial mechanism of homeostatic regulation. Amongst different cellular processes known to be influenced by redox signaling, T-cell activation is one of the most established. Numerous studies reported an indispensible role for ROS as modulators of T-cell receptor-induced transcription. Nevertheless, mechanistic details regarding signaling pathways triggered by ROS are far from being delineated. The nature and interplay between enzymatic sources involved in the generation of "oxidative signals" are also a matter of ongoing research. In particular, active participation of the mitochondrial respiratory chain as ROS producer constitutes an intriguing issue with various implications for bioenergetics of activated T cells as well as for T-cell-mediated pathologies. The aim of the current review is to address these interesting concepts.
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Affiliation(s)
- Marcin M Kamiński
- Tumour Immunology Program, Division of Immunogenetics (D030), German Cancer Research Center (DKFZ), Heidelberg, Germany,
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Mondal R, Ghosh SK. Accumulation of mutations over the complete mitochondrial genome in tobacco-related oral cancer from northeast India. ACTA ACUST UNITED AC 2013; 24:432-9. [PMID: 23350716 DOI: 10.3109/19401736.2012.760551] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Northeast India has one of the world's highest incidences of oral cancer and 90% of them are related to tobacco. We examined the complete mitochondrial genome to determine hot spot mutations in oral cancer. The complete mitochondrial genome was sequenced using PGM™ from 10 patients matched blood and tumour tissue. Overall, 26 somatic mutations were found of which nine mutations in d-loop and 17 mutations in the coding region. The mutations at nucleotide positions 16294, 16325 and 16463 in d-loop and 4136, 13542 and 13869 in coding region are probably an indication to be a hot spot mutation in oral cancer. The knowledge about role, patterns and timing of mitochondrial mutations may serve to be facilitating clinical applications and hot spot mutations may be helpful in assessing cancer risk in tumour.
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Affiliation(s)
- Rosy Mondal
- Department of Biochemistry and Molecular and Cellular Biology, Universidad de Zaragoza, CIBER de Enfermedades Raras, Zaragoza, Spain.
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Mondal R, Ghosh SK, Talukdar FR, Laskar RS. Association of mitochondrial D-loop mutations with GSTM1 and GSTT1 polymorphisms in oral carcinoma: a case control study from northeast India. Oral Oncol 2012; 49:345-53. [PMID: 23265943 DOI: 10.1016/j.oraloncology.2012.11.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Revised: 11/10/2012] [Accepted: 11/18/2012] [Indexed: 11/28/2022]
Abstract
OBJECTIVES Mitochondrial dysfunction is a hallmark of cancer cells. Tobacco consumption in various forms is one of the major risk factors for the development of oral squamous cell carcinoma which makes the mitochondrial DNA susceptible to damage by reactive oxygen species. The GSTT1 and GSTM1 members of the glutathione S-transferase multigene family are candidate carcinogen metabolizing genes. Here we determined the hot spot mutations in the D-loop region and revealing correlation if any, with clinical parameters, along with analysing the genetic polymorphism of GSTT1 and GSTM1 and its susceptibility towards oral cancer. MATERIALS AND METHODS To determine the hot spot mutations 25 matched tissue samples of OSCC patients with 25 control subjects were used for PCR and direct sequencing. Analysis for GSTM1 and GSTT1 gene polymorphism was done by multiplex PCR. RESULTS Several mutations were found within the D-loop region among which mutations at nt146, nt152 and nt196 are found to be hot spot (P<0.0001, P<0.0001 and P<0.001 respectively). A significant association was found between the numbers of D-loop mutation and GSTM1 (OR=2.03; 95% CI, 1.04-3.96, P=0.003), GSTT1 (OR=1.73; 95% CI, 1.10-2.71, P=0.0027) null genotypes respectively. We observed a significant correlation between the increased number of D-loop mutations with the advancement in tumour stage of the patients (P=0.009, r=0.48). CONCLUSION The association of null genotypes and mutations can be used as a possible biomarker for early detection and preventive measure of oral cancer for those habituated to tobacco consumption.
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Affiliation(s)
- Rosy Mondal
- Department of Biotechnology, Assam University (A Central University), Silchar 788011, Assam, India.
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Li H, Hong ZH. Mitochondrial DNA mutations in human tumor cells. Oncol Lett 2012; 4:868-872. [PMID: 23162613 DOI: 10.3892/ol.2012.874] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2012] [Accepted: 08/20/2012] [Indexed: 02/02/2023] Open
Abstract
Mitochondria play significant roles in cellular energy metabolism, free radical generation and apoptosis. The dysfunction of mitochondria is correlated with the origin and progression of tumors; thus, mutations in the mitochondrial genome that affect mitochondrial function may be one of the causal factors of tumorigenesis. Although the role of mitochondrial DNA (mtDNA) mutations in carcinogenesis has been investigated extensively by various approaches, the conclusions remain controversial to date. This review briefly summarizes the recent progress in this field.
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Affiliation(s)
- Hui Li
- Department of Genetics and Developmental Biology, Southeast University School of Medicine; ; The Key Laboratory of Developmental Genes and Human Disease, Ministry of Education, Southeast University, Nanjing, Jiangsu 210009, P.R. China
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Pereira L, Soares P, Máximo V, Samuels DC. Somatic mitochondrial DNA mutations in cancer escape purifying selection and high pathogenicity mutations lead to the oncocytic phenotype: pathogenicity analysis of reported somatic mtDNA mutations in tumors. BMC Cancer 2012; 12:53. [PMID: 22299657 PMCID: PMC3342922 DOI: 10.1186/1471-2407-12-53] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2011] [Accepted: 02/02/2012] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The presence of somatic mitochondrial DNA (mtDNA) mutations in cancer cells has been interpreted in controversial ways, ranging from random neutral accumulation of mutations, to positive selection for high pathogenicity, or conversely to purifying selection against high pathogenicity variants as occurs at the population level. METHODS Here we evaluated the predicted pathogenicity of somatic mtDNA mutations described in cancer and compare these to the distribution of variations observed in the global human population and all possible protein variations that could occur in human mtDNA. We focus on oncocytic tumors, which are clearly associated with mitochondrial dysfunction. The protein variant pathogenicity was predicted using two computational methods, MutPred and SNPs&GO. RESULTS The pathogenicity score of the somatic mtDNA variants were significantly higher in oncocytic tumors compared to non-oncocytic tumors. Variations in subunits of Complex I of the electron transfer chain were significantly more common in tumors with the oncocytic phenotype, while variations in Complex V subunits were significantly more common in non-oncocytic tumors. CONCLUSIONS Our results show that the somatic mtDNA mutations reported over all tumors are indistinguishable from a random selection from the set of all possible amino acid variations, and have therefore escaped the effects of purifying selection that act strongly at the population level. We show that the pathogenicity of somatic mtDNA mutations is a determining factor for the oncocytic phenotype. The opposite associations of the Complex I and Complex V variants with the oncocytic and non-oncocytic tumors implies that low mitochondrial membrane potential may play an important role in determining the oncocytic phenotype.
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Affiliation(s)
- Luísa Pereira
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University Medical Center, Nashville, TN, USA
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Zeng A, Liu X, Shen L, Li W, Ding Z, Bai Y, Lu J. Analysis of mitochondrial DNA variations in a Chinese family with spinocerebellar ataxia. J Clin Neurosci 2011; 19:60-4. [PMID: 22169599 DOI: 10.1016/j.jocn.2011.05.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 05/03/2011] [Accepted: 05/06/2011] [Indexed: 11/25/2022]
Abstract
Mitochondrial dysfunction and mitochondrial DNA (mtDNA) variations have been shown to have a role in several neurological diseases. To determine whether there is an association between mtDNA variations and spinocerebellar ataxia (SCA), we analyzed the mtDNA main control region (D-loop), as well as mtDNA content and the prevalence of the common deletion, in blood samples from members of a large Chinese family (14 individuals with SCA and 13 healthy individuals). All 14 individuals with SCA were genotyped as SCA3. Thirteen mtDNA haplotypes were identified among the 27 subjects. We detected no mutations in the mtDNA D-loop region and found no significant differences in mtDNA copy number or common deletion level between patients and their healthy relatives. Contrary to some previous reports, our study showed that mtDNA variations seem to be a rare event in individuals with SCA3.
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Affiliation(s)
- Aiping Zeng
- Wenling Hospital of Wenzhou Medical College, Wenling, Zhejiang, China
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Bi R, Zhang AM, Yao YG. Leber's Hereditary Optic Neuropathy. Ophthalmology 2011; 118:1489-1489.e1. [DOI: 10.1016/j.ophtha.2011.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2011] [Accepted: 04/05/2011] [Indexed: 10/27/2022] Open
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