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Aaltio J, Euro L, Tynninen O, Vu HS, Ni M, DeBerardinis RJ, Suomalainen A, Isohanni P. Niacin supplementation in a child with novel MTTN variant m.5670A>G causing early onset mitochondrial myopathy and NAD + deficiency. Neuromuscul Disord 2024; 43:14-19. [PMID: 39173541 DOI: 10.1016/j.nmd.2024.07.005] [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: 03/14/2024] [Revised: 07/07/2024] [Accepted: 07/09/2024] [Indexed: 08/24/2024]
Abstract
Myopathy is a common manifestation in mitochondrial disorders, but the pathomechanisms are still insufficiently studied in children. Here, we report a severe, progressive mitochondrial myopathy in a four-year-old child, who died at eight years. He developed progressive loss of muscle strength with nocturnal hypoventilation and dilated cardiomyopathy. Skeletal muscle showed ragged red fibers and severe combined respiratory chain deficiency. Mitochondrial DNA sequencing revealed a novel m.5670A>G mutation in mitochondrial tRNAAsn (MTTN) with 88 % heteroplasmy in muscle. The proband also had systemic NAD+ deficiency but rescuing this with the NAD+ precursor niacin did not stop disease progression. Targeted metabolomics revealed an overall shift of metabolism towards controls after niacin supplementation, with normalized tryptophan metabolites and lipid-metabolic markers, but most amino acids did not respond to niacin therapy. To conclude, we report a new MTTN mutation, secondary NAD+ deficiency in childhood-onset mitochondrial myopathy with metabolic but meager clinical response to niacin supplementation.
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Affiliation(s)
- Juho Aaltio
- Research Programs Unit, Stem Cells and Metabolism Research, University of Helsinki, Helsinki, Finland.
| | - Liliya Euro
- Research Programs Unit, Stem Cells and Metabolism Research, University of Helsinki, Helsinki, Finland
| | - Olli Tynninen
- Department of Pathology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Hieu S Vu
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Min Ni
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Anu Suomalainen
- Research Programs Unit, Stem Cells and Metabolism Research, University of Helsinki, Helsinki, Finland; HUS Diagnostic Centre, Helsinki University Hospital, Helsinki, Finland; HiLife, University of Helsinki, Helsinki, Finland
| | - Pirjo Isohanni
- Research Programs Unit, Stem Cells and Metabolism Research, University of Helsinki, Helsinki, Finland; Child Neurology, Children's Hospital, Pediatric Research Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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Ding Y, Yu XJ, Guo QX, Leng JH. Functional analysis of the novel mitochondrial tRNA Trp and tRNA Ser(AGY) variants associated with type 2 diabetes mellitus. World J Diabetes 2024; 15:1753-1763. [PMID: 39192858 PMCID: PMC11346085 DOI: 10.4239/wjd.v15.i8.1753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 05/09/2024] [Accepted: 06/18/2024] [Indexed: 07/25/2024] Open
Abstract
BACKGROUND Mutations in mitochondrial tRNA (mt-tRNA) genes that result in mitochondrial dysfunction play important roles in type 2 diabetes mellitus (T2DM). We pre-viously reported a large Chinese pedigree with maternally inherited T2DM that harbors novel mt-tRNA Trp A5514G and tRNA Ser(AGY) C12237T variants, however, the effects of these mt-tRNA variants on T2DM progression are largely unknown. AIM To assess the potential pathogenicity of T2DM-associated m.A5514G and m.C12237T variants at genetic, molecular, and biochemical levels. METHODS Cytoplasmic hybrid (cybrid) cells carrying both m.A5514G and m.C12237T variants, and healthy control cells without these mitochondrial DNA (mtDNA) variants were generated using trans-mitochondrial technology. Mitochondrial features, including mt-tRNA steady-state level, levels of adenosine triphosphate (ATP), mitochondrial membrane potential (MMP), reactive oxygen species (ROS), mtDNA copy number, nicotinamide adenine dinucleotide (NAD+)/NADH ratio, enzymatic activities of respiratory chain complexes (RCCs), 8-hydroxy-deo-xyguanine (8-OhdG), malondialdehyde (MDA), and superoxide dismutase (SOD) were examined in cell lines with and without these mt-tRNA variants. RESULTS Compared with control cells, the m.A5514G variant caused an approximately 35% reduction in the steady-state level of mt-tRNA Trp (P < 0.0001); however, the m.C12237T variant did not affect the mt-tRNA Ser(AGY) steady-state level (P = 0.5849). Biochemical analysis revealed that cells with both m.A5514G and m.C12237T variants exhibited more severe mitochondrial dysfunctions and elevated oxidative stress than control cells: ATP, MMP, NAD+/NADH ratio, enzyme activities of RCCs and SOD levels were markedly decreased in mutant cells (P < 0.05 for all measures). By contrast, the levels of ROS, 8-OhdG and MDA were significantly increased (P < 0.05 for all measures), but mtDNA copy number was not affected by m.A5514G and m.C12237T variants (P = 0.5942). CONCLUSION The m.A5514G variant impaired mt-tRNA Trp metabolism, which subsequently caused mitochondrial dysfunction. The m.C12237T variant did not alter the steady-state level of mt-tRNA Ser(AGY), indicating that it may be a modifier of the m.A5514G variant. The m.A5514G variant may exacerbate the pathogenesis and progression of T2DM in this Chinese pedigree.
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Affiliation(s)
- Yu Ding
- Central Laboratory, Hangzhou First People’s Hospital, Hangzhou 310006, Zhejiang Province, China
| | - Xue-Jiao Yu
- Clinical Laboratory, Quzhou People’s Hospital, Quzhou 324000, Zhejiang Province, China
| | - Qin-Xian Guo
- Central Laboratory, Hangzhou First People’s Hospital, Hangzhou 310006, Zhejiang Province, China
| | - Jian-Hang Leng
- Central Laboratory, Hangzhou First People’s Hospital, Hangzhou 310006, Zhejiang Province, China
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Wang C, Deng X, Li L, Li M. Maternally Inherited Essential Hypertension May Be Associated with the Mutations in Mitochondrial tRNA Glu Gene. Pharmgenomics Pers Med 2024; 17:13-26. [PMID: 38222291 PMCID: PMC10787565 DOI: 10.2147/pgpm.s436235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Accepted: 12/21/2023] [Indexed: 01/16/2024] Open
Abstract
Background Mitochondrial DNA (mtDNA) mutations are associated with essential hypertension (EH), but the molecular mechanism remains largely unknown. Objective The aim of this study is to explore the association between mtDNA mutations and EH. Methods Two maternally inherited families with EH are underwent clinical, genetic and biochemical assessments. mtDNA mutations are screened by PCR-Sanger sequencing and phylogenetic, and bioinformatics analyses are performed to evaluate the pathogenicity of mtDNA mutations. We also generate cytoplasmic hybrid (cybrid) cell lines to analysis mitochondrial functions. Results Matrilineal relatives exhibit variable degree of clinical phenotypes. Molecular analysis reveals the presence of m.A14693G and m.A14696G mutations in two pedigrees. Notably, the m.A14693G mutation occurs at position 54 in the TψC loop of tRNAGlu, a position which is critical for post-transcriptionally modification of tRNAGlu. While the m.A14696G mutation creates a novel base-pairing (51C-64G). Bioinformatic analysis shows that these mutations alter tRNAGlu secondary structure. Additionally, patients with tRNAGlu mutations exhibit markedly decreased in mtDNA copy number, mitochondrial membrane potential (MMP) and ATP, whereas the levels of reactive oxygen species (ROS) increase significantly. Conclusion The m.A14696G and m.A14693G mutations lead to failure in tRNAGlu metabolism and cause mitochondrial dysfunction that is responsible for EH.
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Affiliation(s)
- Chun Wang
- Department of Integrated TCM & Western Medicine, Mengcheng County Second People’s Hospital, Anhui, 233500, People’s Republic of China
| | - Xin Deng
- Department of Integrated TCM & Western Medicine, Mengcheng County Second People’s Hospital, Anhui, 233500, People’s Republic of China
| | - Lei Li
- Department of Cardiology, Mengcheng County Second People’s Hospital, Anhui, 233500, People’s Republic of China
| | - Mei Li
- Department of Pharmacy, Mengcheng County Second People’s Hospital, Anhui, 233500, People’s Republic of China
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Ghirigato E, Terenzi F, Baglivo M, Zanetti N, Baldo F, Murru FM, Bobbo M, Barbi E, Zeviani M, Bruno I, Lamantea E. A new family with a case of severe early-onset muscle fatigue and a peculiar maternally inherited painful swelling in chewing muscles associated with homoplasmic m.15992A>T mutation in mitochondrial tRNA Pro. Neuromuscul Disord 2023; 33:972-977. [PMID: 38030461 DOI: 10.1016/j.nmd.2023.11.001] [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: 04/27/2023] [Revised: 09/12/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
A 16-year-old boy was evaluated for a history of exercise-induced fatigability associated with nausea even after minimal effort, lower limbs muscle hypotrophy, and swelling of the masseter muscles after chewing. Laboratory tests were remarkable for hyperlactatemia and metabolic acidosis after short physical activity. The muscle biopsy showed non-specific mitochondrial alterations and an increase in intrafibral lipids. Biochemical analysis showed reduced activity of the respiratory chain complexes. Mitochondrial DNA sequencing revealed the presence of a homoplasmic variant m.15992A>T in the MT-TP gene, coding for the mt-tRNAPro in the patient, in his mother and in his brother. Pathogenic or likely pathogenic variants in MT-TP gene are rare. They are responsible for different clinical presentation, almost ever involving the muscle tissue. We report the first family with exercise-induced muscle weakness and swelling of the chewing muscles due to m.15992A>T variant in absence of J1c10 haplogroup, confirming its pathogenicity.
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Affiliation(s)
| | | | - Mirko Baglivo
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Nadia Zanetti
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Francesco Baldo
- Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy.
| | - Flora Maria Murru
- Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Marco Bobbo
- Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Egidio Barbi
- University of Trieste, Italy; Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Massimo Zeviani
- Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Irene Bruno
- Institute for Maternal and Child Health IRCCS Burlo Garofolo, Trieste, Italy
| | - Eleonora Lamantea
- Unit of Medical Genetics and Neurogenetics, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
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Bibi S, Abbas G, Khan MZ, Nawaz T, Ullah Q, Uddin A, Khan MF, Ghafoor SU, Nadeem MS, Tabassum S, Zahoor M. The mutational analysis of mitochondrial DNA in maternal inheritance of polycystic ovarian syndrome. Front Endocrinol (Lausanne) 2023; 14:1093353. [PMID: 37674615 PMCID: PMC10477912 DOI: 10.3389/fendo.2023.1093353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 04/17/2023] [Indexed: 09/08/2023] Open
Abstract
Introduction Polycystic Ovarian Syndrome (PCOS) is a globally prevalent condition that leads to infertility in women. While environmental factors contribute to PCOS, maternal genetics also play a significant role. Currently, there is no definitive test for identifying predisposition to PCOS. Hence, our objective is to discover novel maternal genetic risk factors for PCOS by investigating the genomes of patients from Pakistan. Methods We utilized Next-Generation Sequencing (NGS) to sequence the complete mitochondrial DNA of three PCOS patients. Subsequently, we employed MitoTIP (Mitochondrial tRNA Informatics Predictor) and PON-mt-tRNA tools to identify variations in the mitochondrial DNA. Our analysis focused on the genes MT-RNR1, MT-RNR2, MT-ATP6, MT-TL2, and MT-CYTB, which displayed common variations in all three genomes. Additionally, we observed individual variations. The D-loop region exhibited the highest frequency of mutations, followed by the non-coding regions of RNR1 and RNR2 genes. Moreover, we detected frameshift mutations in the mitochondrially encoded NADH Dehydrogenase 2 (MT-ND2) and mitochondrially encoded NADH Dehydrogenase 5 (ND5) genes within individual genomes. Results Our analysis unveiled six regions with common variations in the mitochondrial DNA of all three PCOS patients. Notably, the MT-RNR1, MT-RNR2, MT-ATP6, MT-TL2, and MT-CYTB genes exhibited these variations. Additionally, we identified individual variations in the mitochondrial DNA. The D-loop region displayed the highest mutation frequency, followed by the non-coding regions of RNR1 and RNR2 genes. Furthermore, frameshift mutations were detected in the MT-ND2 and ND5 genes within individual genomes. Conclusion Through our study, we have identified variations in mitochondrial DNA that may be associated with the development of PCOS and have the potential to serve as predisposition tests. Our findings highlight the presence of novel mutations in the MT-RNR1, MT-RNR2, MT-ATP6, MT-TL2, and MT-CYTB genes, as well as frameshift mutations in the MT-ND2 and ND5 genes. Pathogenicity analysis indicated that most variants were likely to result in benign cysts. However, the frameshift mutations in the ND2 gene were associated with a high risk of complications and pathogenicity in PCOS. This is the first report identifying these mutations and their association with PCOS, contributing to our understanding of the genetic factors underlying the condition.
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Affiliation(s)
- Shaheen Bibi
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - Ghulam Abbas
- Department of Biotechnology, University of Agriculture, Dera Ismail Khan, Pakistan
| | - Muhammad Zahoor Khan
- Faculty of Veterinary and Animal Science, University of Agriculture, Dera Ismail Khan, Pakistan
| | - Tanzeela Nawaz
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - Qudrat Ullah
- Faculty of Veterinary and Animal Science, University of Agriculture, Dera Ismail Khan, Pakistan
| | - Aziz Uddin
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | | | - Sajid Ul Ghafoor
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdul-Aziz University, Jeddah, Saudi Arabia
| | - Sadia Tabassum
- Department of Zoology, Hazara University, Mansehra, Pakistan
| | - Muhammad Zahoor
- Department of Molecular Medicine, Institute of Basic Medical Sciences, University of Oslo, Oslo, Norway
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Ding H, Zhao Y, Jiang Z, Zhou D, Zhu R. Analysis of Mitochondrial Transfer RNA Mutations in Breast Cancer. Balkan J Med Genet 2023; 25:15-22. [PMID: 37265965 PMCID: PMC10230833 DOI: 10.2478/bjmg-2022-0020] [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: 06/03/2023] Open
Abstract
Damage of mitochondrial functions caused by mitochondrial DNA (mtDNA) pathogenic mutations had long been proposed to be involved in breast carcinogenesis. However, the detailed pathological mechanism remained deeply undetermined. In this case-control study, we screened the frequencies of mitochondrial tRNA (mt-tRNA) mutations in 80 breast cancer tissues and matched normal adjacent tissues. PCR and Sanger sequence revealed five possible pathogenic mutations: tRNAVal G1606A, tRNAIle A4300G, tRNASer(UCN) T7505C, tRNAGlu A14693G and tRNAThr G15927A. We noticed that these mutations resided at extremely conserved positions of tRNAs and would affect tRNAs transcription or modifications. Furthermore, functional analysis suggested that patients with these mt-tRNA mutations exhibited much lower levels of mtDNA copy number and ATP, as compared with controls (p<0.05). Therefore, it can be speculated that these mutations may impair mitochondrial protein synthesis and oxidative phosphorylation (OXPHOS) complexes, which caused mitochondrial dysfunctions that were involved in the breast carcinogenesis. Taken together, our data indicated that mutations in mt-tRNA were the important contributors to breast cancer, and mutational analyses of mt-tRNA genes were critical for prevention of breast cancer.
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Affiliation(s)
- H.J. Ding
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
| | - Y.P. Zhao
- Department of Pharmacy, Shaoxing Hospital of Traditional Chinese Medicine Affiliated to Zhejiang Chinese Medical University, Shaoxing, China
| | - Z.C. Jiang
- Department of Pathology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - D.T. Zhou
- Department of Pharmacy, The First People’s Hospital of Kaili, Kaili, China
| | - R. Zhu
- School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, China
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Wu G, Shen Y, Zhu F, Tao W, Zhou Y, Ke S, Jiang H. Comprehensive Diagnostic Criteria for MELAS Syndrome; a Case Study Involving an Elderly Patient With MT-TWm.5541C>T Mutation. Neurologist 2023; 28:190-194. [PMID: 36125978 PMCID: PMC10158598 DOI: 10.1097/nrl.0000000000000457] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
INTRODUCTION The mitochondrial encephalopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome is a matrilineal hereditary multisystem disease caused by mutations in the mitochondrial DNA. Although the initial diagnostic criteria correlate with a range of clinical phenotypes, including clinical onset after the age of 40, there is still lack of a unified single diagnostic standard for MELAS. CASE REPORT A 71-year-old female patient with recurrent stroke was reported. Magnetic resonance imaging showed a cerebral gyrus-like diffusion weighted imaging high signal lesion in the parietal-occipital lobe and the area of this lesion expanded with disease progression. The MRS result showed significantly inverted Lac/Lip peaks. The nucleic acid sequencing result displayed a MT-TWm.5541C>T mutation, and a 12.86% mutation rate in the blood sample. The patient had a 6-year history of type 2 diabetes. CONCLUSION Patients with the MELAS syndrome may present with a variety of clinical manifestations. Our data demonstrated that, for patients with atypical cerebral infarction and suspected MELAS syndrome, gene sequencing and muscle biopsy should be performed in time. This case provides a reference for the diagnostic criteria of MELAS syndrome.
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Affiliation(s)
- Gang Wu
- Department of Neurology
- Department of Pharmacy, Taizhou Hospital of Zhejiang Province affiliated to Wenzhou Medical University, Linhai, Zhejiang, China
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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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Mitochondrial tRNAGln 4394C>T Mutation May Contribute to the Clinical Expression of 1555A>G-Induced Deafness. Genes (Basel) 2022; 13:genes13101794. [PMID: 36292680 PMCID: PMC9602358 DOI: 10.3390/genes13101794] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/08/2022] [Accepted: 09/12/2022] [Indexed: 11/17/2022] Open
Abstract
The mitochondrial 1555A>G mutation plays a critical role in aminoglycoside-induced and non-syndromic hearing loss (AINSHL). Previous studies have suggested that mitochondrial secondary variants may modulate the clinical expression of m.1555A>G-induced deafness, but the molecular mechanism has remained largely undetermined. In this study, we investigated the contribution of a deafness-associated tRNAGln 4394C>T mutation to the clinical expression of the m.1555A>G mutation. Interestingly, a three-generation family with both the m.1555A>G and m.4394C>T mutations exhibited a higher penetrance of hearing loss than another family harboring only the m.1555A>G mutation. At the molecular level, the m.4394C>T mutation resides within a very conserved nucleotide of tRNAGln, which forms a new base-pairing (7T-66A) and may affect tRNA structure and function. Using trans-mitochondrial cybrid cells derived from three subjects with both the m.1555A>G and m.4394C>T mutations, three patients with only the m.1555A>G mutation and three control subjects without these primary mutations, we observed that cells with both the m.1555A>G and m.4394C>T mutations exhibited more severely impaired mitochondrial functions than those with only the m.1555A>G mutation. Furthermore, a marked decrease in mitochondrial RNA transcripts and respiratory chain enzymes was observed in cells harboring both the m.1555A>G and m.4394C>T mutations. Thus, our data suggest that the m.4394C>T mutation may play a synergistic role in the m.1555A>G mutation, enhancing mitochondrial dysfunctions and contributing to a high penetrance of hearing loss in families with both mtDNA pathogenic mutations.
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Miyamoto A, Tomotaka U, Takaaki K, Kenichi M, Chimi M. Molecular characterization of two pedigrees with maternally inherited diabetes mellitus. Mitochondrial DNA B Resour 2022. [DOI: 10.1080/23802359.2022.2050474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Akira Miyamoto
- Faculty of Rehabilitation, Kobe International University, Hyogo, Japan
| | - Ueda Tomotaka
- Faculty of Rehabilitation, Nishikyushu University, Saga, Japan
| | - Kubo Takaaki
- Faculty of health science, Kumamoto Health Science University, Kumamoto, Japan
| | - Mori Kenichi
- Omote Orthopedic Osteoporosis Clinic, Toyonaka, Japan
| | - Miyamoto Chimi
- Department of Occupational Therapy, Faculty of Health Science, Aino University, Osaka, Japan
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Hippen M, Zsurka G, Peeva V, Machts J, Schwiecker K, Debska-Vielhaber G, Wiesner RJ, Vielhaber S, Kunz WS. Novel Pathogenic Sequence Variation m.5789T>C Causes NARP Syndrome and Promotes Formation of Deletions of the Mitochondrial Genome. Neurol Genet 2022; 8:e660. [PMID: 35252560 PMCID: PMC8893589 DOI: 10.1212/nxg.0000000000000660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 01/10/2022] [Indexed: 11/15/2022]
Abstract
Background and Objectives We report the pathogenic sequence variant m.5789T>C in the anticodon stem of the mitochondrial tRNA for cysteine as a novel cause of neuropathy, ataxia, and retinitis pigmentosa (NARP), which is usually associated with pathogenic variants in the MT-ATP6 gene. Methods To address the correlation of oxidative phosphorylation deficiency with mutation loads, we performed genotyping on single laser-dissected skeletal muscle fibers. Stability of the mitochondrial tRNACys was investigated by Northern blotting. Accompanying deletions of the mitochondrial genome were detected by long-range PCR and their breakpoints were determined by sequencing of single-molecule amplicons. Results The sequence variant m.5789T>C, originating from the patient's mother, decreases the stability of the mitochondrial tRNA for cysteine by disrupting the anticodon stem, which subsequently leads to a combined oxidative phosphorylation deficiency. In parallel, we observed a prominent cluster of low-abundance somatic deletions with breakpoints in the immediate vicinity of the m.5789T>C variant. Strikingly, all deletion-carrying mitochondrial DNA (mtDNA) species, in which the corresponding nucleotide position was not removed, harbored the mutant allele, and none carried the wild-type allele. Discussion In addition to providing evidence for the novel association of a tRNA sequence alteration with NARP syndrome, our observations support the hypothesis that single nucleotide changes can lead to increased occurrence of site-specific mtDNA deletions through the formation of an imperfect repeat. This finding might be relevant for understanding mechanisms of deletion generation in the human mitochondrial genome.
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Affiliation(s)
- Marius Hippen
- Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany
| | - Gábor Zsurka
- Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany
| | - Viktoriya Peeva
- Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany
| | - Judith Machts
- Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany
| | - Kati Schwiecker
- Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany
| | - Grazyna Debska-Vielhaber
- Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany
| | - Rudolf J Wiesner
- Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany
| | - Stefan Vielhaber
- Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany
| | - Wolfram S Kunz
- Division of Neurochemistry (M.H., G.Z., V.P., W.S.K.), Institute of Experimental Epileptology and Cognition Research, University of Bonn; Department of Epileptology (G.Z., W.S.K.), University of Bonn; Center for Behavioral Brain Sciences (CBBS) (J.M.), Magdeburg; Department of Neurology (K.S., G.D.-V., S.V.), University of Magdeburg; and Institute of Vegetative Physiology (R.J.W.), University of Cologne, Germany
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12
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Valiente-Pallejà A, Tortajada J, Bulduk BK, Vilella E, Garrabou G, Muntané G, Martorell L. Comprehensive summary of mitochondrial DNA alterations in the postmortem human brain: A systematic review. EBioMedicine 2022; 76:103815. [PMID: 35085849 PMCID: PMC8790490 DOI: 10.1016/j.ebiom.2022.103815] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/24/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) encodes 37 genes necessary for synthesizing 13 essential subunits of the oxidative phosphorylation system. mtDNA alterations are known to cause mitochondrial disease (MitD), a clinically heterogeneous group of disorders that often present with neuropsychiatric symptoms. Understanding the nature and frequency of mtDNA alterations in health and disease could be a cornerstone in disentangling the relationship between biochemical findings and clinical symptoms of brain disorders. This systematic review aimed to summarize the mtDNA alterations in human brain tissue reported to date that have implications for further research on the pathophysiological significance of mtDNA alterations in brain functioning. METHODS We searched the PubMed and Embase databases using distinct terms related to postmortem human brain and mtDNA up to June 10, 2021. Reports were eligible if they were empirical studies analysing mtDNA in postmortem human brains. FINDINGS A total of 158 of 637 studies fulfilled the inclusion criteria and were clustered into the following groups: MitD (48 entries), neurological diseases (NeuD, 55 entries), psychiatric diseases (PsyD, 15 entries), a miscellaneous group with controls and other clinical diseases (5 entries), ageing (20 entries), and technical issues (5 entries). Ten entries were ascribed to more than one group. Pathogenic single nucleotide variants (pSNVs), both homo- or heteroplasmic variants, have been widely reported in MitD, with heteroplasmy levels varying among brain regions; however, pSNVs are rarer in NeuD, PsyD and ageing. A lower mtDNA copy number (CN) in disease was described in most, but not all, of the identified studies. mtDNA deletions were identified in individuals in the four clinical categories and ageing. Notably, brain samples showed significantly more mtDNA deletions and at higher heteroplasmy percentages than blood samples, and several of the deletions present in the brain were not detected in the blood. Finally, mtDNA heteroplasmy, mtDNA CN and the deletion levels varied depending on the brain region studied. INTERPRETATION mtDNA alterations are well known to affect human tissues, including the brain. In general, we found that studies of MitD, NeuD, PsyD, and ageing were highly variable in terms of the type of disease or ageing process investigated, number of screened individuals, studied brain regions and technology used. In NeuD and PsyD, no particular type of mtDNA alteration could be unequivocally assigned to any specific disease or diagnostic group. However, the presence of mtDNA deletions and mtDNA CN variation imply a role for mtDNA in NeuD and PsyD. Heteroplasmy levels and threshold effects, affected brain regions, and mitotic segregation patterns of mtDNA alterations may be involved in the complex inheritance of NeuD and PsyD and in the ageing process. Therefore, more information is needed regarding the type of mtDNA alteration, the affected brain regions, the heteroplasmy levels, and their relationship with clinical phenotypes and the ageing process. FUNDING Hospital Universitari Institut Pere Mata; Institut d'Investigació Sanitària Pere Virgili; Instituto de Salud Carlos III, Ministerio de Ciencia e Innovación (PI18/00514).
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Affiliation(s)
- Alba Valiente-Pallejà
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Juan Tortajada
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Bengisu K Bulduk
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Elisabet Vilella
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain
| | - Glòria Garrabou
- Laboratory of Muscle Research and Mitochondrial Function, Department of Internal Medicine-Hospital Clínic of Barcelona (HCB); Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS); Faculty of Medicine and Health Sciences, Universitat de Barcelona (UB), 08036 Barcelona, Catalonia, Spain; Biomedical Network Research Centre on Rare Diseases (CIBERER), 28029 Madrid, Spain
| | - Gerard Muntané
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain; Institute of Evolutionary Biology (IBE), Universitat Pompeu Fabra (UPF), 08003 Barcelona, Catalonia, Spain
| | - Lourdes Martorell
- Research Department, Hospital Universitari Institut Pere Mata (HUIPM); Institut d'Investigació Sanitària Pere Virgili (IISPV); Faculty of Medicine and Health Sciences, Universitat Rovira i Virgili (URV), 43201 Reus, Catalonia, Spain; Biomedical Network Research Centre on Mental Health (CIBERSAM), 28029 Madrid, Spain.
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13
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Molecular Genetics Overview of Primary Mitochondrial Myopathies. J Clin Med 2022; 11:jcm11030632. [PMID: 35160083 PMCID: PMC8836969 DOI: 10.3390/jcm11030632] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 01/13/2022] [Accepted: 01/20/2022] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial disorders are the most common inherited conditions, characterized by defects in oxidative phosphorylation and caused by mutations in nuclear or mitochondrial genes. Due to its high energy request, skeletal muscle is typically involved. According to the International Workshop of Experts in Mitochondrial Diseases held in Rome in 2016, the term Primary Mitochondrial Myopathy (PMM) should refer to those mitochondrial disorders affecting principally, but not exclusively, the skeletal muscle. The clinical presentation may include general isolated myopathy with muscle weakness, exercise intolerance, chronic ophthalmoplegia/ophthalmoparesis (cPEO) and eyelids ptosis, or multisystem conditions where there is a coexistence with extramuscular signs and symptoms. In recent years, new therapeutic targets have been identified leading to the launch of some promising clinical trials that have mainly focused on treating muscle symptoms and that require populations with defined genotype. Advantages in next-generation sequencing techniques have substantially improved diagnosis. So far, an increasing number of mutations have been identified as responsible for mitochondrial disorders. In this review, we focused on the principal molecular genetic alterations in PMM. Accordingly, we carried out a comprehensive review of the literature and briefly discussed the possible approaches which could guide the clinician to a genetic diagnosis.
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14
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Jiang Z, Cai X, Kong J, Zhang R, Ding Y. Maternally transmitted diabetes mellitus may be associated with mitochondrial ND5 T12338C and tRNA Ala T5587C variants. Ir J Med Sci 2022; 191:2625-2633. [PMID: 34993838 DOI: 10.1007/s11845-021-02911-w] [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: 11/08/2021] [Accepted: 12/25/2021] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Mutations/variants in mitochondrial genomes are found to be associated with type 2 diabetes mellitus (T2DM), but the pathophysiology of this disease remains largely unknown. AIM The aim of this study is to investigate the relationship between mitochondrial DNA (mtDNA) variants and T2DM. METHODOLOGY A maternally inherited T2DM pedigree is underwent clinical, genetic, and molecular assessment. Moreover, the complete mitochondrial genomes of the matrilineal relatives of this family are PCR amplified and sequenced. We also utilize the phylogenetic conservation analysis, haplogroup classification, and the pathogenicity scoring system to determine the T2DM-associated potential pathogenic mtDNA variants. RESULT Four of seven matrilineal relatives of this pedigree suffered from T2DM with variable ages of onset. Screening for the entire mtDNA genes of matrilineal members reveals co-existence of ND5 T12338C and tRNAAla T5587C variants, as well as 21 genetic polymorphisms which belong to East Asian haplogroup F2. Interestingly, the T12338C variant causes the alternation of first amino acid Met to Thr, shortened two amino acids of ND5 protein. Furthermore, T5587C variant is located at position 73 in the 3'end of mt-tRNAAla and may have structural and functional consequences. CONCLUSIONS The co-occurrence of ND5 T12338C and tRNAAla T5587C variants may impair the mitochondrial function, which are associated with the development of T2DM in this family.
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Affiliation(s)
- Zhaochang Jiang
- Department of Pathology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaobo Cai
- Department of Pathology, Taizhou Central Hospital, Taizhou University Hospital, Taizhou, China
| | - Jing Kong
- Department of Endocrinology and Metabolism, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Ruyi Zhang
- Department of Pathology, Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Ding
- Central Laboratory, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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15
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Cardiomyopathies. Cardiovasc Pathol 2022. [DOI: 10.1016/b978-0-12-822224-9.00014-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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16
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Yang L, Guo Q, Leng J, Wang K, Ding Y. Late onset of type 2 diabetes is associated with mitochondrial tRNA Trp A5514G and tRNA Ser(AGY) C12237T mutations. J Clin Lab Anal 2021; 36:e24102. [PMID: 34811812 PMCID: PMC8761459 DOI: 10.1002/jcla.24102] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 10/19/2021] [Accepted: 10/26/2021] [Indexed: 12/16/2022] Open
Abstract
Background Mitochondrial dysfunctions caused by mitochondrial DNA (mtDNA) pathogenic mutations play putative roles in type 2 diabetes mellitus (T2DM) progression. But the underlying mechanism remains poorly understood. Methods A large Chinese family with maternally inherited diabetes and deafness (MIDD) underwent clinical, genetic, and molecular assessment. PCR and sequence analysis are carried out to detect mtDNA variants in affected family members, in addition, phylogenetic conservation analysis, haplogroup classification, and pathogenicity scoring system are performed. Moreover, the GJB2, GJB3, GJB6, and TRMU genes mutations are screened by PCR‐Sanger sequencing. Results Six of 18 matrilineal subjects manifested different clinical phenotypes of diabetes. The average age at onset of diabetic patients is 52 years. Screening for the entire mitochondrial genomes suggests the co‐existence of two possibly pathogenic mutations: tRNATrp A5514G and tRNASer(AGY) C12237T, which belongs to East Asia haplogroup G2a. By molecular level, m.A5514G mutation resides at acceptor stem of tRNATrp (position 3), which is critical for steady‐state level of tRNATrp. Conversely, m.C12237T mutation occurs in the variable region of tRNASer(AGY) (position 31), which creates a novel base‐pairing (11A‐31T). Thus, the mitochondrial dysfunctions caused by tRNATrp A5514G and tRNASer(AGY) C12237T mutations, may be associated with T2DM in this pedigree. But we do not find any functional mutations in those nuclear genes. Conclusion Our findings suggest that m.A5514G and m.C12337T mutations are associated with T2DM, screening for mt‐tRNA mutations is useful for molecular diagnosis and prevention of mitochondrial diabetes.
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Affiliation(s)
- Liuchun Yang
- Central Laboratory, the Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China
| | - Qinxian Guo
- Central Laboratory, the Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianhang Leng
- Central Laboratory, the Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Keyi Wang
- Central Laboratory, the Fourth School of Clinical Medicine, Zhejiang Chinese Medical University, Hangzhou, China.,Central Laboratory, the Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yu Ding
- Central Laboratory, the Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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17
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Sukri A, Noorizhab MNF, Teh LK, Salleh MZ. Insight of the mitochondrial genomes of the Orang Asli and Malays: The heterogeneity and the disease-associated variants. Mitochondrion 2021; 62:74-84. [PMID: 34748985 DOI: 10.1016/j.mito.2021.10.010] [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: 03/11/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 11/27/2022]
Abstract
Orang Asli are the oldest inhabitants in Peninsular Malaysia that forms as a national minority while the Malays are the majority. The study aimed to screen the mitochondrial genomes of the Orang Asli and the Malays to discover the disease-associated variants. A total of 99 Orang Asli from six tribes (Bateq, Cheq Wong, Orang Kanaq, Kensiu, Lanoh, and Semai) were recruited. Mitochondrial genome sequencing was conducted using a next-generation sequencing platform. Furthermore, we retrieved mitochondrial DNA sequences from the Malays for comparison. The clinical significance, pathogenicity prediction and frequency of variants were determined using online tools. Variants associated with mitochondrial diseases were detected in the 2 populations. A high frequency of variants associated with mitochondrial diseases, breast cancer, prostate cancer, and cervical cancer were detected in the Orang Asli and modern Malays. As medicine evolves to adopt prediction and prevention of diseases, this study highlights the need for intervention to adopt genomics medicine to strategise better healthcare management as a way forward for Precision Health.
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Affiliation(s)
- Asif Sukri
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia
| | - Mohd Nur Fakhruzzaman Noorizhab
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia; Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia
| | - Lay Kek Teh
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia; Faculty of Pharmacy, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia
| | - Mohd Zaki Salleh
- Integrative Pharmacogenomics Institute, Universiti Teknologi MARA Cawangan Selangor, Puncak Alam Campus, 42300 Puncak Alam, Selangor, Malaysia.
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18
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Klink GV, O'Keefe H, Gogna A, Bazykin GA, Elson JL. A broad comparative genomics approach to understanding the pathogenicity of Complex I mutations. Sci Rep 2021; 11:19578. [PMID: 34599203 PMCID: PMC8486755 DOI: 10.1038/s41598-021-98360-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/01/2021] [Indexed: 12/29/2022] Open
Abstract
Disease caused by mutations of mitochondrial DNA (mtDNA) are highly variable in both presentation and penetrance. Over the last 30 years, clinical recognition of this group of diseases has increased. It has been suggested that haplogroup background could influence the penetrance and presentation of disease-causing mutations; however, to date there is only one well-established example of such an effect: the increased penetrance of two Complex I Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducts the most extensive investigation to date into the importance of haplogroup context in the pathogenicity of mtDNA mutations in Complex I. We searched for proven human point mutations across more than 900 metazoans finding human disease-causing mutations and potential masking variants. We found more than a half of human pathogenic variants as compensated pathogenic deviations (CPD) in at least in one animal species from our multiple sequence alignments. Some variants were found in many species, and some were even the most prevalent amino acids across our dataset. Variants were also found in other primates, and in such cases, we looked for non-human amino acids in sites with high probability to interact with the CPD in folded protein. Using this "local interactions" approach allowed us to find potential masking substitutions in other amino acid sites. We suggest that the masking variants might arise in humans, resulting in variability of mutation effect in our species.
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Affiliation(s)
- Galya V Klink
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Hannah O'Keefe
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amrita Gogna
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Georgii A Bazykin
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation.
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation.
| | - Joanna L Elson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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19
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Ratnaike TE, Greene D, Wei W, Sanchis-Juan A, Schon KR, van den Ameele J, Raymond L, Horvath R, Turro E, Chinnery PF. MitoPhen database: a human phenotype ontology-based approach to identify mitochondrial DNA diseases. Nucleic Acids Res 2021; 49:9686-9695. [PMID: 34428295 PMCID: PMC8464050 DOI: 10.1093/nar/gkab726] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/03/2021] [Accepted: 08/18/2021] [Indexed: 12/23/2022] Open
Abstract
Diagnosing mitochondrial disorders remains challenging. This is partly because the clinical phenotypes of patients overlap with those of other sporadic and inherited disorders. Although the widespread availability of genetic testing has increased the rate of diagnosis, the combination of phenotypic and genetic heterogeneity still makes it difficult to reach a timely molecular diagnosis with confidence. An objective, systematic method for describing the phenotypic spectra for each variant provides a potential solution to this problem. We curated the clinical phenotypes of 6688 published individuals with 89 pathogenic mitochondrial DNA (mtDNA) mutations, collating 26 348 human phenotype ontology (HPO) terms to establish the MitoPhen database. This enabled a hypothesis-free definition of mtDNA clinical syndromes, an overview of heteroplasmy-phenotype relationships, the identification of under-recognized phenotypes, and provides a publicly available reference dataset for objective clinical comparison with new patients using the HPO. Studying 77 patients with independently confirmed positive mtDNA diagnoses and 1083 confirmed rare disease cases with a non-mitochondrial nuclear genetic diagnosis, we show that HPO-based phenotype similarity scores can distinguish these two classes of rare disease patients with a false discovery rate <10% at a sensitivity of 80%. Enriching the MitoPhen database with more patients will improve predictions for increasingly rare variants.
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Affiliation(s)
- Thiloka E Ratnaike
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Department of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UK
| | - Daniel Greene
- Department of Haematology, University of Cambridge, NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK.,Medical Research Council Biostatistics Unit, Cambridge Biomedical Campus, Cambridge CB2 0SR, UK
| | - Wei Wei
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Alba Sanchis-Juan
- Department of Haematology, University of Cambridge, NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge CB2 0PT, UK
| | - Katherine R Schon
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Jelle van den Ameele
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Lucy Raymond
- Department of Medical Genetics, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Rita Horvath
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Ernest Turro
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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20
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Cell reprogramming shapes the mitochondrial DNA landscape. Nat Commun 2021; 12:5241. [PMID: 34475388 PMCID: PMC8413449 DOI: 10.1038/s41467-021-25482-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/14/2021] [Indexed: 12/25/2022] Open
Abstract
Individual induced pluripotent stem cells (iPSCs) show considerable phenotypic heterogeneity, but the reasons for this are not fully understood. Comprehensively analysing the mitochondrial genome (mtDNA) in 146 iPSC and fibroblast lines from 151 donors, we show that most age-related fibroblast mtDNA mutations are lost during reprogramming. However, iPSC-specific mutations are seen in 76.6% (108/141) of iPSC lines at a mutation rate of 8.62 × 10−5/base pair. The mutations observed in iPSC lines affect a higher proportion of mtDNA molecules, favouring non-synonymous protein-coding and tRNA variants, including known disease-causing mutations. Analysing 11,538 single cells shows stable heteroplasmy in sub-clones derived from the original donor during differentiation, with mtDNA variants influencing the expression of key genes involved in mitochondrial metabolism and epidermal cell differentiation. Thus, the dynamic mtDNA landscape contributes to the heterogeneity of human iPSCs and should be considered when using reprogrammed cells experimentally or as a therapy. Here the authors describe high depth mitochondrial DNA (mtDNA) sequence analysis of 146 human induced pluripotent stem cell (hiPSC) lines as well as single cell RNA-seq (scRNAseq) of hiPSCs undergoing differentiation from 125 donors; reporting mtDNA diversity and some variants favoured after reprogramming.
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21
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Shuai J, Shi J, Liang Y, Ji F, Gu L, Yuan Z. Mutational analysis of mitochondrial tRNA genes in 138 patients with Leber's hereditary optic neuropathy. Ir J Med Sci 2021; 191:865-876. [PMID: 34053002 DOI: 10.1007/s11845-021-02656-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 05/19/2021] [Indexed: 02/06/2023]
Abstract
INTRODUCTION Mutations in mitochondrial DNA (mtDNA) are the most important causes for Leber's hereditary optic neuropathy (LHON). Of these, three primary mtDNA mutations account for more than 90% cases of this disease. However, to date, little is known regarding the relationship between mitochondrial tRNA (mt-tRNA) variants and LHON. AIM In this study, we aimed to investigate the association between mt-tRNA variants and LHON. METHODOLOGY One hundred thirty-eight LHON patients lacking three primary mutations (ND1 3460G > A, ND4 11778Gxs > A, and ND6 14484 T > C), as well as 266 controls were enrolled in this study. PCR-Sanger sequencing was performed to screen the mt-tRNA variants. Moreover, the phylogenetic analysis, pathogenicity scoring system, as well as mitochondrial functions were performed. RESULTS We identified 8 possible pathogenic variants: tRNAPhe 593 T > C, tRNALeu(UUR) 3275C > T, tRNAGln 4363 T > C, tRNAMet 4435A > G, tRNAAla 5587 T > C, tRNAGlu 14693A > G, tRNAThr 15927G > A, and 15951A > G, which may change the structural and functional impact on the corresponding tRNAs, and subsequently lead to a failure in tRNA metabolism. Furthermore, significant reductions in mitochondrial ATP and MMP levels and an overproduction of ROS were observed in cybrid cells containing these mt-tRNA variants, suggesting that these variants may lead to mitochondrial dysfunction which was responsible for LHON. CONCLUSION Our study indicated that mt-tRNA variants were associated with LHON, and screening for mt-tRNA variants were recommended for early detection, diagnosis, and prevention of maternally inherited LHON.
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Affiliation(s)
- Jie Shuai
- Department of Ophthalmology, the Affiliated Hospital of Nantong University, Nantong, China
| | - Jian Shi
- Department of Ophthalmology, the Affiliated Hospital of Nantong University, Nantong, China
| | - Ya Liang
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Fangfang Ji
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China
| | - Luo Gu
- Department of Physiology, Nanjing Medical University, Nanjing, China
| | - Zhilan Yuan
- Department of Ophthalmology, the First Affiliated Hospital of Nanjing Medical University, 300 Guangzhou Road, Nanjing, Jiangsu Province, China.
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22
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Pienaar IS, Mohammed R, Courtley R, Gledson MR, Reynolds R, Nicholas R, Elson JL. Investigation of the correlation between mildly deleterious mtDNA Variations and the clinical progression of multiple sclerosis. Mult Scler Relat Disord 2021; 53:103055. [PMID: 34119746 DOI: 10.1016/j.msard.2021.103055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Evidence suggests that mitochondrial DNA (mtDNA) variation at a population level may influence susceptibility to, or the clinical progression of Multiple Sclerosis (MS). OBJECTIVE To determine if mtDNA population variation is linked to the clinical progress of MS. METHODS Using the complete mtDNA sequences of 217 MS patients, we applied the new 'variant load' model, designed as a framework by which to examine the role of mtDNA variation in the context of complex clinical disease. RESULTS No significant association was detected between mtDNA 'variant load'and the clinical measures of progression. CONCLUSION Our results suggest that mtDNA population variation does not play a substantial role in the clinical progression of MS; however, modest effects and/or effects in a subgroup of patients cannot be entirely excluded. Results do not exclude the possibility of detecting an association between variation and more strictly quantified variables obtained from histopathologically-stained specimens. The results further illustrate the method's applicabilityto other disease phenotypes.
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Affiliation(s)
- Ilse S Pienaar
- School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Rean Mohammed
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Rebecca Courtley
- Northern Genetics Service, Newcastle Hospitals NHS Foundation Trust Newcastle upon Tyne, United Kingdom
| | - Michael R Gledson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard Reynolds
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Centre for Molecular Neuropathology, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Richard Nicholas
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Joanna L Elson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa.
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23
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Ji K, Wang W, Lin Y, Xu X, Liu F, Wang D, Zhao Y, Yan C. Mitochondrial encephalopathy Due to a Novel Pathogenic Mitochondrial tRNA Gln m.4349C>T Variant. Ann Clin Transl Neurol 2021; 7:980-991. [PMID: 32588991 PMCID: PMC7318088 DOI: 10.1002/acn3.51069] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 05/02/2020] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVE Mitochondrial diseases are a group of genetic diseases caused by mutations in mitochondrial DNA and nuclear DNA, among which, mutations in mitochondrial tRNA genes possessing prominent status. In most of the cases, however, the detailed molecular pathogenesis of these tRNA gene mutations remains unclear. METHODS We performed the clinical emulation, muscle histochemistry, northern blotting analysis of tRNA levels, biochemical measurement of respiratory chain complex activities and mitochondrial respirations in muscle tissue and cybrid cells. RESULTS We found a novel m.4349C>T mutation in mitochondrial tRNAGln gene in a patient present with encephalopathy, epilepsy, and deafness. We demonstrated molecular pathomechanisms of this mutation. This mutation firstly disturbed the translation machinery of mitochondrial tRNAGln and impaired mitochondrial respiratory chain complex activities, followed by remarkable mitochondrial dysfunction and ROS production. INTERPRETATION This study illustrated the pathogenicity of a novel m.4349C>T mutation and provided a better understanding of the phenotype associated with mutations in mitochondrial tRNAGln gene.
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Affiliation(s)
- Kunqian Ji
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, Shandong, 250000, China
| | - Wei Wang
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, Shandong, 250000, China
| | - Yan Lin
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, Shandong, 250000, China
| | - Xuebi Xu
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, Shandong, 250000, China
| | - Fuchen Liu
- Department of Neurobiology, Yale University School of Medicine, New Haven, CT, 06511, USA
| | - Dongdong Wang
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, Shandong, 250000, China
| | - Yuying Zhao
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, Shandong, 250000, China
| | - Chuanzhu Yan
- Research Institute of Neuromuscular and Neurodegenerative Diseases and Department of Neurology, Qilu Hospital, Shandong University, Jinan, Shandong, 250000, China.,Mitochondrial Medicine Laboratory, Qilu Hospital (Qingdao), Shandong University, Qingdao, Shandong, 266035, China.,Brain Science Research Institute, Shandong University, Jinan, Shandong, 250000, China
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24
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Pozzi A, Dowling DK. Small mitochondrial RNAs as mediators of nuclear gene regulation, and potential implications for human health. Bioessays 2021; 43:e2000265. [PMID: 33763872 DOI: 10.1002/bies.202000265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
Much research has focused on the effects of pathogenic mitochondrial mutations on health. Notwithstanding, the mechanisms regulating the link between these mutations and their effects remain elusive in several cases. Here, we propose that certain mitochondrial mutations may disrupt function of a set of mitochondrial-transcribed small RNAs, perturbing communication between mitochondria and nucleus, leading to disease. Our hypothesis synthesises two lines of supporting evidence. First, several mitochondrial mutations cannot be directly linked to effects on energy production or protein synthesis. Second, emerging studies have described the existence of small RNAs encoded by the mitochondria and proposed their involvement in RNA interference. We present a roadmap to testing this hypothesis.
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Affiliation(s)
- Andrea Pozzi
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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25
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Tang Z, Tang X, Xue L, Guan M. [A non-invasive method for detecting mitochondrial tRNA Thr15927G>A mutation]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2021; 41:151-156. [PMID: 33509769 DOI: 10.12122/j.issn.1673-4254.2021.01.23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To explore the feasibility of detecting maternal hereditary mitochondrial tRNAThr15927G>A (m.15927G>A) mutation using buccal swabs. METHODS We performed sequence analysis of mitochondrial DNA in blood samples from 2070 cases of maternal hereditary mitochondrial disease in the First Affiliated Hospital of Wenzhou Medical University, and identified 3 patients with m.15927G>A mutation.Buccal swabs and blood samples were obtained from the 3 patients (mutation group) and 3 normal volunteers (control group).After extracting whole genomic DNA from all the samples, the DNA concentration and purity were analyzed.The PCR products were subjected to dot blot hybridization, Southern blot hybridization, and DNA sequencing analysis to verify the feasibility of detecting m.15927G>A mutation using buccal swabs. RESULTS There was no significant difference in DNA concentration extracted from buccal swabs and blood samples in either the mutation group or the control group (P > 0.05), but the purity of manually extracted oral mucosa DNA was significantly lower than that of whole blood and oral mucosa DNA extracted using commercial kits (P < 0.05).Dot blot hybridization and Southern blot hybridization both yielded positive results in the control group but negative results in the mutation group.DNA sequencing identified m.15927G>A mutation in all the samples from the mutation group. CONCLUSIONS Buccal swabs collection accurate is an accurate and sensitive method for the detection of m.15927G>A mutation.
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Affiliation(s)
- Zhining Tang
- School of Laboratory Medicine and Life Sciences, Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiaowen Tang
- School of Laboratory Medicine and Life Sciences, Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Ling Xue
- School of Laboratory Medicine and Life Sciences, Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou 325035, China
| | - Minxin Guan
- School of Laboratory Medicine and Life Sciences, Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou 325035, China
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26
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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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27
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A mitochondrial myopathy-associated tRNA Ser(UCN) 7453G>A mutation alters tRNA metabolism and mitochondrial function. Mitochondrion 2020; 57:1-8. [PMID: 33279600 DOI: 10.1016/j.mito.2020.11.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/09/2020] [Accepted: 11/23/2020] [Indexed: 12/25/2022]
Abstract
BACKGROUND Mitochondrial disorders are a group of heterogeneous diseases characterized by biochemical disturbances in oxidative phosphorylation (OXPHOS). Mutations in mitochondrial transfer RNA (mt-tRNA) genes are the most frequently in mitochondrial disease. However, few studies have detailed the molecular mechanisms behind these mutations. METHODS We performed clinical evaluation, genetic analysis, muscle histochemistry, and molecular and biochemical investigations in muscle tissue and proband-derived cybrid cell lines. RESULTS We found a mitochondrial tRNASer(UCN) mutation (m.7453G>A) in a 15-year-old patient with severe mitochondrial myopathy. We demonstrated that this mutation caused impairment of mitochondrial translation, respiratory deficiency, overproduction of reactive oxygen species (ROS), and decreased mitochondrial membrane potential (MMP), which ultimately led to severe mitochondrial myopathy. CONCLUSION Our findings offer valuable new insights into the tRNASer(UCN) m.7453G>A mutation for both the pathogenic mechanism and functional consequences.
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28
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Campbell T, Lou X, Slone J, Brown J, Bromwell M, Liu J, Bai R, Haude K, Balog A, Cui H, Zou W, Yang L, Al-Beshri A, Huang T. Mitochondrial genome variant m.3250T>C as a possible risk factor for mitochondrial cardiomyopathy. Hum Mutat 2020; 42:177-188. [PMID: 33259687 DOI: 10.1002/humu.24143] [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: 06/25/2020] [Revised: 10/28/2020] [Accepted: 11/19/2020] [Indexed: 11/11/2022]
Abstract
The MT-TL1 gene codes for the mitochondrial leucine transfer RNA (tRNALeu(UUR) ) necessary for mitochondrial translation. Pathogenic variants in the MT-TL1 gene result in mitochondriopathy in humans. The m.3250T>C variant in the MT-TL1 gene has been previously associated with exercise intolerance and mitochondrial myopathy, yet disease classification for this variant has not been consistently reported. Molecular studies suggest the m.3250T>C variant does not alter tRNALeu(UUR) structure but may have a modest impact on aminoacylation capacity. However, functional studies are limited. Our study aimed to further define the clinical presentation, inheritance pattern, and molecular pathology of the m.3250T>C variant. Families with the m.3250T>C variant were recruited from the Mitochondrial Disease Clinic at Cincinnati Children's Hospital Medical Center and GeneDx laboratory database. Affected individuals most frequently presented with cardiac findings, exercise intolerance, and muscle weakness. Hypertrophic cardiomyopathy was the most frequent cardiac finding. Many asymptomatic individuals had homoplasmic or near homoplasmic levels of the m.3250T>C variant, suggesting the penetrance is incomplete. Patient-derived fibroblasts demonstrated lowered ATP production and increased levels of reactive oxygen species. Our results demonstrate that the m.3250T>C variant exhibits incomplete penetrance and may be a possible cause of cardiomyopathy by impacting cellular respiration in mitochondria.
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Affiliation(s)
- Teresa Campbell
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Xiaoting Lou
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jesse Slone
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jenice Brown
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Meghan Bromwell
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Jie Liu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | | | | | | | - Hong Cui
- GeneDx, Gaithersburg, Maryland, USA
| | - Weiwei Zou
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Obstetrics and Gynecology, Reproductive Medicine Center, The First Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Li Yang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA.,Department of Pediatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Ali Al-Beshri
- Internal Medicine and Medical Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
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29
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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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30
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Yu XJ, Ding Y. The roles of mitochondrial tRNA mutations in non-dystrophic myotonias. Mitochondrial DNA B Resour 2020; 5:3796-3801. [PMID: 33367105 PMCID: PMC7682739 DOI: 10.1080/23802359.2020.1839364] [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: 11/03/2022] Open
Abstract
According a recent report by Heidari et al., a mutational screening for candidate pathogenic mitochondrial tRNA (mt-tRNA) mutations were performed in 45 Iranian patients with non-dystrophic myotonia (NDM) and 70 control subjects. Through PCR amplification and direct sequence analysis, nine mt-tRNA mutations were identified: tRNAMet T4454C, tRNATrp A5568G, tRNACys T5794C, tRNAArg A10438T and T10462C, tRNALeu(CUN) A12308G, tRNAThr A15907G, A15924G and G15928A. However, through the database searches and phylogenetic conservation analysis, we noticed that the tRNAThr A15924G, G15928A and tRNALeu(CUN) A12308G mutations should be classified 'pathogenic'. Thus, the roles of mt-tRNA mutations in clinical expression of NDM needed to be further experimentally addressed.
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Affiliation(s)
- Xue-Jiao Yu
- Department of Clinical Laboratory, Quzhou People's Hospital, Quzhou, China
| | - Yu Ding
- Central Laboratory, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
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31
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McCormick EM, Lott MT, Dulik MC, Shen L, Attimonelli M, Vitale O, Karaa A, Bai R, Pineda-Alvarez DE, Singh LN, Stanley CM, Wong S, Bhardwaj A, Merkurjev D, Mao R, Sondheimer N, Zhang S, Procaccio V, Wallace DC, Gai X, Falk MJ. Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation. Hum Mutat 2020; 41:2028-2057. [PMID: 32906214 DOI: 10.1002/humu.24107] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.
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Affiliation(s)
- Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew C Dulik
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Ornella Vitale
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Amel Karaa
- Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christine M Stanley
- Variantyx, Inc, Framingham, Massachusetts, USA.,QNA Diagnostics, Cambridge, Massachusetts, USA
| | | | - Anshu Bhardwaj
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Daria Merkurjev
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Rong Mao
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Neal Sondheimer
- Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, Angers, France
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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32
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Toncheva D, Serbezov D, Karachanak-Yankova S, Nesheva D. Ancient mitochondrial DNA pathogenic variants putatively associated with mitochondrial disease. PLoS One 2020; 15:e0233666. [PMID: 32970680 PMCID: PMC7514063 DOI: 10.1371/journal.pone.0233666] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2020] [Accepted: 08/09/2020] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial DNA variants associated with diseases are widely studied in contemporary populations, but their prevalence has not yet been investigated in ancient populations. The publicly available AmtDB database contains 1443 ancient mtDNA Eurasian genomes from different periods. The objective of this study was to use this data to establish the presence of pathogenic mtDNA variants putatively associated with mitochondrial diseases in ancient populations. The clinical significance, pathogenicity prediction and contemporary frequency of mtDNA variants were determined using online platforms. The analyzed ancient mtDNAs contain six variants designated as being "confirmed pathogenic" in modern patients. The oldest of these, m.7510T>C in the MT-TS1 gene, was found in a sample from the Neolithic period, dated 5800-5400 BCE. All six have well established clinical association, and their pathogenic effect is corroborated by very low population frequencies in contemporary populations. Analysis of the geographic location of the ancient samples, contemporary epidemiological trends and probable haplogroup association indicate diverse spatiotemporal dynamics of these variants. The dynamics in the prevalence and distribution is conceivably result of de novo mutations or human migrations and subsequent evolutionary processes. In addition, ten variants designated as possibly or likely pathogenic were found, but the clinical effect of these is not yet well established and further research is warranted. All detected mutations putatively associated with mitochondrial disease in ancient mtDNA samples are in tRNA coding genes. Most of these mutations are in a mt-tRNA type (Model 2) that is characterized by loss of D-loop/T-loop interaction. Exposing pathogenic variants in ancient human populations expands our understanding of their origin and prevalence dynamics.
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Affiliation(s)
- Draga Toncheva
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
- Bulgarian Academy of Sciences–BAS, Sofia, Bulgaria
- * E-mail:
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
| | - Sena Karachanak-Yankova
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
- Department of Genetics, Faculty of biology, Sofia University “St. Kliment Ohridski”, Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University of Sofia, Bulgarian Academy of Science, Sofia, Bulgaria
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Homoplasmic deleterious MT-ATP6/8 mutations in adult patients. Mitochondrion 2020; 55:64-77. [PMID: 32858252 DOI: 10.1016/j.mito.2020.08.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 07/13/2020] [Accepted: 08/14/2020] [Indexed: 01/10/2023]
Abstract
To address the frequency of complex V defects, we systematically sequenced MT-ATP6/8 genes in 512 consecutive patients. We performed functional analysis in muscle or fibroblasts for 12 out of 27 putative homoplasmic mutations and in cybrids for four. Fibroblasts, muscle and cybrids with known deleterious mutations underwent parallel analysis. It included oxidative phosphorylation spectrophotometric assays, western blots, structural analysis, ATP production, glycolysis and cell proliferation evaluation. We demonstrated the deleterious nature of three original mutations. Striking gradation in severity of the mutations consequences and differences between muscle, fibroblasts and cybrids implied a likely under-diagnosis of human complex V defects.
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Lim AZ, McMacken G, Rastelli F, Oláhová M, Baty K, Hopton S, Falkous G, Töpf A, Lochmüller H, Marini-Bettolo C, McFarland R, Taylor RW. A novel, pathogenic dinucleotide deletion in the mitochondrial MT-TY gene causing myasthenia-like features. Neuromuscul Disord 2020; 30:661-668. [PMID: 32684384 PMCID: PMC7477489 DOI: 10.1016/j.nmd.2020.06.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 06/16/2020] [Accepted: 06/17/2020] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA)-related diseases often pose a diagnostic challenge and require rigorous clinical and laboratory investigation. Pathogenic variants in the mitochondrial tRNA gene MT-TY, which encodes the tRNATyr, are a rare cause of mitochondrial disease. Here we describe a novel m.5860delTA anticodon variant in the MT-TY gene in a patient who initially presented with features akin to a childhood onset myasthenic syndrome. Using histochemical, immunohistochemical and protein studies we demonstrate that this mutation leads to severe biochemical defects of mitochondrial translation, which is reflected in the early onset and progressive phenotype. This case highlights the clinical overlap between mtDNA-related diseases and other neuromuscular disorders, and demonstrates the potential pitfalls in analysis of next generation sequencing results, given whole exome sequencing of a blood DNA sample failed to make a genetics diagnosis. Muscle biopsy remains an important requirement in the diagnosis of mitochondrial disease and in establishing the pathogenicity of novel mtDNA variants.
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Affiliation(s)
- Albert Z Lim
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Grace McMacken
- The John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK; Department of Neurosciences, Royal Victoria Hospital, Belfast Health and Social Care Trust, Belfast, UK
| | - Francesca Rastelli
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Karen Baty
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne, UK
| | - Sila Hopton
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne, UK
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne, UK
| | - Ana Töpf
- The John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Hanns Lochmüller
- Department of Neuropediatrics and Muscle Disorders, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany; Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain; Research Institute, Children's Hospital of Eastern Ontario, Ottawa, Canada; Division of Neurology, Department of Medicine, Ottawa University, Ottawa, Canada
| | - Chiara Marini-Bettolo
- The John Walton Muscular Dystrophy Research Centre, Newcastle University, Newcastle upon Tyne, UK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom.
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, The Medical School, Newcastle University, Newcastle upon Tyne, UK; NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne, UK; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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Auré K, Fayet G, Chicherin I, Rucheton B, Filaut S, Heckel AM, Eichler J, Caillon F, Péréon Y, Entelis N, Tarassov I, Lombès A. Homoplasmic mitochondrial tRNA Pro mutation causing exercise-induced muscle swelling and fatigue. NEUROLOGY-GENETICS 2020; 6:e480. [PMID: 32802947 PMCID: PMC7371370 DOI: 10.1212/nxg.0000000000000480] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 06/02/2020] [Indexed: 01/15/2023]
Abstract
Objective To demonstrate the causal role in disease of the MT-TP m.15992A>T mutation observed in patients from 5 independent families. Methods Lactate measurement, muscle histology, and mitochondrial activities in patients; PCR-based analyses of the size, amount, and sequence of muscle mitochondrial DNA (mtDNA) and proportion of the mutation; respiration, mitochondrial activities, proteins, translation, transfer RNA (tRNA) levels, and base modification state in skin fibroblasts and cybrids; and reactive oxygen species production, proliferation in the absence of glucose, and plasma membrane potential in cybrids. Results All patients presented with severe exercise intolerance and hyperlactatemia. They were associated with prominent exercise-induced muscle swelling, conspicuous in masseter muscles (2 families), and/or with congenital cataract (2 families). MRI confirmed exercise-induced muscle edema. Muscle disclosed severe combined respiratory defect. Muscle mtDNA had normal size and amount. Its sequence was almost identical in all patients, defining the haplotype as J1c10, and sharing 31 variants, only 1 of which, MT-TP m.15992A>T, was likely pathogenic. The mutation was homoplasmic in all tissues and family members. Fibroblasts and cybrids with homoplasmic mutation had defective respiration, low complex III activity, and decreased tRNAPro amount. Their respiratory complexes amount and tRNAPro aminoacylation appeared normal. Low proliferation in the absence of glucose demonstrated the relevance of the defects on cybrid biology while abnormal loss of cell volume when faced to plasma membrane depolarization provided a link to the muscle edema observed in patients. Conclusions The homoplasmic MT-TP m.15992A>T mutation in the J1c10 haplotype causes exercise-induced muscle swelling and fatigue.
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Affiliation(s)
- Karine Auré
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Guillemette Fayet
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Ivan Chicherin
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Benoit Rucheton
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Sandrine Filaut
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Anne-Marie Heckel
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Julie Eichler
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Florence Caillon
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Yann Péréon
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Nina Entelis
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Ivan Tarassov
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
| | - Anne Lombès
- Inserm U1016 Institut Cochin (K.A., B.R., A.L.), INSERM, Paris; Department of Neurophysiology (K.A.), Foch Hospital, Suresnes; Centre de Référence Maladies Neuromusculaires Hôtel-Dieu AOC (G.F., Y.P.), CHU Nantes; CNRS UMR 7156 GMGM (I.C., A.-M.H., J.E., N.E., I.T.), University of Strasbourg; Service de Biochimie Métabolique CHU Pitié-Salpêtrière (B.R., S.F.), AP-HP, Paris; Service de Radiologie et Imagerie Médicale Hôtel-Dieu (F.C.), CHU Nantes; CNRS UMR 8104 (A.L.); Université Paris-Descartes-Paris5 (A.L.), Paris, France; and Present Address: M.V. Lomonossov State University (I.C.), Moscow, Russia
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Boguszewska K, Szewczuk M, Kaźmierczak-Barańska J, Karwowski BT. The Similarities between Human Mitochondria and Bacteria in the Context of Structure, Genome, and Base Excision Repair System. Molecules 2020; 25:E2857. [PMID: 32575813 PMCID: PMC7356350 DOI: 10.3390/molecules25122857] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/17/2020] [Accepted: 06/19/2020] [Indexed: 02/06/2023] Open
Abstract
Mitochondria emerged from bacterial ancestors during endosymbiosis and are crucial for cellular processes such as energy production and homeostasis, stress responses, cell survival, and more. They are the site of aerobic respiration and adenosine triphosphate (ATP) production in eukaryotes. However, oxidative phosphorylation (OXPHOS) is also the source of reactive oxygen species (ROS), which are both important and dangerous for the cell. Human mitochondria contain mitochondrial DNA (mtDNA), and its integrity may be endangered by the action of ROS. Fortunately, human mitochondria have repair mechanisms that allow protecting mtDNA and repairing lesions that may contribute to the occurrence of mutations. Mutagenesis of the mitochondrial genome may manifest in the form of pathological states such as mitochondrial, neurodegenerative, and/or cardiovascular diseases, premature aging, and cancer. The review describes the mitochondrial structure, genome, and the main mitochondrial repair mechanism (base excision repair (BER)) of oxidative lesions in the context of common features between human mitochondria and bacteria. The authors present a holistic view of the similarities of mitochondria and bacteria to show that bacteria may be an interesting experimental model for studying mitochondrial diseases, especially those where the mechanism of DNA repair is impaired.
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Affiliation(s)
| | | | | | - Bolesław T. Karwowski
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland; (K.B.); (M.S.); (J.K.-B.)
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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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Ding Y, Teng YS, Zhuo GC, Xia BH, Leng JH. The Mitochondrial tRNAHis G12192A Mutation May Modulate the Clinical Expression of Deafness-Associated tRNAThr G15927A Mutation in a Chinese Pedigree. Curr Mol Med 2020; 19:136-146. [PMID: 30854964 DOI: 10.2174/1566524019666190308121552] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 03/02/2019] [Accepted: 03/04/2019] [Indexed: 12/19/2022]
Abstract
BACKGROUND Mutations in mitochondrial tRNA (mt-tRNA) genes have been found to be associated with both syndromic and non-syndromic hearing impairment. However, the pathophysiology underlying mt-tRNA mutations in clinical expression of hearing loss remains poorly understood. OBJECTIVE The aim of this study was to explore the potential association between mttRNA mutations and hearing loss. METHODS AND RESULTS We reported here the molecular features of a pedigree with maternally transmitted non-syndromic hearing loss. Among 12 matrilineal relatives, five of them suffered variable degree of hearing impairment, but none of them had any medical history of using aminoglycosides antibiotics (AmAn). Genetic screening of the complete mitochondrial genomes from the matrilineal relatives identified the coexistence of mt-tRNAHis G12192A and mt-tRNAThr G15927A mutations, together with a set of polymorphisms belonging to human mitochondrial haplogroup B5b1b. Interestingly, the G12192A mutation occurred 2-bp from the 3' end of the TψC loop of mt-tRNAHis, which was evolutionarily conserved from various species. In addition, the well-known G15927A mutation, which disrupted the highly conserved C-G base-pairing at the anticodon stem of mt-tRNAThr, may lead to the failure in mt-tRNA metabolism. Furthermore, a significant decreased in ATP production and an increased ROS generation were observed in polymononuclear leukocytes (PMNs) which were isolated from the deaf patients carrying these mt-tRNA mutations, suggested that the G12192A and G15927A mutations may cause mitochondrial dysfunction that was responsible for deafness. However, the absence of any functional mutations/variants in GJB2, GJB3, GJB6 and TRMU genes suggested that the nuclear genes may not play important roles in the clinical expression of non-syndromic hearing loss in this family. CONCLUSION Our data indicated that mt-tRNAHis G12192A mutation may increase the penetrance and expressivity of deafness-associated m-tRNAThr G15927A mutation in this family.
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Affiliation(s)
- Yu Ding
- Central Laboratory, Hangzhou First People's Hospital, Zhejiang University, School of Medicine, Hangzhou, China
| | - Yao-Shu Teng
- Department of Otolaryngology, Hangzhou First People's Hospital, Zhejiang University, School of Medicine, Hangzhou, China
| | - Guang-Chao Zhuo
- Central Laboratory, Hangzhou First People's Hospital, Zhejiang University, School of Medicine, Hangzhou, China
| | - Bo-Hou Xia
- Department of Pharmacy, Hunan Chinese Medical University, Changsha, China
| | - Jian-Hang Leng
- Central Laboratory, Hangzhou First People's Hospital, Zhejiang University, School of Medicine, Hangzhou, China
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Screening for deafness-associated mitochondrial 12S rRNA mutations by using a multiplex allele-specific PCR method. Biosci Rep 2020; 40:224124. [PMID: 32400865 PMCID: PMC7263198 DOI: 10.1042/bsr20200778] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/30/2020] [Accepted: 05/12/2020] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial 12S rRNA A1555G and C1494T mutations are the major contributors to hearing loss. As patients with these mutations are sensitive to aminoglycosides, mutational screening for 12S rRNA is therefore recommended before the use of aminoglycosides. Most recently, we developed a novel multiplex allele-specific PCR (MAS-PCR) that can be used for detecting A1555G and C1494T mutations. In the present study, we employed this MAS-PCR to screen the 12S rRNA mutations in 500 deaf patients and 300 controls from 5 community hospitals. After PCR and electrophoresis, two patients with A1555G and one patient with C1494T were identified, this was consistent with Sanger sequence results. We further traced the origin of three Chinese pedigrees. Clinical evaluation revealed variable phenotypes of hearing loss including severity, age at onset and audiometric configuration in these patients. Sequence analysis of the mitochondrial genomes from matrilineal relatives suggested the presence of three evolutionarily conserved mutations: tRNACys T5802C, tRNALys A8343G and tRNAThr G15930A, which may result the failure in tRNAs metabolism and lead to mitochondrial dysfunction that was responsible for deafness. However, the lack of any functional variants in GJB2, GJB3, GJB6 and TRMU suggested that nuclear genes may not play active roles in deafness expression. Hence, aminoglycosides and mitochondrial genetic background may contribute to the clinical expression of A1555G/C1494T-induced deafness. Our data indicated that the MAS-PCR was a fast, convenience method for screening the 12S rRNA mutations, which was useful for early detection and prevention of mitochondrial deafness.
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40
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Preste R, Vitale O, Clima R, Gasparre G, Attimonelli M. HmtVar: a new resource for human mitochondrial variations and pathogenicity data. Nucleic Acids Res 2020; 47:D1202-D1210. [PMID: 30371888 PMCID: PMC6323908 DOI: 10.1093/nar/gky1024] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Accepted: 10/18/2018] [Indexed: 12/12/2022] Open
Abstract
Interest in human mitochondrial genetic data is constantly increasing among both clinicians and researchers, due to the involvement of mitochondrial DNA (mtDNA) in a number of physiological and pathological processes. Thanks to new sequencing technologies and modern databases, the large amount of information on mtDNA variability may be exploited to gain insights into the relationship between mtDNA variants, phenotypes and diseases. To facilitate this process, we have developed the HmtVar resource, a variant-focused database that allows the exploration of a dataset of over 40 000 human mitochondrial variants. Mitochondrial variation data, initially gathered from the HmtDB platform, are integrated with in-house pathogenicity assessments based on various evaluation criteria and with a set of additional annotations from third-party resources. The result is a comprehensive collection of information of crucial importance for human mitochondrial variation studies and investigation of common and rare diseases in which the mitochondrion may be involved. HmtVar is accessible at https://www.hmtvar.uniba.it and data may be retrieved using either a web interface through the Query page or a state-of-the-art API for programmatic access.
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Affiliation(s)
- Roberto Preste
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari 70126, Italy
| | - Ornella Vitale
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari 70126, Italy
| | - Rosanna Clima
- Department of Medical and Surgical Sciences - DIMEC, Medical Genetics Unit, University of Bologna, Bologna 40126, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences - DIMEC, Medical Genetics Unit, University of Bologna, Bologna 40126, Italy
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, Bari 70126, Italy
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41
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Wong LJC, Chen T, Schmitt ES, Wang J, Zhang S, Landsverk M, Li F, Tang S, Wang Y, Zhang VW, Craigen WJ. Response to Bai et al. Genet Med 2020; 22:1420-1421. [PMID: 32418988 DOI: 10.1038/s41436-020-0805-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 03/31/2020] [Indexed: 11/09/2022] Open
Affiliation(s)
- Lee-Jun C Wong
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA. .,Baylor Genetics Laboratory, Houston, TX, USA.
| | - Ting Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Endocrinology, Genetics and Metabolism, Children's Hospital of Soochow University, Suzhou, China
| | - Eric S Schmitt
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Jing Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shulin Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Department of Pathology and Laboratory Medicine, UKHealthCare, University of Kentucky, Lexington, USA
| | - Megan Landsverk
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Global Laboratory Services/Diagnostics, Perkin Elmer, Waltham, MA, USA
| | - Fangyuan Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Sema4, Branford, CT, USA
| | - Sha Tang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,WuXi NextCODE, Cambridge, MA, USA
| | - Yue Wang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
| | - Victor Wei Zhang
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,AmCare Genomics Lab, Guangzhou, China
| | - William J Craigen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.,Baylor Genetics Laboratory, Houston, TX, USA
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42
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Peng W, Zhong Y, Zhao X, Yuan J. Low penetrance of hearing loss in two Chinese families carrying the mitochondrial tRNASer(UCN) mutations. Mol Med Rep 2020; 22:77-86. [PMID: 32377700 PMCID: PMC7248462 DOI: 10.3892/mmr.2020.11100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Accepted: 02/20/2020] [Indexed: 01/07/2023] Open
Abstract
Mutations in mitochondrial DNA (mtDNA), especially in mitochondrial 12S rRNA and transfer RNA(tRNA)Ser(UCN) genes, are important causes of non-syndromic hearing loss. However, the molecular mechanism underlying mt-tRNA mutations in clinical hearing impairment are not fully understood. The present study assessed the molecular characterization of two Chinese families with non-syndromic hearing loss, who both exhibited very low penetrance of deafness (9.1 and 12.5% for Family 1 and 2, respectively). Mutational analysis of the complete mtDNA genes identified the presence of cytochrome c oxidase 1/tRNASer(UCN) G7444A and tRNASer(UCN) C7492T mutations, together with polymorphisms belonging to human mitochondrial haplogroup D4 and G2b, respectively. Moreover, the G7444A and C7492T mutations occurred at highly conserved tRNASer(UCN) nucleotides and may cause tRNA metabolism failure, which is involved in mitochondrial translation defects. Therefore, the G7444A and C7492T mutations may lead to the mitochondrial dysfunction that responsible for deafness. However, the absence of any functional variants in Gap junction β-2, Solute Carrier Family 26 Member 4 and TRNA 5-methylaminomethyl-2-thiouridylate methyltransferase suggested that nuclear genes may not play active roles in the occurrence of deafness. In the present study, the observed incomplete penetrance of hearing loss and mild mitochondrial dysfunction indicated that mtDNA G7444A and C7492T mutations are insufficient to produce the deafness phenotype. Therefore, other risk factors such as environmental factors and epigenetic regulation may be involved in the pathogenesis of hearing loss in the families recruited in the present study.
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Affiliation(s)
- Wei Peng
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Yi Zhong
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Xueyan Zhao
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
| | - Jie Yuan
- Department of Otorhinolaryngology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430022, P.R. China
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43
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Poole OV, Horga A, Hardy SA, Bugiardini E, Woodward CE, Hargreaves IP, Merve A, Quinlivan R, Taylor RW, Hanna MG, Pitceathly RDS. Multisystem mitochondrial disease caused by a rare m.10038G>A mitochondrial tRNA Gly ( MT-TG) variant. Neurol Genet 2020; 6:e413. [PMID: 32337339 PMCID: PMC7164964 DOI: 10.1212/nxg.0000000000000413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 01/23/2020] [Indexed: 11/15/2022]
Affiliation(s)
- Olivia V Poole
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Alejandro Horga
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Steven A Hardy
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Enrico Bugiardini
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Cathy E Woodward
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Iain P Hargreaves
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Ashirwad Merve
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Rosaline Quinlivan
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Robert W Taylor
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Michael G Hanna
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases (O.V.P., A.H., E.B., R.Q., M.G.H., R.D.S.P.), UCL Queen Square Institute of Neurology and The National Hospital for Neurology and Neurosurgery, London, United Kingdom; Wellcome Centre for Mitochondrial Research (S.A.H., R.W.T.), Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne; Neurogenetics Unit (C.E.W.), and Neurometabolic Unit (I.P.H.), The National Hospital for Neurology and Neurosurgery; Division of Neuropathology (A.M.), UCL Queen Square Institute of Neurology; Department of Histopathology (A.M.), Camelia Botnar Laboratory, Great Ormond Street Hospital; and Dubowitz Neuromuscular Centre (R.Q.), Great Ormond Street Hospital, London, United Kingdom
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44
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Joshi PR, Baty K, Hopton S, Cordts I, Falkous G, Schoser B, Blakely EL, Taylor RW, Deschauer M. Progressive external ophthalmoplegia due to a recurrent de novo m.15990C>T MT-TP (mt-tRNA Pro) gene variant. Neuromuscul Disord 2020; 30:346-350. [PMID: 32305257 DOI: 10.1016/j.nmd.2020.02.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Revised: 02/11/2020] [Accepted: 02/27/2020] [Indexed: 11/25/2022]
Abstract
Progressive external ophthalmoplegia is typically associated with single or multiple mtDNA deletions but occasionally mtDNA single nucleotide variants within mitochondrial transfer RNAs (mt-tRNAs) are identified. We report a 34-year-old female sporadic patient with progressive external ophthalmoplegia accompanied by exercise intolerance but neither fixed weakness nor multisystemic involvement. Histopathologically, abundant COX-deficient fibres were present in muscle with immunofluorescence analysis confirming the loss of mitochondrial complex I and IV proteins. Molecular genetic analysis identified a rare heteroplasmic m.15990C>T mt-tRNAPro variant reported previously in a single patient with childhood-onset myopathy. The variant in our patient was restricted to muscle. Single muscle fibre analysis identified higher heteroplasmy load in COX-deficient fibres than COX-normal fibres, confirming segregation of high heteroplasmic load with a biochemical defect. Our case highlights the phenotypic variability typically observed with pathogenic mt-tRNA mutations, whilst the identification of a second case with the m.15990C>T mutation not only confirms pathogenicity but shows that de novo mt-tRNA point mutations can arise in multiple, unrelated patients.
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Affiliation(s)
- Pushpa Raj Joshi
- Department of Neurology, Martin-Luther-University Halle-Wittenberg, Germany.
| | - Karen Baty
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Sila Hopton
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Isabell Cordts
- Department of Neurology, Technical University Munich, School of Medicine, Munich, Germany
| | - Gavin Falkous
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Benedikt Schoser
- Department of Neurology, Friedrich-Baur-Institute, University of Munich, Munich, Germany
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, United Kingdom; NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom; Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Marcus Deschauer
- Department of Neurology, Technical University Munich, School of Medicine, Munich, Germany
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45
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O'Donnell L, Blakely EL, Baty K, Alexander M, Bogdanova-Mihaylova P, Craig J, Walsh R, Brett F, Taylor RW, Murphy SM. Chronic Progressive External Ophthalmoplegia due to a Rare de novo m.12334G>A MT-TL2 Mitochondrial DNA Variant1. J Neuromuscul Dis 2020; 7:355-360. [PMID: 32310184 DOI: 10.3233/jnd-200486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We describe a patient with chronic progressive external ophthalmoplegia (CPEO) due to a rare mitochondrial genetic variant. Muscle biopsy revealed numerous cytochrome c oxidase (COX)-deficient fibres, prompting sequencing of the entire mitochondrial genome in muscle which revealed a rare m.12334G>A variant in the mitochondrial (mt-) tRNALeu(CUN)(MT-TL2) gene. Analysis of several tissues showed this to be a de novo mutational event. Single fibre studies confirmed the segregation of high m.12334G>A heteroplasmy levels with the COX histochemical defect, confirming pathogenicity of the m.12334G>A MT-TL2 variant. This case illustrates the importance of pursuing molecular genetic analysis in clinically-affected tissues when mitochondrial disease is suspected.
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Affiliation(s)
- Luke O'Donnell
- Department of Neurology, Tallaght University Hospital, Tallaght, Dublin, Ireland
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Karen Baty
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Michael Alexander
- Department of Neurophysiology, Tallaght University Hospital, Tallaght, Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | | | - John Craig
- Department of Neurology, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Ronan Walsh
- Department of Neurology, Hermitage Medical Clinic, Dublin, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Sinead M Murphy
- Department of Neurology, Tallaght University Hospital, Tallaght, Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, The University of Dublin, Dublin, Ireland
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Thompson K, Collier JJ, Glasgow RIC, Robertson FM, Pyle A, Blakely EL, Alston CL, Oláhová M, McFarland R, Taylor RW. Recent advances in understanding the molecular genetic basis of mitochondrial disease. J Inherit Metab Dis 2020; 43:36-50. [PMID: 31021000 PMCID: PMC7041634 DOI: 10.1002/jimd.12104] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 04/03/2019] [Accepted: 04/24/2019] [Indexed: 12/22/2022]
Abstract
Mitochondrial disease is hugely diverse with respect to associated clinical presentations and underlying genetic causes, with pathogenic variants in over 300 disease genes currently described. Approximately half of these have been discovered in the last decade due to the increasingly widespread application of next generation sequencing technologies, in particular unbiased, whole exome-and latterly, whole genome sequencing. These technologies allow more genetic data to be collected from patients with mitochondrial disorders, continually improving the diagnostic success rate in a clinical setting. Despite these significant advances, some patients still remain without a definitive genetic diagnosis. Large datasets containing many variants of unknown significance have become a major challenge with next generation sequencing strategies and these require significant functional validation to confirm pathogenicity. This interface between diagnostics and research is critical in continuing to expand the list of known pathogenic variants and concomitantly enhance our knowledge of mitochondrial biology. The increasing use of whole exome sequencing, whole genome sequencing and other "omics" techniques such as transcriptomics and proteomics will generate even more data and allow further interrogation and validation of genetic causes, including those outside of coding regions. This will improve diagnostic yields still further and emphasizes the integral role that functional assessment of variant causality plays in this process-the overarching focus of this review.
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Affiliation(s)
- Kyle Thompson
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Jack J. Collier
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Ruth I. C. Glasgow
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Fiona M. Robertson
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
| | - Emma L. Blakely
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Charlotte L. Alston
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Robert McFarland
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Institute of NeuroscienceNewcastle UniversityNewcastle upon TyneUK
- NHS Highly Specialised Mitochondrial Diagnostic LaboratoryNewcastle upon Tyne Hospitals NHS Foundation TrustNewcastle upon TyneUK
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47
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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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O'Keefe H, Queen R, Lord P, Elson JL. What can a comparative genomics approach tell us about the pathogenicity of mtDNA mutations in human populations? Evol Appl 2019; 12:1912-1930. [PMID: 31700535 PMCID: PMC6824070 DOI: 10.1111/eva.12851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/13/2019] [Accepted: 07/17/2019] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial disorders are heterogeneous, showing variable presentation and penetrance. Over the last three decades, our ability to recognize mitochondrial patients and diagnose these mutations, linking genotype to phenotype, has greatly improved. However, it has become increasingly clear that these strides in diagnostics have not benefited all population groups. Recent studies have demonstrated that patients from genetically understudied populations, in particular those of black African heritage, are less likely to receive a diagnosis of mtDNA disease. It has been suggested that haplogroup context might influence the presentation and penetrance of mtDNA disease; thus, the spectrum of mutations that are associated with disease in different populations. However, to date there is only one well-established example of such an effect: the increased penetrance of two Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducted the most extensive investigation to date into the importance of haplogroup context on the pathogenicity of mtDNA mutations. We searched for proven human point mutations across 726 multiple sequence alignments derived from 33 non-human species absent of disease. A total of 58 pathogenic point mutations arise in the sequences of these species. We assessed the sequence context and found evidence of population variants that could modulate the phenotypic expression of these point mutations masking the pathogenic effects seen in humans. This supports the theory that sequence context is influential in the presentation of mtDNA disease and has implications for diagnostic practices. We have shown that our current understanding of the pathogenicity of mtDNA point mutations, primarily built on studies of individuals with haplogroups HVUKTJ, will not present a complete picture. This will have the effect of creating a diagnostic inequality, whereby individuals who do not belong to these lineages are less likely to receive a genetic diagnosis.
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Affiliation(s)
- Hannah O'Keefe
- Institute of Genetic MedicineNewcastle UniversityNewcastle‐upon‐TyneUK
- School of ComputingNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Rachel Queen
- Bioinformatics Core FacilityNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Phillip Lord
- School of ComputingNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Joanna L. Elson
- Institute of Genetic MedicineNewcastle UniversityNewcastle‐upon‐TyneUK
- Centre for Human MetabonomicsNorth‐West UniversityPotchefstroomSouth Africa
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Yang P, Wu P, Liu X, Feng J, Zheng S, Wang Y, Fan Z. Mitochondrial tRNASer(UCN) 7471delC may be a novel mutation associated with maternally transmitted hypertension. Ir J Med Sci 2019; 189:489-496. [DOI: 10.1007/s11845-019-02143-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 11/14/2019] [Indexed: 02/07/2023]
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Ding Y, Ye YF, Li MY, Xia BH, Leng JH. Mitochondrial tRNAAla 5601C>T variant may affect the clinical expression of the LHON‑related ND4 11778G>A mutation in a family. Mol Med Rep 2019; 21:201-208. [PMID: 31939618 PMCID: PMC6896293 DOI: 10.3892/mmr.2019.10844] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/09/2019] [Indexed: 01/21/2023] Open
Abstract
Certain mutations in mitochondrial DNA (mtDNA) are associated with Leber's hereditary optic neuropathy (LHON). In particular, the well-known NADH dehydrogenase 4 (ND4) m.11778G>A mutation is one of the most common LHON-associated primary mutations worldwide. However, how specific mtDNA mutations, or variants, affect LHON penetrance is not fully understood. The aim of the current study was to explore the relationship between mtDNA mutations and LHON, and to provide useful information for early detection and prevention of this disease. Following the molecular characterization of a Han Chinese family with maternally inherited LHON, four out of eight matrilineal relatives demonstrated varying degrees of both visual impairment and age of onset. Through PCR amplification of mitochondrial genomes and direct Sanger sequencing analysis, a homoplasmic mitochondrial-encoded ND4 m.11778G>A mutation, alongside a set of genetic variations belonging to human mtDNA haplogroup B5b1 were identified. Among these sequence variants, alanine transfer RNA (tRNA)Ala m.5601C>T was of particular interest. This variant occurred at position 59 in the TψC loop and altered the base pairing, which led to mitochondrial RNA (mt-RNA) metabolism failure and defects in mitochondrial protein synthesis. Bioinformatics analysis suggested that the m.5601C>T variant altered tRNAAla structure. Therefore, impaired mitochondrial functions caused by the ND4 m.11778G>A mutation may be enhanced by the mt-tRNAAla m.5601C>T variant. These findings suggested that the tRNAAla m.5601C>T variant might modulate the clinical manifestation of the LHON-associated primary mutation.
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Affiliation(s)
- Yu Ding
- Central Laboratory, School of Medicine, Hangzhou First People's Hospital, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Yu-Feng Ye
- Department of Ophthalmology, School of Medicine, Hangzhou First People's Hospital, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
| | - Mei-Ya Li
- Analytical Testing Center, Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310053, P.R. China
| | - Bo-Hou Xia
- Department of Pharmacy, Hunan Chinese Medical University, Changsha, Hunan 410208, P.R. China
| | - Jian-Hang Leng
- Central Laboratory, School of Medicine, Hangzhou First People's Hospital, Zhejiang University, Hangzhou, Zhejiang 310006, P.R. China
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