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Yin X, Dong Q, Fan S, Yang L, Li H, Jin Y, Laurentinah MR, Chen X, Sysa A, Fang H, Lyu J, Yu Y, Wang Y. A novel pathogenic mitochondrial DNA variant m.4344T>C in tRNA Gln causes developmental delay. J Hum Genet 2024; 69:381-389. [PMID: 38730005 DOI: 10.1038/s10038-024-01254-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 05/12/2024]
Abstract
Mitochondrial diseases are a group of genetic diseases caused by mutations in mitochondrial DNA and nuclear DNA. However, the genetic spectrum of this disease is not yet complete. In this study, we identified a novel variant m.4344T>C in mitochondrial tRNAGln from a patient with developmental delay. The mutant loads of m.4344T>C were 95% and 89% in the patient's blood and oral epithelial cells, respectively. Multialignment analysis showed high evolutionary conservation of this nucleotide. TrRosettaRNA predicted that m.4344T>C variant would introduce an additional hydrogen bond and alter the conformation of the T-loop. The transmitochondrial cybrid-based study demonstrated that m.4344T>C variant impaired the steady-state level of mitochondrial tRNAGln and decreased the contents of mitochondrial OXPHOS complexes I, III, and IV, resulting in defective mitochondrial respiration, elevated mitochondrial ROS production, reduced mitochondrial membrane potential and decreased mitochondrial ATP levels. Altogether, this is the first report in patient carrying the m.4344T>C variant. Our data uncover the pathogenesis of the m.4344T>C variant and expand the genetic mutation spectrum of mitochondrial diseases, thus contributing to the clinical diagnosis of mitochondrial tRNAGln gene variants-associated mitochondrial diseases.
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Affiliation(s)
- Xiaojie Yin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Qiyu Dong
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Shuanglong Fan
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Lina Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Hao Li
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Yijun Jin
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Mahlatsi Refiloe Laurentinah
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Xiandan Chen
- International Sakharov Environmental Institute of Belarusian State University, Minsk, 220070, Republic of Belarus
| | - Aliaksei Sysa
- International Sakharov Environmental Institute of Belarusian State University, Minsk, 220070, Republic of Belarus
| | - Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310053, Zhejiang, China.
| | - Yongguo Yu
- Department of Pediatric Endocrinology and Genetics, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Institute for Pediatric Research, Shanghai, 200092, China.
- Shanghai Key Laboratory of Pediatric Gastroenterology and Nutrition, Shanghai, 200092, China.
| | - Ya Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life sciences, Wenzhou Medical University, Wenzhou, 325035, Zhejiang, China.
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Antolínez-Fernández Á, Esteban-Ramos P, Fernández-Moreno MÁ, Clemente P. Molecular pathways in mitochondrial disorders due to a defective mitochondrial protein synthesis. Front Cell Dev Biol 2024; 12:1410245. [PMID: 38855161 PMCID: PMC11157125 DOI: 10.3389/fcell.2024.1410245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/09/2024] [Indexed: 06/11/2024] Open
Abstract
Mitochondria play a central role in cellular metabolism producing the necessary ATP through oxidative phosphorylation. As a remnant of their prokaryotic past, mitochondria contain their own genome, which encodes 13 subunits of the oxidative phosphorylation system, as well as the tRNAs and rRNAs necessary for their translation in the organelle. Mitochondrial protein synthesis depends on the import of a vast array of nuclear-encoded proteins including the mitochondrial ribosome protein components, translation factors, aminoacyl-tRNA synthetases or assembly factors among others. Cryo-EM studies have improved our understanding of the composition of the mitochondrial ribosome and the factors required for mitochondrial protein synthesis and the advances in next-generation sequencing techniques have allowed for the identification of a growing number of genes involved in mitochondrial pathologies with a defective translation. These disorders are often multisystemic, affecting those tissues with a higher energy demand, and often present with neurodegenerative phenotypes. In this article, we review the known proteins required for mitochondrial translation, the disorders that derive from a defective mitochondrial protein synthesis and the animal models that have been established for their study.
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Affiliation(s)
- Álvaro Antolínez-Fernández
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Esteban-Ramos
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Miguel Ángel Fernández-Moreno
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paula Clemente
- Instituto de Investigaciones Biomédicas Sols-Morreale (IIBM), Universidad Autónoma de Madrid-Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Departamento de Bioquímica, Universidad Autónoma de Madrid, Madrid, Spain
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3
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Ferreira T, Rodriguez S. Mitochondrial DNA: Inherent Complexities Relevant to Genetic Analyses. Genes (Basel) 2024; 15:617. [PMID: 38790246 PMCID: PMC11121663 DOI: 10.3390/genes15050617] [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: 04/17/2024] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/26/2024] Open
Abstract
Mitochondrial DNA (mtDNA) exhibits distinct characteristics distinguishing it from the nuclear genome, necessitating specific analytical methods in genetic studies. This comprehensive review explores the complex role of mtDNA in a variety of genetic studies, including genome-wide, epigenome-wide, and phenome-wide association studies, with a focus on its implications for human traits and diseases. Here, we discuss the structure and gene-encoding properties of mtDNA, along with the influence of environmental factors and epigenetic modifications on its function and variability. Particularly significant are the challenges posed by mtDNA's high mutation rate, heteroplasmy, and copy number variations, and their impact on disease susceptibility and population genetic analyses. The review also highlights recent advances in methodological approaches that enhance our understanding of mtDNA associations, advocating for refined genetic research techniques that accommodate its complexities. By providing a comprehensive overview of the intricacies of mtDNA, this paper underscores the need for an integrated approach to genetic studies that considers the unique properties of mitochondrial genetics. Our findings aim to inform future research and encourage the development of innovative methodologies to better interpret the broad implications of mtDNA in human health and disease.
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Affiliation(s)
- Tomas Ferreira
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge CB2 0SL, UK
| | - Santiago Rodriguez
- Bristol Medical School, University of Bristol, Bristol BS8 1UD, UK
- MRC Integrative Epidemiology Unit, Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 1QU, UK
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Li X, Shang J, Li S, Wang Y. Identification of a Novel Mitochondrial tRNA Mutation in Chinese Family with Type 2 Diabetes Mellitus. Pharmgenomics Pers Med 2024; 17:149-161. [PMID: 38645701 PMCID: PMC11032666 DOI: 10.2147/pgpm.s438978] [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: 10/21/2023] [Accepted: 01/29/2024] [Indexed: 04/23/2024] Open
Abstract
Background Mutations in mitochondrial tRNA (mt-tRNA) could be the origin of some type 2 diabetes mellitus (T2DM) cases, but the mechanism remained largely unknown. Aim The aim of this study was to assess the impact of a novel mitochondrial tRNACys/tRNATyr A5826G mutation on the development and progression of T2DM. Methods A four-generation Han Chinese family with maternally inherited diabetes underwent clinical, genetic and biochemical analyses. The mitochondrial DNA (mtDNA) mutations of three matrilineal relatives were screened by PCR-Sanger sequencing. Furthermore, to see whether m.A5826G mutations affected mitochondrial functions, the cybrid cell lines were derived from three subjects with m.A5826G mutation and three controls without this mutation. ATP was evaluated by luminescent cell viability assay, mitochondrial membrane potential (MMP), and reactive oxygen species (ROS) were determined by flow cytometry. The student's two-tailed, unpaired t-test was used to assess the statistical significance between the control and mutant results. Results The age at onset of diabetes in this pedigree varied from 40 to 63 years, with an average of 54 years. Mutational analysis of mitochondrial genomes revealed the presence of a novel m.A5826G mutation. Interestingly, the m.A5826G mutation occurred at the conjunction between tRNACys and tRNATyr, a very conserved position that was critical for tRNAs processing and functions. Using trans-mitochondrial cybrid cells, we found that mutant cells carrying the m.A5826G showed approximately 36.5% and 22.4% reductions in ATP and MMP, respectively. By contrast, mitochondrial ROS levels increased approximately 33.3%, as compared with the wild type cells. Conclusion A novel m.A5826G mutation was identified in a pedigree with T2DM, and this mutation would lead to mitochondrial dysfunction. Thus, the genetic spectrum of mitochondrial diabetes was expanded by including m.A5826G mutation in tRNACys/tRNATyr, our study provided novel insight into the molecular pathogenesis, early diagnosis, prevention and clinical treatment for mitochondrial diabetes.
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Affiliation(s)
- Xing Li
- Department of Endocrinology, Ordos Center Hospital, Ordos, Inner Mongolian, 017010, People’s Republic of China
| | - Jinyao Shang
- Department of Endocrinology, Ordos Center Hospital, Ordos, Inner Mongolian, 017010, People’s Republic of China
| | - Shuang Li
- Department of Endocrinology, Ordos Center Hospital, Ordos, Inner Mongolian, 017010, People’s Republic of China
| | - Yue Wang
- Department of Endocrinology, Ordos Center Hospital, Ordos, Inner Mongolian, 017010, People’s Republic of China
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Martins ARP, Warren NB, McMillan WO, Barrett RDH. Spatiotemporal dynamics in butterfly hybrid zones. INSECT SCIENCE 2024; 31:328-353. [PMID: 37596954 DOI: 10.1111/1744-7917.13262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 07/13/2023] [Accepted: 07/21/2023] [Indexed: 08/21/2023]
Abstract
Evaluating whether hybrid zones are stable or mobile can provide novel insights for evolution and conservation biology. Butterflies exhibit high sensitivity to environmental changes and represent an important model system for the study of hybrid zone origins and maintenance. Here, we review the literature exploring butterfly hybrid zones, with a special focus on their spatiotemporal dynamics and the potential mechanisms that could lead to their movement or stability. We then compare different lines of evidence used to investigate hybrid zone dynamics and discuss the strengths and weaknesses of each approach. Our goal with this review is to reveal general conditions associated with the stability or mobility of butterfly hybrid zones by synthesizing evidence obtained using different types of data sampled across multiple regions and spatial scales. Finally, we discuss spatiotemporal dynamics in the context of a speciation/divergence continuum, the relevance of hybrid zones for conservation biology, and recommend key topics for future investigation.
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Affiliation(s)
- Ananda R Pereira Martins
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Natalie B Warren
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
| | - W Owen McMillan
- Smithsonian Tropical Research Institute, Gamboa, Panama City, Panama
| | - Rowan D H Barrett
- Redpath Museum, McGill University, 859 Sherbrooke Street West, Montreal, Quebec, Canada
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6
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Rivetti S, Romano A, Mastrangelo S, Attinà G, Maurizi P, Ruggiero A. Aminoglycosides-Related Ototoxicity: Mechanisms, Risk Factors, and Prevention in Pediatric Patients. Pharmaceuticals (Basel) 2023; 16:1353. [PMID: 37895824 PMCID: PMC10610175 DOI: 10.3390/ph16101353] [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: 07/08/2023] [Revised: 09/17/2023] [Accepted: 09/21/2023] [Indexed: 10/29/2023] Open
Abstract
Aminoglycosides are broad-spectrum antibiotics largely used in children, but they have potential toxic side effects, including ototoxicity. Ototoxicity from aminoglycosides is permanent and is a consequence of its action on the inner ear cells via multiple mechanisms. Both uncontrollable risk factors and controllable risk factors are involved in the pathogenesis of aminoglycoside-related ototoxicity and, because of the irreversibility of ototoxicity, an important undertaking for preventing ototoxicity includes antibiotic stewardship to limit the use of aminoglycosides. Aminoglycosides are fundamental in the treatment of numerous infectious conditions at neonatal and pediatric age. In childhood, normal auditory function ensures adequate neurocognitive and social development. Hearing damage from aminoglycosides can therefore strongly affect the normal growth of the child. This review describes the molecular mechanisms of aminoglycoside-related ototoxicity and analyzes the risk factors and the potential otoprotective strategies in pediatric patients.
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Affiliation(s)
- Serena Rivetti
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
| | - Alberto Romano
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
| | - Stefano Mastrangelo
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Giorgio Attinà
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
| | - Palma Maurizi
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
| | - Antonio Ruggiero
- Pediatric Oncology Unit, Fondazione Policlinico Universitario Agostino Gemelli IRCCS, 00168 Rome, Italy; (S.R.); (A.R.); (S.M.); (G.A.); (P.M.)
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy
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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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Sun X, Ye G, Mai Y, Shu Y, Wang L, Zhang J. Parkin exerts the tumor-suppressive effect through targeting mitochondria. Med Res Rev 2023. [PMID: 36916678 DOI: 10.1002/med.21938] [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: 01/11/2022] [Revised: 12/10/2022] [Accepted: 02/26/2023] [Indexed: 03/16/2023]
Abstract
The role of PARKIN in Parkinson's disease is well established but its role in cancer has recently emerged. PARKIN serves as a tumor suppressor in many cancers and loses the tumor-suppressive function due to loss of heterozygosity and DNA copy number. But how PARKIN protects against cancer is poorly understood. Through the analysis of PARKIN substrates and their association with mitochondria, this viewpoint discussed that PARKIN exerts its anti-cancer activity through targeting mitochondria. Mitochondria function as a convergence point for many signaling pathways and biological processes, including apoptosis, cell cycle, mitophagy, energy metabolism, oxidative stress, calcium homeostasis, inflammation, and so forth. PARKIN participates in these processes through regulating its mitochondrial targets. Conversely, these mitochondrial substrates also influence the function of PARKIN under different cellular circumstances. We believe that future studies in this area may lead to novel therapeutic targets and strategies for cancer therapy.
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Affiliation(s)
- Xin Sun
- Department of Medical Oncology, Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Guiqin Ye
- Department of Medical Oncology, Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.,Hangzhou Medical College, Hangzhou, China
| | - Yuanyuan Mai
- Department of Medical Oncology, Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China.,Hangzhou Medical College, Hangzhou, China
| | - Yuhan Shu
- Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, China
| | - Lei Wang
- Department of Medical Oncology, Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
| | - Jianbin Zhang
- Department of Medical Oncology, Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Cancer Center, Zhejiang Provincial People's Hospital (Affiliated People's Hospital, Hangzhou Medical College), Hangzhou, China
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9
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Liu Y, Zhao S, Chen X, Bian Y, Cao Y, Xu P, Zhang C, Zhang J, Zhao S, Zhao H. Variations in mitochondrial DNA coding and D-loop region are associated with early embryonic development defects in infertile women. Hum Genet 2023; 142:193-200. [PMID: 36352239 DOI: 10.1007/s00439-022-02505-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 10/31/2022] [Indexed: 11/11/2022]
Abstract
Mitochondrial DNA (mtDNA) plays a critical role in oocyte maturation, fertilization, and early embryonic development. Defects in mtDNA may determine the alteration of the mitochondrial function, affecting cellular oxidative phosphorylation and ATP supply, leading to impaired oocyte maturation, abnormal fertilization, and low embryonic developmental potential, ultimately leading to female infertility. This case-control study was established to investigate the correlation between mtDNA variations and early embryonic development defects. Peripheral blood was collected for next-generation sequencing from women who suffered the repeated failures of in vitro fertilization (IVF) and/or intracytoplasmic sperm injection (ICSI) cycles due to early embryonic development defects as well as in-house healthy controls, and the sequencing results were statistically analyzed for all subjects. This study found that infertile women with early embryonic development defects carried more mtDNA variants, especially in the D-loop region, ATP6 gene, and CYTB gene. By univariate logistic regression analysis, 16 mtDNA variants were associated with an increased risk of early embryonic development defects (OR > 1, p < 0.05). Furthermore, we identified 16 potentially pathogenic mtDNA variants only in infertile cases. The data proved that mtDNA variations were associated with early embryonic development defects in infertile Chinese women.
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Affiliation(s)
- Yuqing Liu
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Shuai Zhao
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Xiaolei Chen
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Yuehong Bian
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Yongzhi Cao
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Peiwen Xu
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Changming Zhang
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Jiangtao Zhang
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Shigang Zhao
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China.,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China.,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China.,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China.,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China.,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China
| | - Han Zhao
- Center for Reproductive Medicine, Shandong University, 157 Jingliu Road, Jinan, 250021, Shandong, China. .,Key Laboratory of Reproductive Endocrinology of Ministry of Education, Shandong University, Jinan, 250012, Shandong, China. .,Shandong Key Laboratory of Reproductive Medicine, Jinan, 250012, Shandong, China. .,Shandong Provincial Clinical Research Center for Reproductive Health, Jinan, 250012, Shandong, China. .,Shandong Technology Innovation Center for Reproductive Health, Jinan, 250012, Shandong, China. .,National Research Center for Assisted Reproductive Technology and Reproductive Genetics, Shandong University, Jinan, 250012, Shandong, China.
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10
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Nucleotide-based genetic networks: Methods and applications. J Biosci 2022. [PMID: 36226367 PMCID: PMC9554864 DOI: 10.1007/s12038-022-00290-7] [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] [Indexed: 11/21/2022]
Abstract
Genomic variations have been acclaimed as among the key players in understanding the biological mechanisms behind migration, evolution, and adaptation to extreme conditions. Due to stochastic evolutionary forces, the frequency of polymorphisms is affected by changes in the frequency of nearby polymorphisms in the same DNA sample, making them connected in terms of evolution. This article presents all the ingredients to understand the cumulative effects and complex behaviors of genetic variations in the human mitochondrial genome by analyzing co-occurrence networks of nucleotides, and shows key results obtained from such analyses. The article emphasizes recent investigations of these co-occurrence networks, describing the role of interactions between nucleotides in fundamental processes of human migration and viral evolution. The corresponding co-mutation-based genetic networks revealed genetic signatures of human adaptation in extreme environments. This article provides the methods of constructing such networks in detail, along with their graph-theoretical properties, and applications of the genomic networks in understanding the role of nucleotide co-evolution in evolution of the whole genome.
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11
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Sun S, Xiao N, Sha Z. Complete mitochondrial genomes of four deep-sea echinoids: conserved mitogenome organization and new insights into the phylogeny and evolution of Echinoidea. PeerJ 2022; 10:e13730. [PMID: 35919401 PMCID: PMC9339218 DOI: 10.7717/peerj.13730] [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] [Received: 04/22/2022] [Accepted: 06/23/2022] [Indexed: 01/17/2023] Open
Abstract
Echinoids are an important component in benthic marine environments, which occur at all depths from the shallow-water hard substrates to abyssal depths. To date, the phylogeny of the sea urchins and the macro-evolutionary processes of deep-sea and shallow water groups have not yet been fully resolved. In the present study, we sequenced the complete mitochondrial genomes (mitogenomes) of four deep-sea sea urchins (Echinoidea), which were the first representatives of the orders Aspidodiadematoida, Pedinoida and Echinothurioida, respectively. The gene content and arrangement were highly conserved in echinoid mitogenomes. The tRNA-Ser AGY with DHU arm was detected in the newly sequenced echinoid mitogenomes, representing an ancestral structure of tRNA-Ser AGY. No difference was found between deep-sea and shallow water groups in terms of base composition and codon usage. The phylogenetic analysis showed that all the orders except Spatangoida were monophyletic. The basal position of Cidaroida was supported. The closest relationship of Scutelloida and Echinolampadoida was confirmed. Our phylogenetic analysis shed new light on the position of Arbacioida, which supported that Arbacioida was most related with the irregular sea urchins instead of Stomopneustoida. The position Aspidodiadematoida (((Aspidodiadematoida + Pedinoida) + Echinothurioida) + Diadematoida) revealed by mitogenomic data discredited the hypothesis based on morphological evidences. The macro-evolutionary pattern revealed no simple onshore-offshore or an opposite hypothesis. But the basal position of the deep-sea lineages indicated the important role of deep sea in generating the current diversity of the class Echinoidea.
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Affiliation(s)
- Shao’e Sun
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Ning Xiao
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Zhongli Sha
- Department of Marine Organism Taxonomy and Phylogeny, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China,Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China,College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
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12
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Hou L, Hu C, Ji L, Wang Q, Liang M. The Mitochondrial tRNA Phe 625G>A Mutation in Three Han Chinese Families With Cholecystolithiasis. Front Genet 2022; 13:814729. [PMID: 35719381 PMCID: PMC9198646 DOI: 10.3389/fgene.2022.814729] [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] [Received: 11/18/2021] [Accepted: 04/19/2022] [Indexed: 11/16/2022] Open
Abstract
In this study, we assessed three Chinese families with inherited cholecystolithiasis and conducted the clinical, genetic, and molecular characterization of these subjects. Eight of eighteen matrilineal relatives had a clinical phenotype in these three families. Sequence analysis of complete mitochondrial genomes in these probands identified the homoplasmic tRNAPhe 625 G > A mutation and distinct sets of mtDNA polymorphisms belonging to haplogroups H2, F4b, and M10a. The 625G > A mutation disturbed the classic G-C base-pairings at a highly conserved position 49 in the T-stem of mitochondrial tRNAs. Molecular dynamics simulation showed that the structure of tRNAphe with 625 G > A mutation was noticeably remodeled while compared with the isoform of the wild type. The occurrence of tRNAPhe 625 G > A mutation in these various genetically unrelated subjects strongly indicates that this mutation is involved in the pathogenesis of cholecystolithiasis. This is the first evidence that tRNA mutations are associated with cholecystolithiasis, and it provided more insights into the genetic mechanism of cholecystolithiasis.
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Affiliation(s)
- Lingling Hou
- Department of Medical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Cuifang Hu
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, China
| | - Lili Ji
- Department of Medical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qiongdan Wang
- Department of Medical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Min Liang
- Department of Medical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China.,Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, China
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13
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Gu P, Wang G, Gao X, Kang D, Dai P, Huang S. Clinical and molecular findings in a Chinese family with a de novo mitochondrial A1555G mutation. BMC Med Genomics 2022; 15:121. [PMID: 35614445 PMCID: PMC9131558 DOI: 10.1186/s12920-022-01276-y] [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] [Received: 09/20/2021] [Accepted: 05/17/2022] [Indexed: 11/10/2022] Open
Abstract
Background The mitochondrial 12S rRNA A1555G mutation is the most prevalent deafness-causing mitochondrial DNA (mtDNA) mutation and is inherited maternally. Studies have suggested that A1555G mutations have multiple origins, although there is no direct evidence of this. Here, we identified a family with a de novo A1555G mutation. Method Based on detailed mtDNA analyses of the family members using next-generation sequencing with 1% sensitivity to mutated mtDNA, the level of heteroplasmy in terms of the A1555G mutation in blood DNA samples was quantified. Results An individual harbored a heterogeneous A1555G mutation, at 28.68% heteroplasmy. The individual’s son was also a heterogeneous carrier, with 7.25% heteroplasmy. The individual’s brother and mother did not carry the A1555G mutation, and both had less than 1% mitochondrial 12S rRNA A1555G heteroplasmy. Conclusion The A1555G mutation arose de novo in this family. This is the first report of a family with a de novo A1555G mutation, providing direct evidence of its multipoint origin. This is important for both diagnostic investigations and genetic counselling.
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Affiliation(s)
- Ping Gu
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China.,Department of Otolaryngology, Shenzhen Children's Hospital, Shenzhen, 518038, People's Republic of China
| | - Guojian Wang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China
| | - Xue Gao
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China
| | - Dongyang Kang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China.,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China.,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China
| | - Pu Dai
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China. .,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China. .,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China.
| | - Shasha Huang
- College of Otolaryngology Head and Neck Surgery, Chinese PLA General Hospital, Chinese PLA Medical School, Do.28 Fuxing Road, Beijing, 100853, People's Republic of China. .,National Clinical Research Center for Otolaryngologic Diseases, State Key Lab of Hearing Science, Ministry of Education, Beijing, People's Republic of China. .,Beijing Key Lab of Hearing Impairment Prevention and Treatment, Beijing, People's Republic of China.
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14
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Ji Y, Zhang J, Liang M, Meng F, Zhang M, Mo JQ, Wang M, Guan MX. Mitochondrial tRNA variants in 811 Chinese probands with Leber's hereditary optic neuropathy. Mitochondrion 2022; 65:56-66. [PMID: 35623556 DOI: 10.1016/j.mito.2022.05.003] [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: 03/08/2022] [Revised: 04/26/2022] [Accepted: 05/22/2022] [Indexed: 11/27/2022]
Abstract
Leber's hereditary optic neuropathy (LHON) is the maternal inheritance of eye disorder. LHON-linked mitochondrial DNA (mtDNA) mutations affect the ND1, ND4 or ND6 genes encoding essential subunits of complex I. However, the role of mitochondrial tRNA defects in the pathogenesis of LHON is poorly understood. In this report, Sanger sequence analysis of 22 mitochondrial tRNA genes identified 139 variants in a cohort of 811 Han Chinese probands and 485 control Chinese subjects. Among these, 32 (4 known and 28 novel/putative) tRNA variants in 69 probands may contribute to pathogenesis of LHON, as these exhibited (1) present in <1% of controls; (2) evolutionary conservation; (3) potential and significance of structural and functional modifications. Such variants may have potentially compromised structural and functional aspects in the processing of tRNAs, structure stability, tRNA charging, or codon-anticodon interactions during translation. These 32 variants presented either singly or with multiple mutations, with the primary LHON-linked ND1 3640G>A, ND4 11778G>A or ND6 14484T>C mutations in the probands. The thirty-eight pedigrees carrying only one of tRNA variants exhibited relatively low penetrances of LHON, ranging from 5.7% to 42.9%, with an average of 19%. Strikingly, the average penetrances of optic neuropathy among 33 Chinese families carrying both a known/putative tRNA variant and a primary LHON-associated mtDNA mutation were 40.1%. These findings suggested that mitochondrial tRNA variants represent a significant causative factor for LHON, accounting for 8.75% cases in this cohort. These new insights may lead to beneficial applications in the pathophysiology, disease management, and genetic counseling of LHON.
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Affiliation(s)
- Yanchun Ji
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China; Institute of Genetics, Zhejiang University, School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Juanjuan Zhang
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Min Liang
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang 325027, China
| | - Feilong Meng
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China; Institute of Genetics, Zhejiang University, School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Minglian Zhang
- Department of Ophthalmology, Hebei Provincial Eye Hospital, Xingtai, Hebei 051730, China
| | - Jun Q Mo
- Department of Pathology, Rady Children's Hospital, University of California at San Diego School of Medicine, San Diego, California 92123, USA
| | - Meng Wang
- Institute of Genetics, Zhejiang University, School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine and National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310058, China; Institute of Genetics, Zhejiang University, School of Medicine, Hangzhou, Zhejiang 310058, China; Zhejiang Provincial Key Laboratory of Genetic & Developmental Disorders, Zhejiang University, Hangzhou, Zhejiang 310058, China; Division of Mitochondrial Biomedicine, Joint Institute of Genetics and Genome Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang, China.
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15
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Verma RK, Kalyakulina A, Mishra A, Ivanchenko M, Jalan S. Role of mitochondrial genetic interactions in determining adaptation to high altitude human population. Sci Rep 2022; 12:2046. [PMID: 35132109 PMCID: PMC8821606 DOI: 10.1038/s41598-022-05719-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 12/17/2021] [Indexed: 12/13/2022] Open
Abstract
Physiological and haplogroup studies performed to understand high-altitude adaptation in humans are limited to individual genes and polymorphic sites. Due to stochastic evolutionary forces, the frequency of a polymorphism is affected by changes in the frequency of a near-by polymorphism on the same DNA sample making them connected in terms of evolution. Here, first, we provide a method to model these mitochondrial polymorphisms as "co-mutation networks" for three high-altitude populations, Tibetan, Ethiopian and Andean. Then, by transforming these co-mutation networks into weighted and undirected gene-gene interaction (GGI) networks, we were able to identify functionally enriched genetic interactions of CYB and CO3 genes in Tibetan and Andean populations, while NADH dehydrogenase genes in the Ethiopian population playing a significant role in high altitude adaptation. These co-mutation based genetic networks provide insights into the role of different set of genes in high-altitude adaptation in human sub-populations.
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Affiliation(s)
- Rahul K Verma
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Alena Kalyakulina
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia
| | - Ankit Mishra
- Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India
| | - Mikhail Ivanchenko
- Department of Applied Mathematics and Centre of Bioinformatics, Lobachevsky State University of Nizhny Novgorod, Nizhny Novgorod, Russia.,Laboratory of Systems Medicine of Healthy Aging and Department of Applied Mathematics, Lobachevsky University, Nizhny Novgorod, Russia
| | - Sarika Jalan
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India. .,Complex Systems Lab, Department of Physics, Indian Institute of Technology Indore, Khandwa Road, Simrol, Indore, 453552, India.
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16
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Qi Y, Wu Z, Bai Y, Jiao Y, Li P. Screening for Mitochondrial tRNA Mutations in 318 Patients with Dilated Cardiomyopathy. Hum Hered 2022; 87:000521615. [PMID: 34991096 DOI: 10.1159/000521615] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 11/25/2021] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Dilated cardiomyopathy (DCM) is a complex cardiovascular disease with unknown etiology. Although nuclear genes play active roles in DCM, mitochondrial dysfunction was believed to be involved in the pathogenesis of DCM. The objective of this study is to analysis the association between mitochondrial tRNA (mt-tRNA) mutations and DCM. MATERIAL AND METHODS We performed a mutational analysis of mt-tRNA genes in a cohort of 318 patients with DCM and 200 age- and gender-matched control subjects. To further assess their pathogenicity, phylogenetic analysis and mitochondrial functions including mtDNA copy number, ATP and ROS were analyzed. RESULTS 7 possible pathogenic mutations: MT-TL1 3302A>G, MT-TI 4295A>G, MT-TM 4435A>G, MT-TA 5655T>C, MT-TH 12201T>C, MT-TE 14692A>G and MT-TT 15927G>A were identified in DCM group but absent in controls. These mutations occurred at extremely conserved nucleotides of corresponding tRNAs, and led to the failure in tRNAs metabolism. Moreover, a significant reduction in ATP and mtDNA copy number, whereas a markedly increased in ROS level were observed in polymononuclear leukocytes (PMNs) derived from the DCM patients carrying these mt-tRNA mutations, suggesting that these mutations may cause mitochondrial dysfunction that was responsible for DCM. CONCLUSIONS Our data indicated that mt-tRNA mutations may be the molecular basis for DCM, which shaded novel insight into the pathophysiology of DCM that was manifestated by mitochondrial dysfunction.
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17
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Ding Y, Zhang S, Guo Q, Zheng H. Mitochondrial Diabetes is Associated with tRNA Leu(UUR) A3243G and ND6 T14502C Mutations. Diabetes Metab Syndr Obes 2022; 15:1687-1701. [PMID: 35685248 PMCID: PMC9172734 DOI: 10.2147/dmso.s363978] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Mutations in mitochondrial DNA (mtDNA) are associated with type 2 diabetes mellitus (T2DM). In particular, m.A3243G is the most common T2DM-related mtDNA mutation in many families worldwide. However, the clinical features and pathophysiology of m.A3243G-induced T2DM are largely undefined. METHODS Two pedigrees with maternally inherited T2DM were underwent clinical, molecular and biochemical assessments. The mtDNA genes were PCR amplified and sequenced. Mitochondrial adenosine triphosphate (ATP) and reactive oxygen species (ROS) were measured in polymononuclear leukocytes derived from three patients with both the m.A3243G and m.T14502C mutations, three patients with only the m.A3243G mutation and three controls without these mutations. Moreover, GJB2, GJB3 and GJB6 mutations were screened by PCR-Sanger sequencing. RESULTS Members of the two pedigrees manifestated variable clinical phenotypes including diabetes and hearing and vision impairments. The age at onset of T2DM varied from 31 to 66 years, with an average of 41 years. Mutational analysis of mitochondrial genomes indicated the presence of the m.A3243G mutation in both pedigrees. Matrilineal relatives in one of the pedigrees harbored the coexisting of m.A3243G and m.T14502C mutations. Remarkably, the m.T14502C mutation, which causes the substitution of a conserved isoleucine for valine at position 58 in ND6 mRNA, may affect the mitochondrial respiratory chain functions. Biochemical analysis revealed that cell lines bearing both the m.A3243G and m.T14502C mutations exhibited greater reductions in ATP levels and increased ROS production compared with those carrying only the m.A3243G mutation. However, we did not find any mutations in the GJB2, GJB3 and GJB6 genes. CONCLUSION Our study indicated that mitochondrial diabetes is associated with the tRNALeu(UUR) A3243G and ND6 T14502C mutations.
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Affiliation(s)
- Yu Ding
- Central Laboratory, Hangzhou First People’s Hospital, Hangzhou, 310006, Zhejiang, People’s Republic of China
- Correspondence: Yu Ding, Central Laboratory, Hangzhou First People’s Hospital, Hangzhou, 310006, Zhejiang, People’s Republic of China, Tel/Fax +86-571-56005600, Email
| | - Shunrong Zhang
- Department of Geriatrics, Hangzhou First People’s Hospital, Hangzhou, 310006, Zhejiang, People’s Republic of China
| | - Qinxian Guo
- Central Laboratory, Hangzhou First People’s Hospital, Hangzhou, 310006, Zhejiang, People’s Republic of China
| | - Hui Zheng
- Central Laboratory, Hangzhou First People’s Hospital, Hangzhou, 310006, Zhejiang, People’s Republic of China
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18
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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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19
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De Luise M, Iommarini L, Marchio L, Tedesco G, Coadă CA, Repaci A, Turchetti D, Tardio ML, Salfi N, Pagotto U, Kurelac I, Porcelli AM, Gasparre G. Pathogenic Mitochondrial DNA Mutation Load Inversely Correlates with Malignant Features in Familial Oncocytic Parathyroid Tumors Associated with Hyperparathyroidism-Jaw Tumor Syndrome. Cells 2021; 10:2920. [PMID: 34831144 PMCID: PMC8616364 DOI: 10.3390/cells10112920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 11/23/2022] Open
Abstract
While somatic disruptive mitochondrial DNA (mtDNA) mutations that severely affect the respiratory chain are counter-selected in most human neoplasms, they are the genetic hallmark of indolent oncocytomas, where they appear to contribute to reduce tumorigenic potential. A correlation between mtDNA mutation type and load, and the clinical outcome of a tumor, corroborated by functional studies, is currently lacking. Recurrent familial oncocytomas are extremely rare entities, and they offer the chance to investigate the determinants of oncocytic transformation and the role of both germline and somatic mtDNA mutations in cancer. We here report the first family with Hyperparathyroidism-Jaw Tumor (HPT-JT) syndrome showing the inherited predisposition of four individuals to develop parathyroid oncocytic tumors. MtDNA sequencing revealed a rare ribosomal RNA mutation in the germline of all HPT-JT affected individuals whose pathogenicity was functionally evaluated via cybridization technique, and which was counter-selected in the most aggressive infiltrating carcinoma, but positively selected in adenomas. In all tumors different somatic mutations accumulated on this genetic background, with an inverse clear-cut correlation between the load of pathogenic mtDNA mutations and the indolent behavior of neoplasms, highlighting the importance of the former both as modifiers of cancer fate and as prognostic markers.
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Affiliation(s)
- Monica De Luise
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Luisa Iommarini
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
| | - Lorena Marchio
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Greta Tedesco
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Camelia Alexandra Coadă
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Andrea Repaci
- Division of Endocrinology and Diabetes Prevention and Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Daniela Turchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Division of Medical Genetics, IRCSS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy
| | - Maria Lucia Tardio
- Unit of Pathology, IRCCS S.Orsola University Hospital, 40138 Bologna, Italy;
| | - Nunzio Salfi
- Pathology Unit, IRCCS Giannina Gaslini Children’s Research Hospital, 16147 Genova, Italy;
| | - Uberto Pagotto
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Division of Endocrinology and Diabetes Prevention and Care, IRCCS Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Ivana Kurelac
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
| | - Anna Maria Porcelli
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy
- Interdepartmental Center of Industrial Research (CIRI) Life Science and Health Technologies, University of Bologna, 40064 Ozzano dell’Emilia, Italy
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40138 Bologna, Italy; (M.D.L.); (L.M.); (G.T.); (C.A.C.); (D.T.); (U.P.); (I.K.)
- Center for Applied Biomedical Research (CRBA), University of Bologna, 40138 Bologna, Italy; (L.I.); (A.M.P.)
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Lin L, Zhang D, Jin Q, Teng Y, Yao X, Zhao T, Xu X, Jin Y. Mutational Analysis of Mitochondrial tRNA Genes in 200 Patients with Type 2 Diabetes Mellitus. Int J Gen Med 2021; 14:5719-5735. [PMID: 34557026 PMCID: PMC8454214 DOI: 10.2147/ijgm.s330973] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 08/25/2021] [Indexed: 12/12/2022] Open
Abstract
Objective Previous studies showed that variants in mitochondrial DNA (mtDNA) are associated with type 2 diabetes mellitus (T2DM). However, the relationships between mitochondrial tRNA (mt-tRNA) variants and T2DM remain poorly understood. Methods In this study, we performed a mutational screening of 22 mt-tRNA genes in a cohort of 200 Han Chinese subjects with T2DM and 200 control subjects through PCR–Sanger sequencing. The identified mt-tRNA variants were assessed for their pathogenicity via the phylogenetic approach, structural and functional analysis. Furthermore, two Han Chinese pedigrees with maternally inherited diabetes and deafness (MIDD) were reported by clinical and genetic assessments. Results A total of 49 genetic variants in mt-tRNA genes were identified; among them, 31 variants (17 pathogenic/likely pathogenic) were absent in controls, located at extremely conserved nucleotides, may have potential structural and functional significance, thereby considered to be T2DM-associated variants. In addition, sequence analysis of entire mitochondrial genomes of the matrilineal relatives from two MIDD pedigrees revealed the occurrence of tRNALeu(UUR) A3243G and T3290C mutations, as well as sets of polymorphisms belonging to mitochondrial haplogroups F2 and D4. However, the lack of any functional variants in connexin 26 gene (GJB2) and tRNA 5-methylaminomethyl-2-thiouridylate (TRMU) suggested that nuclear genes may not play active roles in clinical expression of MIDD in these pedigrees. Conclusion Our data indicated that mt-tRNA variants were associated with T2DM, screening for mt-tRNA pathogenic mutations was recommended for early detection and prevention of mitochondrial diabetes.
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Affiliation(s)
- Liangyan Lin
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Dongdong Zhang
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Qingsong Jin
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Yaqin Teng
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Xiaoyan Yao
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Tiantian Zhao
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
| | - Xinmiao Xu
- Department of Endocrinology, Yantai Yeda Hospital, Yantai, Shandong, People's Republic of China
| | - Yongjun Jin
- Department of Endocrinology and Metabolism, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, People's Republic of China
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21
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Abstract
Variation in the mitochondrial DNA (mtDNA) sequence is common in certain tumours. Two classes of cancer mtDNA variants can be identified: de novo mutations that act as 'inducers' of carcinogenesis and functional variants that act as 'adaptors', permitting cancer cells to thrive in different environments. These mtDNA variants have three origins: inherited variants, which run in families, somatic mutations arising within each cell or individual, and variants that are also associated with ancient mtDNA lineages (haplogroups) and are thought to permit adaptation to changing tissue or geographic environments. In addition to mtDNA sequence variation, mtDNA copy number and perhaps transfer of mtDNA sequences into the nucleus can contribute to certain cancers. Strong functional relevance of mtDNA variation has been demonstrated in oncocytoma and prostate cancer, while mtDNA variation has been reported in multiple other cancer types. Alterations in nuclear DNA-encoded mitochondrial genes have confirmed the importance of mitochondrial metabolism in cancer, affecting mitochondrial reactive oxygen species production, redox state and mitochondrial intermediates that act as substrates for chromatin-modifying enzymes. Hence, subtle changes in the mitochondrial genotype can have profound effects on the nucleus, as well as carcinogenesis and cancer progression.
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Affiliation(s)
- Piotr K Kopinski
- Howard Hughes Medical Institute, University of Pennsylvania, Philadelphia, PA, USA
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA, USA.
- Department of Pediatrics, Division of Human Genetics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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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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Investigating the importance of individual mitochondrial genotype in susceptibility to drug-induced toxicity. Biochem Soc Trans 2021; 48:787-797. [PMID: 32453388 PMCID: PMC7329340 DOI: 10.1042/bst20190233] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 12/13/2022]
Abstract
The mitochondrion is an essential organelle responsible for generating cellular energy. Additionally, mitochondria are a source of inter-individual variation as they contain their own genome. Evidence has revealed that mitochondrial DNA (mtDNA) variation can confer differences in mitochondrial function and importantly, these differences may be a factor underlying the idiosyncrasies associated with unpredictable drug-induced toxicities. Thus far, preclinical and clinical data are limited but have revealed evidence in support of an association between mitochondrial haplogroup and susceptibility to specific adverse drug reactions. In particular, clinical studies have reported associations between mitochondrial haplogroup and antiretroviral therapy, chemotherapy and antibiotic-induced toxicity, although study limitations and conflicting findings mean that the importance of mtDNA variation to toxicity remains unclear. Several studies have used transmitochondrial cybrid cells as personalised models with which to study the impact of mitochondrial genetic variation. Cybrids allow the effects of mtDNA to be assessed against a stable nuclear background and thus the in vitro elucidation of the fundamental mechanistic basis of such differences. Overall, the current evidence supports the tenet that mitochondrial genetics represent an exciting area within the field of personalised medicine and drug toxicity. However, further research effort is required to confirm its importance. In particular, efforts should focus upon translational research to connect preclinical and clinical data that can inform whether mitochondrial genetics can be useful to identify at risk individuals or inform risk assessment during drug development.
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Mohamed WKE, Arnoux M, Cardoso THS, Almutery A, Tlili A. Mitochondrial mutations in non-syndromic hearing loss at UAE. Int J Pediatr Otorhinolaryngol 2020; 138:110286. [PMID: 32871514 DOI: 10.1016/j.ijporl.2020.110286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 07/08/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
Abstract
INTRODUCTION Hearing loss (HL) is a common sensory disorder over the world, and it has been estimated that genetic etiology is involved in more than 50% of the cases in developed countries. Both nuclear and mitochondrial genes were reported as responsible for hereditary HL. Mitochondrial mutations leading to HL have so far been reported in the MT-RNR1 gene, mitochondrially encoded 12S rRNA. METHODS To study the molecular contribution of mitochondrial 12S rRNA gene mutations in UAE-HL, a cohort of 74 unrelated UAE patients with no gap junction protein beta 2 (GJB2) mutations were selected for mitochondrial 12S rRNA gene mutational screening using Sanger sequencing and whole-exome sequencing. Detected DNA variants were analyzed by bioinformatics tools to predict their pathogenic effects. RESULTS Our analysis revealed the presence of two known deafness mutations; m.669T > C and m.827A > G in two different deaf individuals. Furthermore, whole-exome sequencing was done for these two patients and showed the absence of any nuclear mutations. Our study supports the pathogenic effect of the m.669T > C and m.827A > G mutations and showed that mitochondrial mutations have a contribution of 2.7% in our cohort. CONCLUSIONS This is the first report of mtDNA mutations in the UAE which revealed that both variants m.669T > C and m.827A > G should be included in the molecular diagnosis of patients with maternally inherited HL in UAE.
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Affiliation(s)
- Walaa Kamal Eldin Mohamed
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates; Laboratory for Immuno Bioengineering Research and Applications, Division of Engineering, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates; Departament de Genètica I de Microbiologia, Facultat de Biociències, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marc Arnoux
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Thyago H S Cardoso
- Departamento de Bioquímica, Universidade Federal De Sao Paulo, Sao Paulo, Brazil
| | - Abdullah Almutery
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates; Human Genetics & Stem Research Group, Research Institute of Sciences & Engineering, University of Sharjah, Sharjah, United Arab Emirates
| | - Abdelaziz Tlili
- Department of Applied Biology, College of Sciences, University of Sharjah, Sharjah, United Arab Emirates; Human Genetics & Stem Research Group, Research Institute of Sciences & Engineering, University of Sharjah, Sharjah, United Arab Emirates.
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Hill GE. Genetic hitchhiking, mitonuclear coadaptation, and the origins of mt DNA barcode gaps. Ecol Evol 2020; 10:9048-9059. [PMID: 32953045 PMCID: PMC7487244 DOI: 10.1002/ece3.6640] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 07/02/2020] [Accepted: 07/06/2020] [Indexed: 01/02/2023] Open
Abstract
DNA barcoding based on mitochondrial (mt) nucleotide sequences is an enigma. Neutral models of mt evolution predict DNA barcoding cannot work for recently diverged taxa, and yet, mt DNA barcoding accurately delimits species for many bilaterian animals. Meanwhile, mt DNA barcoding often fails for plants and fungi. I propose that because mt gene products must cofunction with nuclear gene products, the evolution of mt genomes is best understood with full consideration of the two environments that impose selective pressure on mt genes: the external environment and the internal genomic environment. Moreover, it is critical to fully consider the potential for adaptive evolution of not just protein products of mt genes but also of mt transfer RNAs and mt ribosomal RNAs. The tight linkage of genes on mt genomes that do not engage in recombination could facilitate selective sweeps whenever there is positive selection on any element in the mt genome, leading to the purging of mt genetic diversity within a population and to the rapid fixation of novel mt DNA sequences. Accordingly, the most important factor determining whether or not mt DNA sequences diagnose species boundaries may be the extent to which the mt chromosomes engage in recombination.
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Rauf S, Zahra N, Malik SS, Zahra SAE, Sughra K, Khan MR. Extraction of Mitochondrial Genome from Whole Genome Next Generation Sequencing Data and Unveiling of Forensically Relevant Markers. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420080128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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27
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Kurbalija Novičić Z, Bodén R, Kozarski K, Jelić M, Jovanović VM, Cunningham JL. Lithium influences whole-organism metabolic rate in Drosophila subobscura. J Neurosci Res 2020; 99:407-418. [PMID: 32729199 DOI: 10.1002/jnr.24678] [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: 10/26/2019] [Revised: 05/25/2020] [Accepted: 05/28/2020] [Indexed: 11/09/2022]
Abstract
Lithium is widely used to treat bipolar disorder. However, the efficacy and vulnerability as to its side effects are known to differ. Although the specific biochemical mechanism of action is still elusive, lithium may influence mitochondrial function, and consequently, metabolism. Lithium exposure in this study was conducted on a unique set of mito-nuclear introgression lines of Drosophila subobscura to disentangle the independent effects of mitochondrial DNA (mtDNA) against a common nuclear DNA background. The study addressed three issues: (a) whether lithium has a dose-dependent effect on whole-organism metabolic rate, (b) whether mtDNA haplotypes show divergent metabolic efficiency measured by metabolic rate to lithium exposure and (c) whether lithium influences the whole-organism metabolic rate across sexes. The results confirm that lithium influenced the whole-organism metabolic rate, showing a subtle balance between efficacy and adverse effects within a narrow dose range. In addition, lithium exposure was found to influence metabolism differently based on mtDNA haplotypes and sex. This preliminary research may have a range of biological implications for the role of mitochondrial variability in psychiatric disease and treatment by contributing to the understanding and predicting of the lithium treatment response and risk for toxic side effects.
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Affiliation(s)
- Zorana Kurbalija Novičić
- Department of Neuroscience, Psychiatry, Uppsala University Hospital, Uppsala, Sweden.,Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Uppsala, Sweden
| | - Robert Bodén
- Department of Neuroscience, Psychiatry, Uppsala University Hospital, Uppsala, Sweden
| | - Ksenija Kozarski
- Department of Neuroscience, Psychiatry, Uppsala University Hospital, Uppsala, Sweden
| | - Mihailo Jelić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Vladimir M Jovanović
- Bioinformatics Solution Center, Freie Universität Berlin, Berlin, Germany.,Human Biology Group, Freie Universität Berlin, Berlin, Germany.,Institute for Zoology, Freie Universität Berlin, Berlin, Germany.,Department of Biology, Chemistry and Pharmacy, Freie Universität Berlin, Berlin, Germany
| | - Janet L Cunningham
- Department of Neuroscience, Psychiatry, Uppsala University Hospital, Uppsala, Sweden
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Zheng J, Bai X, Xiao Y, Ji Y, Meng F, Aishanjiang M, Gao Y, Wang H, Fu Y, Guan MX. Mitochondrial tRNA mutations in 887 Chinese subjects with hearing loss. Mitochondrion 2020; 52:163-172. [PMID: 32169613 DOI: 10.1016/j.mito.2020.03.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 01/13/2020] [Accepted: 03/09/2020] [Indexed: 01/24/2023]
Abstract
Mutations in the mitochondrial tRNAs have been reported to be the important cause of hearing loss. However, only a few cases have been identified thus far and the prevalence of mitochondrial tRNA mutations in hearing-impaired patients remain unclear. Here we performed the mutational analysis of 22 mitochondrial tRNA genes in a large cohort of 887 Han Chinese subjects with hearing loss by Sanger sequencing. The systemic evaluation of putative pathogenic variants was further carried out by frequency in controls (<1%), phylogenetic analysis, structural analysisandfunctionalprediction. As a result, a total of 147 variants on 22 tRNA genes were identified. Among these, 39 tRNA mutations (10 pathogenic and 29 likely pathogenic) which absent or present <1% in 773 Chinese controls, localized at highly conserved nucleotides, or changed the modified nucleotides, could have potential structural alterations and functional significance, thereby considered to be deafness-associated mutations. Furthermore, 44 subjects carried one of these 39 pathogenic/likely pathogenic tRNA mutations with a total prevalence of 4.96%. However, the phenotypic variability and incomplete penetrance of hearing loss in pedigrees carrying these tRNA mutations indicate the involvement of modifier factors, such as nuclear encoded genes associated with mitochondrion biogenesis, mitochondrial haplotypes, epigenetic and environmental factors. Thus, our data provide the evidence that mitochondrial tRNA mutations are the important causes of hearing loss among Chinese population. These findings further increase our knowledge on the clinical relevance of tRNA mutations in the mitochondrial genome, and should be helpful to elucidate the pathogenesis of maternal hearing loss.
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Affiliation(s)
- Jing Zheng
- Division of Medical Genetics and Genomics, and Department of Genetic and Metabolic Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaohui Bai
- Department of Otorhinolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, Shandong 250022, China
| | - Yun Xiao
- Division of Medical Genetics and Genomics, and Department of Genetic and Metabolic Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Department of Otorhinolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, Shandong 250022, China
| | - Yanchun Ji
- Division of Medical Genetics and Genomics, and Department of Genetic and Metabolic Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Feilong Meng
- Division of Medical Genetics and Genomics, and Department of Genetic and Metabolic Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Maerhaba Aishanjiang
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yinglong Gao
- Division of Medical Genetics and Genomics, and Department of Genetic and Metabolic Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Haibo Wang
- Department of Otorhinolaryngology-Head and Neck Surgery, Shandong Provincial ENT Hospital, Shandong University, Jinan, Shandong 250022, China.
| | - Yong Fu
- Division of Medical Genetics and Genomics, and Department of Genetic and Metabolic Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Department of Otorhinolaryngology Head and Neck Surgery, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China.
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, and Department of Genetic and Metabolic Diseases, The Children's Hospital, Zhejiang University School of Medicine, National Clinical Research Center for Child Health, Hangzhou, Zhejiang 310052, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
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Gao Z, Yuan YS. Screening for mitochondrial 12S rRNA C1494T mutation in 655 patients with non-syndromic hearing loss: An observational study. Medicine (Baltimore) 2020; 99:e19373. [PMID: 32221064 PMCID: PMC7220552 DOI: 10.1097/md.0000000000019373] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Mutations in mitochondrial DNA, especially in 12S rRNA gene, are the most important causes for hearing loss. In particular, the A1555G and C1494T mutations have been found to be associated with both aminoglycoside-induced and non-syndromic hearing loss in many families worldwide. To determine the frequency of C1494T mutation in deaf patients, in the current study, we screened this mutation in 655 patients with non-syndromic hearing loss and 300 control subjects. After PCR amplification of mitochondrial 12S rRNA gene and direct sequence analysis, we found that there were 2 patients carrying the C1494T mutation; however, this mutation was not detected in 300 healthy subjects. Further genetic counseling suggested that only 1 patient had an obvious family history of hearing impairment. Clinical evaluation showed that 3 of 10 matrilineal relatives suffered from hearing loss, with different age at onset of hearing loss. Molecular analysis revealed the presence of homoplasmic 12S rRNA C1494T and ND5 T12338C mutations, together with a set of polymorphisms belonging to human mitochondrial haplogroup F2. Interestingly, T12338C mutation resulted in the replacement of the first amino acid, a translation-initiating methionine with a threonine, shortening 2 amino acids of ND5 polypeptide. Moreover, this mutation is located in 2 nucleotides adjacent to the 3' end of the mt-tRNALeu(CUN) gene. Therefore, this mutation may alter ND5 mRNA metabolism and the processing of RNA precursors. Thus, the combination of T12338C and C1494T mutations may contribute to deafness expression in this family. Taken together, our data suggested that the C1494T mutation was the molecular basis for hearing loss, screening for the mitochondrial DNA pathogenic mutations was recommended for early detection, prevention, and diagnosis of mitochondrial deafness.
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Affiliation(s)
- Zhen Gao
- Department of Otology and Skull Base Surgery, Eye & ENT Hospital
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China
| | - Ya-Sheng Yuan
- Department of Otology and Skull Base Surgery, Eye & ENT Hospital
- NHC Key Laboratory of Hearing Medicine, Fudan University, Shanghai, China
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30
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Kurbalija Novičić Z, Sayadi A, Jelić M, Arnqvist G. Negative frequency dependent selection contributes to the maintenance of a global polymorphism in mitochondrial DNA. BMC Evol Biol 2020; 20:20. [PMID: 32019493 PMCID: PMC7001298 DOI: 10.1186/s12862-020-1581-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 01/13/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the forces that maintain diversity across a range of scales is at the very heart of biology. Frequency-dependent processes are generally recognized as the most central process for the maintenance of ecological diversity. The same is, however, not generally true for genetic diversity. Negative frequency dependent selection, where rare genotypes have an advantage, is often regarded as a relatively weak force in maintaining genetic variation in life history traits because recombination disassociates alleles across many genes. Yet, many regions of the genome show low rates of recombination and genetic variation in such regions (i.e., supergenes) may in theory be upheld by frequency dependent selection. RESULTS We studied what is essentially a ubiquitous life history supergene (i.e., mitochondrial DNA) in the fruit fly Drosophila subobscura, showing sympatric polymorphism with two main mtDNA genotypes co-occurring in populations world-wide. Using an experimental evolution approach involving manipulations of genotype starting frequencies, we show that negative frequency dependent selection indeed acts to maintain genetic variation in this region. Moreover, the strength of selection was affected by food resource conditions. CONCLUSIONS Our work provides novel experimental support for the view that balancing selection through negative frequency dependency acts to maintain genetic variation in life history genes. We suggest that the emergence of negative frequency dependent selection on mtDNA is symptomatic of the fundamental link between ecological processes related to resource use and the maintenance of genetic variation.
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Affiliation(s)
- Zorana Kurbalija Novičić
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.,Department of Neuroscience, Psychiatry, Uppsala University Hospital, Entrance 10, 751 85, Uppsala, Sweden
| | - Ahmed Sayadi
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden
| | - Mihailo Jelić
- Faculty of Biology, University of Belgrade, Studentski trg 16, Belgrade, 11000, Serbia
| | - Göran Arnqvist
- Animal Ecology, Department of Ecology and Genetics, Evolutionary Biology Center, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.
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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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Kiiskilä J, Moilanen JS, Kytövuori L, Niemi AK, Majamaa K. Analysis of functional variants in mitochondrial DNA of Finnish athletes. BMC Genomics 2019; 20:784. [PMID: 31664900 PMCID: PMC6819560 DOI: 10.1186/s12864-019-6171-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/04/2019] [Indexed: 11/15/2022] Open
Abstract
Background We have previously reported on paucity of mitochondrial DNA (mtDNA) haplogroups J and K among Finnish endurance athletes. Here we aimed to further explore differences in mtDNA variants between elite endurance and sprint athletes. For this purpose, we determined the rate of functional variants and the mutational load in mtDNA of Finnish athletes (n = 141) and controls (n = 77) and determined the sequence variation in haplogroups. Results The distribution of rare and common functional variants differed between endurance athletes, sprint athletes and the controls (p = 0.04) so that rare variants occurred at a higher frequency among endurance athletes. Furthermore, the ratio between rare and common functional variants in haplogroups J and K was 0.42 of that in the remaining haplogroups (p = 0.0005). The subjects with haplogroup J and K also showed a higher mean level of nonsynonymous mutational load attributed to common variants than subjects with the other haplogroups. Interestingly, two of the rare variants detected in the sprint athletes were the disease-causing mutations m.3243A > G in MT-TL1 and m.1555A > G in MT-RNR1. Conclusions We propose that endurance athletes harbor an excess of rare mtDNA variants that may be beneficial for oxidative phosphorylation, while sprint athletes may tolerate deleterious mtDNA variants that have detrimental effect on oxidative phosphorylation system. Some of the nonsynonymous mutations defining haplogroup J and K may produce an uncoupling effect on oxidative phosphorylation thus favoring sprint rather than endurance performance.
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Affiliation(s)
- Jukka Kiiskilä
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland. .,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland.
| | - Jukka S Moilanen
- PEDEGO Research Unit, Medical Research Center Oulu, University of Oulu, Oulu, Finland.,Department of Clinical Genetics, Oulu University Hospital, Oulu, Finland
| | - Laura Kytövuori
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
| | - Anna-Kaisa Niemi
- Division of Neonatology, Rady Children's Hospital San Diego, University of California San Diego, San Diego, California, USA
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Neurology and Medical Research Center, Oulu University Hospital, Oulu, Finland
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Lyu Y, Xu M, Chen J, Ji Y, Guan MX, Zhang J. Frequency and spectrum of MT-TT variants associated with Leber's hereditary optic neuropathy in a Chinese cohort of subjects. MITOCHONDRIAL DNA PART B-RESOURCES 2019; 4:2266-2280. [PMID: 33365504 PMCID: PMC7687527 DOI: 10.1080/23802359.2019.1627921] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Leber’s hereditary optic neuropathy (LHON) is a maternally inherited eye disease. In our previous investigations, we have reported the spectrum and frequency of mitochondrial MT-ND1, MT-ND4 and MT-ND6 gene in Chinese LHON population. This study aimed to assess the molecular epidemiology of MT-TT mutations in Chinese families with LHON. A cohort of 352 Chinese Han probands lacking the known LHON-associated mtDNA mutations and 376 control subjects underwent molecular analysis of mtDNA. All variants were evaluated for evolutionary conservation, structural and functional consequences. Fifteen variants were identified in the MT-TT gene by mitochondrial genome analysis of LHON pedigrees, which was substantially higher than that of individuals from general Chinese populations. The incidences of the two known LHON-associated mutations, m.15927G > A and m.15951A > G, were 2.27% and 1.14%, respectively. Nine putative LHON-associated variants were identified in 20 probands, translated into 2.1% cases of this cohort. Moreover, mtDNAs in 41 probands carrying the MT-TT mutation(s) were widely dispersed among nine Eastern Asian haplogroups. Our results suggest that the MT-TT gene is a mutational hotspot for these 352 Chinese families lacking the known LHON-associated mutations. These data further showed the molecular epidemiology of MT-TT mutations in Chinese Han LHON pedigrees.
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Affiliation(s)
- Yuanyuan Lyu
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,School of Laboratory Medicine and Life Sciences, Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Man Xu
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,School of Laboratory Medicine and Life Sciences, Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jie Chen
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,School of Laboratory Medicine and Life Sciences, Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - YanChun Ji
- School of Medicine, Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China
| | - Min-Xin Guan
- School of Laboratory Medicine and Life Sciences, Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China.,School of Medicine, Institute of Genetics, Zhejiang University, Hangzhou, Zhejiang, China
| | - Juanjuan Zhang
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,School of Laboratory Medicine and Life Sciences, Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
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Tseng CC, Chen CJ, Yen JH, Huang HY, Chang JG, Chang SJ, Liao WT. Next-generation sequencing profiling of mitochondrial genomes in gout. Arthritis Res Ther 2018; 20:137. [PMID: 29976239 PMCID: PMC6034246 DOI: 10.1186/s13075-018-1637-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Accepted: 05/29/2018] [Indexed: 12/16/2022] Open
Abstract
Background Accumulating evidence implicates mitochondrial DNA (mtDNA) alleles, which are independent of the nuclear genome, in disease, especially in human metabolic diseases. However, this area of investigation has lagged behind in researching the nuclear alleles in complex traits, for example, in gout. Methods Next-generation sequencing was utilized to investigate the relationship between mtDNA alleles and phenotypic variations in 52 male patients with gout and 104 age-matched male non-gout controls from the Taiwan Biobank whole-genome sequencing samples. Differences from a reference sequence (GRCh38) were identified. The sequence kernel association test (SKAT) was applied to identify gout-associated alleles in mitochondrial genes. The tools Polymorphism Phenotyping, Sorting Intolerant From Tolerant (SIFT), Predict the pathology of Mutations (PMUT), Human Mitochondrial Genome Database (mtDB), Multiple Alignment using Fast Fourier Transform (MAFFT), and Mammalian Mitochondrial tRNA Genes (Mamit-tRNA) were used to evaluate pathogenicity of alleles. Validation of selected alleles by quantitative polymerase chain reaction of single nucleotide polymorphisms (qPCR SNPs) was also performed. Results We identified 456 alleles in patients with gout and 640 alleles in non-gout controls with 274 alleles shared by both. Mitochondrial genes were associated with gout, with MT-CO3, MT-TA, MT-TC, and MT-TT containing potentially pathogenic gout-associated alleles and displaying evidence of gene-gene interactions. All heteroplasmy levels of potentially pathogenic alleles exceeded metabolic thresholds for pathogenicity. Validation assays confirmed the next-generation sequencing results of selected alleles. Among them, potentially pathogenic MT-CO3 alleles correlated with high-density lipoprotein (HDL) levels (P = 0.034). Conclusion This study provided two scientific insights. First, this was the most extensive mitochondrial genomic profiling associated with gout. Second, our results supported the roles of mitochondria in gout and HDL, and this comprehensive analysis framework can be applied to other diseases in which mitochondrial dysfunction has been implicated. Electronic supplementary material The online version of this article (10.1186/s13075-018-1637-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chia-Chun Tseng
- Department of Internal Medicine, Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung, Taiwan
| | - Chung-Jen Chen
- Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Department of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jeng-Hsien Yen
- Division of Rheumatology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.,Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Hsi-Yuan Huang
- Department of Laboratory Medicine and Epigenome Research Center, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Jan-Gowth Chang
- Department of Laboratory Medicine and Epigenome Research Center, China Medical University Hospital, China Medical University, Taichung, Taiwan
| | - Shun-Jen Chang
- Department of Kinesiology, Health and Leisure Studies, National University of Kaohsiung, Kaohsiung, Taiwan.
| | - Wei-Ting Liao
- Department of Biotechnology, College of Life Science, Kaohsiung Medical University, Kaohsiung, Taiwan. .,Department of Medical Research, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan.
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Wu L, Li R, Chen J, Chen Y, Yang M, Wu Q. Analysis of mitochondrial A1555G mutation in infants with hearing impairment. Exp Ther Med 2018; 15:5307-5313. [PMID: 29805548 PMCID: PMC5958681 DOI: 10.3892/etm.2018.6078] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2017] [Accepted: 02/23/2018] [Indexed: 11/06/2022] Open
Abstract
Mutations in the mitochondrial 12S ribosomal RNA gene have been identified to be associated with deafness. Among these, the A to G transition at position 1555 is one of the most common pathogenic mutations associated with hearing loss. In order to evaluate the allele frequency of this mutation in infants with hearing loss, the A1555G mutation was screened in 300 deaf children and 100 age- and sex-matched healthy subjects. Consequently, 5 patients with this mutation were identified, whereas the mutation was absent in healthy controls. Among the patients with the mutation, only one had an obvious family history of hearing impairment. Notably, this pedigree manifested a high penetrance of deafness. In particular, the penetrance of deafness was 80 and 40%, when the aminoglycoside antibiotics (AmAn) was included or excluded, respectively. Clinical evaluation of this family exhibited a wide degree of hearing loss. Furthermore, screening for the complete mitochondrial genes revealed the occurrence of A1555G and transfer (t)RNAThr T15943C mutations, together with other genetic variations belonging to East Asian haplogroup C. Notably, the T15943C mutation, located at the T arm of tRNAThr, could disrupt the 63T-55A base-pairing and impair tRNA metabolism. Therefore, it was hypothesized that the combination of A1555G and T15943C mutations may result in mitochondrial dysfunction that is responsible for deafness. Screening for A1555G, as well as other potential pathogenic mutations in the mitochondrial genome, is critical for clinical diagnosis and prevention of hearing impairment.
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Affiliation(s)
- Lihua Wu
- Department of Otolaryngology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Ruiyu Li
- Department of Otolaryngology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Juan Chen
- Department of Otolaryngology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Yanping Chen
- Department of Obstetrics, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Meijun Yang
- Department of Neonatology, Shengli Clinical Medical College of Fujian Medical University, Fujian Provincial Hospital, Fuzhou, Fujian 350001, P.R. China
| | - Qing Wu
- Department of Neonatology, Fujian Provincial Maternal and Child Health Care Hospital, Fuzhou, Fujian 350001, P.R. China
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Celie BM, Mariman A, Boone J, Delesie L, Tobback E, Seneca S, De Paepe B, Vogelaers D, Van Coster RN, Bourgois JG. Near-Infrared Spectroscopy Screening to Allow Detection of Pathogenic Mitochondrial DNA Variants in Individuals with Unexplained Abnormal Fatigue: A Preliminary Study. APPLIED SPECTROSCOPY 2018; 72:715-724. [PMID: 29336589 DOI: 10.1177/0003702818756647] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Unexplained abnormal fatigue is characterized by chronic fatigue persisting for at least six months and not sufficiently explained by any recognized medical condition. In this pilot study, twelve individuals with abnormal fatigue remaining unexplained after thorough screening were investigated using a near-infrared (NIR) spectroscopy handgrip test. Four of them were found to have an abnormal oxygen extraction pattern similar to participants with documented mitochondrial myopathy. In three of the four individuals, diverse mitochondrial abnormalities were documented by spectrophotometric, immunocytological, fluorescent, and morphological analyses performed in skeletal muscle and in cultured skin fibroblasts. Three of the four participants with decreased muscular oxygen extraction were each shown to harbor a different homoplasmic pathogenic mitochondrial DNA point mutation (m.961T > C, m.1555A > G, m.14484T > C). In the fourth participant, the presence of multiple large mitochondrial DNA deletions was suspected in muscle tissue. In contrast, none of the eight abnormally fatigued participants with normal NIR spectroscopy results harbored either a pathogenic mitochondrial DNA point mutation or large deletions ( P < 0.001). This pilot study shows that NIR spectroscopy may serve as a noninvasive screening tool to delineate a subgroup (of participants) with mitochondrial dysfunction among the large group of individuals with unexplained abnormal fatigue.
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Affiliation(s)
- Bert M Celie
- 1 26656 Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - An Mariman
- 2 Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
- 3 Center for Neurophysiologic Monitoring, Ghent University Hospital, Ghent, Belgium
| | - Jan Boone
- 1 26656 Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
- 4 Centre of Sports Medicine, Ghent University Hospital, Ghent, Belgium
| | - Liesbeth Delesie
- 2 Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Els Tobback
- 2 Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
- 3 Center for Neurophysiologic Monitoring, Ghent University Hospital, Ghent, Belgium
| | - Sara Seneca
- 5 Centre for Medical Genetics, University Hospital Brussels, Neurogenetics Research Group, Reproduction Genetics and Regenerative Medicine Research Group, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Boel De Paepe
- 6 60200 Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Dirk Vogelaers
- 2 Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
- 3 Center for Neurophysiologic Monitoring, Ghent University Hospital, Ghent, Belgium
| | - Rudy N Van Coster
- 6 60200 Department of Pediatrics, Division of Pediatric Neurology and Metabolism, Ghent University Hospital, Ghent, Belgium
| | - Jan G Bourgois
- 1 26656 Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
- 4 Centre of Sports Medicine, Ghent University Hospital, Ghent, Belgium
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Sonney S, Leipzig J, Lott MT, Zhang S, Procaccio V, Wallace DC, Sondheimer N. Predicting the pathogenicity of novel variants in mitochondrial tRNA with MitoTIP. PLoS Comput Biol 2017; 13:e1005867. [PMID: 29227991 PMCID: PMC5739504 DOI: 10.1371/journal.pcbi.1005867] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 12/21/2017] [Accepted: 11/02/2017] [Indexed: 11/18/2022] Open
Abstract
Novel or rare variants in mitochondrial tRNA sequences may be observed after mitochondrial DNA analysis. Determining whether these variants are pathogenic is critical, but confirmation of the effect of a variant on mitochondrial function can be challenging. We have used available databases of benign and pathogenic variants, alignment between diverse tRNAs, structural information and comparative genomics to predict the impact of all possible single-base variants and deletions. The Mitochondrial tRNA Informatics Predictor (MitoTIP) is available through MITOMAP at www.mitomap.org. The source code for MitoTIP is available at www.github.com/sonneysa/MitoTIP.
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Affiliation(s)
- Sanjay Sonney
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jeremy Leipzig
- Department of Biomedical and Health Informatics, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Marie T. Lott
- The Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Shiping Zhang
- The Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Vincent Procaccio
- UMR CNRS 6015-INSERM U1083, MitoVasc Institute, Angers University Hospital, Angers, France
| | - Douglas C. Wallace
- The Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
- Department of Pathology, The University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Neal Sondheimer
- Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Paediatrics, The University of Toronto, Toronto, Ontario, Canada
- * E-mail:
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Zhang J, Ji Y, Liu X, Chen J, Wang B, Zhang M, Guan MX. Leber's hereditary optic neuropathy caused by a mutation in mitochondrial tRNA Thr in eight Chinese pedigrees. Mitochondrion 2017; 42:84-91. [PMID: 29225014 DOI: 10.1016/j.mito.2017.12.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 11/09/2017] [Accepted: 12/06/2017] [Indexed: 01/09/2023]
Abstract
PURPOSE The purpose of this study was to investigate the pathophysiology underlying Leber's hereditary optic neuropathy (LHON)-associated mitochondrial tRNA mutation. METHODS Severn hundred ninety-seven Han Chinese subjects underwent clinical and genetic evaluation and analysis of mitochondrial DNA (mtDNA). The cybrid cell lines were constructed by transferring mitochondria from lymphoblastoid cell lines derived from a Chinese family into mtDNA-less (ρo) cells. These cell lines were assayed by tRNA Northern blot and Western blot analyses, respiratory enzymatic activities, the rate of ATP production and the generation of reactive oxygen species. RESULTS The tRNAThr 15927G>A mutation was identified in eight probands with suggestively maternal inheritance among 352 Han Chinese probands lacking these known LHON-associated mtDNA mutations. The m.15927G>A mutation affected a highly conserved guanine at position 42 at the anticodon-stem of tRNAThr, destabilizing the conservative base pairing (28C-42G). We therefore hypothesized that the m.15927G>A mutation, and altered the structure and function of tRNAThr. Northern blot analysis revealed 60% decrease in the steady-state level of tRNAThr in the mutant cell lines. Western blot analysis showed the variable reductions of 4 mtDNA encoding proteins, especially for marked decrease of ND1 and CYTB observed in mutant cell lines. Furthermore, we demonstrated that the m.15927G>A mutation decreased the activities of mitochondrial complexes I and III, markedly diminished mitochondrial ATP levels, and increased the production of reactive oxygen species in the mutant cells. CONCLUSIONS Our data demonstrated the first mitochondrial tRNA mutation leading to LHON. Our findings may provide new insights into the understanding of pathophysiology of LHON.
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Affiliation(s)
- Juanjuan Zhang
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China; Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yanchun Ji
- Division of Medical Genetics and Genomics, Zhejiang Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaoling Liu
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jie Chen
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Bibin Wang
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Minglian Zhang
- Department of Ophthalmology, Hebei Provincial Eye Hospital, Xingtai, Hebei, China
| | - Min-Xin Guan
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Division of Medical Genetics and Genomics, Zhejiang Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Department of Ophthalmology, Hebei Provincial Eye Hospital, Xingtai, Hebei, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou, China.
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Lv ZY, Xu XM, Cao XF, Wang Q, Sun DF, Tian WJ, Yang Y, Wang YZ, Hao YL. Mitochondrial mutations in 12S rRNA and 16S rRNA presenting as chronic progressive external ophthalmoplegia (CPEO) plus: A case report. Medicine (Baltimore) 2017; 96:e8869. [PMID: 29310369 PMCID: PMC5728770 DOI: 10.1097/md.0000000000008869] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
RATIONALE Chronic progressive external ophthalmoplegia (CPEO) is a classical mitochondrial ocular disorder characterized by bilateral progressive ptosis and ophthalmoplegia. Kearns -Sayre syndrome (KSS) is a multisystem disorder with PEO, cardiac conduction block, and pigmentary retinopathy. A few individuals with CPEO have other manifestations of KSS, but do not meet all the clinical diagnosis criteria, and this is called "CPEO plus." PATIENT CONCERNS We report a 48-year-old woman exhibiting limb weakness, ptosis, ophthalmoparesis, and cerebellar dysfunctions. DIAGNOSES The patient was diagnosed as exhibiting CPEO plus syndrome. INTERVENTIONS The patient underwent clinical, genetic, histological, and histochemical analysis. She was treated orally with CoQ10, vitamin Bs, L-carnitine, and vitamin E. OUTCOMES The patient's serum creatine kinase levels, electrocardiography, and nerve conduction study results were normal; an electromyogram revealed myopathic findings. Magnetic resonance imaging showed global brain atrophy, particularly in the brainstem and cerebellum areas. A muscle biopsy showed the presence of abundant ragged red fibers. Sequencing of the mitochondrial DNA from the skeletal muscle biopsy revealed C960del mutation in 12S rRNA and homozygous mutation C2835T in 16S rRNA. She took medicines on schedule, the clinical features were similar as 2 years ago. LESSONS This is the first report of 2 rRNA mutations in a patient with MRI findings showing global brain atrophy, particularly in brainstem and cerebellum areas. Early recognition and appropriate treatment is crucial. This case highlights the cerebellar ataxia can occur in CPEO plus.
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Zhou M, Wang M, Xue L, Lin Z, He Q, Shi W, Chen Y, Jin X, Li H, Jiang P, Guan MX. A hypertension-associated mitochondrial DNA mutation alters the tertiary interaction and function of tRNA Leu(UUR). J Biol Chem 2017; 292:13934-13946. [PMID: 28679533 DOI: 10.1074/jbc.m117.787028] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 07/03/2017] [Indexed: 01/10/2023] Open
Abstract
Several mitochondrial tRNA mutations have been associated with hypertension, but their pathophysiology remains poorly understood. In this report, we identified a novel homoplasmic 3253T→C mutation in the mitochondrial tRNALeu(UUR) gene in a Han Chinese family with maternally inherited hypertension. The m.3253T→C mutation affected a highly conserved uridine at position 22 at the D-stem of tRNALeu(UUR), introducing a G-C base pairing (G13-C22) at the D-stem and a tertiary base pairing (C22-G46) between the D-stem and the variable loop. We therefore hypothesized that the m.3253T→C mutation altered both the structure and function of tRNALeu(UUR) Using cytoplasmic hybrid (cybrid) cell lines derived from this Chinese family, we demonstrated that the m.3253T→C mutation perturbed the conformation and stability of tRNALeu(UUR), as suggested by faster electrophoretic mobility of mutated tRNA relative to the wild-type molecule. Northern blot analysis revealed an ∼45% decrease in the steady-state level of tRNALeu(UUR) in the mutant cell lines carrying the m.3253T→C mutation, as compared with control cell lines. Moreover, an ∼35% reduction in aminoacylation efficiency of tRNALeu(UUR) was observed in the m.3253T→C mutant cells. These alterations in tRNALeu(UUR) metabolism impaired mitochondrial translation, especially for those polypeptides with a high proportion of Leu(UUR) codons, such as ND6. Furthermore, we demonstrated that the m.3253T→C mutation decreased the activities of mitochondrial complexes I and V, markedly diminished mitochondrial ATP levels and membrane potential, and increased the production of reactive oxygen species in the cells. In conclusion, our findings may provide new insights into the pathophysiology of maternally inherited hypertension.
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Affiliation(s)
- Mi Zhou
- From the Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China,; Institute of Genetics and Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Meng Wang
- From the Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China,; Institute of Genetics and Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Ling Xue
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou 325600, Zhejiang, China
| | - Zhi Lin
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou 325600, Zhejiang, China
| | - Qiufen He
- Institute of Genetics and Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Wenwen Shi
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou 325600, Zhejiang, China
| | - Yaru Chen
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou 325600, Zhejiang, China
| | - Xiaofen Jin
- Institute of Genetics and Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Haiying Li
- Department of Cardiology, First Affiliated Hospital, Wenzhou Medical University, Wenzhou 325600, Zhejiang, China
| | - Pingping Jiang
- From the Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China,; Institute of Genetics and Zhejiang University, Hangzhou 310058, Zhejiang, China
| | - Min-Xin Guan
- From the Division of Medical Genetics and Genomics, Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China,; Institute of Genetics and Zhejiang University, Hangzhou 310058, Zhejiang, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Zhejiang University, Hangzhou 310058, Zhejiang, China,; Joint Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Hangzhou 310058, Zhejiang, China.
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Gao Z, Chen Y, Guan MX. Mitochondrial DNA mutations associated with aminoglycoside induced ototoxicity. J Otol 2017; 12:1-8. [PMID: 29937831 PMCID: PMC6011804 DOI: 10.1016/j.joto.2017.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 11/25/2022] Open
Abstract
Aminoglycosides (AmAn) are widely used for their great efficiency against gram-negative bacterial infections. However, they can also induce ototoxic hearing loss, which has affected millions of people around the world. As previously reported, individuals bearing mitochondrial DNA mutations in the 12S rRNA gene, such as m.1555A>G and m.1494C>T, are more prone to AmAn-induced ototoxicity. These mutations cause human mitochondrial ribosomes to more closely resemble bacterial ribosomes and enable a stronger aminoglycoside interaction. Consequently, exposure to AmAn can induce or worsen hearing loss in these individuals. Furthermore, a wide range of severity and penetrance of hearing loss was observed among families carrying these mutations. Studies have revealed that these mitochondria mutations are the primary molecular mechanism of genetic susceptibility to AmAn ototoxicity, though nuclear modifier genes and mitochondrial haplotypes are known to modulate the phenotypic manifestation.
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Affiliation(s)
- Zewen Gao
- Division of Clinical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Ye Chen
- Division of Clinical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Min-Xin Guan
- Division of Clinical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
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42
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Abstract
The report in 1988 that Leber Hereditary Optic Neuropathy (LHON) was the product of mitochondrial DNA (mtDNA) mutations provided the first demonstration of the clinical relevance of inherited mtDNA variation. From LHON studies, the medical importance was demonstrated for the mtDNA showing its coding for the most important energy genes, its maternal inheritance, its high mutation rate, its presence in hundreds to thousands of copies per cell, its quantitatively segregation of biallelic genotypes during both mitosis and meiosis, its preferential effect on the most energetic tissues including the eye and brain, its wide range of functional polymorphisms that predispose to common diseases, and its accumulation of mutations within somatic tissues providing the aging clock. These features of mtDNA genetics, in combination with the genetics of the 1-2000 nuclear DNA (nDNA) coded mitochondrial genes, is not only explaining the genetics of LHON but also providing a model for understanding the complexity of many common diseases. With the maturation of LHON biology and genetics, novel animal models for complex disease have been developed and new therapeutic targets and strategies envisioned, both pharmacological and genetic. Multiple somatic gene therapy approaches are being developed for LHON which are applicable to other mtDNA diseases. Moreover, the unique cytoplasmic genetics of the mtDNA has permitted the first successful human germline gene therapy via spindle nDNA transfer from mtDNA mutant oocytes to enucleated normal mtDNA oocytes. Such LHON lessons are actively being applied to common ophthalmological diseases like glaucoma and neurological diseases like Parkinsonism.
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43
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Su X, Wang W, Ruan G, Liang M, Zheng J, Chen Y, Wu H, Fahey TJ, Guan M, Teng L. A Comprehensive Characterization of Mitochondrial Genome in Papillary Thyroid Cancer. Int J Mol Sci 2016; 17:ijms17101594. [PMID: 27735863 PMCID: PMC5085627 DOI: 10.3390/ijms17101594] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Revised: 08/17/2016] [Accepted: 09/08/2016] [Indexed: 01/24/2023] Open
Abstract
Nuclear genetic alterations have been widely investigated in papillary thyroid cancer (PTC), however, the characteristics of the mitochondrial genome remain uncertain. We sequenced the entire mitochondrial genome of 66 PTCs, 16 normal thyroid tissues and 376 blood samples of healthy individuals. There were 2508 variations (543 sites) detected in PTCs, among which 33 variations were novel. Nearly half of the PTCs (31/66) had heteroplasmic variations. Among the 31 PTCs, 28 specimens harbored a total of 52 somatic mutations distributed in 44 sites. Thirty-three variations including seven nonsense, 11 frameshift and 15 non-synonymous variations selected by bioinformatic software were regarded as pathogenic. These 33 pathogenic mutations were associated with older age (p = 0.0176) and advanced tumor stage (p = 0.0218). In addition, they tended to be novel (p = 0.0003), heteroplasmic (p = 0.0343) and somatic (p = 0.0018). The mtDNA copy number increased in more than two-third (46/66) of PTCs, and the average content in tumors was nearly four times higher than that in adjacent normal tissues (p < 0.0001). Three sub-haplogroups of N (A4, B4a and B4g) and eight single-nucleotide polymorphisms (mtSNPs) (A16164G, C16266T, G5460A, T6680C, G9123A, A14587G, T16362C, and G709A) were associated with the occurrence of PTC. Here we report a comprehensive characterization of the mitochondrial genome and demonstrate its significance in pathogenesis and progression of PTC. This can help to clarify the molecular mechanisms underlying PTC and offer potential biomarkers or therapeutic targets for future clinical practice.
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Affiliation(s)
- Xingyun Su
- Department of Surgical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Weibin Wang
- Department of Surgical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Guodong Ruan
- Department of Oncology, the Second Hospital of Shaoxing, Shaoxing 312000, China.
| | - Min Liang
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Jing Zheng
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Ye Chen
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Huiling Wu
- Department of Plastic Surgery, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
| | - Thomas J Fahey
- Department of Surgery, New York Presbyterian Hospital and Weill Medical College of Cornell University, New York, NY 10021, USA.
| | - Minxin Guan
- Institute of Genetics, School of Medicine, Zhejiang University, Hangzhou 310058, China.
| | - Lisong Teng
- Department of Surgical Oncology, First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China.
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Xue L, Wang M, Li H, Wang H, Jiang F, Hou L, Geng J, Lin Z, Peng Y, Zhou H, Yu H, Jiang P, Mo JQ, Guan MX. Mitochondrial tRNA mutations in 2070 Chinese Han subjects with hypertension. Mitochondrion 2016; 30:208-21. [PMID: 27544295 DOI: 10.1016/j.mito.2016.08.008] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 07/21/2016] [Accepted: 08/16/2016] [Indexed: 12/28/2022]
Abstract
BACKGROUND Mitochondria have the profound impact on vascular function in both health and disease. However, mitochondrial genetic determinants for the development of hypertension remain poorly explored. METHODS AND RESULTS The Sanger sequence analysis of 22 mitochondrial tRNA genes were performed in a cohort of 2070 Han Chinese hypertensive and 512 control subjects. This analysis identified 165 variants among 22 tRNA genes. These variants were evaluated for the pathogenicity using the following criteria: (1) present in <1% of the controls; (2) evolutional conservation; (3) potential structural and functional alterations. We identified 47 (5 known and 42 novel/putative) hypertension-associated tRNA variants in 80 hypertensive subjects. These variants could have potential structural alterations and functional significance of tRNAs. By using lymphoblastoid cell lines derived from 6 probands carrying one of 6 represented variants (tRNA(Ala) 5655T>C, tRNA(Gly) 10003T>C, tRNA(Leu(UUR)) 3253T>C, tRNA(Asp) 7551A>G, tRNA(Glu) 14692A>G, tRNA(Thr) 15909A>G) and 6 control subjects lacking these variants, we showed marked reductions in the steady-state level of corresponding 5 tRNAs, but not tRNA(Thr), in mutant cell lines, compared with control cells lines. The various decreases in the activities of complexes I, III and IV were observed in mutant cells carrying one of five tRNA variants, except tRNA(Thr) 15909A>G variant. The deficient respirations were responsible for the decrease in the mitochondrial ATP production and increasing production of reactive oxygen species in mutant cell lines carrying one of five tRNA variants. CONCLUSION Mitochondrial tRNA variants are the important causes of hypertension, accounting for 3.9% cases of 2070 Han Chinese hypertensive subjects. Our findings may provide new insights into the pathophysiology of hypertension that were manifested by mitochondrial dysfunction.
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Affiliation(s)
- Ling Xue
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Meng Wang
- Institute of Genetics, Zhejiang University, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Haiying Li
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Department of Cardiology, The First Affiliated Hospital, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Heng Wang
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Feng Jiang
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lingling Hou
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Junwei Geng
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Zhi Lin
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Yanyan Peng
- Institute of Genetics, Zhejiang University, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Hong Zhou
- Institute of Genetics, Zhejiang University, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Han Yu
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Pingping Jiang
- Institute of Genetics, Zhejiang University, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jun Qin Mo
- Department of Pathology, Rady Children's Hospital, University of California San Diego School of Medicine, San Diego, CA, USA
| | - Min-Xin Guan
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China; Institute of Genetics, Zhejiang University, Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China; Division of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China; Joining Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang, China.
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45
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Jiang P, Liang M, Zhang C, Zhao X, He Q, Cui L, Liu X, Sun YH, Fu Q, Ji Y, Bai Y, Huang T, Guan MX. Biochemical evidence for a mitochondrial genetic modifier in the phenotypic manifestation of Leber's hereditary optic neuropathy-associated mitochondrial DNA mutation. Hum Mol Genet 2016; 25:3613-3625. [PMID: 27427386 DOI: 10.1093/hmg/ddw199] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 06/08/2016] [Accepted: 06/21/2016] [Indexed: 02/01/2023] Open
Abstract
Leber's hereditary optic neuropathy (LHON) is the most common mitochondrial disease. Mitochondrial modifiers are proposed to modify the phenotypic expression of primary LHON-associated mitochondrial DNA (mtDNA) mutations. In this study, we demonstrated that the LHON susceptibility allele (m.14502T > C, p. 58I > V) in the ND6 gene modulated the phenotypic expression of primary LHON-associated m.11778G > A mutation. Twenty-two Han Chinese pedigrees carrying m.14502T > C and m.11778G > A mutations exhibited significantly higher penetrance of optic neuropathy than those carrying only m.11778G > A mutation. We performed functional assays using the cybrid cell models, generated by fusing mtDNA-less ρo cells with enucleated cells from LHON patients carrying both m.11778G > A and m.14502T > C mutations, only m.14502T > C or m.11778G > A mutation and a control belonging to the same mtDNA haplogroup. These cybrids cell lines bearing m.14502T > C mutation exhibited mild effects on mitochondrial functions compared with those carrying only m.11778G > A mutation. However, more severe mitochondrial dysfunctions were observed in cell lines bearing both m.14502T > C and m.11778G > A mutations than those carrying only m.11778G > A or m.14502T > C mutation. In particular, the m.14502T > C mutation altered assemble of complex I, thereby aggravating the respiratory phenotypes associated with m.11778G > A mutation, resulted in a more defective complex I. Furthermore, more reductions in the levels of mitochondrial ATP and increasing production of reactive oxygen species were also observed in mutant cells bearing both m.14502T > C and m.11778G > A mutation than those carrying only 11778G > A mutation. Our findings provided new insights into the pathophysiology of LHON that were manifested by interaction between primary and secondary mtDNA mutations.
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Affiliation(s)
- Pingping Jiang
- Divsion of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Min Liang
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Department of Clinical Laboratory, The First Affiliated Hospital.,School of Ophthalmology and Optometry
| | - Chaofan Zhang
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaoxu Zhao
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Qiufen He
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Limei Cui
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Xiaoling Liu
- School of Ophthalmology and Optometry.,Attardi Institute of Mitochondrial Biomedicine, School of Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang 325035, China
| | - Yan-Hong Sun
- Department of Ophthalmology, Beijing University of Chinese Medicine and Pharmacology, Beijing 100029, China
| | - Qun Fu
- Department of Ophthalmology, The Third Affiliated Hospital, Xinxiang Medical College, Xinxiang, Henan 45300, China
| | - Yanchun Ji
- Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Yidong Bai
- Department of Cellular & Structural Biology, University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, OH 45229, USA
| | - Min-Xin Guan
- Divsion of Medical Genetics and Genomics, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China .,Institute of Genetics, Zhejiang University and Department of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China.,Joining Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang 310058, China
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46
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Lv F, Qian G, You W, Lin H, Wang XF, Qiu GS, Jiang YS, Pang LX, Kang YM, Jia BF, Xu JZ, Yu Y. Variants in mitochondrial tRNA gene may not be associated with thyroid carcinoma. Balkan J Med Genet 2016; 18:59-64. [PMID: 27785398 PMCID: PMC5026273 DOI: 10.1515/bjmg-2015-0090] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Thyroid cancer is a very common form of endocrine system malignancy. To date, the molecular mechanism underlying thyroid cancer remains poorly understood. Studies of oncocytic tumors have led to a hypothesis which proposes that defects in oxidative phosphorylation (OX- PHOS) may result in a compensatory increase in mitochondrial replication and gene expression. As a result, mitochondrial DNA (mtDNA) mutation analysis has become a useful tool to explore the molecular basis of this disease. Among these mutations, mitochondrial transfer RNAs (mttRNAs) are the hot spots for pathogenic mutations associated with thyroid cancer. However, due to its high mutation rate, the role of mt-tRNA variants in thyroid cancer is still controversial. To address this problem, in this study, we reassessed seven reported mt-tRNA variants: tRNAAsp G7521A, tRNAArg T10411C and T10463C, tRNALeu(CUN) A12308G, tRNAIle G4292C and C4312T, and tRNAAla T5655C, in clinical manifestations of thyroid cancer. We first performed the phylogenetic conservation analysis for these variants; moreover, we used a bioinformatic tool to compare the minimum free energy (G) of mt-tRNA with and without mutations. Most strikingly, none of these variants caused the significant change of the G between the wild-type and the mutant form, suggesting that they may not play an important roles in thyroid cancer. In addition, we screened the frequency of the “pathogenic” A12308G alternation in 300 patients with thyroid cancer and 200 healthy controls. We found that there were five patients and three control subjects carrying this variant. It seemed that the A12308G variant may be a common polymorphism in the human population. Taken together, our study indicated that variants in mt-tRNA genes may not play active roles in patients with thyroid cancer.
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Affiliation(s)
- F Lv
- Department of Breast Surgery, Henan Provincial People’s Hospital, Zhengzhou, People’s Republic of China
| | - G Qian
- Department of Endocrinology, Ningbo Fourth Hospital, Xiangshan, People’s Republic of China
| | - W You
- Department of Breast Surgery, Henan Provincial People’s Hospital, Zhengzhou, People’s Republic of China
| | - H Lin
- College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - XF Wang
- College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - GS Qiu
- Department of Endocrinology, Ningbo Fourth Hospital, Xiangshan, People’s Republic of China
| | - YS Jiang
- Department of Endocrinology, Ningbo Fourth Hospital, Xiangshan, People’s Republic of China
| | - LX Pang
- College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, People’s Republic of China
| | - YM Kang
- School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, People’s Republic of China
| | - BF Jia
- School of Basic Medical Sciences, Inner Mongolia Medical University, Hohhot, People’s Republic of China
| | - JZ Xu
- Department of Clinical Pharmacy, the Affiliated Wenling Hospital of Wenzhou Medial University, Wenling, People’s Republic of China
| | - Y Yu
- Department of Breast Surgery, Henan Provincial People’s Hospital, Zhengzhou, People’s Republic of China
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47
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Allele-specific PCR for detecting the deafness-associated mitochondrial 12S rRNA mutations. Gene 2016; 591:148-152. [PMID: 27397648 DOI: 10.1016/j.gene.2016.07.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/22/2016] [Accepted: 07/05/2016] [Indexed: 01/19/2023]
Abstract
Mutations in mitochondrial 12S rRNA (MT-RNR1) are the important causes of sensorineural hearing loss. Of these mutations, the homoplasmic m.1555A>G or m.1494C>T mutation in the highly conserved A-site of MT-RNR1 gene has been found to be associated with both aminoglycoside-induced and non-syndromic hearing loss in many families worldwide. Since the m.1555A>G and m.1494C>T mutations are sensitive to ototoxic drugs, therefore, screening for the presence of these mutations is important for early diagnosis and prevention of deafness. For this purpose, we recently developed a novel allele-specific PCR (AS-PCR) which is able to simultaneously detect these mutations. To assess its accuracy, in this study, we employed this method to screen the frequency of m.1555A>G and m.1494C>T mutations in 200 deafness patients and 120 healthy subjects. Consequently, four m.1555A>G and four m.1494C>T mutations were identified; among these, only one patient with the m.1494C>T mutation had an obvious family history of hearing loss. Strikingly, clinical evaluation showed that this family exhibited a high penetrance of hearing loss. In particular, the penetrances of hearing loss were 80% with the aminoglycoside included and 20% when excluded. PCR-Sanger sequencing of the mitochondrial genomes confirmed the presence of the m.1494C>T mutation and identified a set of polymorphisms belonging to mitochondrial haplogroup A. However, the lack of functional variants in mitochondrial and nuclear modified genes (GJB2 and TRMU) in this family indicated that mitochondrial haplogroup and nuclear genes may not play important roles in the phenotypic expression of the m.1494C>T mutation. Thus, other modification factors, such as environmental factor, aminoglycosides or epigenetic modification may have contributed to the high penetrance of hearing loss in this family. Taken together, our data showed that this assay is an effective approach that could be used for detection the deafness-associated MT-RNR1 mutations.
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48
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A Hypertension-Associated tRNAAla Mutation Alters tRNA Metabolism and Mitochondrial Function. Mol Cell Biol 2016; 36:1920-30. [PMID: 27161322 PMCID: PMC4936059 DOI: 10.1128/mcb.00199-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 05/04/2016] [Indexed: 01/11/2023] Open
Abstract
In this report, we investigated the pathophysiology of a novel hypertension-associated mitochondrial tRNAAla 5655A → G (m.5655A → G) mutation. The destabilization of a highly conserved base pairing (A1-U72) at the aminoacyl acceptor stem by an m.5655A → G mutation altered the tRNAAla function. An in vitro processing analysis showed that the m.5655A → G mutation reduced the efficiency of tRNAAla precursor 5′ end cleavage catalyzed by RNase P. By using cybrids constructed by transferring mitochondria from lymphoblastoid cell lines derived from a Chinese family into mitochondrial DNA (mtDNA)-less (ρo) cells, we showed a 41% reduction in the steady-state level of tRNAAla in mutant cybrids. The mutation caused an improperly aminoacylated tRNAAla, as suggested by aberrantly aminoacylated tRNAAla and slower electrophoretic mobility of mutated tRNA. A failure in tRNAAla metabolism contributed to variable reductions in six mtDNA-encoded polypeptides in mutant cells, ranging from 21% to 37.5%, with an average of a 29.1% reduction, compared to levels of the controls. The impaired translation caused reduced activities of mitochondrial respiration chains. Furthermore, marked decreases in the levels of mitochondrial ATP and membrane potential were observed in mutant cells. These caused increases in the production of reactive oxygen species in the mutant cybrids. The data provide evidence for the association of the tRNAAla 5655A → G mutation with hypertension.
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49
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Sun GJ, He F, Yao HM, Han ZY, Lu WJ, Chen XJ, Wang ZB, Qiu CG. Assessment of mitochondrial DNA mutations in Chinese family with essential hypertension. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 27:1740-1741. [PMID: 25242182 DOI: 10.3109/19401736.2014.961148] [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: 06/03/2023]
Abstract
Mitochondrial DNA (MtDNA) mutations played an important role in the development of essential hypertension. Mitochondrial tRNA point mutations, caused the failure in tRNA metabolism, responsible for the pathogenesis of this complex disease. In this study, we evaluated the possible role of the 4329C >G mutation in the clinical expression of hypertension in a Chinese family. Analysis of the complete mtDNA sequence variants showed that other mutations may play synergic roles in the phenotypic manifestation of hypertension. In addition, other potential pitfalls were also discussed in this context.
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Affiliation(s)
- Guo-Ju Sun
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Fei He
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Hai-Mu Yao
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Zhan-Ying Han
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Wen-Jie Lu
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Xiao-Jie Chen
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Zheng-Bin Wang
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
| | - Chun-Guang Qiu
- a Department of Cardiology , The First Affiliated Hospital of Zhengzhou University , Zhengzhou , Henan , P.R. China
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Liu Y, Li Y, Wang X, Ma Q, Zhu C, Li Z, Yin T, Yang J, Chen Y, Guan M. Mitochondrial tRNA mutations in Chinese hypertensive individuals. Mitochondrion 2016; 28:1-7. [PMID: 26923935 DOI: 10.1016/j.mito.2016.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2013] [Revised: 12/23/2015] [Accepted: 02/24/2016] [Indexed: 10/22/2022]
Abstract
PURPOSE Hypertension is a very important risk factor for cardiac vascular disease. The previous studies showed that mitochondrial DNA mutations are associated with cardiovascular disease, including hypertension. METHODS In this study we did systematical analysis on the total 22 mitochondrial tRNAs and the clinical, genetic and molecular changes of 140 Chinese hypertension and 124 controls. RESULTS This analysis identified 22 nucleotide changes among 15 different tRNA genes. There are 15 mutations with CI (Conservation index) larger than 75%. Of these, there are 26 patients with CI larger than 75% in the HTN group, higher than the 6 subjects in the control group (P=0.00). The tRNA(Phe) G586A, tRNA(Lys) G8313A and tRNA(His) G12147A mutations create highly conservative base-pairings on the D-stem, tRNA(Lys) G8342A on the T-stem, tRNA(Phe) T616C, tRNA(Ala) T5628C, tRNA(Tyr) G5856A and tRNA(Thr) A15924G on the AC stem, tRNA(Leu(CUN)) G12300A on the AC loop, tRNA(Met) C4467T, tRNA(Trp) T5578C, tRNA(Lys) A8296G, tRNA(Arg) T10463C and tRNA(Thr) C15891T on ACC stem, and tRNA(Ser(UCN)) C7492T on D-A junction, while the other tRNA variants were polymorphisms. The pedigrees of PLAH78 carrying the T5578C, PLAH84 carrying the C4467T, PLAH60 carrying the T5628C and PLAH118 carrying the C7492T mutation exhibited maternal transmission of essential hypertension. Sequence analysis of their mitochondrial genomes revealed the presence of T5578C, C4467T, T5628C or C7492T mutations but the absence of other functionally significant mutations in all matrilineal relatives of these families. CONCLUSIONS These tRNAs mutations, associated with altered structures of tRNAs and mitochondrial dysfunction, may contribute to the hypertension in Chinese population. A lot of work still should be done for the mechanism and functional effect of the mtDNA mutation on hypertension.
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Affiliation(s)
- Yuqi Liu
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Yang Li
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Xin Wang
- Department of Health Statistics, Fourth Military Medical University, Chinese PLA Police Force Center for Disease Control and Prevention, Xi'an, Shanxi Province, China
| | - Qinha Ma
- Department of cardiology, Yishui Center hospital of Shandong Province, Linyi, China
| | - Chao Zhu
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Zongbin Li
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Tong Yin
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Jie Yang
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China
| | - Yundai Chen
- Department of Cardiology, Chinese PLA General Hospital, Beijing, China.
| | - Minxin Guan
- Institute of Genetics, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang, China; Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA; Division of Pathology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA.
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