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Chermakani P, Gowri P, Mahesh Kumar S, Sundaresan P. Exploring mito-nuclear genetic factors in Leber's hereditary optic neuropathy: insights from comprehensive profiling of unique cases. EXCLI JOURNAL 2023; 22:1077-1091. [PMID: 38054206 PMCID: PMC10694345 DOI: 10.17179/excli2023-6297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 10/06/2023] [Indexed: 12/07/2023]
Abstract
Leber's hereditary optic neuropathy (LHON) is a mitochondrial complex I disorder and causes inexorable painless vision loss. Recent studies from India reported that a significant proportion of LHON patients lack primary mitochondrial DNA mutations, suggesting that alternative genetic factors contribute to disease development. Therefore, this study investigated the genetic profile of LHON-affected individuals in order to understand the role of mito-nuclear genetic factors in LHON. A total of thirty probands displaying symptoms consistent with LHON have undergone whole mitochondrial and whole exome sequencing. Interestingly, whole mtDNA sequencing revealed primary mtDNA mutations in 30 % of the probands (n=9), secondary mtDNA mutations in 40 % of the probands (n=12) and no mitochondrial changes in 30 % of individuals (n=9). Further, WES analysis determined pathogenic mutations in 11 different nuclear genes, especially in cases with secondary mtDNA mutations (n=6) or no mtDNA mutations (n=6). These findings provide valuable insight into LHON genetic predisposition, particularly in cases lacking primary mtDNA mutations. See also Figure 1(Fig. 1).
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Affiliation(s)
- Prakash Chermakani
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
- Department of Molecular Biology, Aravind Medical Research Foundation - Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India
| | - Poigaialwar Gowri
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
- Department of Molecular Biology, Aravind Medical Research Foundation - Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India
| | | | - Periasamy Sundaresan
- Department of Molecular Genetics, Aravind Medical Research Foundation, Madurai, Tamil Nadu, India
- Department of Molecular Biology, Aravind Medical Research Foundation - Affiliated to Alagappa University, Karaikudi, Tamil Nadu, India
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Yao S, Zhang X, Jin X, Yang M, Li Y, Yang L, Xu J, Lei B. Proteomic Profiling Reveals Increased Glycolysis, Decreased Oxidoreductase Activity and Fatty Acid Degradation in Skin Derived Fibroblasts from LHON Patients Bearing m.G11778A. Biomolecules 2022; 12:1568. [PMID: 36358916 PMCID: PMC9687919 DOI: 10.3390/biom12111568] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/23/2022] [Accepted: 10/24/2022] [Indexed: 04/28/2024] Open
Abstract
LHON is a common blinding inherited optic neuropathy caused by mutations in mitochondrial genes. In this study, by using skin fibroblasts derived from LHON patients with the most common m.G11778A mutation and healthy objects, we performed proteomic analysis to document changes in molecular proteins, signaling pathways and cellular activities. Furthermore, the results were confirmed by functional studies. A total of 860 differential expression proteins were identified, containing 624 upregulated and 236 downregulated proteins. Bioinformatics analysis revealed increased glycolysis in LHON fibroblasts. A glycolysis stress test showed that ECAR (extra-cellular acidification rate) values increased, indicating an enhanced level of glycolysis in LHON fibroblasts. Downregulated proteins were mainly enriched in oxidoreductase activity. Cellular experiments verified high levels of ROS in LHON fibroblasts, indicating the presence of oxidative damage. KEGG analysis also showed the metabolic disturbance of fatty acid in LHON cells. This study provided a proteomic profile of skin fibroblasts derived from LHON patients bearing m.G11778A. Increased levels of glycolysis, decreased oxidoreductase activity and fatty acid metabolism could represent the in-depth mechanisms of mitochondrial dysfunction mediated by the mutation. The results provided further evidence that LHON fibroblast could be an alternative model for investigating the devastating disease.
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Affiliation(s)
- Shun Yao
- Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Xiaoli Zhang
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Xiuxiu Jin
- Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Mingzhu Yang
- Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Ya Li
- Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
| | - Lin Yang
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Jin Xu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
| | - Bo Lei
- Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Henan Eye Hospital, Henan Provincial People’s Hospital, Zhengzhou 450003, China
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou 450052, China
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Zhao LJ, Zhang ZL, Fu Y. Novel m.4268T>C mutation in the mitochondrial tRNA Ile gene is associated with hearing loss in two Chinese families. World J Clin Cases 2022; 10:205-216. [PMID: 35071519 PMCID: PMC8727281 DOI: 10.12998/wjcc.v10.i1.205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 07/23/2021] [Accepted: 11/29/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Herein, we report the genetic, clinical, molecular and biochemical features of two Han Chinese pedigrees with suggested maternally transmitted non-syndromic hearing loss.
AIM To investigate the pathophysiology of hearing loss associated with mitochondrial tRNA mutations.
METHODS Sixteen subjects from two Chinese families with hearing loss underwent clinical, genetic, molecular, and biochemical evaluations. Biochemical characterizations included the measurements of tRNA levels using lymphoblastoid cell lines derived from five affected matrilineal relatives of these families and three control subjects.
RESULTS Three of the 16 matrilineal relatives in these families exhibited a variable seriousness and age-at-onset (8 years) of deafness. Analysis of mtDNA mutation identified the novel homoplasmic tRNAIle 4268T>C mutation in two families both belonging to haplogroup D4j. The 4268T>C mutation is located in a highly conserved base pairing (6U–67A) of tRNAIle. The elimination of 6U–67A base-pairing may change the tRNAIle metabolism. Functional mutation was supported by an approximately 64.6% reduction in the level of tRNAIle observed in the lymphoblastoid cell lines with the 4268T>C mutation, in contrast to the wild-type cell lines. The reduced level of tRNA was below the proposed threshold for normal respiration in lymphoblastoid cells. However, genotyping analysis did not detect any mutations in the prominent deafness-causing gene GJB2 in any members of the family.
CONCLUSION These data show that the novel tRNAIle 4268T>C mutation was involved in maternally transmitted deafness. However, epigenetic, other genetic, or environmental factors may be attributed to the phenotypic variability. These findings will be useful for understanding families with maternally inherited deafness.
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Affiliation(s)
- Li-Jing Zhao
- Department of Otorhinolaryngology Head and Neck Surgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang Province, China
| | - Zhi-Li Zhang
- Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310003, Zhejiang Province, China
| | - Yong Fu
- Department of Otorhinolaryngology Head and Neck Surgery, The Children’s Hospital, Zhejiang University School of Medicine, Hangzhou 310009, Zhejiang Province, China
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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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Li JK, Li W, Gao FJ, Qu SF, Hu FY, Zhang SH, Li LL, Wang ZW, Qiu Y, Wang LS, Huang J, Wu JH, Chen F. Mutation Screening of mtDNA Combined Targeted Exon Sequencing in a Cohort With Suspected Hereditary Optic Neuropathy. Transl Vis Sci Technol 2020; 9:11. [PMID: 32855858 PMCID: PMC7422818 DOI: 10.1167/tvst.9.8.11] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 04/23/2020] [Indexed: 12/02/2022] Open
Abstract
Purpose Leber hereditary optic neuropathy (LHON) and autosomal dominant optic atrophy (ADOA) are the two commonest forms of hereditary optic neuropathy. The aim of this study was to comprehensively investigate the incidence and spectrum of mutations in patients with suspected hereditary optic neuropathy by combining mitochondrial DNA (mtDNA) genome-wide and targeted exon sequencing. Methods A cohort of 1101 subjects were recruited to participate in the study, comprising 177 families (177 probands and their family members, a total of 537 subjects, including 254 patients) and 164 sporadic cases with suspected hereditary optic neuropathy, and 400 unrelated control subjects for genetic analysis: all subjects (including control subjects) underwent a comprehensive ophthalmologic examination and were subjected to sequencing analysis of mtDNA genome-wide and targeted exon. Overall, targeted exon sequencing was used to screen 792 genes associated with common hereditary eye diseases, and the mtDNA genome-wide were screened by next-generation sequencing. Results We found variants detected in 168 (40.2%, 168/418) of the 418 patients screened. Among these, 132 cases (78.6%, 132/168) were detected with known LHON disease-causing mtDNA variants; 40 cases (23.8%, 40/168) were detected with nuclear DNA (ntDNA) variants, which included 36 cases (21.4%, 36/168) with detected OPA1 mutations, 4 patients (2.4%, 4/168) with detected OPA3 mutations, and 2 patients (1.2%, 2/168) with detected TMEM126A homozygous mutation. Coexistence variation (mtDNA/mtDNA [n = 16], ntDNA/ntDNA [n = 4], mtDNA/ntDNA [n = 7]) was found in 27 patients (16.4%, 27/165), including mtDNA/ntDNA coexistence variation that was detected in seven patients. Among these ntDNA mutations, 38 distinct disease-causing variants, including autosomal recessive heterozygous mutations, were detected, which included 22 novel variants and two de novo variants. Total haplogroup distribution showed that 34.5% (29/84) and 28.6% (24/84) of the affected subjects with m.11778G>A belonged to haplogroup D and M, with a high frequency of subhaplogroups D4, D5, and M7. Conclusions The LHON-mtDNA mutations are the commonest genetic defects in this Chinese cohort, followed by the OPA1 mutations. To our knowledge, this is the first comprehensive study of LHON, ADOA, and autosomal recessive optic atrophy combined with mtDNA genome-wide and targeted exon sequencing, as well as haplogroup analysis, in a large cohort of Chinese patients with suspected hereditary optic neuropathy. Our findings provide a powerful basis for genetic counseling in patients with suspected hereditary optic neuropathy. Translational Relevance We applied mtDNA genome-wide sequencing combined with panel-based targeted exon sequencing to explore the pathogenic variation spectrum and genetic characteristics of patients with suspected hereditary optic neuropathy, providing a comprehensive research strategy for clinical assistant diagnosis, treatment, and genetic counseling.
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Affiliation(s)
- Jian-Kang Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong.,BGI-Shenzhen, Shenzhen, China
| | - Wei Li
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Feng-Juan Gao
- Eye Institute, Eye, Ear, Nose and Throat Hospital, College of Medicine, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
| | - Shou-Fang Qu
- National Institutes for Food and Drug Control, Tiantan Xili Dongcheng District, Beijing, China
| | - Fang-Yuan Hu
- Eye Institute, Eye, Ear, Nose and Throat Hospital, College of Medicine, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
| | - Sheng-Hai Zhang
- Eye Institute, Eye, Ear, Nose and Throat Hospital, College of Medicine, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
| | - Li-Li Li
- National Institutes for Food and Drug Control, Tiantan Xili Dongcheng District, Beijing, China
| | - Zi-Wei Wang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,BGI-Shenzhen, Shenzhen, China
| | - Yong Qiu
- BGI-Shenzhen, Shenzhen, China.,MGI, BGI-Shenzhen, Shenzhen, China
| | - Lu-Sheng Wang
- Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong.,BGI-Shenzhen, Shenzhen, China
| | - Jie Huang
- National Institutes for Food and Drug Control, Tiantan Xili Dongcheng District, Beijing, China
| | - Ji-Hong Wu
- Eye Institute, Eye, Ear, Nose and Throat Hospital, College of Medicine, Fudan University, Shanghai, China.,Shanghai Key Laboratory of Visual Impairment and Restoration, Science and Technology Commission of Shanghai Municipality, Shanghai, China
| | - Fang Chen
- BGI-Shenzhen, Shenzhen, China.,MGI, BGI-Shenzhen, Shenzhen, China
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Wassmer SJ, De Repentigny Y, Sheppard D, Lagali PS, Fang L, Coupland SG, Kothary R, Guy J, Hauswirth WW, Tsilfidis C. XIAP Protects Retinal Ganglion Cells in the Mutant ND4 Mouse Model of Leber Hereditary Optic Neuropathy. Invest Ophthalmol Vis Sci 2020; 61:49. [PMID: 32735323 PMCID: PMC7425697 DOI: 10.1167/iovs.61.8.49] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Purpose Leber hereditary optic neuropathy (LHON) is a genetic form of vision loss that occurs primarily owing to mutations in the nicotinamide adenine dinucleotide dehydrogenase (ND) subunits that make up complex I of the electron transport chain. LHON mutations result in the apoptotic death of retinal ganglion cells. We tested the hypothesis that gene therapy with the X-linked inhibitor of apoptosis (XIAP) would prevent retinal ganglion cell apoptosis and reduce disease progression in a vector-induced mouse model of LHON that carries the ND4 mutation. Methods Adeno-associated virus (AAV) encoding full length hemagglutinin-tagged XIAP (AAV2.HA-XIAP) or green fluorescent protein (AAV2.GFP) was injected into the vitreous of DBA/1J mice. Two weeks later, the LHON phenotype was induced by AAV delivery of mutant ND4 (AAV2.mND4FLAG) to the vitreous. Retinal function was assessed by pattern electroretinography. Optic nerves were harvested at 4 months, and the effects of XIAP therapy on nerve fiber layer and optic nerve integrity were evaluated using immunohistochemistry, transmission electron microscopy and magnetic resonance imaging. Results During LHON disease progression, retinal ganglion cell axons are lost. Apoptotic cell bodies are seen in the nuclei of astrocytes or oligodendrocytes in the optic nerve, and there is thinning of the optic nerve and the nerve fiber layer of the retina. At 4 months after disease onset, XIAP gene therapy protects the nerve fiber layer and optic nerve architecture by preserving axon health. XIAP also decreases nuclear fragmentation in resident astrocytes or oligodendrocytes and decreases glial cell infiltration. Conclusions XIAP therapy improves optic nerve health and delays disease progression in LHON.
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Li K, Wu L, Liu J, Lin W, Qi Q, Zhao T. Maternally Inherited Diabetes Mellitus Associated with a Novel m.15897G>A Mutation in Mitochondrial tRNA Thr Gene. J Diabetes Res 2020; 2020:2057187. [PMID: 32083134 PMCID: PMC7011485 DOI: 10.1155/2020/2057187] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/06/2019] [Accepted: 12/26/2019] [Indexed: 12/17/2022] Open
Abstract
We report here the clinical, genetic, and molecular characteristics of type 2 diabetes in a Chinese family. There are differences in the severity and age of onset in diabetes among these families. By molecular analysis of the complete mitochondrial genome in this family, we identified the homoplasmic m.15897G>A mutation underwent sequence analysis of whole mitochondrial DNA genome, which localized at conventional position ten of tRNAThr, and distinct sets of mtDNA polymorphisms belonging to haplogroup D4b1. This mutation has been implicated to be important for tRNA identity and stability. Using cybrid cell models, the decreased efficiency of mitochondrial tRNAThr levels caused by the m.15897G>A mutation results in respiratory deficiency, protein synthesis and assembly, mitochondrial ATP synthesis, and mitochondrial membrane potential. These mitochondrial dysfunctions caused an increase in the production of reactive oxygen species in the mutant cell lines. These data provide a direct evidence that a novel tRNA mutation was associated with T2DM. Thus, our findings provide a new insight into the understanding of pathophysiology of maternally inherited diabetes.
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Affiliation(s)
- Ke Li
- Department of Plastic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215006, China
- Department of Plastic and Burn Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Lijun Wu
- Department of Plastic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Jianjiang Liu
- Department of Plastic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Wei Lin
- Department of Plastic and Burn Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Qiang Qi
- Department of Plastic and Burn Surgery, The First Affiliated Hospital of Soochow University, Suzhou 215006, China
| | - Tianlan Zhao
- Department of Plastic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou 215006, China
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Klink GV, Golovin AV, Bazykin GA. Substitutions into amino acids that are pathogenic in human mitochondrial proteins are more frequent in lineages closely related to human than in distant lineages. PeerJ 2017; 5:e4143. [PMID: 29250469 PMCID: PMC5731343 DOI: 10.7717/peerj.4143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 11/16/2017] [Indexed: 11/23/2022] Open
Abstract
Propensities for different amino acids within a protein site change in the course of evolution, so that an amino acid deleterious in a particular species may be acceptable at the same site in a different species. Here, we study the amino acid-changing variants in human mitochondrial genes, and analyze their occurrence in non-human species. We show that substitutions giving rise to such variants tend to occur in lineages closely related to human more frequently than in more distantly related lineages, indicating that a human variant is more likely to be deleterious in more distant species. Unexpectedly, substitutions giving rise to amino acids that correspond to alleles pathogenic in humans also more frequently occur in more closely related lineages. Therefore, a pathogenic variant still tends to be more acceptable in human mitochondria than a variant that may only be fit after a substantial perturbation of the protein structure.
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Affiliation(s)
- Galya V. Klink
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Andrey V. Golovin
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Georgii A. Bazykin
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation
- Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation
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Analysis of Genetic Mutations in a Cohort of Hereditary Optic Neuropathy in Shanghai, China. J Ophthalmol 2017; 2017:6186052. [PMID: 29348930 PMCID: PMC5733633 DOI: 10.1155/2017/6186052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2017] [Revised: 10/29/2017] [Accepted: 11/06/2017] [Indexed: 12/01/2022] Open
Abstract
Purpose To evaluate the clinical classification and characteristics of hereditary optic neuropathy patients in a single center in China. Method Retrospective case study. Patients diagnosed with hereditary optic neuropathy between January 2014 and December 2015 in the neuro-ophthalmology division in Shanghai Eye and ENT Hospital of Fudan University were recruited. Clinical features as well as visual field, brain/orbital MRI, and spectrum domain optical coherence tomography (SD-OCT) were analyzed. Results Eighty-two patients diagnosed by gene test were evaluated, including 66 males and 16 females. The mean age of the patients was 19.4 years (range, 5–46 years). A total of 158 eyes were analyzed, including 6 unilateral, 61 bilateral, and 15 sequential. The median duration of the disease was 0.5 year (range, 0.1–20 years). Genetic test identified 68 patients with Leber hereditary optic neuropathy, 9 with dominant optic neuropathy, and 2 with a Wolfram gene mutation. There was also one case of hereditary spastic paraplegia, spinocerebellar ataxia, and polymicrogyria with optic nerve atrophy, respectively. Conclusion Leber hereditary optic neuropathy is the most common detected type of hereditary optic neuropathy in Shanghai, China. The detection of other autosomal mutations in hereditary optic neuropathy is limited by the currently available technique.
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Ji J, Xu M, Huang Z, Li L, Zheng H, Yang S, Li S, Jin L, Ling X, Xia Y, Lu C, Wang X. Mitochondrial DNA sequencing and large-scale genotyping identifies MT-ND4 gene mutation m.11696G>A associated with idiopathic oligoasthenospermia. Oncotarget 2017; 8:52975-52982. [PMID: 28881787 PMCID: PMC5581086 DOI: 10.18632/oncotarget.17675] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/13/2017] [Indexed: 01/07/2023] Open
Abstract
Genetic variants of mitochondrial DNA (mtDNA) were implicated to be associated with male infertility. Our previous whole mitochondrial genome sequencing and association study has identified two susceptibility mtDNA variants for oligoasthenospermia in Han Chinese men. In this study, we tested promising associations in an extended validation using 670 idiopathic oligoasthenospermia cases and 793 healthy controls to identify additional risk variants. We found that the genetic variant of m.11696G>A showed significantly higher frequency in the case group than that in the control group (odds ratio (OR) 2.21, 95% CI 1.21-4.04) (P=7.90×10−3). To elucidate the exact role of the genetic variants in spermatogenesis, two main sperm parameters (sperm count and motility) were taken into account. We found that m.11696G>A was associated with low sperm motility, with the OR of 2.38 (95 % CI 1.27-4.46) (P =5.22×10−3). These results advance our understanding of the genetic susceptibility to oligoasthenospermia and more functional studies are needed to provide insights into its pathogenic mechanism.
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Affiliation(s)
- Juan Ji
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China.,Department of Children Health Care, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Miaofei Xu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Zhenyao Huang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Lei Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Hongxiang Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Shuping Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Shilin Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200433, China
| | - Xiufeng Ling
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Department of Children Health Care, Nanjing Maternity and Child Health Care Hospital Affiliated to Nanjing Medical University, Nanjing 210029, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Institute of Toxicology, Nanjing Medical University, Nanjing 210029, China.,Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing 210029, China
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Yu L, Wang G. Complete mitochondrial genome of Ctenopharyngodon idella var. Gold grass carp and its intraspecific comparison. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:372-374. [PMID: 27211306 DOI: 10.3109/19401736.2015.1126828] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
We determined the complete mitochondrial genome (Mitogome) of Ctenopharyngodon idella var. gold grass carp (C. idella var.) (Accession No.:KT894100) and compered it with a previously published mitogenome (Accession No.:NC010288.1) of Chinese common grass carp. The total length of mitogenome is 16 609 bp with 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes and a control region. The nucleotide compositions of the L-strand are 31.87% for A, 26.20% for T, 15.68% for G, 26.26% for C. Most of the protein-coding genes began with an ATG start codon except for COX1 and ND3 gene. The sequence similarity was 99.81% between each other. There were 32 variation loci obtained, including of 23 transitions, 7 transversions and 2 INDELs.
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Affiliation(s)
- Lingyun Yu
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation Ministry of Agriculture , Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences , Guangzhou , China
| | - Guangjun Wang
- a Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation Ministry of Agriculture , Pearl River Fisheries Research Institute of Chinese Academy of Fishery Sciences , Guangzhou , China
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