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Chen Z, Chen L, Tan J, Mao Y, Hao M, Li Y, Wang Y, Li J, Wang J, Jin L, Zheng HX. Natural selection shaped the protective effect of the mtDNA lineage against obesity in Han Chinese populations. J Genet Genomics 2024:S1673-8527(24)00129-2. [PMID: 38880354 DOI: 10.1016/j.jgg.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/18/2024]
Abstract
Mitochondria play a key role in lipid metabolism, and mitochondrial DNA (mtDNA) mutations are thus considered to affect obesity susceptibility by altering oxidative phosphorylation and mitochondrial function. In this study, we investigated mtDNA variants that may affect obesity risk in 2,877 Han Chinese individuals from three independent populations. The association analysis of 16 basal mtDNA haplogroups with body mass index (BMI), waist circumference (WC) and waist-to-hip ratio (WHR) revealed that only haplogroup M7 was significantly negatively correlated with all three adiposity-related anthropometric traits in the overall cohort (P=0.003 for BMI, P=1×10-5 for WC, P=0.005 for WHR), which was verified by the analysis of a single population, i.e., the Zhengzhou population. Furthermore, subhaplogroup analysis suggested that M7b1a1 was the most likely haplogroup associated with a decreased obesity risk, and the variation T12811C (causing Y159H in ND5) harbored in M7b1a1 may be the most likely candidate for altering mitochondrial function. Specifically, we found that proportionally more nonsynonymous mutations accumulated in M7b1a1 carriers, indicating that M7b1a1 was either under positive selection or subject to a relaxation of selective constraints. We also found that nuclear variants, especially in DACT2 and PIEZO1, may functionally interact with M7b1a1.
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Affiliation(s)
- Ziwei Chen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Lu Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Jingze Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yizhen Mao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Meng Hao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Yi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Jinxi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China; Research Unit of Dissecting Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China.
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China; Research Unit of Dissecting Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China.
| | - Hong-Xiang Zheng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
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Iverson ENK, Criswell A, Havird JC. Stronger evidence for relaxed selection than adaptive evolution in high-elevation animal mtDNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.20.576402. [PMID: 38328137 PMCID: PMC10849488 DOI: 10.1101/2024.01.20.576402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Mitochondrial (mt) genes are the subject of many adaptive hypotheses due to the key role of mitochondria in energy production and metabolism. One widespread adaptive hypothesis is that selection imposed by life at high elevation leads to the rapid fixation of beneficial alleles in mtDNA, reflected in the increased rates of mtDNA evolution documented in many high-elevation species. However, the assumption that fast mtDNA evolution is caused by positive, rather than relaxed purifying selection has rarely been tested. Here, we calculated the dN/dS ratio, a metric of nonsynonymous substitution bias, and explicitly tested for relaxed selection in the mtDNA of over 700 species of terrestrial vertebrates, freshwater fishes, and arthropods, with information on elevation and latitudinal range limits, range sizes, and body sizes. We confirmed that mitochondrial genomes of high-elevation taxa have slightly higher dN/dS ratios compared to low-elevation relatives. High-elevation species tend to have smaller ranges, which predict higher dN/dS ratios and more relaxed selection across species and clades, while absolute elevation and latitude do not predict higher dN/dS. We also find a positive relationship between body mass and dN/dS, supporting a role for small effective population size leading to relaxed selection. We conclude that higher mt dN/dS among high-elevation species is more likely to reflect relaxed selection due to smaller ranges and reduced effective population size than adaptation to the environment. Our results highlight the importance of rigorously testing adaptive stories against non-adaptive alternative hypotheses, especially in mt genomes.
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Affiliation(s)
- Erik N K Iverson
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Abby Criswell
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
| | - Justin C Havird
- Department of Integrative Biology, the University of Texas at Austin, Austin, TX, United States
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3
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Saha T, Bhowmick B, Sengupta D, Banerjee S, Mitra R, Sarkar A, Chaudhuri T, Bhattacharjee G, Nath S, Roychoudhury S, Sengupta M. No association of the common Asian mitochondrial DNA haplogroups with lung cancer in East Indian population. J Basic Clin Physiol Pharmacol 2023; 34:663-668. [PMID: 35338796 DOI: 10.1515/jbcpp-2021-0352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/02/2022] [Indexed: 11/15/2022]
Abstract
OBJECTIVES Mitochondrial dysfunction has long been associated with the pathogenesis of lung cancer (LC). Mitochondrial DNA (mtDNA) haplogroups have been reported to modify the risk of LC in a few different populations; however, no study has been done among the Indians. Here, we explore the relationship between mtDNA haplogroups and LC in a representative eastern Indian sample set. METHODS Different combinations of six mtDNA SNPs, which define the major Asian mtDNA haplogroups M and N, and their sub-haplogroups D, G, M7, R, and F were genotyped via polymerase chain reaction (PCR) - restriction fragment length polymorphism (RFLP) - sequencing approach in 94 smoker LC patients and 100 healthy smoker controls from an eastern Indian cohort. RESULTS The distribution of 7 mtDNA haplogroups did not show any significant differences between patients and controls (p<0.05). We did not find sub-haplogroup M7 in our study population. CONCLUSIONS Our study is the first to indicate that the major Asian mtDNA haplogroups have no significant (p<0.05) association with LC in East Indian population.
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Affiliation(s)
- Tania Saha
- Department of Genetics, University of Calcutta, Kolkata, West Bengal, India
| | - Bismoy Bhowmick
- Department of Genetics, University of Calcutta, Kolkata, West Bengal, India
| | - Debmalya Sengupta
- Department of Genetics, University of Calcutta, Kolkata, West Bengal, India
| | - Souradeep Banerjee
- Department of Genetics, University of Calcutta, Kolkata, West Bengal, India
| | - Ritabrata Mitra
- Department of Pulmonary medicine (Chest), IPGMER, Kolkata, West Bengal, India
| | - Abhijit Sarkar
- Department of Radiotherapy, SGCCRI, Kolkata, West Bengal, India
| | | | | | - Somsubhra Nath
- Molecular Biology and Basic Research Division, SGCCRI, Kolkata, West Bengal, India
| | | | - Mainak Sengupta
- Department of Genetics, University of Calcutta, Kolkata, West Bengal, India
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4
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Bodenstein DF, Powlowski P, Zachos KA, El Soufi El Sabbagh D, Jeong H, Attisano L, Edgar L, Wallace DC, Andreazza AC. Optimization of differential filtration-based mitochondrial isolation for mitochondrial transplant to cerebral organoids. Stem Cell Res Ther 2023; 14:202. [PMID: 37580812 PMCID: PMC10426050 DOI: 10.1186/s13287-023-03436-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 07/27/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Mitochondrial dysfunction is involved in several diseases ranging from genetic mitochondrial disorders to chronic metabolic diseases. An emerging approach to potentially treat mitochondrial dysfunction is the transplantation of autologous live mitochondria to promote cell regeneration. We tested the differential filtration-based mitochondrial isolation protocol established by the McCully laboratory for use in cellular models but found whole cell contaminants in the mitochondrial isolate. METHODS Therefore, we explored alternative types of 5-μm filters (filters A and B) for isolation of mitochondria from multiple cell lines including HEK293 cells and induced pluripotent stem cells (iPSCs). MitoTracker™ staining combined with flow cytometry was used to quantify the concentration of viable mitochondria. A proof-of-principle mitochondrial transplant was performed using mitoDsRed2-tagged mitochondria into a H9-derived cerebral organoid. RESULTS We found that filter B provided the highest quality mitochondria as compared to the 5-μm filter used in the original protocol. Using this method, mitochondria were also successfully isolated from induced pluripotent stem cells. To test for viability, mitoDsRed2-tagged mitochondria were isolated and transplanted into H9-derived cerebral organoids and observed that mitochondria were engulfed as indicated by immunofluorescent co-localization of TOMM20 and MAP2. CONCLUSIONS Thus, use of filter B in a differential filtration approach is ideal for isolating pure and viable mitochondria from cells, allowing us to begin evaluating long-term integration and safety of mitochondrial transplant using cellular sources.
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Affiliation(s)
- David F Bodenstein
- Department of Pharmacology and Toxicology, University of Toronto, Medical Science Building, Room 4211, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Pavel Powlowski
- Department of Pharmacology and Toxicology, University of Toronto, Medical Science Building, Room 4211, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Kassandra A Zachos
- Department of Pharmacology and Toxicology, University of Toronto, Medical Science Building, Room 4211, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Dana El Soufi El Sabbagh
- Department of Pharmacology and Toxicology, University of Toronto, Medical Science Building, Room 4211, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Hyunjin Jeong
- Department of Pharmacology and Toxicology, University of Toronto, Medical Science Building, Room 4211, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
- Donnelly Centre, University of Toronto, Toronto, ON, Canada
| | - Landon Edgar
- Department of Pharmacology and Toxicology, University of Toronto, Medical Science Building, Room 4211, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada
- Department of Chemistry, University of Toronto, Toronto, ON, Canada
| | - Douglas C Wallace
- Department of Biological Chemistry, Center for Molecular and Mitochondrial Medicine and Genetics, University of California, Irvine, CA, USA
- Division of Human Genetics, Department of Pediatrics, Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, USA
- Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Ana Cristina Andreazza
- Department of Pharmacology and Toxicology, University of Toronto, Medical Science Building, Room 4211, 1 King's College Circle, Toronto, ON, M5S 1A8, Canada.
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada.
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5
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St John JC, Okada T, Andreas E, Penn A. The role of mtDNA in oocyte quality and embryo development. Mol Reprod Dev 2023; 90:621-633. [PMID: 35986715 PMCID: PMC10952685 DOI: 10.1002/mrd.23640] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 09/02/2023]
Abstract
The mitochondrial genome resides in the mitochondria present in nearly all cell types. The porcine (Sus scrofa) mitochondrial genome is circa 16.7 kb in size and exists in the multimeric format in cells. Individual cell types have different numbers of mitochondrial DNA (mtDNA) copy number based on their requirements for ATP produced by oxidative phosphorylation. The oocyte has the largest number of mtDNA of any cell type. During oogenesis, the oocyte sets mtDNA copy number in order that sufficient copies are available to support subsequent developmental events. It also initiates a program of epigenetic patterning that regulates, for example, DNA methylation levels of the nuclear genome. Once fertilized, the nuclear and mitochondrial genomes establish synchrony to ensure that the embryo and fetus can complete each developmental milestone. However, altering the oocyte's mtDNA copy number by mitochondrial supplementation can affect the programming and gene expression profiles of the developing embryo and, in oocytes deficient of mtDNA, it appears to have a positive impact on the embryo development rates and gene expression profiles. Furthermore, mtDNA haplotypes, which define common maternal origins, appear to affect developmental outcomes and certain reproductive traits. Nevertheless, the manipulation of the mitochondrial content of an oocyte might have a developmental advantage.
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Affiliation(s)
- Justin C. St John
- The Mitochondrial Genetics Group, The School of Biomedicine and The Robinson Research InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Takashi Okada
- The Mitochondrial Genetics Group, The School of Biomedicine and The Robinson Research InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Eryk Andreas
- The Mitochondrial Genetics Group, The School of Biomedicine and The Robinson Research InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Alexander Penn
- The Mitochondrial Genetics Group, The School of Biomedicine and The Robinson Research InstituteThe University of AdelaideAdelaideSouth AustraliaAustralia
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Abstract
Mitochondrial optic neuropathies have a leading role in the field of mitochondrial medicine ever since 1988, when the first mutation in mitochondrial DNA was associated with Leber's hereditary optic neuropathy (LHON). Autosomal dominant optic atrophy (DOA) was subsequently associated in 2000 with mutations in the nuclear DNA affecting the OPA1 gene. LHON and DOA are both characterized by selective neurodegeneration of retinal ganglion cells (RGCs) triggered by mitochondrial dysfunction. This is centered on respiratory complex I impairment in LHON and defective mitochondrial dynamics in OPA1-related DOA, leading to distinct clinical phenotypes. LHON is a subacute, rapid, severe loss of central vision involving both eyes within weeks or months, with age of onset between 15 and 35 years old. DOA is a more slowly progressive optic neuropathy, usually apparent in early childhood. LHON is characterized by marked incomplete penetrance and a clear male predilection. The introduction of next-generation sequencing has greatly expanded the genetic causes for other rare forms of mitochondrial optic neuropathies, including recessive and X-linked, further emphasizing the exquisite sensitivity of RGCs to compromised mitochondrial function. All forms of mitochondrial optic neuropathies, including LHON and DOA, can manifest either as pure optic atrophy or as a more severe multisystemic syndrome. Mitochondrial optic neuropathies are currently at the forefront of a number of therapeutic programs, including gene therapy, with idebenone being the only approved drug for a mitochondrial disorder.
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Affiliation(s)
- Valerio Carelli
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy; IRCCS Istituto di Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy.
| | - Chiara La Morgia
- Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy; IRCCS Istituto di Scienze Neurologiche di Bologna, Programma di Neurogenetica, Bologna, Italy
| | - Patrick Yu-Wai-Man
- John van Geest Centre for Brain Repair and MRC Mitochondrial Biology Unit, Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom; Cambridge Eye Unit, Addenbrooke's Hospital, Cambridge University Hospitals, Cambridge, United Kingdom; Moorfields Eye Hospital NHS Foundation Trust, London, United Kingdom; Institute of Ophthalmology, University College London, London, United Kingdom
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7
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Chiaratti MR, Chinnery PF. Modulating mitochondrial DNA mutations: factors shaping heteroplasmy in the germ line and somatic cells. Pharmacol Res 2022; 185:106466. [PMID: 36174964 DOI: 10.1016/j.phrs.2022.106466] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
Until recently it was thought that most humans only harbor one type of mitochondrial DNA (mtDNA), however, deep sequencing and single-cell analysis has shown the converse - that mixed populations of mtDNA (heteroplasmy) are the norm. This is important because heteroplasmy levels can change dramatically during transmission in the female germ line, leading to high levels causing severe mitochondrial diseases. There is also emerging evidence that low level mtDNA mutations contribute to common late onset diseases such as neurodegenerative disorders and cardiometabolic diseases because the inherited mutation levels can change within developing organs and non-dividing cells over time. Initial predictions suggested that the segregation of mtDNA heteroplasmy was largely stochastic, with an equal tendency for levels to increase or decrease. However, transgenic animal work and single-cell analysis have shown this not to be the case during germ-line transmission and in somatic tissues during life. Mutation levels in specific mtDNA regions can increase or decrease in different contexts and the underlying molecular mechanisms are starting to be unraveled. In this review we provide a synthesis of recent literature on the mechanisms of selection for and against mtDNA variants. We identify the most pertinent gaps in our understanding and suggest ways these could be addressed using state of the art techniques.
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Affiliation(s)
- Marcos R Chiaratti
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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8
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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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9
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Müller-Nedebock AC, Pfaff AL, Pienaar IS, Kõks S, van der Westhuizen FH, Elson JL, Bardien S. Mitochondrial DNA variation in Parkinson’s disease: Analysis of “out-of-place” population variants as a risk factor. Front Aging Neurosci 2022; 14:921412. [PMID: 35912088 PMCID: PMC9330142 DOI: 10.3389/fnagi.2022.921412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 06/30/2022] [Indexed: 12/17/2022] Open
Abstract
Mitochondrial DNA (mtDNA), a potential source of mitochondrial dysfunction, has been implicated in Parkinson’s disease (PD). However, many previous studies investigating associations between mtDNA population variation and PD reported inconsistent or contradictory findings. Here, we investigated an alternative hypothesis to determine whether mtDNA variation could play a significant role in PD risk. Emerging evidence suggests that haplogroup-defining mtDNA variants may have pathogenic potential if they occur “out-of-place” on a different maternal lineage. We hypothesized that the mtDNA of PD cases would be enriched for out-of-place variation in genes encoding components of the oxidative phosphorylation complexes. We tested this hypothesis with a unique dataset comprising whole mitochondrial genomes of 70 African ancestry PD cases, two African ancestry control groups (n = 78 and n = 53) and a replication group of 281 European ancestry PD cases and 140 controls from the Parkinson’s Progression Markers Initiative cohort. Significantly more African ancestry PD cases had out-of-place variants than controls from the second control group (P < 0.0125), although this association was not observed in the first control group nor the replication group. As the first mtDNA study to include African ancestry PD cases and to explore out-of-place variation in a PD context, we found evidence that such variation might be significant in this context, thereby warranting further replication in larger cohorts.
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Affiliation(s)
- Amica C. Müller-Nedebock
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council, Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
| | - Abigail L. Pfaff
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | - Ilse S. Pienaar
- Institute of Clinical Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Sulev Kõks
- Perron Institute for Neurological and Translational Science, Nedlands, WA, Australia
- Centre for Molecular Medicine and Innovative Therapeutics, Murdoch University, Murdoch, WA, Australia
| | | | - Joanna L. Elson
- Human Metabolomics, North-West University, Potchefstroom, South Africa
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- South African Medical Research Council, Stellenbosch University Genomics of Brain Disorders Research Unit, Stellenbosch University, Cape Town, South Africa
- *Correspondence: Soraya Bardien,
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10
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Emser SV, Schaschl H, Millesi E, Steinborn R. Extension of Mitogenome Enrichment Based on Single Long-Range PCR: mtDNAs and Putative Mitochondrial-Derived Peptides of Five Rodent Hibernators. Front Genet 2021; 12:685806. [PMID: 35027919 PMCID: PMC8749263 DOI: 10.3389/fgene.2021.685806] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 11/10/2021] [Indexed: 12/14/2022] Open
Abstract
Enriching mitochondrial DNA (mtDNA) for sequencing entire mitochondrial genomes (mitogenomes) can be achieved by single long-range PCR. This avoids interference from the omnipresent nuclear mtDNA sequences (NUMTs). The approach is currently restricted to the use of samples collected from humans and ray-finned fishes. Here, we extended the use of single long-range PCR by introducing back-to-back oligonucleotides that target a sequence of extraordinary homology across vertebrates. The assay was applied to five hibernating rodents, namely alpine marmot, Arctic and European ground squirrels, and common and garden dormice, four of which have not been fully sequenced before. Analysis of the novel mitogenomes focussed on the prediction of mitochondrial-derived peptides (MDPs) providing another level of information encoded by mtDNA. The comparison of MOTS-c, SHLP4 and SHLP6 sequences across vertebrate species identified segments of high homology that argue for future experimentation. In addition, we evaluated four candidate polymorphisms replacing an amino acid in mitochondrially encoded subunits of the oxidative phosphorylation (OXPHOS) system that were reported in relation to cold-adaptation. No obvious pattern was found for the diverse sets of mammalian species that either apply daily or multiday torpor or otherwise cope with cold. In summary, our single long-range PCR assay applying a pair of back-to-back primers that target a consensus sequence motif of Vertebrata has potential to amplify (intact) mitochondrial rings present in templates from a taxonomically diverse range of vertebrates. It could be promising for studying novel mitogenomes, mitotypes of a population and mitochondrial heteroplasmy in a sensitive, straightforward and flexible manner.
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Affiliation(s)
- Sarah V. Emser
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Helmut Schaschl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Eva Millesi
- Department of Behavioral and Cognitive Biology, University of Vienna, Vienna, Austria
| | - Ralf Steinborn
- Genomics Core Facility, VetCore, University of Veterinary Medicine, Vienna, Austria
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11
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Wu Y, Wang XH, Li XH, Song LY, Yu SL, Fang ZC, Liu YQ, Yuan LY, Peng CY, Zhang SY, Cheng W, Ma HC, Wang LF, Tang JM, Wang YF, Ji FY. Common mtDNA variations at C5178a and A249d/T6392C/G10310A decrease the risk of severe COVID-19 in a Han Chinese population from Central China. Mil Med Res 2021; 8:57. [PMID: 34724985 PMCID: PMC8558762 DOI: 10.1186/s40779-021-00351-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 10/21/2021] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Mitochondria have been shown to play vital roles during severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and coronavirus disease 2019 (COVID-19) development. Currently, it is unclear whether mitochondrial DNA (mtDNA) variants, which define mtDNA haplogroups and determine oxidative phosphorylation performance and reactive oxygen species production, are associated with COVID-19 risk. METHODS A population-based case-control study was conducted to compare the distribution of mtDNA variations defining mtDNA haplogroups between healthy controls (n = 615) and COVID-19 patients (n = 536). COVID-19 patients were diagnosed based on molecular diagnostics of the viral genome by qPCR and chest X-ray or computed tomography scanning. The exclusion criteria for the healthy controls were any history of disease in the month preceding the study assessment. MtDNA variants defining mtDNA haplogroups were identified by PCR-RFLPs and HVS-I sequencing and determined based on mtDNA phylogenetic analysis using Mitomap Phylogeny. Student's t-test was used for continuous variables, and Pearson's chi-squared test or Fisher's exact test was used for categorical variables. To assess the independent effect of each mtDNA variant defining mtDNA haplogroups, multivariate logistic regression analyses were performed to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) with adjustments for possible confounding factors of age, sex, smoking and diseases (including cardiopulmonary diseases, diabetes, obesity and hypertension) as determined through clinical and radiographic examinations. RESULTS Multivariate logistic regression analyses revealed that the most common investigated mtDNA variations (> 10% in the control population) at C5178a (in NADH dehydrogenase subunit 2 gene, ND2) and A249d (in the displacement loop region, D-loop)/T6392C (in cytochrome c oxidase I gene, CO1)/G10310A (in ND3) were associated with a reduced risk of severe COVID-19 (OR = 0.590, 95% CI 0.428-0.814, P = 0.001; and OR = 0.654, 95% CI 0.457-0.936, P = 0.020, respectively), while A4833G (ND2), A4715G (ND2), T3394C (ND1) and G5417A (ND2)/C16257a (D-loop)/C16261T (D-loop) were related to an increased risk of severe COVID-19 (OR = 2.336, 95% CI 1.179-4.608, P = 0.015; OR = 2.033, 95% CI 1.242-3.322, P = 0.005; OR = 3.040, 95% CI 1.522-6.061, P = 0.002; and OR = 2.890, 95% CI 1.199-6.993, P = 0.018, respectively). CONCLUSIONS This is the first study to explore the association of mtDNA variants with individual's risk of developing severe COVID-19. Based on the case-control study, we concluded that the common mtDNA variants at C5178a and A249d/T6392C/G10310A might contribute to an individual's resistance to developing severe COVID-19, whereas A4833G, A4715G, T3394C and G5417A/C16257a/C16261T might increase an individual's risk of developing severe COVID-19.
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Affiliation(s)
- Yi Wu
- Department of Medical Biology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xian-Hui Wang
- Institute of Biomedical Research, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Xi-Hua Li
- Department of Medical Biology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Li-Yuan Song
- Department of Medical Biology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Shi-Long Yu
- Institute of Human Respiratory Disease, Xinqiao Hospital, The Army Medical University (Third Military Medical University), 400037, Chongqing, China
| | - Zhi-Cheng Fang
- Department of Emergency Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Yu-Quan Liu
- Department of Geriatric Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Le-Yong Yuan
- Department of Immunology, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Chun-Yan Peng
- Department of Laboratory Medicine, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.,Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Shen-Yi Zhang
- Department of Medical Biology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Wang Cheng
- Department of Medical Biology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Hong-Chao Ma
- Department of Medical Biology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Li-Feng Wang
- Department of Medical Biology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China
| | - Jun-Ming Tang
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
| | - Yun-Fu Wang
- Department of Neurology, Taihe Hospital, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
| | - Fu-Yun Ji
- Department of Medical Biology, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China. .,Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Science, Hubei University of Medicine, Shiyan, 442000, Hubei, China.
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12
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Klink GV, O'Keefe H, Gogna A, Bazykin GA, Elson JL. A broad comparative genomics approach to understanding the pathogenicity of Complex I mutations. Sci Rep 2021; 11:19578. [PMID: 34599203 PMCID: PMC8486755 DOI: 10.1038/s41598-021-98360-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Accepted: 09/01/2021] [Indexed: 12/29/2022] Open
Abstract
Disease caused by mutations of mitochondrial DNA (mtDNA) are highly variable in both presentation and penetrance. Over the last 30 years, clinical recognition of this group of diseases has increased. It has been suggested that haplogroup background could influence the penetrance and presentation of disease-causing mutations; however, to date there is only one well-established example of such an effect: the increased penetrance of two Complex I Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducts the most extensive investigation to date into the importance of haplogroup context in the pathogenicity of mtDNA mutations in Complex I. We searched for proven human point mutations across more than 900 metazoans finding human disease-causing mutations and potential masking variants. We found more than a half of human pathogenic variants as compensated pathogenic deviations (CPD) in at least in one animal species from our multiple sequence alignments. Some variants were found in many species, and some were even the most prevalent amino acids across our dataset. Variants were also found in other primates, and in such cases, we looked for non-human amino acids in sites with high probability to interact with the CPD in folded protein. Using this "local interactions" approach allowed us to find potential masking substitutions in other amino acid sites. We suggest that the masking variants might arise in humans, resulting in variability of mutation effect in our species.
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Affiliation(s)
- Galya V Klink
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation
| | - Hannah O'Keefe
- Population Health Sciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Amrita Gogna
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Georgii A Bazykin
- Sector of Molecular Evolution, Institute for Information Transmission Problems (Kharkevich Institute) of the Russian Academy of Sciences, Moscow, Russian Federation.
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Skolkovo, Russian Federation.
| | - Joanna L Elson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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13
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Cai N, Gomez-Duran A, Yonova-Doing E, Kundu K, Burgess AI, Golder ZJ, Calabrese C, Bonder MJ, Camacho M, Lawson RA, Li L, Williams-Gray CH, Di Angelantonio E, Roberts DJ, Watkins NA, Ouwehand WH, Butterworth AS, Stewart ID, Pietzner M, Wareham NJ, Langenberg C, Danesh J, Walter K, Rothwell PM, Howson JMM, Stegle O, Chinnery PF, Soranzo N. Mitochondrial DNA variants modulate N-formylmethionine, proteostasis and risk of late-onset human diseases. Nat Med 2021; 27:1564-1575. [PMID: 34426706 DOI: 10.1038/s41591-021-01441-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 06/15/2021] [Indexed: 02/02/2023]
Abstract
Mitochondrial DNA (mtDNA) variants influence the risk of late-onset human diseases, but the reasons for this are poorly understood. Undertaking a hypothesis-free analysis of 5,689 blood-derived biomarkers with mtDNA variants in 16,220 healthy donors, here we show that variants defining mtDNA haplogroups Uk and H4 modulate the level of circulating N-formylmethionine (fMet), which initiates mitochondrial protein translation. In human cytoplasmic hybrid (cybrid) lines, fMet modulated both mitochondrial and cytosolic proteins on multiple levels, through transcription, post-translational modification and proteolysis by an N-degron pathway, abolishing known differences between mtDNA haplogroups. In a further 11,966 individuals, fMet levels contributed to all-cause mortality and the disease risk of several common cardiovascular disorders. Together, these findings indicate that fMet plays a key role in common age-related disease through pleiotropic effects on cell proteostasis.
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Affiliation(s)
- Na Cai
- Human Genetics Department, Wellcome Sanger Institute (WT), Hinxton, UK.,European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.,Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | - Aurora Gomez-Duran
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Centro de Investigaciones Biológicas Margarita Salas, Consejo Superior de Investigaciones Científicas (CIB-CSIC), Madrid, Spain
| | - Ekaterina Yonova-Doing
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Primary Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Kousik Kundu
- Human Genetics Department, Wellcome Sanger Institute (WT), Hinxton, UK
| | - Annette I Burgess
- Wolfson Centre for Prevention of Stroke and Dementia, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Zoe J Golder
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Claudia Calabrese
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Marc J Bonder
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK.,Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marta Camacho
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Rachael A Lawson
- Translational and Clinical Research Institute, Newcastle University, Newcastle, UK
| | - Lixin Li
- Wolfson Centre for Prevention of Stroke and Dementia, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Caroline H Williams-Gray
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | | | - Emanuele Di Angelantonio
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Primary Public Health and Primary Care, University of Cambridge, Cambridge, UK.,British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.,National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - David J Roberts
- National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.,NHS Blood and Transplant-Oxford Centre, John Radcliffe Hospital, Oxford, UK.,Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Nick A Watkins
- NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK
| | - Willem H Ouwehand
- Human Genetics Department, Wellcome Sanger Institute (WT), Hinxton, UK.,British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.,NHS Blood and Transplant, Cambridge Biomedical Campus, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
| | - Adam S Butterworth
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Primary Public Health and Primary Care, University of Cambridge, Cambridge, UK.,British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.,National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | | | - Maik Pietzner
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | - Nick J Wareham
- MRC Epidemiology Unit, University of Cambridge, Cambridge, UK
| | | | - John Danesh
- Human Genetics Department, Wellcome Sanger Institute (WT), Hinxton, UK.,British Heart Foundation Cardiovascular Epidemiology Unit, Department of Primary Public Health and Primary Care, University of Cambridge, Cambridge, UK.,British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK.,National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK.,Health Data Research UK Cambridge, Wellcome Genome Campus and University of Cambridge, Cambridge, UK
| | - Klaudia Walter
- Human Genetics Department, Wellcome Sanger Institute (WT), Hinxton, UK
| | - Peter M Rothwell
- Wolfson Centre for Prevention of Stroke and Dementia, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK
| | - Joanna M M Howson
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Primary Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Oliver Stegle
- European Bioinformatics Institute (EMBL-EBI), Hinxton, UK. .,Division of Computational Genomics and Systems Genetics, German Cancer Research Center (DKFZ), Heidelberg, Germany. .,European Molecular Biology Laboratory, Heidelberg, Germany.
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK. .,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
| | - Nicole Soranzo
- Human Genetics Department, Wellcome Sanger Institute (WT), Hinxton, UK. .,British Heart Foundation Centre of Research Excellence, University of Cambridge, Cambridge, UK. .,National Institute for Health Research Blood and Transplant Research Unit in Donor Health and Genomics, University of Cambridge, Cambridge, UK. .,Department of Haematology, University of Cambridge, Cambridge, UK. .,Genomics Research Centre, Human Technopole, Milan, Italy.
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14
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Gutiérrez Cortés N, Pertuiset C, Dumon E, Börlin M, Da Costa B, Le Guédard M, Stojkovic T, Loundon N, Rouillon I, Nadjar Y, Letellier T, Jonard L, Marlin S, Rocher C. Mutation m.3395A > G in MT-ND1 leads to variable pathologic manifestations. Hum Mol Genet 2021; 29:980-989. [PMID: 32011699 DOI: 10.1093/hmg/ddaa020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 01/27/2020] [Accepted: 01/31/2020] [Indexed: 11/12/2022] Open
Abstract
A non-synonymous mtDNA mutation, m.3395A > G, which changes tyrosine in position 30 to cysteine in p.MT-ND1, was found in several patients with a wide range of clinical phenotypes such as deafness, diabetes and cerebellar syndrome but no Leber's hereditary optic neuropathy. Although this mutation has already been described, its pathogenicity has not been demonstrated. Here, it was found isolated for the first time, allowing a study to investigate its pathogenicity. To do so, we constructed cybrid cell lines and carried out a functional study to assess the possible consequences of the mutation on mitochondrial bioenergetics. Results obtained demonstrated that this mutation causes an important dysfunction of the mitochondrial respiratory chain with a decrease in both activity and quantity of complex I due to a diminution of p.MT-ND1 quantity. However, no subcomplexes were found in cybrids carrying the mutation, indicating that the quality of the complex I assembly is not affected. Moreover, based on the crystal structure of p.MT-ND1 and the data found in the literature, we propose a hypothesis for the mechanism of the degradation of p.MT-ND1. Our study provides new insights into the pathophysiology of mitochondrial diseases and in particular of MT-ND1 mutations.
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Affiliation(s)
- Nicolás Gutiérrez Cortés
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Claire Pertuiset
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Elodie Dumon
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Marine Börlin
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Barbara Da Costa
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
| | - Marina Le Guédard
- Laboratoire de Biogenèse Membranaire, CNRS UMR 5200, Université de Bordeaux, INRA Bordeaux Aquitaine, Villenave d'Ornon, France.,LEB Aquitaine Transfert-ADERA, FR-33883 Villenave d'Ornon, Cedex, France
| | - Tanya Stojkovic
- APHP, Centre de Référence des Maladies Neuromusculaires Ile de France Nord Est, G-H Pitié-Salpêtrière, 75013 Paris, France
| | - Natalie Loundon
- Otorhinolaryngologie Pédiatrique, Centre de Référence des Surdités Génétiques, Hôpital Necker, AP-HP, Paris, France
| | - Isabelle Rouillon
- Otorhinolaryngologie Pédiatrique, Centre de Référence des Surdités Génétiques, Hôpital Necker, AP-HP, Paris, France
| | - Yann Nadjar
- Neurologie, GH Pitié Salpêtrière, 75013 Paris, France
| | - Thierry Letellier
- Equipe de Médecine Evolutive, AMIS, UMR 5288 CNRS/Université Paul Sabatier, 31073 Toulouse, France
| | - Laurence Jonard
- Service de Génétique Moléculaire, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France
| | - Sandrine Marlin
- Service de Génétique Moléculaire, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France.,Centre de Référence des Surdités Génétiques, Service de Génétique Médicale, Hôpital Necker-Enfants Malades, Assistance Publique-Hôpitaux de Paris, 75015 Paris, France.,UMR 1163, Université Paris Descartes, Sorbonne Paris Cité, Institut IMAGINE, 24 Boulevard du Montparnasse, 75015 Paris, France
| | - Christophe Rocher
- INSERM-U688 Physiopathologie Mitochondriale, Université Bordeaux Segalen, 146 rue Léo Saignat, 33076 Bordeaux, France
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15
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Yonova-Doing E, Calabrese C, Gomez-Duran A, Schon K, Wei W, Karthikeyan S, Chinnery PF, Howson JMM. An atlas of mitochondrial DNA genotype-phenotype associations in the UK Biobank. Nat Genet 2021; 53:982-993. [PMID: 34002094 PMCID: PMC7611844 DOI: 10.1038/s41588-021-00868-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 04/07/2021] [Indexed: 02/03/2023]
Abstract
Mitochondrial DNA (mtDNA) variation in common diseases has been underexplored, partly due to a lack of genotype calling and quality-control procedures. Developing an at-scale workflow for mtDNA variant analyses, we show correlations between nuclear and mitochondrial genomic structures within subpopulations of Great Britain and establish a UK Biobank reference atlas of mtDNA-phenotype associations. A total of 260 mtDNA-phenotype associations were new (P < 1 × 10-5), including rs2853822 /m.8655 C>T (MT-ATP6) with type 2 diabetes, rs878966690 /m.13117 A>G (MT-ND5) with multiple sclerosis, 6 mtDNA associations with adult height, 24 mtDNA associations with 2 liver biomarkers and 16 mtDNA associations with parameters of renal function. Rare-variant gene-based tests implicated complex I genes modulating mean corpuscular volume and mean corpuscular hemoglobin. Seven traits had both rare and common mtDNA associations, where rare variants tended to have larger effects than common variants. Our work illustrates the value of studying mtDNA variants in common complex diseases and lays foundations for future large-scale mtDNA association studies.
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Affiliation(s)
- Ekaterina Yonova-Doing
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
| | - Claudia Calabrese
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Aurora Gomez-Duran
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
- Centro de Investigaciones Biológicas "Margarita Salas", Consejo Superior de Investigaciones Científicas (CIB-CSIC), Madrid, Spain
| | - Katherine Schon
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Wei Wei
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Savita Karthikeyan
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
| | - Joanna M M Howson
- British Heart Foundation Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK.
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16
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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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17
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Burskaia V, Artyushin I, Potapova NA, Konovalov K, Bazykin GA. Convergent Adaptation in Mitochondria of Phylogenetically Distant Birds: Does it Exist? Genome Biol Evol 2021; 13:6284172. [PMID: 34037779 PMCID: PMC8271140 DOI: 10.1093/gbe/evab113] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/15/2021] [Indexed: 11/24/2022] Open
Abstract
In a wide range of taxa, proteins encoded by mitochondrial genomes are involved in adaptation to lifestyle that requires oxygen starvation or elevation of metabolism rate. It remains poorly understood to what extent adaptation to similar conditions is associated with parallel changes in these proteins. We search for a genetic signal of parallel or convergent evolution in recurrent molecular adaptation to high altitude, migration, diving, wintering, unusual flight abilities, or loss of flight in mitochondrial genomes of birds. Developing on previous work, we design an approach for the detection of recurrent coincident changes in genotype and phenotype, indicative of an association between the two. We describe a number of candidate sites involved in recurrent adaptation in ND genes. However, we find that the majority of convergence events can be explained by random coincidences without invoking adaptation.
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Affiliation(s)
- Valentina Burskaia
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia.,Molecular Evolution Laboratory, Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
| | - Ilja Artyushin
- Department of Vertebrate Zoology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Nadezhda A Potapova
- Molecular Evolution Laboratory, Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
| | - Kirill Konovalov
- Department of Chemistry, Hong Kong University of Science and Technology, Kowloon, Hong Kong
| | - Georgii A Bazykin
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, Moscow Oblast, Russia.,Molecular Evolution Laboratory, Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevitch Institute), Moscow, Russia
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18
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Sharma S, Singh Y, Sandhir R, Singh S, Ganju L, Kumar B, Varshney R. Mitochondrial DNA mutations contribute to high altitude pulmonary edema via increased oxidative stress and metabolic reprogramming during hypobaric hypoxia. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2021; 1862:148431. [PMID: 33862004 DOI: 10.1016/j.bbabio.2021.148431] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 03/27/2021] [Accepted: 04/07/2021] [Indexed: 10/21/2022]
Abstract
High altitude pulmonary edema (HAPE) is experienced by non-acclimatized sea level individuals on exposure to high altitude hypoxic conditions. Available evidence suggests that genetic factors and perturbed mitochondrial redox status may play an important role in HAPE pathophysiology. However, the precise mechanism has not been fully understood. In the present study, sequencing of mitochondrial DNA (mtDNA) from HAPE subjects and acclimatized controls was performed to identify pathogenic mutations and to determine their role in HAPE. Hypobaric hypoxia induced oxidative stress and metabolic alterations were also assessed in HAPE subjects. mtDNA copy number, mitochondrial oxidative phosphorylation (mtOXPHOS) activity, mitochondrial biogenesis were measured to determine mitochondrial functions. The data revealed that the mutations in Complex I genes affects the secondary structure of protein in HAPE subjects. Further, increased oxidative stress during hypobaric hypoxia, reduced mitochondrial biogenesis and mtOXPHOS activity induced metabolic reprogramming appears to contribute to mitochondrial dysfunctions in HAPE individuals. Haplogroup analysis suggests that mtDNA haplogroup H2a2a1 has potential contribution in the pathobiology of HAPE in lowlanders. This study also suggests contribution of altered mitochondrial functions in HAPE susceptibility.
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Affiliation(s)
- Swati Sharma
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India; Department of Biochemistry, Basic Medical Sciences Block II, Panjab University, Chandigarh 160014, India
| | - Yamini Singh
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India.
| | - Rajat Sandhir
- Department of Biochemistry, Basic Medical Sciences Block II, Panjab University, Chandigarh 160014, India
| | - Sayar Singh
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Lilly Ganju
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Bhuvnesh Kumar
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
| | - Rajeev Varshney
- Defence Institute of Physiology and Allied Sciences (DIPAS), Defence R&D Organization (DRDO), Lucknow Road, Timarpur, Delhi 110054, India
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19
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Pozzi A, Dowling DK. Small mitochondrial RNAs as mediators of nuclear gene regulation, and potential implications for human health. Bioessays 2021; 43:e2000265. [PMID: 33763872 DOI: 10.1002/bies.202000265] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 03/03/2021] [Accepted: 03/05/2021] [Indexed: 02/06/2023]
Abstract
Much research has focused on the effects of pathogenic mitochondrial mutations on health. Notwithstanding, the mechanisms regulating the link between these mutations and their effects remain elusive in several cases. Here, we propose that certain mitochondrial mutations may disrupt function of a set of mitochondrial-transcribed small RNAs, perturbing communication between mitochondria and nucleus, leading to disease. Our hypothesis synthesises two lines of supporting evidence. First, several mitochondrial mutations cannot be directly linked to effects on energy production or protein synthesis. Second, emerging studies have described the existence of small RNAs encoded by the mitochondria and proposed their involvement in RNA interference. We present a roadmap to testing this hypothesis.
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Affiliation(s)
- Andrea Pozzi
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Melbourne, Victoria, Australia
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20
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Iannello M, Bettinazzi S, Breton S, Ghiselli F, Milani L. A Naturally Heteroplasmic Clam Provides Clues about the Effects of Genetic Bottleneck on Paternal mtDNA. Genome Biol Evol 2021; 13:6130822. [PMID: 33555290 PMCID: PMC7936021 DOI: 10.1093/gbe/evab022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is present in multiple copies within an organism. Since these copies are not identical, a single individual carries a heterogeneous population of mtDNAs, a condition known as heteroplasmy. Several factors play a role in the dynamics of the within-organism mtDNA population: among them, genetic bottlenecks, selection, and strictly maternal inheritance are known to shape the levels of heteroplasmy across mtDNAs. In Metazoa, the only evolutionarily stable exception to the strictly maternal inheritance of mitochondria is the doubly uniparental inheritance (DUI), reported in 100+ bivalve species. In DUI species, there are two highly divergent mtDNA lineages, one inherited through oocyte mitochondria (F-type) and the other through sperm mitochondria (M-type). Having both parents contributing to the mtDNA pool of the progeny makes DUI a unique system to study the dynamics of mtDNA populations. Since, in bivalves, the spermatozoon has few mitochondria (4–5), M-type mtDNA faces a tight bottleneck during embryo segregation, one of the narrowest mitochondrial bottlenecks investigated so far. Here, we analyzed the F- and M-type mtDNA variability within individuals of the DUI species Ruditapes philippinarum and investigated for the first time the effects of such a narrow bottleneck affecting mtDNA populations. As a potential consequence of this narrow bottleneck, the M-type mtDNA shows a large variability in different tissues, a condition so pronounced that it leads to genotypes from different tissues of the same individual not to cluster together. We believe that such results may help understanding the effect of low population size on mtDNA bottleneck.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Stefano Bettinazzi
- Department of Biological Sciences, University of Montreal, Quebec, Canada
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Quebec, Canada
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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21
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Gusdon AM, Hui Y, Chen J, Mathews CE, Qu S. Mitochondrial haplogroup G is associated with nonalcoholic fatty liver disease, while haplogroup A mitigates the effects of PNPLA3. Endocrinol Diabetes Metab 2021; 4:e00187. [PMID: 33532620 PMCID: PMC7831202 DOI: 10.1002/edm2.187] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/05/2020] [Accepted: 08/29/2020] [Indexed: 12/17/2022] Open
Abstract
Objectives Mitochondrial dysfunction plays a pivotal role in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). We hypothesized that mitochondrial DNA (mtDNA) haplogroups affect the risk of NAFLD in Han Chinese patients and interact with PNPLA3 genotypes. Design NAFLD and control patients were recruited from a tertiary care centre. The mitochondrial genome was amplified in overlapping segments and sequenced. Mitochondrial haplogroups were determined using Mitomaster. PNPLA3 rs738409 genotyping was performed using restriction fragment length polymorphism analysis. Patients We enrolled 655 NAFLD patients and 504 controls. Results More NAFLD patients encoded haplogroup G; odds ratio (OR) 1.85 (95% confidence interval [CI] 1.16, 2.80). Subhaplogroup G3 was present more frequently in NAFLD patients (25.8% vs 6.5%). The PNPLA3 CG genotype resulted in an OR of 1.66 (95% CI 1.25, 2.21), and the GG genotype resulted in an OR of 2.33 (95% CI 1.72, 3.17) for NAFLD. Patients with mitochondrial haplogroup A had a significantly higher frequency of genotype GG. Among patients with haplogroup A, no PNPLA3 genotype was associated with increased NAFLD risk (CG: OR 1.17, 95% CI 0.55, 2.34; GG: OR 1.04 95% CI 0.66, 2.65). Excluding haplogroup A, the OR for CG was 1.58 (95% CI 1.18, 2.12), and the OR for GG was 1.81 (95% CI 1.30, 2.51). Conclusion Haplogroup G was associated with an increased risk of NAFLD PNPLA3 GG genotype was overrepresented among patients encoding haplogroup A and was not associated with NAFLD risk among haplogroup A patients. Mitochondrial genetics influence NAFLD risk and interact with PNPLA3 genotypes.
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Affiliation(s)
- Aaron M. Gusdon
- Department of NeurosurgeryMischer Neuroscience AssociatesUniversity of Texas Health Science Center at HoustonHoustonTXUSA
| | - You Hui
- Department of EndocrinologyShanghai Tenth People's HospitalTongji UniversityShanghaiChina
| | - Jing Chen
- Department of Pathology, Immunology and Laboratory MedicineUniversity of Florida College of MedicineGainesvilleFLUSA
| | - Clayton E. Mathews
- Department of Pathology, Immunology and Laboratory MedicineUniversity of Florida College of MedicineGainesvilleFLUSA
| | - Shen Qu
- Department of EndocrinologyShanghai Tenth People's HospitalTongji UniversityShanghaiChina
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22
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Sun D, Niu Z, Zheng HX, Wu F, Jiang L, Han TQ, Wei Y, Wang J, Jin L. A Mitochondrial DNA Variant Elevates the Risk of Gallstone Disease by Altering Mitochondrial Function. Cell Mol Gastroenterol Hepatol 2020; 11:1211-1226.e15. [PMID: 33279689 PMCID: PMC8053626 DOI: 10.1016/j.jcmgh.2020.11.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND AIMS Gallstone disease (cholelithiasis) is a cholesterol-related metabolic disorders with strong familial predisposition. Mitochondrial DNA (mtDNA) variants accumulated during human evolution are associated with some metabolic disorders related to modified mitochondrial function. The mechanistic links between mtDNA variants and gallstone formation need further exploration. METHODS In this study, we explored the possible associations of mtDNA variants with gallstone disease by comparing 104 probands and 300 controls in a Chinese population. We constructed corresponding cybrids using trans-mitochondrial technology to investigate the underlying mechanisms of these associations. Mitochondrial respiratory chain complex activity and function and cholesterol metabolism were assessed in the trans-mitochondrial cell models. RESULTS Here, we found a significant association of mtDNA 827A>G with an increased risk of familial gallstone disease in a Chinese population (odds ratio [OR]: 4.5, 95% confidence interval [CI]: 2.1-9.4, P=1.2×10-4). Compared with 827A cybrids (haplogroups B4a and B4c), 827G cybrids (haplogroups B4b and B4d) had impaired mitochondrial respiratory chain complex activity and function and activated JNK and AMPK signaling pathways. Additionally, the 827G cybrids showed disturbances in cholesterol transport and accelerated development of gallstones. Specifically, cholesterol transport through the transporter ABCG5/8 was increased via activation of the AMPK signaling pathway in 827G cybrids. CONCLUSIONS Our findings reveal that mtDNA 827A>G induces aberrant mitochondrial function and abnormal cholesterol transport, resulting in increased occurrence of gallstones. The results provide an important biological basis for the clinical diagnosis and prevention of gallstone disease in the future.
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Affiliation(s)
- Dayan Sun
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Zhenmin Niu
- Shanghai-MOST Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai and Shanghai Academy of Science and Technology, Shanghai, China
| | - Hong-Xiang Zheng
- Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China; Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Fei Wu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Liuyiqi Jiang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Tian-Quan Han
- Shanghai Institute of Digestive Surgery, Department of Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Yang Wei
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China; Taizhou Institute of Health Sciences, Fudan University, Taizhou, China.
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China; Research Unit of Dissecting the Population Genetics and Developing New Technologies for Treatment and Prevention of Skin Phenotypes and Dermatological Diseases (2019RU058), Chinese Academy of Medical Sciences, Shanghai, China; Taizhou Institute of Health Sciences, Fudan University, Taizhou, China.
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23
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McCormick EM, Lott MT, Dulik MC, Shen L, Attimonelli M, Vitale O, Karaa A, Bai R, Pineda-Alvarez DE, Singh LN, Stanley CM, Wong S, Bhardwaj A, Merkurjev D, Mao R, Sondheimer N, Zhang S, Procaccio V, Wallace DC, Gai X, Falk MJ. Specifications of the ACMG/AMP standards and guidelines for mitochondrial DNA variant interpretation. Hum Mutat 2020; 41:2028-2057. [PMID: 32906214 DOI: 10.1002/humu.24107] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 08/20/2020] [Accepted: 08/28/2020] [Indexed: 12/12/2022]
Abstract
Mitochondrial DNA (mtDNA) variant pathogenicity interpretation has special considerations given unique features of the mtDNA genome, including maternal inheritance, variant heteroplasmy, threshold effect, absence of splicing, and contextual effects of haplogroups. Currently, there are insufficient standardized criteria for mtDNA variant assessment, which leads to inconsistencies in clinical variant pathogenicity reporting. An international working group of mtDNA experts was assembled within the Mitochondrial Disease Sequence Data Resource Consortium and obtained Expert Panel status from ClinGen. This group reviewed the 2015 American College of Medical Genetics and Association of Molecular Pathology standards and guidelines that are widely used for clinical interpretation of DNA sequence variants and provided further specifications for additional and specific guidance related to mtDNA variant classification. These Expert Panel consensus specifications allow for consistent consideration of the unique aspects of the mtDNA genome that directly influence variant assessment, including addressing mtDNA genome composition and structure, haplogroups and phylogeny, maternal inheritance, heteroplasmy, and functional analyses unique to mtDNA, as well as specifications for utilization of mtDNA genomic databases and computational algorithms.
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Affiliation(s)
- Elizabeth M McCormick
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Marie T Lott
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Matthew C Dulik
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA.,Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Lishuang Shen
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Ornella Vitale
- Department of Biosciences, Biotechnology, and Biopharmaceutics, University of Bari "A. Moro", Bari, Italy
| | - Amel Karaa
- Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | | | | | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Christine M Stanley
- Variantyx, Inc, Framingham, Massachusetts, USA.,QNA Diagnostics, Cambridge, Massachusetts, USA
| | | | - Anshu Bhardwaj
- CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Daria Merkurjev
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA
| | - Rong Mao
- ARUP Institute for Clinical and Experimental Pathology, ARUP Laboratories, Salt Lake City, Utah, USA.,Department of Pathology, University of Utah, Salt Lake City, Utah, USA
| | - Neal Sondheimer
- Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Shiping Zhang
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Biomedical and Health Informatics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Vincent Procaccio
- Department of Biochemistry and Genetics, MitoVasc Institute, UMR CNRS 6015- INSERM U1083, CHU Angers, Angers, France
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Xiaowu Gai
- Center for Personalized Medicine, Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California, USA.,Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Marni J Falk
- Mitochondrial Medicine Frontier Program, Division of Human Genetics, Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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24
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Płoszaj T, Antosik K, Młudzik P, Traczyk-Borszyńska M, Borowiec M. Clinical use of NGS data from the targeted gene panel for mitochondrial diseases screening. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE 2020; 194:105529. [PMID: 32470904 DOI: 10.1016/j.cmpb.2020.105529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/09/2020] [Accepted: 05/01/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND AND OBJECTIVE Mitochondrial diseases are a frequent cause of inherited genetic disorders caused by mutations in both the mitochondrial and nuclear human genome. The new technique of high-throughput sequencing, which is used more and more frequently around the world, is most often focused on nuclear DNA. In some cases, such data after proper IT processing could also allow to determine alterations in mtDNA genome. In our work, we want to verify that off-target reads from targeted gene panels are sufficient data to determine pathogenic variants in the mitochondrial genome. METHODS We analyzed 50 patients who underwent routine diagnostics with the Illumina's TruSight One Sequencing Panel. In the entire bioinformatic analysis process, we have used only free, user-friendly and generally available online tools that do not require specialized IT knowledge. RESULTS Most of the data obtained were suitable for determining the presence of homoplasmic variants in mtDNA; 84% of the data met the minimum 20-fold coverage requirement as defined in the scientific literature for clinical data. We managed to identify 16 pathogenic variants in the examined genetic material (mtDNA) according to the ClinVar database. CONCLUSIONS In conclusion, we have outlined that off-target reads from targeted gene panel (TruSight One Sequencing Panel) may also be suitable for determining potentially pathogenic homoplasmic variants in mtDNA. We also described a simple pipeline based only on free tools available online. Introducing such a pipeline into a standard procedure of clinical units which carry out such research undoubtedly can extend the diagnostic potential by information about mtDNA, especially when it is based on purely free tools that do not require specialized bioinformatic knowledge.
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Affiliation(s)
- Tomasz Płoszaj
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland.
| | - Karolina Antosik
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland
| | - Paulina Młudzik
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland
| | | | - Maciej Borowiec
- Department of Clinical Genetics, Medical University of Lodz, Pomorska 251, 92-213 Lodz, Poland
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25
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Stewart JB, Chinnery PF. Extreme heterogeneity of human mitochondrial DNA from organelles to populations. Nat Rev Genet 2020; 22:106-118. [PMID: 32989265 DOI: 10.1038/s41576-020-00284-x] [Citation(s) in RCA: 108] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2020] [Indexed: 02/06/2023]
Abstract
Contrary to the long-held view that most humans harbour only identical mitochondrial genomes, deep resequencing has uncovered unanticipated extreme genetic variation within mitochondrial DNA (mtDNA). Most, if not all, humans contain multiple mtDNA genotypes (heteroplasmy); specific patterns of variants accumulate in different tissues, including cancers, over time; and some variants are preferentially passed down or suppressed in the maternal germ line. These findings cast light on the origin and spread of mtDNA mutations at multiple scales, from the organelle to the human population, and challenge the conventional view that high percentages of a mutation are required before a new variant has functional consequences.
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Affiliation(s)
- James B Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany.,Wellcome Centre for Mitochondrial Research, Newcastle University Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK. .,Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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26
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Whole Mitochondrial Genome Analysis in Serbian Cases of Leber's Hereditary Optic Neuropathy. Genes (Basel) 2020; 11:genes11091037. [PMID: 32887465 PMCID: PMC7565519 DOI: 10.3390/genes11091037] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 08/19/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Leber’s hereditary optic neuropathy (LHON) is a maternally inherited disorder that affects central vision in young adults and is typically associated with mitochondrial DNA (mtDNA) mutations. This study is based on a mutational screening of entire mtDNA in eight Serbian probands clinically and genetically diagnosed with LHON and four of their family members, who are asymptomatic mutation carriers. All obtained sequence variants were compared to human mtDNA databases, and their potential pathogenic characteristics were assessed by bioinformatics tools. Mitochondrial haplogroup analysis was performed by MITOMASTER. Our study revealed two well-known primary LHON mutations, m.11778G>A and m.3460G>A, and one rare LHON mutation, m.8836A>G. Various secondary mutations were detected in association with the primary mutations. MITOMASTER analysis showed that the two well-known primary mutations belong to the R haplogroup, while the rare LHON m.8836A>G was detected within the N1b haplogroup. Our results support the need for further studies of genetic background and its role in the penetrance and severity of LHON.
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27
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Medini H, Cohen T, Mishmar D. Mitochondria Are Fundamental for the Emergence of Metazoans: On Metabolism, Genomic Regulation, and the Birth of Complex Organisms. Annu Rev Genet 2020; 54:151-166. [PMID: 32857636 DOI: 10.1146/annurev-genet-021920-105545] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Out of many intracellular bacteria, only the mitochondria and chloroplasts abandoned their independence billions of years ago and became endosymbionts within the host eukaryotic cell. Consequently, one cannot grow eukaryotic cells without their mitochondria, and the mitochondria cannot divide outside of the cell, thus reflecting interdependence. Here, we argue that such interdependence underlies the fundamental role of mitochondrial activities in the emergence of metazoans. Several lines of evidence support our hypothesis: (a) Differentiation and embryogenesis rely on mitochondrial function; (b) mitochondrial metabolites are primary precursors for epigenetic modifications (such as methyl and acetyl), which are critical for chromatin remodeling and gene expression, particularly during differentiation and embryogenesis; and (c) mitonuclear coregulation adapted to accommodate both housekeeping and tissue-dependent metabolic needs. We discuss the evolution of the unique mitochondrial genetic system, mitochondrial metabolites, mitonuclear coregulation, and their critical roles in the emergence of metazoans and in human disorders.
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Affiliation(s)
- Hadar Medini
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
| | - Tal Cohen
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501 Israel;
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28
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Mitochondrial DNA genomes revealed different patterns of high-altitude adaptation in high-altitude Tajiks compared with Tibetans and Sherpas. Sci Rep 2020; 10:10592. [PMID: 32601317 PMCID: PMC7324373 DOI: 10.1038/s41598-020-67519-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 06/05/2020] [Indexed: 02/06/2023] Open
Abstract
High-altitude Tajiks (HA-Tajiks), Tibetans and Sherpas are three groups of high-altitude native people in China. The differences in the mtDNA genome between the three populations and the role of the mtDNA genome in the high-altitude adaptation of HA-Tajiks were seldom investigated. In this study, 80 HA-Tajiks were enrolled, and their whole mtDNA genomes were sequenced. The haplogroup of each subject was determined by comparison to the revised Cambridge Reference Sequence (rCRS). Ten additional populations from East Asia and Central Asia, including Tibetans and Sherpas, were selected as references. The top haplogroup was U, followed by H, T and J. Principle component analysis and genetic distance analysis indicated that HA-Tajiks showed a close relationship with Wakhi Tajiks, Pamiri Tajiks and Sarikoli Tajiks, indicating that they should be considered one nation scattered around the Pamirs. The difference in the mtDNA genome between HA-Tajiks and Sherpas was significantly greater than that between HA-Tajiks and Tibetans. Among the 13 genes related to the OXPHOS pathway encoded by the mtDNA genome, HA-Tajiks showed more significant differences in ND3 and CYTB compared to Tibetans. Compared to Sherpas, HA-Tajiks showed more significant differences in ND1, ND2, COX1, ATP8, ATP6, ND3, ND4L, ND4, ND5 and CYTB. The associated functional changes and underlying molecular mechanisms should be explored by molecular and biochemical investigations in further studies.
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29
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Klucnika A, Ma H. A battle for transmission: the cooperative and selfish animal mitochondrial genomes. Open Biol 2020; 9:180267. [PMID: 30890027 PMCID: PMC6451365 DOI: 10.1098/rsob.180267] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial genome is an evolutionarily persistent and cooperative component of metazoan cells that contributes to energy production and many other cellular processes. Despite sharing the same host as the nuclear genome, the multi-copy mitochondrial DNA (mtDNA) follows very different rules of replication and transmission, which translate into differences in the patterns of selection. On one hand, mtDNA is dependent on the host for its transmission, so selections would favour genomes that boost organismal fitness. On the other hand, genetic heterogeneity within an individual allows different mitochondrial genomes to compete for transmission. This intra-organismal competition could select for the best replicator, which does not necessarily give the fittest organisms, resulting in mito-nuclear conflict. In this review, we discuss the recent advances in our understanding of the mechanisms and opposing forces governing mtDNA transmission and selection in bilaterians, and what the implications of these are for mtDNA evolution and mitochondrial replacement therapy.
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Affiliation(s)
- Anna Klucnika
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
| | - Hansong Ma
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
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30
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Ji Y, Zhang J, Yu J, Wang Y, Lu Y, Liang M, Li Q, Jin X, Wei Y, Meng F, Gao Y, Cang X, Tong Y, Liu X, Zhang M, Jiang P, Zhu T, Mo JQ, Huang T, Jiang P, Guan MX. Contribution of mitochondrial ND1 3394T>C mutation to the phenotypic manifestation of Leber's hereditary optic neuropathy. Hum Mol Genet 2020; 28:1515-1529. [PMID: 30597069 DOI: 10.1093/hmg/ddy450] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 11/05/2018] [Accepted: 12/22/2018] [Indexed: 11/14/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations have been associated with Leber's hereditary optic neuropathy (LHON) and their pathophysiology remains poorly understood. In this study, we investigated the pathophysiology of a LHON susceptibility allele (m.3394T>C, p.30Y>H) in the Mitochondrial (MT)-ND1 gene. The incidence of m.3394T>C mutation was 2.7% in the cohort of 1741 probands with LHON. Extremely low penetrances of LHON were observed in 26 pedigrees carrying only m.3394T>C mutation, while 21 families bearing m.3394T>C, together with m.11778G>A or m.14484T>C mutation, exhibited higher penetrance of LHON than those in families carrying single mtDNA mutation(s). The m.3394T>C mutation disrupted the specific electrostatic interactions between Y30 of p.MT-ND1 with the sidechain of E4 and backbone carbonyl group of M1 of NDUFA1 (NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 1) of complex I, thereby altering the structure and function of complex I. We demonstrated that these cybrids bearing only m.3394T>C mutation caused mild mitochondrial dysfunctions and those harboring both m.3394T>C and m.11778G>A mutations exhibited greater mitochondrial dysfunctions than cybrids carrying only m.11778G>A mutation. In particular, the m.3394T>C mutation altered the stability of p.MT-ND1 and complex I assembly. Furthermore, the m.3394T>C mutation decreased the activities of mitochondrial complexes I, diminished mitochondrial ATP levels and membrane potential and increased the production of reactive oxygen species in the cybrids. These m.3394T>C mutation-induced alterations aggravated mitochondrial dysfunctions associated with the m.11778G>A mutation. These resultant biochemical defects contributed to higher penetrance of LHON in these families carrying both mtDNA mutations. Our findings provide new insights into the pathophysiology of LHON arising from the synergy between mitochondrial ND1 and ND4 mutations.
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Affiliation(s)
- Yanchun Ji
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Juanjuan Zhang
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jialing Yu
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Ying Wang
- Department of Ophthalmology, Chinese Academy of Traditional Chinese Medicine, Beijing, China
| | - Yuanyuan Lu
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Min Liang
- Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qiang Li
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaofen Jin
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinsheng Wei
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Feilong Meng
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yinglong Gao
- Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Xiaohui Cang
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yi Tong
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiaoling Liu
- School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China.,Attardi Institute of Mitochondrial Biomedicine, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Minglian Zhang
- Department of Ophthalmology, Hebei Provincial Eye Hospital, Xingtai, Hebei, China
| | - Peifang Jiang
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Tao Zhu
- Department of Critical Care Medicine, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Jun Qin Mo
- Department of Pathology, Rady Children's Hospital, University of California School of Medicine, San Diego, California, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Pingping Jiang
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Min-Xin Guan
- Division of Medical Genetics and Genomics, the Children's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Institute of Genetics, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Key Lab of Reproductive Genetics, Ministry of Education of PRC, Zhejiang University, Hangzhou, China.,Joint Institute of Genetics and Genomic Medicine between Zhejiang University and University of Toronto, Hangzhou, Zhejiang, China
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Jaber SM, Yadava N, Polster BM. Mapping mitochondrial respiratory chain deficiencies by respirometry: Beyond the Mito Stress Test. Exp Neurol 2020; 328:113282. [PMID: 32165258 DOI: 10.1016/j.expneurol.2020.113282] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/01/2020] [Accepted: 03/08/2020] [Indexed: 02/06/2023]
Abstract
Cell-based respirometers, such as the Seahorse Extracellular Flux Analyzer, are valuable tools to assess the functionality of mitochondria within adherent neurons, as well as other cell types. The Mito Stress Test is the most frequently employed protocol of drug additions to evaluate mitochondrial bioenergetic function. Sequential exposure of cells to an ATP synthase inhibitor such as oligomycin and an uncoupler such as FCCP cause changes in oxygen consumption rate that allow estimation of the cellular efficiency and capacity for mitochondrial ATP synthesis. While a useful first step in assessing whether an experimental treatment or genetic manipulation affects mitochondrial energetics, the Mito Stress Test does not identify specific sites of altered respiratory chain function. This article discusses limitations of the Mito Stress Test, proposes a refined protocol for comparing cell populations that requires independent drug titrations at multiple cell densities, and describes a stepwise series of respirometry-based assays that "map" locations of electron transport deficiency. These include strategies to test for cytochrome c release, to probe the functionality of specific electron transport chain complexes within intact or permeabilized cells, and to measure NADH oxidation by the linked activity of Complexes I, III, and IV. To illustrate utility, we show that although UK5099 and ABT-737 each decrease the spare respiratory capacity of cortical neurons, the stepwise assays reveal different underlying mechanisms consistent with their established drug targets: deficient Complex I substrate supply induced by the mitochondrial pyruvate carrier inhibitor UK5099 and cytochrome c release induced by the anti-apoptotic BCL-2 family protein inhibitor ABT-737.
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Affiliation(s)
- Sausan M Jaber
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Nagendra Yadava
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Brian M Polster
- Department of Anesthesiology and Center for Shock, Trauma and Anesthesiology Research, University of Maryland School of Medicine, Baltimore, MD 21201, USA; Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA.
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Russlies J, Fähnrich A, Witte M, Yin J, Benoit S, Gläser R, Günter C, Eming R, Erdmann J, Gola D, Gupta Y, Holtsche MM, Kern JS, König IR, Kiritsi D, Lieb W, Sadik CD, Sárdy M, Schauer F, van Beek N, Weidinger A, Worm M, Zillikens D, Schmidt E, Busch H, Ibrahim SM, Hirose M. Polymorphisms in the Mitochondrial Genome Are Associated With Bullous Pemphigoid in Germans. Front Immunol 2019; 10:2200. [PMID: 31824475 PMCID: PMC6883920 DOI: 10.3389/fimmu.2019.02200] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/30/2019] [Indexed: 01/06/2023] Open
Abstract
Bullous pemphigoid (BP) is the most prevalent autoimmune skin blistering disease and is characterized by the generation of autoantibodies against the hemidesmosomal proteins BP180 (type XVII collagen) and BP230. Most intriguingly, BP is distinct from other autoimmune diseases because it predominantly affects elderly individuals above the age of 75 years, raising the question why autoantibodies and the clinical lesions of BP emerges mostly in this later stage of life, even in individuals harboring known putative BP-associated germline gene variants. The mitochondrial genome (mtDNA) is a potential candidate to provide additional insights into the BP etiology; however, the mtDNA has not been extensively explored to date. Therefore, we sequenced the whole mtDNA of German BP patients (n = 180) and age- and sex-matched healthy controls (n = 188) using next generation sequencing (NGS) technology, followed by the replication study using Sanger sequencing of an additional independent BP (n = 89) and control cohort (n = 104). While the BP and control groups showed comparable mitochondrial haplogroup distributions, the haplogroup T exhibited a tendency of higher frequency in BP patients suffering from neurodegenerative diseases (ND) compared to BP patients without ND (50%; 3 in 6 BP with haplogroup T). A total of four single nucleotide polymorphisms (SNPs) in the mtDNA, namely, m.16263T>C, m.16051A>G, and m.16162A>G in the D-loop region of the mtDNA, and m.11914G>A in the mitochondrially encoded NADH:ubiquinone oxidoreductase core subunit 4 gene (MT-ND4), were found to be significantly associated with BP based on the meta-analysis of our NGS data and the Sanger sequencing data (p = 0.0017, p = 0.0129, p = 0.0076, and p = 0.0132, respectively, Peto's test). More specifically, the three SNPs in the D-loop region were negatively, and the SNP in the MT-ND4 gene was positively associated with BP. Our study is the first to interrogate the whole mtDNA in BP patients and controls and to implicate multiple novel mtDNA variants in disease susceptibility. Studies using larger cohorts and more diverse populations are warranted to explore the functional consequences of the mtDNA variants identified in this study on immune and skin cells to understand their contributions to BP pathology.
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Affiliation(s)
- Juliane Russlies
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
| | - Anke Fähnrich
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Institute for Cardiogenetics, University of Luebeck, Luebeck, Germany
| | - Mareike Witte
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Department of Dermatology, University of Luebeck, Luebeck, Germany
| | - Junping Yin
- Research Center Borstel, Leibniz-Center for Medicine and Bioscience, Borstel, Germany
| | - Sandrine Benoit
- Department of Dermatology, Venereology and Allergology, University Hospital Würzburg, Würzburg, Germany
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
| | - Regine Gläser
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Venereology and Allergology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Claudia Günter
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, University Hospital of Dresden, Dresden, Germany
| | - Rüdiger Eming
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology and Allergology, Phillips-Universität Marburg, Marburg, Germany
| | - Jeanette Erdmann
- Institute for Cardiogenetics, University of Luebeck, Luebeck, Germany
| | - Damian Gola
- Institute of Medical Biometry and Statistics, University of Luebeck, Luebeck, Germany
| | - Yask Gupta
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
| | | | - Johannes S. Kern
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
- Dermatology Department, Faculty of Medicine, Dentistry and Health Sciences, The Royal Melbourne Hospital, University of Melbourne, Melbourne, VIC, Australia
| | - Inke R. König
- Institute of Medical Biometry and Statistics, University of Luebeck, Luebeck, Germany
| | - Dimitra Kiritsi
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Wolfgang Lieb
- Institute of Epidemiology, Christian-Albrecht University of Kiel, Kiel, Germany
- Popgen Biobank, Christian-Albrecht University of Kiel, Kiel, Germany
| | | | - Miklós Sárdy
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Venereology and Dermatooncology, Semmelweis University, Budapest, Hungary
- Department of Dermatology and Allergy, University Hospital, LMU Munich, Munich, Germany
| | - Franziska Schauer
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Faculty of Medicine, Medical Center-University of Freiburg, University of Freiburg, Freiburg, Germany
| | - Nina van Beek
- Department of Dermatology, University of Luebeck, Luebeck, Germany
| | - Anke Weidinger
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Venereology and Allergology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Margitta Worm
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
- Department of Dermatology, Venereology and Allergology, Allergy Center Charité, Charité Medical University Berlin, Berlin, Germany
| | - Detlef Zillikens
- Department of Dermatology, University of Luebeck, Luebeck, Germany
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
| | - Enno Schmidt
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Department of Dermatology, University of Luebeck, Luebeck, Germany
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
| | - Hauke Busch
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- Institute for Cardiogenetics, University of Luebeck, Luebeck, Germany
| | - Saleh M. Ibrahim
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
- The German Autoimmune Bullous Disease Genetic Study Group, Germany
| | - Misa Hirose
- Luebeck Institute of Experimental Dermatology, University of Luebeck, Luebeck, Germany
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Wang M, Wang Z, He G, Wang S, Zou X, Liu J, Wang F, Ye Z, Hou Y. Whole mitochondrial genome analysis of highland Tibetan ethnicity using massively parallel sequencing. Forensic Sci Int Genet 2019; 44:102197. [PMID: 31756629 DOI: 10.1016/j.fsigen.2019.102197] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 01/12/2023]
Abstract
Mitochondrial DNA (mtDNA) is a key player in numerous multifaceted and intricate biological processes and plays a pivotal role in dissecting the peopling of different populations, due to its maternally inherited property and comparatively high mutation rate. In this study, 119 Tibetan individuals from the Muli Tibetan Autonomous County of China (average altitude above 3,000 m) were employed in mitochondrial genome (mitogenome) sequencing by massively parallel sequencing (MPS) techniques using the Precision ID mtDNA Whole Genome Panel on an Ion S5XL system. The dataset presented 88 distinct haplotypes, resulting in the haplotype diversity of 0.9909. The majority of haplotypes were assigned to East Asian lineages and the distribution of haplogroups of Muli Tibetan significantly differed from reference Tibetan populations. The maximum parsimony phylogeny reconstructed by 119 newly generated mitogenomes revealed 12 major Muli Tibetan lineages. Intriguingly, a Sherpa-specific sub-haplogroup A15c1 with the lack of mutations at 4216 and 15,924 was discerned in our dataset, which suggested that the maternal gene pool of Sherpas may derive from Tibetan populations. The shared haplogroups between Muli Tibetan and lowland Han Chinese hinted that these lineages may derive from non-Tibetans and have already differentiated before their arrival on the Tibetan Plateau. Furthermore, extensive pairwise population comparisons displayed that Muli Tibetan had a closer genetic relationship with ethnically or linguistically close Nyingtri Tibetan, Nyingtri Lhoba and Chamdo Tibetan populations. Genetic affinity was also observed between the Muli Tibetan and North Han Chinese. Collectively, the results generated in this study enriched the existing forensic mtDNA database and raised additional interest in the application of whole mitogenome sequencing in forensic investigations.
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Affiliation(s)
- Mengge Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Guanglin He
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Shouyu Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Xing Zou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Fei Wang
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Ziwei Ye
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Science & Forensic Medicine, Sichuan University, Chengdu, 610041, 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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Shtolz N, Mishmar D. The Mitochondrial Genome–on Selective Constraints and Signatures at the Organism, Cell, and Single Mitochondrion Levels. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00342] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Yao L, Xu Z, Wan L. Whole Mitochondrial DNA Sequencing Analysis in 47 Han Populations in Southwest China. Med Sci Monit 2019; 25:6482-6490. [PMID: 31464266 PMCID: PMC6733151 DOI: 10.12659/msm.916275] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Mitochondrial DNA (mtDNA) sequencing has been used in many areas, including forensic genetics. Due to the rapid development of sequencing technology, whole mtDNA sequencing is now possible and may be used in epidemiological and forensic studies. This study aimed to use whole mtDNA sequencing to investigate 47 Chongqing Han populations in southwest China and the diversity in the mtGenome reference data. Material/Methods The mtDNA of 47 Chongqing Han populations was generated using the Ion Torrent Personal Genome Machine (PGM) system. The extent of the effects of the mtDNA on the subpopulations was investigated and compared with six other populations from published studies. Pairwise fixation index (FST), a measure of population differentiation due to genetic structure, were calculated. Analysis of molecular variance (AMOVA) was performed, and 1257 hypervariable region data sets were added to the principal component analysis (PCA). Results The whole mtDNA sequencing data of 47 southwest Chinese Han populations were successfully recovered. Expanding the sequencing rage increased the discrimination power of mtDNA from three-times to 25-times based on different populations. The subpopulation effects showed 20 times the differences in match probability when compared with south China regions. Conclusions Whole mtDNA sequencing distinguished between individuals from 47 Chongqing Han populations in southwest China and has potential applications that include high-quality forensic identification.
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Affiliation(s)
- Lan Yao
- College of Basic Medicine, Chongqing Medical University, Chongqing, China (mainland)
| | - Zhen Xu
- Key Laboratory of Forensic Genetics, Institute of Forensic Science, Ministry of Public Security, Beijing, China (mainland)
| | - Lihua Wan
- College of Basic Medicine, Chongqing Medical University, Chongqing, China (mainland)
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Comparative analysis of peripheral blood reveals transcriptomic adaptations to extreme environments on the Qinghai-Tibetan Plateau in the gray wolf (Canis lupus chanco). ORG DIVERS EVOL 2019. [DOI: 10.1007/s13127-019-00405-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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38
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Hill GE, Havird JC, Sloan DB, Burton RS, Greening C, Dowling DK. Assessing the fitness consequences of mitonuclear interactions in natural populations. Biol Rev Camb Philos Soc 2019; 94:1089-1104. [PMID: 30588726 PMCID: PMC6613652 DOI: 10.1111/brv.12493] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 11/27/2018] [Accepted: 11/30/2018] [Indexed: 12/22/2022]
Abstract
Metazoans exist only with a continuous and rich supply of chemical energy from oxidative phosphorylation in mitochondria. The oxidative phosphorylation machinery that mediates energy conservation is encoded by both mitochondrial and nuclear genes, and hence the products of these two genomes must interact closely to achieve coordinated function of core respiratory processes. It follows that selection for efficient respiration will lead to selection for compatible combinations of mitochondrial and nuclear genotypes, and this should facilitate coadaptation between mitochondrial and nuclear genomes (mitonuclear coadaptation). Herein, we outline the modes by which mitochondrial and nuclear genomes may coevolve within natural populations, and we discuss the implications of mitonuclear coadaptation for diverse fields of study in the biological sciences. We identify five themes in the study of mitonuclear interactions that provide a roadmap for both ecological and biomedical studies seeking to measure the contribution of intergenomic coadaptation to the evolution of natural populations. We also explore the wider implications of the fitness consequences of mitonuclear interactions, focusing on central debates within the fields of ecology and biomedicine.
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Affiliation(s)
- Geoffrey E. Hill
- Department of Biological Sciences, Auburn University, United States of America
| | - Justin C. Havird
- Department of Biology, Colorado State University, United States of America
| | - Daniel B. Sloan
- Department of Biology, Colorado State University, United States of America
| | - Ronald S. Burton
- Scripps Institution of Oceanography, University of California, San Diego, United States of America
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Damian K. Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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39
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14th EUNOS Congress: PORTO, PORTUGAL, 16-19 JUNE 2019. Neuroophthalmology 2019; 43:1-221. [PMID: 31528195 PMCID: PMC6736494 DOI: 10.1080/01658107.2019.1608780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022] Open
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40
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Singh LN, Crowston JG, Lopez Sanchez MIG, Van Bergen NJ, Kearns LS, Hewitt AW, Yazar S, Mackey DA, Wallace DC, Trounce IA. Mitochondrial DNA Variation and Disease Susceptibility in Primary Open-Angle Glaucoma. Invest Ophthalmol Vis Sci 2019; 59:4598-4602. [PMID: 30242360 PMCID: PMC6138263 DOI: 10.1167/iovs.18-25085] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Purpose To determine whether mitochondrial DNA haplogroups or rare variants associate with primary open-angle glaucoma in subjects of European descent. Methods A case-control comparison of age- and sex-matched cohorts of 90 primary open-angle glaucoma patients and 95 population controls. Full mitochondrial DNA sequences from peripheral blood were generated by next-generation sequencing and compared to the revised Cambridge Reference Sequence to define mitochondrial haplogroups and variants. Results Most subjects were of the major European haplogroups H, J, K, U, and T. Logistic regression analysis showed haplogroup U to be significantly underrepresented in male primary open-angle glaucoma subjects (odds ratio 0.25; 95% confidence interval [CI] 0.09-0.67; P = 0.007; Bonferroni multiple testing P = 0.022). Variants in the mitochondrial DNA gene MT-ND2 were overrepresented in the control group (P = 0.005; Bonferroni multiple testing correction P = 0.015). Conclusions Mitochondrial DNA ancestral lineages modulate the risk for primary open-angle glaucoma in populations of European descent. Haplogroup U and rare variants in the mitochondrial DNA-encoded MT-ND2 gene may be protective against primary open-angle glaucoma. Larger studies are warranted to explore haplogroup associations with disease risk in different ethnic groups and define biomarkers of primary open-angle glaucoma endophenotypes to target therapeutic strategies.
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Affiliation(s)
- Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, University of Pennsylvania, Philadelphia, United States
| | - Jonathan G Crowston
- Center for Eye Research Australia, Ophthalmology, University of Melbourne Department of Surgery, Melbourne, Australia
| | - M Isabel G Lopez Sanchez
- Center for Eye Research Australia, Ophthalmology, University of Melbourne Department of Surgery, Melbourne, Australia
| | - Nicole J Van Bergen
- Center for Eye Research Australia, Ophthalmology, University of Melbourne Department of Surgery, Melbourne, Australia
| | - Lisa S Kearns
- Center for Eye Research Australia, Ophthalmology, University of Melbourne Department of Surgery, Melbourne, Australia
| | - Alex W Hewitt
- Center for Eye Research Australia, Ophthalmology, University of Melbourne Department of Surgery, Melbourne, Australia.,Menzies Research Institute Tasmania, School of Medicine, University of Tasmania, Hobart, Australia
| | - Seyhan Yazar
- Lions Eye Institute, University of Western Australia, Centre for Ophthalmology and Visual Science, Perth, Australia.,MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom
| | - David A Mackey
- Lions Eye Institute, University of Western Australia, Centre for Ophthalmology and Visual Science, Perth, Australia
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, University of Pennsylvania, Philadelphia, United States.,Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, United States
| | - Ian A Trounce
- Center for Eye Research Australia, Ophthalmology, University of Melbourne Department of Surgery, Melbourne, Australia
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Hwang IW, Kim K, Choi EJ, Jin HJ. Association of mitochondrial haplogroup F with physical performance in Korean population. Genomics Inform 2019; 17:e11. [PMID: 30929412 PMCID: PMC6459174 DOI: 10.5808/gi.2019.17.1.e11] [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: 01/11/2019] [Accepted: 03/20/2019] [Indexed: 11/20/2022] Open
Abstract
Athletic performance is a complex multifactorial trait involving genetic and
environmental factors. The heritability of an athlete status was reported to be
about 70% in a twin study, and at least 155 genetic markers are known to be
related with athlete status. Mitochondrial DNA (mtDNA) encodes essential
proteins for oxidative phosphorylation, which is related to aerobic capacity.
Thus, mtDNA is a candidate marker for determining physical performance. Recent
studies have suggested that polymorphisms of mtDNA are associated with athlete
status and/or physical performance in various populations. Therefore, we
analyzed mtDNA haplogroups to assess their association with the physical
performance of Korean population. The 20 mtDNA haplogroups were determined using
the SNaPshot assay. Our result showed a significant association of the
haplogroup F with athlete status (odds ratio, 3.04; 95% confidence interval,
1.094 to 8.464; p = 0.012). Athletes with haplogroup F (60.64 ±
3.04) also demonstrated a higher Sargent jump than athletes with other
haplogroups (54.28 ± 1.23) (p = 0.041). Thus, our data imply
that haplogroup F may play a crucial role in the physical performance of Korean
athletes. Functional studies with larger sample sizes are necessary to further
substantiate these findings.
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Affiliation(s)
- In Wook Hwang
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan 31116, Korea
| | - Kicheol Kim
- Department of Neurology, Weill Institute for Neurosciences, University of California San Francisco, San Francisco, CA 94158, USA
| | - Eun Ji Choi
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan 31116, Korea
| | - Han Jun Jin
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan 31116, Korea
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Pan J, Wang L, Lu C, Zhu Y, Min Z, Dong X, Sha H. Matching Mitochondrial DNA Haplotypes for Circumventing Tissue-Specific Segregation Bias. iScience 2019; 13:371-379. [PMID: 30897510 PMCID: PMC6426714 DOI: 10.1016/j.isci.2019.03.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 01/13/2019] [Accepted: 03/01/2019] [Indexed: 02/01/2023] Open
Abstract
Mitochondrial DNA (mtDNA) segregation associated with donor-recipient mtDNA mismatch in mitochondria replacement therapy leads to unknown risks. Here, to explore whether matching mtDNA haplotypes contributes to ameliorating segregation, we reproduced various degrees of heteroplasmic mice with three single nucleotide polymorphisms to monitor segregation severity. “Segregation” presented in tissues of heteroplasmic mice containing low-level donor mtDNA heteroplasmy, and disappeared as donor mtDNA heteroplasmy levels ascended. Meanwhile, we found that distribution of donor mtDNA among the blastomeres of preimplantation embryos from the heteroplasmic mice shared the same tendency as that in adult tissues. Statistical analysis showed that no selective replication of donor mtDNA occurred during lifespan. Tracking donor mtDNA distribution showed that uneven distribution of donor mtDNA among embryonic blastomeres gradually became even as donor mtDNA heteroplasmy increased, indicating that the “segregation” in tissues was inherited from the uneven distribution. Our finding suggested that donor-recipient mtDNA matching could circumvent segregation in mitochondria replacement therapy. Matching mitochondrial DNA haplotypes make the nucleus treat different mtDNA the same Similar mtDNA haplotypes prevents tissue-specific segregation bias Low level of mtDNA heteroplasmy results in uneven inheritance rather than segregation
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Affiliation(s)
- Jianxin Pan
- Reproductive Medicine Center, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Li Wang
- Key Lab of Synthetic Biology of CAS, Shanghai Institute for Biological Sciences, Shanghai Research Center of Biotech., Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
| | - Charles Lu
- Reproductive Medicine Center, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai 200032, China; Washington University in St. Louis, Saint Louis 63110, USA
| | - Yanming Zhu
- Reproductive Medicine Center, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Zhunyuan Min
- Reproductive Medicine Center, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Xi Dong
- Reproductive Medicine Center, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai 200032, China.
| | - Hongying Sha
- Reproductive Medicine Center, Zhongshan Hospital, State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai 200032, China.
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43
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McManus MJ, Picard M, Chen HW, De Haas HJ, Potluri P, Leipzig J, Towheed A, Angelin A, Sengupta P, Morrow RM, Kauffman BA, Vermulst M, Narula J, Wallace DC. Mitochondrial DNA Variation Dictates Expressivity and Progression of Nuclear DNA Mutations Causing Cardiomyopathy. Cell Metab 2019; 29:78-90.e5. [PMID: 30174309 PMCID: PMC6717513 DOI: 10.1016/j.cmet.2018.08.002] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2017] [Revised: 02/01/2018] [Accepted: 08/01/2018] [Indexed: 02/03/2023]
Abstract
Nuclear-encoded mutations causing metabolic and degenerative diseases have highly variable expressivity. Patients sharing the homozygous mutation (c.523delC) in the adenine nucleotide translocator 1 gene (SLC25A4, ANT1) develop cardiomyopathy that varies from slowly progressive to fulminant. This variability correlates with the mitochondrial DNA (mtDNA) lineage. To confirm that mtDNA variants can modulate the expressivity of nuclear DNA (nDNA)-encoded diseases, we combined in mice the nDNA Slc25a4-/- null mutation with a homoplasmic mtDNA ND6P25L or COIV421A variant. The ND6P25L variant significantly increased the severity of cardiomyopathy while the COIV421A variant was phenotypically neutral. The adverse Slc25a4-/- and ND6P25L combination was associated with impaired mitochondrial complex I activity, increased oxidative damage, decreased l-Opa1, altered mitochondrial morphology, sensitization of the mitochondrial permeability transition pore, augmented somatic mtDNA mutation levels, and shortened lifespan. The strikingly different phenotypic effects of these mild mtDNA variants demonstrate that mtDNA can be an important modulator of autosomal disease.
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Affiliation(s)
- Meagan J McManus
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Martin Picard
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA; Departments of Psychiatry and Neurology, Columbia University Medical Center, New York, NY 10032, USA
| | - Hsiao-Wen Chen
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Hans J De Haas
- Department of Medicine, Mount Sinai Hospital, New York, NY 10029, USA
| | - Prasanth Potluri
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Jeremy Leipzig
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Atif Towheed
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Alessia Angelin
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Partho Sengupta
- Department of Medicine, Mount Sinai Hospital, New York, NY 10029, USA
| | - Ryan M Morrow
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Brett A Kauffman
- Vascular Medicine Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Marc Vermulst
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA
| | - Jagat Narula
- Department of Medicine, Mount Sinai Hospital, New York, NY 10029, USA
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children's Hospital of Philadelphia and University of Pennsylvania, Colket Translational Research Building, Room 6060, 3501 Civic Center Boulevard, Philadelphia, PA 19104-4302, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Abstract
The maternally inherited mitochondrial DNA (mtDNA) is located inside every mitochondrion, in variable number of copies, and it contains 37 crucial genes for cellular bioenergetics. This chapter will discuss the unique features of this circular genome including heteroplasmy, haplogroups, among others, along with the corresponding clinical relevance for each. The discussion also covers the nuclear-encoded mitochondrial genes (N > 1000) and the epistatic interactions between mtDNA and the nuclear genome. Examples of mitochondrial diseases related to specific mtDNA mutation sites of relevance for humans are provided. This chapter aims to provide an overview of mitochondrial genetics as an emerging hot topic for the future of medicine.
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Affiliation(s)
- Vanessa F Gonçalves
- Molecular Brain Sciences Department, Centre for Addiction and Mental Health, Toronto, Canada.
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Hwang IW, Kwon BN, Kim HJ, Han SH, Lee NR, Lim MH, Kwon HJ, Jin HJ. Assessment of associations between mitochondrial DNA haplogroups and attention deficit and hyperactivity disorder in Korean children. Mitochondrion 2018; 47:174-178. [PMID: 30423452 DOI: 10.1016/j.mito.2018.11.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 09/21/2018] [Accepted: 11/02/2018] [Indexed: 01/05/2023]
Abstract
Attention deficit hyperactivity disorder (ADHD) is a multifactorial disorder with multiple environmental and biological etiologies, including genetic factors. Until now, several genetic variants have been reported to be significantly associated with ADHD. Recently, the relationship between mitochondrial DNA (mtDNA) haplogroups and psychiatric disorders such as schizophrenia has also been reported. However, currently there are no reports pertaining to the genetic association between mtDNA haplogroups and ADHD. Therefore, we performed an mtDNA haplogroup analysis of a total of 472 Korean children (150 Children with ADHD and 322 controls). The 20 East Asian specific mtDNA haplogroups were determined using the SNaPshot assay. We also sequenced the displacement loop (D-loop) region, position 15,971-613. Our results showed that haplogroup B4 was significantly associated with ADHD (OR, 1.90; 95% CI, 1.055-3.429; p = 0.031). A marginally significant association was found in subjects with ADHD and haplogroup B5 (OR, 0.26; 95% CI, 0.059-1.139; p = 0.041). When stratified based on gender, an association was also observed between haplogroup B5 and boys diagnosed with ADHD (OR, 0.17; 95% CI, 0.022-1.340; p = 0.048). Compared with boys, girls with ADHD carried an excess of the haplogroup D4b (OR, 4.83; 95% CI, 1.352-17.272; p = 0.014). Stratified analysis of subtypes also showed significant results (combined: haplogroup B4, p = 0.007; inattentive: haplogroup F, p = 0.022). Our results showed a possible role of mtDNA haplogroups in the genetic etiology of ADHD and ADHD symptoms in Korean children.
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Affiliation(s)
- In Wook Hwang
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Bit Na Kwon
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Hyung Jun Kim
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Seung Hun Han
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Noo Ri Lee
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea
| | - Myung Ho Lim
- Department of Psychology and Psychotherapy, College of Health Sciences, Dankook University, Cheonan, South Korea
| | - Ho Jang Kwon
- Department of Preventive Medicine, College of Medicine, Dankook University, Cheonan, South Korea
| | - Han Jun Jin
- Department of Biological Sciences, College of Natural Science, Dankook University, Cheonan, South Korea.
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46
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Abstract
Inherited mitochondrial DNA (mtDNA) diseases were discovered 30 years ago, and their characterization has provided a new perspective on the etiology of the common metabolic and degenerative diseases, cancer, and aging. The maternally inherited mtDNA contains 37 critical bioenergetic genes that are present in hundreds of copies per cell, but the 'mitochondrial genome' encompasses an additional 1,000-2,000 nuclear DNA (nDNA) mitochondrial genes. The interaction between these two mitochondrial genetic systems provides explanations for phenomena such as the non-Mendelian transmission of the common 'complex' diseases, age-related disease risk and progression, variable penetrance and expressivity, and gene-environment interactions. Thus, mtDNA genetics contributes to the quantitative and environmental components of human genetics that cannot be explained by Mendelian genetics. Because mtDNA is maternally inherited and cytoplasmic, it has fostered the first germline gene therapy, nuclear transplantation. However, effective interventions are still lacking for existing patients with mitochondrial dysfunction.
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Affiliation(s)
- Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia and Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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47
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Haenel GJ, Del Gaizo Moore V. Functional Divergence of Mitochondria and Coevolution of Genomes: Cool Mitochondria in Hot Lizards. Physiol Biochem Zool 2018; 91:1068-1081. [DOI: 10.1086/699918] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ji J, Xu M, Wang R, Wang Y, Qin Y, Li L, Zheng H, Yang S, Li S, Miao D, Jin L, Zhou L, Ling X, Xia Y, Lu C, Wang X. Human mitochondrial DNA haplogroup M8a influences the penetrance of m.8684C>T in Han Chinese men with non-obstructive azoospermia. Reprod Biomed Online 2018; 37:480-488. [PMID: 30236824 DOI: 10.1016/j.rbmo.2018.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Revised: 08/02/2018] [Accepted: 08/03/2018] [Indexed: 11/29/2022]
Abstract
RESEARCH QUESTION What is the role of mitochondrial DNA (mtDNA) in the pathogenesis of non-obstructive azoospermia (NOA)? DESIGN mtDNA genome sequencing followed by an independent population validation were performed in 628 NOA cases and 584 healthy controls. Antioxidant capacity of serum was evaluated in 54 randomly selected cases out of 536 and 49 out of 489 controls. RESULTS In the screening stage, 13 mtDNA haplogroups (hg) were ascertained, and 10 susceptible variants were observed. In the validation stage, hg M8* in individuals was found to be associated with increased risk of NOA [odds ratio (OR) 2.61, 95% confidence interval (CI) 1.47-4.61] (P=0.001). Unexpectedly, the frequency of m.8684C>T, the defining marker for hg M8a, was also higher in NOA (OR 4.14, 95% CI 1.56-11.03) (P=0.002). Subsequently, the frequency distributions were compared among the sub-hg of hg M8* (including hg M8a, C and Z) and, intriguingly, no significance was found in hg C and Z. Additionally, the level of total antioxidant capacity was significantly decreased (P<0.05) compared with the control group. CONCLUSIONS hg M8a background in general played an active role in the penetrance of 8684C>T in NOA, and mtDNA genetic variants (causing low antioxidant levels) might increase mtDNA damage and impair normal spermatogenesis.
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Affiliation(s)
- Juan Ji
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Miaofei Xu
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Rong Wang
- Research Centre for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Ying Wang
- Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Yufeng Qin
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle ParkNC27709, USA
| | - Lei Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Hongxiang Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Shuping Yang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Shilin Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Dengshun Miao
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Research Centre for Bone and Stem Cells, Department of Anatomy, Histology, and Embryology, Nanjing Medical University, Nanjing, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai200433, China
| | - Lin Zhou
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Xiufeng Ling
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Yankai Xia
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China
| | - Chuncheng Lu
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China.
| | - Xinru Wang
- State Key Laboratory of Reproductive Medicine, Nanjing Maternity and Child Health Care Hospital, Obstetrics and Gynecology Hospital Affiliated to Nanjing Medical University, Nanjing Medical University, Nanjing210029, China; Key Laboratory of Modern Toxicology of Ministry of Education, School of Public Health, Nanjing Medical University, Nanjing210029, China.
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Chalkia D, Chang YC, Derbeneva O, Lvova M, Wang P, Mishmar D, Liu X, Singh LN, Chuang LM, Wallace DC. Mitochondrial DNA associations with East Asian metabolic syndrome. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2018; 1859:878-892. [PMID: 29997041 DOI: 10.1016/j.bbabio.2018.07.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/04/2018] [Accepted: 07/04/2018] [Indexed: 01/31/2023]
Abstract
Mitochondrial dysfunction has repeatedly been reported associated with type 2 diabetes mellitus (T2DM) and metabolic syndrome (MS), as have mitochondrial DNA (mtDNA) tRNA and duplication mutations and mtDNA haplogroup lineages. We identified 19 Taiwanese T2DM and MS pedigrees from Taiwan, with putative matrilineal transmission, one of which harbored the pathogenic mtDNA tRNALeu(UUR) nucleotide (nt) 3243A>G mutation on the N9a3 haplogroup background. We then recruited three independent Taiwanese cohorts, two from Taipei (N = 498, mean age 52 and N = 1002, mean age 44) and one from a non-urban environment (N = 501, mean age 57). All three cohorts were assessed for an array of metabolic parameters, their mtDNA haplogroups determined, and the haplogroups correlated with T2DM/MS phenotypes. Logistic regression analysis revealed that mtDNA haplogroups D5, F4, and N9a conferred T2DM protection, while haplogroups F4 and N9a were risk factors for hypertension (HTN), and F4 was a risk factor for obesity (OB). Additionally, the 5263C>T (ND2 A165V) variant commonly associated with F4 was associated with hypertension (HTN). Cybrids were prepared with macro-haplogroup N (defined by variants m.ND3 10398A (114T) and m.ATP6 8701A (59T)) haplogroups B4 and F1 mtDNAs and from macro-haplogroup M (variants m.ND3 10398G (114A) and m.ATP6 8701G (59A)) haplogroup M9 mtDNAs. Additionally, haplogroup B4 and F1 cybrids were prepared with and without the mtDNA variant in ND1 3394T>C (Y30H) reported to be associated with T2DM. Assay of mitochondria complex I in these cybrids revealed that macro-haplogroup N cybrids had lower activity than M cybrids, that haplogroup F cybrids had lower activity than B4 cybrids, and that the ND1 3394T>C (Y30H) variant reduced complex I on both the B4 and F1 background but with very different cumulative effects. These data support the hypothesis that functional mtDNA variants may contribute to the risk of developing T2DM and MS.
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Affiliation(s)
- Dimitra Chalkia
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States of America
| | - Yi-Cheng Chang
- Department of Internal Medicine, National Taiwan University Medical College, Taipei, Taiwan; Graduate Institute of Medical Genomics and Proteomics, National Taiwan University Medical College, Taipei, Taiwan; Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan
| | - Olga Derbeneva
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States of America; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America
| | - Maria Lvova
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States of America
| | - Ping Wang
- Department of Medicine, University of California, Irvine School of Medicine, Irvine, CA 92697, United States of America
| | - Dan Mishmar
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
| | - Xiaogang Liu
- Douglas C. Wallace Institute for Mitochondrial and Epigenomic Information Sciences, The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China; Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China
| | - Larry N Singh
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States of America
| | - Lee-Ming Chuang
- Department of Internal Medicine, National Taiwan University Medical College, Taipei, Taiwan
| | - Douglas C Wallace
- Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, United States of America; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States of America; Douglas C. Wallace Institute for Mitochondrial and Epigenomic Information Sciences, The Key Laboratory of Biomedical Information Engineering of the Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China; Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, PR China.
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Fang H, Hu N, Zhao Q, Wang B, Zhou H, Fu Q, Shen L, Chen X, Shen F, Lyu J. mtDNA Haplogroup N9a Increases the Risk of Type 2 Diabetes by Altering Mitochondrial Function and Intracellular Mitochondrial Signals. Diabetes 2018; 67:1441-1453. [PMID: 29735607 DOI: 10.2337/db17-0974] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Accepted: 04/26/2018] [Indexed: 11/13/2022]
Abstract
Mitochondrial DNA (mtDNA) haplogroups have been associated with the incidence of type 2 diabetes (T2D); however, their underlying role in T2D remains poorly elucidated. Here, we report that mtDNA haplogroup N9a was associated with an increased risk of T2D occurrence in Southern China (odds ratio 1.999 [95% CI 1.229-3.251], P = 0.005). By using transmitochondrial technology, we demonstrated that the activity of respiratory chain complexes was lower in the case of mtDNA haplogroup N9a (N9a1 and N9a10a) than in three non-N9a haplogroups (D4j, G3a2, and Y1) and that this could lead to alterations in mitochondrial function and mitochondrial redox status. Transcriptome analysis revealed that OXPHOS function and metabolic regulation differed markedly between N9a and non-N9a cybrids. Furthermore, in N9a cybrids, insulin-stimulated glucose uptake might be inhibited at least partially through enhanced stimulation of ERK1/2 phosphorylation and subsequent TLR4 activation, which was found to be mediated by the elevated redox status in N9a cybrids. Although it remains unclear whether other signaling pathways (e.g., Wnt pathway) contribute to the T2D susceptibility of haplogroup N9a, our data indicate that in the case of mtDNA haplogroup N9a, T2D is affected, at least partially through ERK1/2 overstimulation and subsequent TLR4 activation.
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Affiliation(s)
- Hezhi Fang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Nianqi Hu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qiongya Zhao
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Bingqian Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Huaibin Zhou
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Qingzi Fu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Lijun Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Xiong Chen
- Department of Endocrinology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Feixia Shen
- Department of Endocrinology, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - Jianxin Lyu
- Key Laboratory of Laboratory Medicine, Ministry of Education, Zhejiang Provincial Key Laboratory of Medical Genetics, College of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, China
- Zhejiang Provincial People's Hospital, Affiliated People's Hospital of Hangzhou Medical College, Hangzhou, Zhejiang, China
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