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Chiang ACY, Ježek J, Mu P, Di Y, Klucnika A, Jabůrek M, Ježek P, Ma H. Two mitochondrial DNA polymorphisms modulate cardiolipin binding and lead to synthetic lethality. Nat Commun 2024; 15:611. [PMID: 38242869 PMCID: PMC10799063 DOI: 10.1038/s41467-024-44964-2] [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: 06/08/2023] [Accepted: 01/10/2024] [Indexed: 01/21/2024] Open
Abstract
Genetic screens have been used extensively to probe interactions between nuclear genes and their impact on phenotypes. Probing interactions between mitochondrial genes and their phenotypic outcome, however, has not been possible due to a lack of tools to map the responsible polymorphisms. Here, using a toolkit we previously established in Drosophila, we isolate over 300 recombinant mitochondrial genomes and map a naturally occurring polymorphism at the cytochrome c oxidase III residue 109 (CoIII109) that fully rescues the lethality and other defects associated with a point mutation in cytochrome c oxidase I (CoIT300I). Through lipidomics profiling, biochemical assays and phenotypic analyses, we show that the CoIII109 polymorphism modulates cardiolipin binding to prevent complex IV instability caused by the CoIT300I mutation. This study demonstrates the feasibility of genetic interaction screens in animal mitochondrial DNA. It unwraps the complex intra-genomic interplays underlying disorders linked to mitochondrial DNA and how they influence disease expression.
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Affiliation(s)
- Ason C Y Chiang
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
| | - Jan Ježek
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- University College London Queen Square Institute of Neurology, Royal Free Hospital, Rowland Hill Street, London, NW3 2PF, UK
| | - Peiqiang Mu
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, South China Agricultural University, Tianhe District, 510642, Guangzhou, Guangdong, P. R. China
| | - Ying Di
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, CB2 0XY, UK
| | - Anna Klucnika
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK
- Laverock Therapeutics, Stevenage Bioscience Catalyst, Gunnels Wood Road, Stevenage, SG1 2FX, UK
| | - Martin Jabůrek
- Laboratory of Mitochondrial Physiology, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Petr Ježek
- Laboratory of Mitochondrial Physiology, Institute of Physiology of the Czech Academy of Sciences, Videnska 1083, 142 20, Prague, Czech Republic
| | - Hansong Ma
- School of Biosciences, University of Birmingham, Birmingham, B15 2TT, UK.
- Wellcome/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge, CB2 1QN, UK.
- Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.
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2
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Mitochondrial DNA population variation is not associated with Alzheimer's in the Japanese population: A consistent finding across global populations. PLoS One 2022; 17:e0276169. [PMID: 36264923 PMCID: PMC9584534 DOI: 10.1371/journal.pone.0276169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 10/02/2022] [Indexed: 11/06/2022] Open
Abstract
Several mitochondrial DNA (mtDNA) haplogroup association studies have suggested that common mtDNA variants are associated with multifactorial diseases, including Alzheimer’s disease (AD). However, such studies have also produced conflicting results. A new mtDNA association model, the ‘variant load model’ (VLM), has been applied to multiple disease phenotypes. Application of the VLM in a 2017 study failed to find different variant loads in AD patients compared to controls, in two cohorts of European origin. The study also suggested a lower variant load in healthy elderly individuals, but could offer no replicate cohort to support this observation. Here, the VLM is applied to Japanese mtDNA sequences; in doing so, we explored the role of mtDNA variation in AD and ageing in a different global population. Consistent with the previous findings using the VLM in two populations of European origin, we found no evidence for an association between rarer, non-haplogroup associated variation and the development of AD. However, the result in the context of ageing that suggested those with fewer mildly deleterious mutations might undergo healthier ageing, was not replicated. In contrast to our previous study, our present results suggest that those living to advanced old age may harbour more mildly deleterious mtDNA variations. Importantly our analysis showed this finding is not primarily being driven by many rare population variants dispersed across the mtDNA, but by a few more frequent variants with high MutPred scores. It is suggested the variants in question do not exert a mildly deleterious effect in their most frequent haplogroup context.
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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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Evaluation of the tRNA-Leu (UUR) gene haplotype profile observed in canine mammary gland tumours based on comparative analysis with the MT-TL1 human gene. ANNALS OF ANIMAL SCIENCE 2022. [DOI: 10.2478/aoas-2022-0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The aetiology and pathogenesis of many canine tumours are likely to be similar to cancers found in humans. This study aimed to evaluate a plausible link between changes in the tRNA-Leu (UUR) gene and the carcinogenesis process in dogs with mammary gland tumours. The whole mitochondrial DNA (mtDNA) isolated from blood and tumour tissues of 13 dogs with malignant mammary gland tumours was sequenced. The present work is the first report showing that some polymorphisms might occur at the corresponding positions in the human and canine mtDNA genome, which in turn may provoke similar deleterious effects. The homology between the human MT-TL1 and canine tRNA-Leu (UUR) genes was 84%. After resequencing of the whole mitochondrial DNA genome with the use of the NGS technology, two polymorphisms in two haplotypes were identified: m.2683G>A (observed in 18 out of 27 samples) and m.2678_2679insG (27 out of 27 samples). The m.2683G>A polymorphism corresponded to a deleterious change at m.3243A>G, which is linked with MELAS (Mitochondrial Encephalomyopathy, Lactic Acidosis, Stroke-like episodes) syndrome and with different types of cancers in humans as well. The comparative analysis of MT-TL1 and tRNA-Leu (UUR) led us to hypothesise that the m.2678_2679insG and m.2683G>A polymorphisms might influence the dog’s condition and might be linked with tumourigenesis, as observed in humans.
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Dawod PGA, Jancic J, Marjanovic A, Brankovic M, Jankovic M, Samardzic J, Gamil Anwar Dawod A, Novakovic I, Abdel Motaleb FI, Radlovic V, Kostic VS, Nikolic D. Mutational Analysis and mtDNA Haplogroup Characterization in Three Serbian Cases of Mitochondrial Encephalomyopathies and Literature Review. Diagnostics (Basel) 2021; 11:1969. [PMID: 34829316 PMCID: PMC8620769 DOI: 10.3390/diagnostics11111969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 10/19/2021] [Accepted: 10/21/2021] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial encephalomyopathies (MEMP) are heterogeneous multisystem disorders frequently associated with mitochondrial DNA (mtDNA) mutations. Clinical presentation varies considerably in age of onset, course, and severity up to death in early childhood. In this study, we performed molecular genetic analysis for mtDNA pathogenic mutation detection in Serbian children, preliminary diagnosed clinically, biochemically and by brain imaging for mitochondrial encephalomyopathies disorders. Sanger sequencing analysis in three Serbian probands revealed two known pathogenic mutations. Two probands had a heteroplasmic point mutation m.3243A>G in the MT-TL1 gene, which confirmed mitochondrial myopathy, encephalopathy, lactic acidosis, and stroke-like episode syndrome (MELAS), while a single case clinically manifested for Leigh syndrome had an almost homoplasmic (close to 100%) m.8993T>G mutation in the MT-ATP6 gene. After full mtDNA MITOMASTER analysis and PhyloTree build 17, we report MELAS' association with haplogroups U and H (U2e and H15 subclades); likewise, the mtDNA-associated Leigh syndrome proband shows a preference for haplogroup H (H34 subclade). Based on clinical-genetic correlation, we suggest that haplogroup H may contribute to the mitochondrial encephalomyopathies' phenotypic variability of the patients in our study. We conclude that genetic studies for the distinctive mitochondrial encephalomyopathies should be well-considered for realizing clinical severity and possible outcomes.
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Affiliation(s)
- Phepy G. A. Dawod
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (P.G.A.D.); (J.J.); (A.M.); (M.B.); (I.N.); (V.R.); (V.S.K.)
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo 11591, Egypt;
| | - Jasna Jancic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (P.G.A.D.); (J.J.); (A.M.); (M.B.); (I.N.); (V.R.); (V.S.K.)
- Clinic of Neurology and Psychiatry of Children and Youth, 11000 Belgrade, Serbia
| | - Ana Marjanovic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (P.G.A.D.); (J.J.); (A.M.); (M.B.); (I.N.); (V.R.); (V.S.K.)
| | - Marija Brankovic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (P.G.A.D.); (J.J.); (A.M.); (M.B.); (I.N.); (V.R.); (V.S.K.)
| | - Milena Jankovic
- Neurology Clinic, Clinical Center of Serbia, 11000 Belgrade, Serbia;
| | - Janko Samardzic
- Institute of Pharmacology, Clinical Pharmacology and Toxicology, Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia;
| | - Ayman Gamil Anwar Dawod
- Internal Medicine, Hepatogastroenterology and Endoscopy Department, Faculty of Medicine, Ain Shams University, Cairo 11591, Egypt;
| | - Ivana Novakovic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (P.G.A.D.); (J.J.); (A.M.); (M.B.); (I.N.); (V.R.); (V.S.K.)
| | - Fayda I. Abdel Motaleb
- Department of Medical Biochemistry and Molecular Biology, Faculty of Medicine, Ain Shams University, Cairo 11591, Egypt;
| | - Vladimir Radlovic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (P.G.A.D.); (J.J.); (A.M.); (M.B.); (I.N.); (V.R.); (V.S.K.)
- Pediatric Surgery Department, University Children’s Hospital, 11000 Belgrade, Serbia
| | - Vladimir S. Kostic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (P.G.A.D.); (J.J.); (A.M.); (M.B.); (I.N.); (V.R.); (V.S.K.)
- Neurology Clinic, Clinical Center of Serbia, 11000 Belgrade, Serbia;
| | - Dejan Nikolic
- Faculty of Medicine, University of Belgrade, 11000 Belgrade, Serbia; (P.G.A.D.); (J.J.); (A.M.); (M.B.); (I.N.); (V.R.); (V.S.K.)
- Physical Medicine and Rehabilitation Department, University Children’s Hospital, Tirsova 10, 11000 Belgrade, Serbia
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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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Kowal K, Tkaczyk-Wlizło A, Pierzchała M, Gawor J, Ślaska B. Molecular differences in mitochondrial DNA genomes of dogs with malignant mammary tumours. Vet Comp Oncol 2021; 20:256-264. [PMID: 34554638 DOI: 10.1111/vco.12772] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 07/01/2021] [Accepted: 09/20/2021] [Indexed: 11/30/2022]
Abstract
The aim of this study was to determine molecular defects in mitochondrial DNA (mtDNA) with the use of large-scale genome analysis in malignant canine mammary gland tumours and indicate whether these changes were linked with the carcinogenesis process. With the use of the NGS technology, we sequenced 27 samples of mtDNA isolated from blood and tumours obtained from 13 dogs with mammary gland tumours. The total number of mutations and polymorphisms in the analysed mitochondrial genomes was 557. We identified 383 single nucleotide polymorphisms (SNP), 32 indels (or length polymorphisms), 4 mutations, 137 heteroplasmic positions and 1 indel mutation. The highest variability (132 changes) was observed in the variable number of tandem repeats (VNTR) region. The heteroplasmy rate in VNTR varied among individuals and even between two tumours in one organism. Our previous study resulted in determination of a probable CpG island in this region, thus it is not excluded that these changes might alter mtDNA methylation. Only the ATP8 gene was not affected by any polymorphisms or mutations, whereas the COX1 gene had the highest number of polymorphisms from all protein-coding genes. One change m.13594G>A was detected in a region spanning two genes: ND5 and ND6, from which a deleterious effect was observed for the ND5 protein. Molecular changes were frequently observed in the TΨC loop, which is thought to interact with ribosomal RNA.
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Affiliation(s)
- Krzysztof Kowal
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Angelika Tkaczyk-Wlizło
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
| | - Mariusz Pierzchała
- Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Jastrzębiec, Poland
| | - Jan Gawor
- DNA Sequencing and Synthesis Facility, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Brygida Ślaska
- Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland
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Dell'Era E, Polidori M, Bernardini M, Capomaccio S, Cappelli K, Balducci F, Mandara MT. Selective symmetrical necrotizing encephalopathy secondary to primary mitochondrial disorder in a cat. J Vet Intern Med 2021; 35:2401-2408. [PMID: 34291836 PMCID: PMC8478069 DOI: 10.1111/jvim.16222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 06/25/2021] [Accepted: 07/12/2021] [Indexed: 11/28/2022] Open
Abstract
A 2‐year‐old female cat was referred for progressive neurological signs indicative of involvement of the prosencephalon, cerebellum, and brainstem. Magnetic resonance imaging identified multifocal, bilateral, symmetrical lesions with strong contrast enhancement, affecting multiple areas of the brain. Neuropathology at necropsy showed demyelination, necrotic lesions, spongiosis, and neuropil edema with reactive astrogliosis and neovascularization. Ultrastructural study indicated mitochondrial polymorphism. Genetic investigations outlined 2 polymorphisms within the tRNA‐Leu(UUR) gene of mitochondrial DNA. Imaging and neuropathological findings were consistent with selective symmetrical necrotizing encephalopathy, for which genetic investigations support mitochondrial pathogenesis.
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Affiliation(s)
- Elena Dell'Era
- Neurology Unit, AniCura Portoni Rossi Veterinary Hospital, Bologna, Italy
| | - Margherita Polidori
- Department of Veterinary Medicine, Neuropathology Laboratory, University of Perugia, Perugia, Italy
| | - Marco Bernardini
- Neurology Unit, AniCura Portoni Rossi Veterinary Hospital, Bologna, Italy.,Department of Animal Medicine, Production and Health, Clinical Section, University of Padua, Legnaro, Italy
| | - Stefano Capomaccio
- Department of Veterinary Medicine, Laboratory of Molecular Biology, University of Perugia, Perugia, Italy
| | - Katia Cappelli
- Department of Veterinary Medicine, Laboratory of Molecular Biology, University of Perugia, Perugia, Italy
| | - Federica Balducci
- Neurology Unit, AniCura Portoni Rossi Veterinary Hospital, Bologna, Italy
| | - Maria T Mandara
- Department of Veterinary Medicine, Neuropathology Laboratory, University of Perugia, Perugia, Italy
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Quantifying Mitochondrial Dynamics in Patient Fibroblasts with Multiple Developmental Defects and Mitochondrial Disorders. Int J Mol Sci 2021; 22:ijms22126263. [PMID: 34200828 PMCID: PMC8230542 DOI: 10.3390/ijms22126263] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 05/31/2021] [Accepted: 06/07/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are dynamic organelles that undergo rounds of fission and fusion and exhibit a wide range of morphologies that contribute to the regulation of different signaling pathways and various cellular functions. It is important to understand the differences between mitochondrial structure in health and disease so that therapies can be developed to maintain the homeostatic balance of mitochondrial dynamics. Mitochondrial disorders are multisystemic and characterized by complex and variable clinical pathologies. The dynamics of mitochondria in mitochondrial disorders is thus worthy of investigation. Therefore, in this study, we performed a comprehensive analysis of mitochondrial dynamics in ten patient-derived fibroblasts containing different mutations and deletions associated with various mitochondrial disorders. Our results suggest that the most predominant morphological signature for mitochondria in the diseased state is fragmentation, with eight out of the ten cell lines exhibiting characteristics consistent with fragmented mitochondria. To our knowledge, this is the first comprehensive study that quantifies mitochondrial dynamics in cell lines with a wide array of developmental and mitochondrial disorders. A more thorough analysis of the correlations between mitochondrial dynamics, mitochondrial genome perturbations, and bioenergetic dysfunction will aid in identifying unique morphological signatures of various mitochondrial disorders in the future.
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Vila-Sanjurjo A, Smith PM, Elson JL. Heterologous Inferential Analysis (HIA) and Other Emerging Concepts: In Understanding Mitochondrial Variation In Pathogenesis: There is no More Low-Hanging Fruit. Methods Mol Biol 2021; 2277:203-245. [PMID: 34080154 DOI: 10.1007/978-1-0716-1270-5_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here we summarize our latest efforts to elucidate the role of mtDNA variants affecting the mitochondrial translation machinery, namely variants mapping to the mt-rRNA and mt-tRNA genes. Evidence is accumulating to suggest that the cellular response to interference with mitochondrial translation is different from that occurring as a result of mutations in genes encoding OXPHOS proteins. As a result, it appears safe to state that a complete view of mitochondrial disease will not be obtained until we understand the effect of mt-rRNA and mt-tRNA variants on mitochondrial protein synthesis. Despite the identification of a large number of potentially pathogenic variants in the mitochondrially encoded rRNA (mt-rRNA) genes, we lack direct methods to firmly establish their pathogenicity. In the absence of such methods, we have devised an indirect approach named heterologous inferential analysis (HIA ) that can be used to make predictions concerning the disruptive potential of a large subset of mt-rRNA variants. We have used HIA to explore the mutational landscape of 12S and 16S mt-rRNA genes. Our HIA studies include a thorough classification of all rare variants reported in the literature as well as others obtained from studies performed in collaboration with physicians. HIA has also been used with non-mammalian mt-rRNA genes to elucidate how mitotypes influence the interaction of the individual and the environment. Regarding mt-tRNA variations, rapidly growing evidence shows that the spectrum of mutations causing mitochondrial disease might differ between the different mitochondrial haplogroups seen in human populations.
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Affiliation(s)
- Antón Vila-Sanjurjo
- Departamento de Bioloxía, Facultade de Ciencias, Centro de Investigacións en Ciencias Avanzadas (CICA), Universidade da Coruña, A Coruña, Spain.
| | - Paul M Smith
- Department of Paediatrics, Royal Aberdeen Children's Hospital, Aberdeen, UK
| | - Joanna L Elson
- Biosciences Institute Newcastle, Newcastle University, Newcastle upon Tyne, UK.
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
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Meldau S, Owen EP, Khan K, Riordan GT. Mitochondrial molecular genetic results in a South African cohort: divergent mitochondrial and nuclear DNA findings. J Clin Pathol 2020; 75:34-38. [PMID: 33115810 DOI: 10.1136/jclinpath-2020-207026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/09/2020] [Accepted: 10/11/2020] [Indexed: 12/22/2022]
Abstract
AIMS Mitochondrial diseases form one of the largest groups of inborn errors of metabolism. The birth prevalence is approximately 1/5000 in well-studied populations, but little has been reported from Sub-Saharan Africa. The aim of this study was to describe the genetics underlying mitochondrial disease in South Africa. METHODS An audit was performed on all mitochondrial disease genetic testing performed in Cape Town, South Africa. RESULTS Of 1614 samples tested for mitochondrial DNA (mtDNA) or nuclear DNA (nDNA) variants in South Africa between 1994 and 2019, there were 155 (9.6 %) positive results. Pathogenic mtDNA variants accounted for 113 (73%)/155, from 96 families. Mitochondrial encephalopathy with lactic acidosis and stroke-like episodes, 37 (33%)/113, Leber's hereditary optic neuropathy, 26 (23%)/113, and single large mtDNA deletions, 22 (20%)/113, accounted for 76%. Thirty eight of 42 nDNA-positive results were homozygous for the MPV17 pathogenic variant c.106C>T (p.[Gln36Ter, Ser25Profs*49]) causing infantile neurohepatopathy, one of the largest homozygous groups reported in the literature. The other nDNA variants were in TAZ1, CPT2, BOLA3 and SERAC1. None were identified in SURF1, POLG or PDHA1. CONCLUSIONS Finding a large group with a homozygous nuclear pathogenic variant emphasises the importance of looking for possible founder effects. The absence of other widely described pathogenic nDNA variants in this cohort may be due to reduced prevalence or insufficient testing. As advances in therapeutics develop, it is critical to develop diagnostic platforms on the African subcontinent so that population-specific genetic variations can be identified.
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Affiliation(s)
- Surita Meldau
- Division of Chemical Pathology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa .,Chemical Pathology, National Health Laboratory Services, Groote Schuur Hospital, Cape Town, South Africa
| | - Elizabeth Patricia Owen
- Division of Chemical Pathology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Chemical Pathology, National Health Laboratory Services, Groote Schuur Hospital, Cape Town, South Africa
| | - Kashief Khan
- Chemical Pathology, National Health Laboratory Services, Groote Schuur Hospital, Cape Town, South Africa
| | - Gillian Tracy Riordan
- Division of Paediatric Neurology, Department of Paediatrics and Child Health, University of Cape Town, Cape Town, Western Cape, South Africa.,Red Cross War Memorial Children's Hospital, Cape Town, South Africa
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12
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Hagen CM, Elson JL, Hedley PL, Aidt FH, Havndrup O, Jensen MK, Kanters JK, Atherton JJ, McGaughran J, Bundgaard H, Christiansen M. Evolutionary dissection of mtDNA hg H: a susceptibility factor for hypertrophic cardiomyopathy. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:238-244. [PMID: 32602800 DOI: 10.1080/24701394.2020.1782897] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Mitochondrial DNA (mtDNA) haplogroup (hg) H has been reported as a susceptibility factor for hypertrophic cardiomyopathy (HCM). This was established in genetic association studies, however, the SNP or SNP's that are associated with the increased risk have not been identified. Hg H is the most frequent European mtDNA hg with greater than 80 subhaplogroups (subhgs) each defined by specific SNPs. We tested the hypothesis that the distribution of H subhgs might differ between HCM patients and controls. The subhg H distribution in 55 HCM index cases was compared to that of two Danish mtDNA hg H control groups (n = 170 and n = 908, respectively). In the HCM group, H and 12 different H subhgs were found. All these, except subhgs H73, were also found in both control groups. The HCM group was also characterized by a higher proportion of H3 compared to H2. In the HCM group the H3/H2 proportion was 1.7, whereas it was 0.45 and 0.54 in the control groups. This tendency was replicated in an independent group of Hg H HCM index cases (n = 39) from Queensland, Australia, where the H3/H2 ratio was 1.5. In conclusion, the H subhgs distribution differs between HCM cases and controls, but the difference is subtle, and the understanding of the pathogenic significance is hampered by the lack of functional studies on the subhgs of H.
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Affiliation(s)
- Christian M Hagen
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Joanna L Elson
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark.,Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Paula L Hedley
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Frederik H Aidt
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark
| | - Ole Havndrup
- Department of Cardiology, Roskilde Hospital, Roskilde, Denmark
| | - Morten K Jensen
- Department of Medicine B, The Heart Center, Copenhagen, Denmark
| | - Jørgen K Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - John J Atherton
- Department of Cardiology, Royal Brisbane Hospital and School of Medicine, University of Queensland, Brisbane, Australia
| | - Julie McGaughran
- Queensland Clinical Genetics Service, Royal Children's Hospital and School of Medicine, Brisbane, Australia
| | | | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institute, Copenhagen, Denmark.,Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
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13
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Dowling DK, Adrian RE. Challenges and Prospects for Testing the Mother's Curse Hypothesis. Integr Comp Biol 2020; 59:875-889. [PMID: 31225591 DOI: 10.1093/icb/icz110] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Maternal inheritance of mitochondrial DNA (mtDNA) renders selection blind to mutations whose effects are limited to males. Evolutionary theory predicts this will lead to the accumulation of a male-specific genetic load within the mitochondrial genomes of populations; that is, a pool of mutations that negatively affects male, but not female, fitness components. This principle has been termed the Mother's Curse hypothesis. While the hypothesis has received some empirical support, its relevance to natural populations of metazoans remains unclear, and these ambiguities are compounded by the lack of a clear predictive framework for studies attempting to test Mother's Curse. Here, we seek to redress this by outlining the core predictions of the hypothesis, as well as the key features of the experimental designs that are required to enable direct testing of the predictions. Our goal is to provide a roadmap for future research seeking to elucidate the evolutionary significance of the Mother's Curse hypothesis.
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Affiliation(s)
- Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Rebecca E Adrian
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
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14
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O'Keefe H, Queen R, Lord P, Elson JL. What can a comparative genomics approach tell us about the pathogenicity of mtDNA mutations in human populations? Evol Appl 2019; 12:1912-1930. [PMID: 31700535 PMCID: PMC6824070 DOI: 10.1111/eva.12851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/13/2019] [Accepted: 07/17/2019] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial disorders are heterogeneous, showing variable presentation and penetrance. Over the last three decades, our ability to recognize mitochondrial patients and diagnose these mutations, linking genotype to phenotype, has greatly improved. However, it has become increasingly clear that these strides in diagnostics have not benefited all population groups. Recent studies have demonstrated that patients from genetically understudied populations, in particular those of black African heritage, are less likely to receive a diagnosis of mtDNA disease. It has been suggested that haplogroup context might influence the presentation and penetrance of mtDNA disease; thus, the spectrum of mutations that are associated with disease in different populations. However, to date there is only one well-established example of such an effect: the increased penetrance of two Leber's hereditary optic neuropathy mutations on a haplogroup J background. This paper conducted the most extensive investigation to date into the importance of haplogroup context on the pathogenicity of mtDNA mutations. We searched for proven human point mutations across 726 multiple sequence alignments derived from 33 non-human species absent of disease. A total of 58 pathogenic point mutations arise in the sequences of these species. We assessed the sequence context and found evidence of population variants that could modulate the phenotypic expression of these point mutations masking the pathogenic effects seen in humans. This supports the theory that sequence context is influential in the presentation of mtDNA disease and has implications for diagnostic practices. We have shown that our current understanding of the pathogenicity of mtDNA point mutations, primarily built on studies of individuals with haplogroups HVUKTJ, will not present a complete picture. This will have the effect of creating a diagnostic inequality, whereby individuals who do not belong to these lineages are less likely to receive a genetic diagnosis.
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Affiliation(s)
- Hannah O'Keefe
- Institute of Genetic MedicineNewcastle UniversityNewcastle‐upon‐TyneUK
- School of ComputingNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Rachel Queen
- Bioinformatics Core FacilityNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Phillip Lord
- School of ComputingNewcastle UniversityNewcastle‐upon‐TyneUK
| | - Joanna L. Elson
- Institute of Genetic MedicineNewcastle UniversityNewcastle‐upon‐TyneUK
- Centre for Human MetabonomicsNorth‐West UniversityPotchefstroomSouth Africa
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15
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Piotrowska-Nowak A, Elson JL, Sobczyk-Kopciol A, Piwonska A, Puch-Walczak A, Drygas W, Ploski R, Bartnik E, Tonska K. New mtDNA Association Model, MutPred Variant Load, Suggests Individuals With Multiple Mildly Deleterious mtDNA Variants Are More Likely to Suffer From Atherosclerosis. Front Genet 2019; 9:702. [PMID: 30671084 PMCID: PMC6332467 DOI: 10.3389/fgene.2018.00702] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 12/14/2018] [Indexed: 12/31/2022] Open
Abstract
The etiology of common complex diseases is multifactorial, involving both genetic, and environmental factors. A role for mitochondrial dysfunction and mitochondrial DNA (mtDNA) variation has been suggested in the pathogenesis of common complex traits. The aim of this study was to investigate a potential role of mtDNA variants in the development of obesity, diabetes, and atherosclerosis in the Polish population. Whole mtDNA sequences from 415 Polish individuals representing three disease cohorts and a control group were obtained using high-throughput sequencing. Two approaches for the assessment of mtDNA variation were applied, traditional mitochondrial haplogroup association analysis and the mutational or variant load model using the MutPred pathogenicity prediction algorithm for amino acid substitutions in humans. We present a possible association between mildly deleterious mtDNA variant load and atherosclerosis that might be due to having more than one likely mildly deleterious non-synonymous substitution. Moreover, it seems largely dependent upon a few common haplogroup associated variants with MutPred score above 0.5.
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Affiliation(s)
| | - Joanna L Elson
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, United Kingdom.,Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa
| | | | - Aleksandra Piwonska
- Department of Epidemiology, Cardiovascular Disease Prevention and Health Promotion, Institute of Cardiology, Warsaw, Poland
| | - Aleksandra Puch-Walczak
- Department of Prevention and Education, Department of Arterial Hypertension and Diabetology, Medical University of Gdansk, Gdansk, Poland
| | - Wojciech Drygas
- Department of Epidemiology, Cardiovascular Disease Prevention and Health Promotion, Institute of Cardiology, Warsaw, Poland
| | - Rafal Ploski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Ewa Bartnik
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland.,Institute of Biochemistry and Biophysics Polish Academy of Sciences, Warsaw, Poland
| | - Katarzyna Tonska
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
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16
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Haplogroup Context is Less Important in the Penetrance of Mitochondrial DNA Complex I Mutations Compared to mt-tRNA Mutations. J Mol Evol 2018; 86:395-403. [PMID: 29987491 PMCID: PMC6061473 DOI: 10.1007/s00239-018-9855-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 06/29/2018] [Indexed: 01/15/2023]
Abstract
Mitochondrial diseases are a highly complex, heterogeneous group of disorders. Mitochondrial DNA variants that are linked to disease can exhibit variable expression and penetrance. This has an implication for mitochondrial diagnostics as variants that cause disease in one individual may not in another. It has been suggested that the sequence context in which a variant arises could influence the genotype-phenotype relationship. However, the consequence of sequence variation between different haplogroups on the expression of disease is not well understood. European haplogroups are the most widely studied. To ensure accurate diagnostics for patients globally, we first need to understand how, if at all, the sequence context in which a variant arises contributes to the manifestion of disease. To help us understand this, we used 2752 sequences from 33 non-human species that do not have disease. We searched for variants in the seven complex I genes that are associated with disease in humans. Our findings indicate that only three reported pathogenic complex I variants have arisen in these species. More importantly, only one of these, m.3308T>C, has arisen with its associated amino acid change in the studied non-human species. With the status of m.3308T>C as a disease causing variant being a matter of debate. This is a stark contrast to previous findings in the mitochondrial tRNA genes and suggests that sequence context may be less important in the complex I genes. This information will help us improve the identification and diagnosis of mitochondrial DNA variants in non-European populations.
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