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Zheng HX, Yan S, Zhang M, Gu Z, Wang J, Jin L. Mitochondrial DNA Genomes Reveal Relaxed Purifying Selection During Human Population Expansion after the Last Glacial Maximum. Mol Biol Evol 2024; 41:msae175. [PMID: 39162340 PMCID: PMC11373649 DOI: 10.1093/molbev/msae175] [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: 11/27/2023] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/21/2024] Open
Abstract
Modern humans have experienced explosive population growth in the past thousand years. We hypothesized that recent human populations have inhabited environments with relaxation of selective constraints, possibly due to the more abundant food supply after the Last Glacial Maximum. The ratio of nonsynonymous to synonymous mutations (N/S ratio) is a useful and common statistic for measuring selective constraints. In this study, we reconstructed a high-resolution phylogenetic tree using a total of 26,419 East Eurasian mitochondrial DNA genomes, which were further classified into expansion and nonexpansion groups on the basis of the frequencies of their founder lineages. We observed a much higher N/S ratio in the expansion group, especially for nonsynonymous mutations with moderately deleterious effects, indicating a weaker effect of purifying selection in the expanded clades. However, this observation on N/S ratio was unlikely in computer simulations where all individuals were under the same selective constraints. Thus, we argue that the expanded populations were subjected to weaker selective constraints than the nonexpanded populations were. The mildly deleterious mutations were retained during population expansion, which could have a profound impact on present-day disease patterns.
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Affiliation(s)
- 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
| | - Shi Yan
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China
| | - Zhenglong Gu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai, China
- Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 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, Beijing, 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, Beijing, China
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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] [Key Words] [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 2877 Han Chinese individuals from three independent populations. The association analysis of 16 basal mtDNA haplogroups with body mass index, waist circumference, and waist-to-hip ratio revealed that only haplogroup M7 was significantly negatively correlated with all three adiposity-related anthropometric traits in the overall cohort, 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 the 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 200438, China
| | - Lu Chen
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Jingze Tan
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai 200438, China
| | - Yizhen Mao
- Ministry of Education Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Meng Hao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai 200438, China
| | - Yi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai 200438, China
| | - Yi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai 200438, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200438, China
| | - Jinxi Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai 200438, China
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai 200438, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200438, 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, Beijing 100730, China.
| | - Li Jin
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute and Center for Evolutionary Biology, Fudan University, Shanghai 200438, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200438, 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, Beijing 100730, 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 200438, China; Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai 200438, China.
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3
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Volpe KE, Samuels DC, Elson JL, Steyn JS, Gebretsadik T, Ellis RJ, Heaton RK, Kallianpur AR, Letendre S, Hulgan T. Mitochondrial DNA mutation pathogenicity score and neurocognitive performance in persons with HIV. Mitochondrion 2024; 74:101820. [PMID: 37989461 PMCID: PMC10872545 DOI: 10.1016/j.mito.2023.11.003] [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: 01/30/2023] [Revised: 10/06/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) genetic variation is associated with neurocognitive (NC) impairment (NCI) in people with HIV (PWH). Other approaches use sequence conservation and protein structure to predict the impact of mtDNA variants on protein function. We examined predicted mtDNA variant pathogenicity in the CHARTER study using MutPred scores, hypothesizing that persons with higher scores (greater predicted pathogenicity) have more NCI. METHODS CHARTER included NC testing in PWH from 2003 to 2007. MutPred scores were assigned to CHARTER participants with mtDNA sequence; any score > 0.5 was considered potentially deleterious. Outcomes at cohort entry were NCI, defined by global and seven NC domain deficit scores, and by mean global and domain NC performance T-scores. Univariate and multivariable regression analyses assessed associations between having a deleterious variant and NCI. Additional models included estimated peripheral blood cell mtDNA copy number. RESULTS Data were available for 744 PWH (357 African ancestry; 317 European; 70 Hispanic). In the overall cohort, PWH having any potentially deleterious variant were less likely to have motor impairment (16 vs. 25 %, p = 0.001). In multivariable analysis, having a deleterious variant remained associated with lower likelihood of motor impairment (adjusted odds ratio 0.59 [95 % CI 0.41-0.88]; p = 0.009), and better motor performance by T-score (β 1.71 [0.31-3.10], p = 0.02). Associations persisted after adjustment for estimated mtDNA quantity. CONCLUSIONS In these PWH, having a potentially deleterious mtDNA variant was associated with less motor impairment. These unexpected findings suggest that potentially deleterious mtDNA variations may confer protection against impaired motor function by as yet unknown mechanisms.
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Affiliation(s)
- Karen E Volpe
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - David C Samuels
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joanna L Elson
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Jannetta S Steyn
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | | | | | | | | | | | - Todd Hulgan
- Vanderbilt University Medical Center, Nashville, TN, USA.
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Shukla P, Mukherjee S, Patil A, Joshi B. Molecular characterization of variants in mitochondrial DNA encoded genes using next generation sequencing analysis and mitochondrial dysfunction in women with PCOS. Gene 2023; 855:147126. [PMID: 36563715 DOI: 10.1016/j.gene.2022.147126] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 12/07/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022]
Abstract
Emerging studies indicates mitochondrial dysfunction and involvement of mitochondrial DNA (mtDNA) variants in the pathogenesis of polycystic ovary syndrome (PCOS). Cumulative effect of mtDNA rare variants are now gaining considerable interest apart from common variants in the pathogenesis of complex diseases. Rare variants may modify the effect of polymorphism or in combination with the common variants may affect the risk of disease. With the evolution of high throughput sequencing techniques, which can be utilized to identify common as well as rare variants along with heteroplasmy levels, comprehensive characterization of the mtDNA variants is possible. Till date, few studies reported common mtDNA variants using traditional sequencing techniques but rare variants in mtDNA encoding genes remain unexplored in women with PCOS. These mtDNA variants may be responsible for mitochondrial dysfunction and may contribute in PCOS pathogenesis. In this study we determined mtDNA copy number, a biomarker of mitochondrial dysfunction and first time analysed variants in mtDNA encoded genes in women with PCOS using mitochondrial Next Generation sequencing (NGS) approach and compared allele frequency from mitochondrial 1000 genome dataset. Variant annotation and prioritization was done using highly automated pipeline, MToolBox that excludes reads mapped from nuclear mitochondrial DNA sequences (NumtS) to identify unique mtDNA reads. The present study identified significant reduction in mtDNA copy number in women with PCOS compared to non-PCOS women. A total of unique 214 prioritized common to rare variants were identified in mtDNA encoded genes, 183 variants in OXPHOS complexes, 14 variants in MT-tRNA and 17 variants in MT-rRNA genes that may be involved in mitochondrial dysfunction in PCOS. Numerous variants were heteroplasmic, pathogenic in nature and occurred in evolutionary conserved region. Heteroplasmic variants were more frequently occurred in MT-CO3 gene. Non-synonymous variants were more than synonymous variants and mainly occurred in OXPHOS complex I and IV. Few variants were found to be associated with diseases in MITOMAP database. The study provides a better understanding towards pathogenesis of PCOS from novel aspects focusing on mitochondrial genetic defects as underlying cause for contributing mitochondrial dysfunction in women with PCOS.
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Affiliation(s)
- Pallavi Shukla
- Department of Molecular Endocrinology, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH), J.M. Street, Parel, Mumbai 400012, India.
| | - Srabani Mukherjee
- Department of Molecular Endocrinology, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH), J.M. Street, Parel, Mumbai 400012, India
| | - Anushree Patil
- Department of Clinical Research, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH), J.M. Street, Parel, Mumbai 400012, India
| | - Beena Joshi
- Department of Operational Research, Indian Council of Medical Research-National Institute for Research in Reproductive and Child Health (ICMR-NIRRCH), J.M. Street, Parel, Mumbai 400012, India
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5
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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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Ahmed Z, Renart EG, Zeeshan S. Genomics pipelines to investigate susceptibility in whole genome and exome sequenced data for variant discovery, annotation, prediction and genotyping. PeerJ 2021; 9:e11724. [PMID: 34395068 PMCID: PMC8320519 DOI: 10.7717/peerj.11724] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 06/14/2021] [Indexed: 12/12/2022] Open
Abstract
Over the last few decades, genomics is leading toward audacious future, and has been changing our views about conducting biomedical research, studying diseases, and understanding diversity in our society across the human species. The whole genome and exome sequencing (WGS/WES) are two of the most popular next-generation sequencing (NGS) methodologies that are currently being used to detect genetic variations of clinical significance. Investigating WGS/WES data for the variant discovery and genotyping is based on the nexus of different data analytic applications. Although several bioinformatics applications have been developed, and many of those are freely available and published. Timely finding and interpreting genetic variants are still challenging tasks among diagnostic laboratories and clinicians. In this study, we are interested in understanding, evaluating, and reporting the current state of solutions available to process the NGS data of variable lengths and types for the identification of variants, alleles, and haplotypes. Residing within the scope, we consulted high quality peer reviewed literature published in last 10 years. We were focused on the standalone and networked bioinformatics applications proposed to efficiently process WGS and WES data, and support downstream analysis for gene-variant discovery, annotation, prediction, and interpretation. We have discussed our findings in this manuscript, which include but not are limited to the set of operations, workflow, data handling, involved tools, technologies and algorithms and limitations of the assessed applications.
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Affiliation(s)
- Zeeshan Ahmed
- Institute for Health, Health Care Policy and Aging Research, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.,Department of Medicine, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Eduard Gibert Renart
- Institute for Health, Health Care Policy and Aging Research, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Saman Zeeshan
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
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7
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Hulgan T, Samuels DC. Mitochondria and Human Immunodeficiency Virus: A Troubled Relationship Enters Its Fourth Decade. Clin Infect Dis 2021; 73:e474-e476. [PMID: 32722791 DOI: 10.1093/cid/ciaa983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 07/09/2020] [Indexed: 11/14/2022] Open
Affiliation(s)
- Todd Hulgan
- Department of Medicine, Division of Infectious Diseases, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
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8
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Pienaar IS, Mohammed R, Courtley R, Gledson MR, Reynolds R, Nicholas R, Elson JL. Investigation of the correlation between mildly deleterious mtDNA Variations and the clinical progression of multiple sclerosis. Mult Scler Relat Disord 2021; 53:103055. [PMID: 34119746 DOI: 10.1016/j.msard.2021.103055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 05/17/2021] [Accepted: 05/26/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Evidence suggests that mitochondrial DNA (mtDNA) variation at a population level may influence susceptibility to, or the clinical progression of Multiple Sclerosis (MS). OBJECTIVE To determine if mtDNA population variation is linked to the clinical progress of MS. METHODS Using the complete mtDNA sequences of 217 MS patients, we applied the new 'variant load' model, designed as a framework by which to examine the role of mtDNA variation in the context of complex clinical disease. RESULTS No significant association was detected between mtDNA 'variant load'and the clinical measures of progression. CONCLUSION Our results suggest that mtDNA population variation does not play a substantial role in the clinical progression of MS; however, modest effects and/or effects in a subgroup of patients cannot be entirely excluded. Results do not exclude the possibility of detecting an association between variation and more strictly quantified variables obtained from histopathologically-stained specimens. The results further illustrate the method's applicabilityto other disease phenotypes.
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Affiliation(s)
- Ilse S Pienaar
- School of Life Sciences, University of Sussex, Falmer, United Kingdom
| | - Rean Mohammed
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Rebecca Courtley
- Northern Genetics Service, Newcastle Hospitals NHS Foundation Trust Newcastle upon Tyne, United Kingdom
| | - Michael R Gledson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Richard Reynolds
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom; Centre for Molecular Neuropathology, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Richard Nicholas
- Department of Brain Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Joanna L Elson
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; Centre for Human Metabolomics, North-West University, Potchefstroom, South Africa.
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9
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Piotrowska-Nowak A, Krawczyński MR, Kosior-Jarecka E, Ambroziak AM, Korwin M, Ołdak M, Tońska K, Bartnik E. Mitochondrial genome variation in male LHON patients with the m.11778G > A mutation. Metab Brain Dis 2020; 35:1317-1327. [PMID: 32740724 PMCID: PMC7584531 DOI: 10.1007/s11011-020-00605-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/21/2020] [Indexed: 11/30/2022]
Abstract
Leber hereditary optic neuropathy (LHON) is a mitochondrial disorder with symptoms limited to a single tissue, optic nerve, resulting in vision loss. In the majority of cases it is caused by one of three point mutations in mitochondrial DNA (mtDNA) but their presence is not sufficient for disease development, since ~50% of men and ~10% women who carry them are affected. Thus additional modifying factors must exist. In this study, we use next generation sequencing to investigate the role of whole mtDNA variation in male Polish patients with LHON and m.11778G > A, the most frequent LHON mutation. We present a possible association between mtDNA haplogroup K and variants in its background, a combination of m.3480A > G, m.9055G > A, m.11299 T > C and m.14167C > T, and LHON mutation. These variants may have a negative effect on m.11778G > A increasing its penetrance and the risk of LHON in the Polish population. Surprisingly, we did not observe associations previously reported for m.11778G > A and LHON in European populations, particularly for haplogroup J as a risk factor, implying that mtDNA variation is much more complex. Our results indicate possible contribution of novel combination of mtDNA genetic factors to the LHON phenotype.
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Affiliation(s)
- Agnieszka Piotrowska-Nowak
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 5a Pawińskiego Street, 02-106 Warsaw, Poland
| | - Maciej R. Krawczyński
- Department of Medical Genetics, Poznań University of Medical Sciences, 8 Rokietnicka Street, 60-806 Poznań, Poland
- Centers for Medical Genetics GENESIS, 4 Grudzieniec Street, 60-601 Poznań, Poland
| | - Ewa Kosior-Jarecka
- Department of Diagnostics and Microsurgery of Glaucoma, Medical University of Lublin, 1 Chmielna Street, 20-079 Lublin, Poland
| | - Anna M. Ambroziak
- Faculty of Physics, University of Warsaw, 5 Pasteur Street, 02-093 Warsaw, Poland
| | - Magdalena Korwin
- Department of Ophthalmology, Medical University of Warsaw, 13 Sierakowskiego Street, 03-709 Warsaw, Poland
| | - Monika Ołdak
- Department of Genetics, Institute of Physiology and Pathology of Hearing, 10 Mochnackiego Street, 02-042 Warsaw, Poland
- Department of Histology and Embryology, Center of Biostructure Research, Medical University of Warsaw, 5 Chałubińskiego Street, 02-004 Warsaw, Poland
| | - Katarzyna Tońska
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 5a Pawińskiego Street, 02-106 Warsaw, Poland
| | - Ewa Bartnik
- Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, 5a Pawińskiego Street, 02-106 Warsaw, Poland
- Institute of Biochemistry and Biophysics Polish Academy of Sciences, 5a Pawińskiego Street, 02-106 Warsaw, Poland
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10
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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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11
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Peng Y, Gao P, Shi L, Chen L, Liu J, Long J. Central and Peripheral Metabolic Defects Contribute to the Pathogenesis of Alzheimer's Disease: Targeting Mitochondria for Diagnosis and Prevention. Antioxid Redox Signal 2020; 32:1188-1236. [PMID: 32050773 PMCID: PMC7196371 DOI: 10.1089/ars.2019.7763] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 12/20/2022]
Abstract
Significance: Epidemiological studies indicate that metabolic disorders are associated with an increased risk for Alzheimer's disease (AD). Metabolic remodeling occurs in the central nervous system (CNS) and periphery, even in the early stages of AD. Mitochondrial dysfunction has been widely accepted as a molecular mechanism underlying metabolic disorders. Therefore, focusing on early metabolic changes, especially from the perspective of mitochondria, could be of interest for early AD diagnosis and intervention. Recent Advances: We and others have identified that the levels of several metabolites are fluctuated in the periphery before their accumulation in the CNS, which plays an important role in the pathogenesis of AD. Mitochondrial remodeling is likely one of the earliest signs of AD, linking nutritional imbalance to cognitive deficits. Notably, by improving mitochondrial function, mitochondrial nutrients efficiently rescue cellular metabolic dysfunction in the CNS and periphery in individuals with AD. Critical Issues: Peripheral metabolic disorders should be intensively explored and evaluated for the early diagnosis of AD. The circulating metabolites derived from mitochondrial remodeling represent novel potential diagnostic biomarkers for AD that are more readily detected than CNS-oriented biomarkers. Moreover, mitochondrial nutrients provide a promising approach to preventing and delaying AD progression. Future Directions: Abnormal mitochondrial metabolism in the CNS and periphery is involved in AD pathogenesis. More clinical studies provide evidence for the suitability and reliability of circulating metabolites and cytokines for the early diagnosis of AD. Targeting mitochondria to rewire cellular metabolism is a promising approach to preventing AD and ameliorating AD-related metabolic disorders.
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Affiliation(s)
- Yunhua Peng
- Center for Mitochondrial Biology & Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Peipei Gao
- Center for Mitochondrial Biology & Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Le Shi
- Center for Mitochondrial Biology & Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Lei Chen
- Center for Mitochondrial Biology & Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Jiankang Liu
- Center for Mitochondrial Biology & Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, China
| | - Jiangang Long
- Center for Mitochondrial Biology & Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, China
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12
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Wang W, Zhao F, Ma X, Perry G, Zhu X. Mitochondria dysfunction in the pathogenesis of Alzheimer's disease: recent advances. Mol Neurodegener 2020; 15:30. [PMID: 32471464 PMCID: PMC7257174 DOI: 10.1186/s13024-020-00376-6] [Citation(s) in RCA: 578] [Impact Index Per Article: 144.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 04/24/2020] [Indexed: 12/22/2022] Open
Abstract
Alzheimer's disease (AD) is one of the most prevalent neurodegenerative diseases, characterized by impaired cognitive function due to progressive loss of neurons in the brain. Under the microscope, neuronal accumulation of abnormal tau proteins and amyloid plaques are two pathological hallmarks in affected brain regions. Although the detailed mechanism of the pathogenesis of AD is still elusive, a large body of evidence suggests that damaged mitochondria likely play fundamental roles in the pathogenesis of AD. It is believed that a healthy pool of mitochondria not only supports neuronal activity by providing enough energy supply and other related mitochondrial functions to neurons, but also guards neurons by minimizing mitochondrial related oxidative damage. In this regard, exploration of the multitude of mitochondrial mechanisms altered in the pathogenesis of AD constitutes novel promising therapeutic targets for the disease. In this review, we will summarize recent progress that underscores the essential role of mitochondria dysfunction in the pathogenesis of AD and discuss mechanisms underlying mitochondrial dysfunction with a focus on the loss of mitochondrial structural and functional integrity in AD including mitochondrial biogenesis and dynamics, axonal transport, ER-mitochondria interaction, mitophagy and mitochondrial proteostasis.
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Affiliation(s)
- Wenzhang Wang
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA.
| | - Fanpeng Zhao
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA
| | - Xiaopin Ma
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA
| | - George Perry
- College of Sciences, University of Texas at San Antonio, San Antonio, TX, USA.
| | - Xiongwei Zhu
- Department of Pathology, Case Western Reserve University, 2103 Cornell Road, Cleveland, OH, 44106, USA.
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13
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Müller-Nedebock AC, Brennan RR, Venter M, Pienaar IS, van der Westhuizen FH, Elson JL, Ross OA, Bardien S. The unresolved role of mitochondrial DNA in Parkinson's disease: An overview of published studies, their limitations, and future prospects. Neurochem Int 2019; 129:104495. [PMID: 31233840 PMCID: PMC6702091 DOI: 10.1016/j.neuint.2019.104495] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 05/27/2019] [Accepted: 06/21/2019] [Indexed: 12/21/2022]
Abstract
Parkinson's disease (PD), a progressive neurodegenerative disorder, has long been associated with mitochondrial dysfunction in both sporadic and familial forms of the disease. Mitochondria are crucial for maintaining cellular homeostasis, and their dysfunction is detrimental to dopaminergic neurons. These neurons are highly dependent on mitochondrial adenosine triphosphate (ATP) and degenerate in PD. Mitochondria contain their own genomes (mtDNA). The role of mtDNA has been investigated in PD on the premise that it encodes vital components of the ATP-generating oxidative phosphorylation (OXPHOS) complexes and accumulates somatic variation with age. However, the association between mtDNA variation and PD remains controversial. Herein, we provide an overview of previously published studies on the role of inherited as well as somatic (acquired) mtDNA changes in PD including point mutations, deletions and depletion. We outline limitations of previous investigations and the difficulties associated with studying mtDNA, which have left its role unresolved in the context of PD. Lastly, we highlight the potential for further research in this field and provide suggestions for future studies. Overall, the mitochondrial genome is indispensable for proper cellular function and its contribution to PD requires further, more extensive investigation.
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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, South Africa
| | | | - Marianne Venter
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Ilse S Pienaar
- School of Life Sciences, University of Sussex, Falmer, BN1 9PH, United Kingdom; Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, United Kingdom
| | | | - Joanna L Elson
- Human Metabolomics, North-West University, Potchefstroom, South Africa; Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, United Kingdom
| | - Owen A Ross
- Department of Neuroscience, Mayo Clinic, Jacksonville, FL, USA; Department of Clinical Genomics, Mayo Clinic, Jacksonville, FL, USA; School of Medicine and Medical Science, University College Dublin, Dublin, Ireland
| | - Soraya Bardien
- Division of Molecular Biology and Human Genetics, Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa.
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14
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Venter M, Tomas C, Pienaar IS, Strassheim V, Erasmus E, Ng WF, Howell N, Newton JL, Van der Westhuizen FH, Elson JL. MtDNA population variation in Myalgic encephalomyelitis/Chronic fatigue syndrome in two populations: a study of mildly deleterious variants. Sci Rep 2019; 9:2914. [PMID: 30814539 PMCID: PMC6393470 DOI: 10.1038/s41598-019-39060-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Accepted: 01/11/2019] [Indexed: 02/07/2023] Open
Abstract
Myalgic Encephalomyelitis (ME), also known as Chronic Fatigue Syndrome (CFS) is a debilitating condition. There is growing interest in a possible etiologic or pathogenic role of mitochondrial dysfunction and mitochondrial DNA (mtDNA) variation in ME/CFS. Supporting such a link, fatigue is common and often severe in patients with mitochondrial disease. We investigate the role of mtDNA variation in ME/CFS. No proven pathogenic mtDNA mutations were found. We then investigated population variation. Two cohorts were analysed, one from the UK (n = 89 moderately affected; 29 severely affected) and the other from South Africa (n = 143 moderately affected). For both cohorts, ME/CFS patients had an excess of individuals without a mildly deleterious population variant. The differences in population variation might reflect a mechanism important to the pathophysiology of ME/CFS.
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Affiliation(s)
- Marianne Venter
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Cara Tomas
- Institute of Cellular Medicine & NIHR Biomedical Research Centre in Ageing and Chronic Disease, Newcastle University, Newcastle-upon-Tyne, United Kingdom
| | - Ilse S Pienaar
- School of Life Sciences, University of Sussex, Falmer, BN1 9PH, United Kingdom
- Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, United Kingdom
| | - Victoria Strassheim
- Institute of Cellular Medicine & NIHR Biomedical Research Centre in Ageing and Chronic Disease, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, United Kingdom
| | - Elardus Erasmus
- Human Metabolomics, North-West University, Potchefstroom, South Africa
| | - Wan-Fai Ng
- Institute of Cellular Medicine & NIHR Biomedical Research Centre in Ageing and Chronic Disease, Newcastle University, Newcastle-upon-Tyne, United Kingdom
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | - Neil Howell
- Department of Radiation Therapy, UTMB, Galveston, Texas, USA
| | - Julia L Newton
- Centre for Neuroinflammation and Neurodegeneration, Imperial College London, London, United Kingdom
- Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle, United Kingdom
| | | | - Joanna L Elson
- Human Metabolomics, North-West University, Potchefstroom, South Africa.
- Institute of Genetic Medicine, Newcastle University, Newcastle-upon-Tyne, United Kingdom.
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15
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Venter M, Malan L, Elson JL, van der Westhuizen FH. Implementing a new variant load model to investigate the role of mtDNA in oxidative stress and inflammation in a bi-ethnic cohort: the SABPA study. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:440-447. [PMID: 30657012 DOI: 10.1080/24701394.2018.1544248] [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] [Indexed: 12/21/2022]
Abstract
Mitochondrial DNA (mtDNA) variation has been implicated in several common complex and degenerative diseases, including cardiovascular disease. Inflammation is seen as part of many of these conditions. Mitochondria feature in inflammatory pathways and it has been suggested that mtDNA variation or released mtDNA might be important in this phenomenon. To determine if mtDNA is involved in the mechanisms leading up to cardiovascular disease, we investigated the role of these variants in seven indicators of oxidative stress and inflammation. This study was done in participants of the Sympathetic Activity and Ambulatory Blood Pressure in Africans (SABPA) cohort, a South African bi-ethnic cohort (N = 363). We applied a variant load hypothesis, which is an alternative approach to, and moves away from the classic haplogroup association approaches, to evaluate the cumulative effect of non-synonymous mtDNA variants on measurements of serum peroxides, nitric oxide metabolites, 8-hydroxy-deoxyguanosine, thiobarbituric acid reactive substances, whole blood reduced glutathione, C-reactive protein, and tumor necrosis factor alpha. We found no significant relationships between non-synonymous mtDNA variants and the seven biochemical parameters investigated here. Non-synonymous mtDNA variants are unlikely to impact on disease in this cohort, to an appreciable or measurable extent.
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Affiliation(s)
- Marianne Venter
- a Human Metabolomics, North-West University , Potchefstroom , South Africa
| | - Leone Malan
- b Hypertension in Africa Research Team (HART), Centre of Excellence , North-West University , Potchefstroom , South Africa
| | - Joanna L Elson
- a Human Metabolomics, North-West University , Potchefstroom , South Africa.,c Institute of Genetic Medicine, Newcastle University , Newcastle-upon-Tyne , United Kingdom
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16
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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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