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Soini HK, Väisänen A, Kärppä M, Hinttala R, Kytövuori L, Moilanen JS, Uusimaa J, Majamaa K. A novel MTTT mutation m.15933G > A revealed in analysis of mitochondrial DNA in patients with suspected mitochondrial disease. BMC MEDICAL GENETICS 2017; 18:14. [PMID: 28187756 PMCID: PMC5303298 DOI: 10.1186/s12881-017-0377-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 02/03/2017] [Indexed: 01/25/2023]
Abstract
Background Mitochondrial diseases present with variable multi-organ symptoms. Common disease-causing mutations in mitochondrial DNA (mtDNA) are regularly screened in diagnostic work-up, but novel mutations may remain unnoticed. Methods Patients (N = 66) with a clinical suspicion of mitochondrial disease were screened for their mtDNA coding region using conformation sensitive gel electrophoresis and sequencing. Long-PCR was used to detect deletions followed by POLG1 sequencing in patients with multiple deletions. Results We discovered three novel mtDNA variants that included m.8743G > C, m.11322A > G and m.15933G > A. The novel MTTT variant m.15933G > A is suggested to be pathogenic. Analysis revealed also multiple mtDNA deletions in two patients and five nonsynonymous variants that were putatively pathogenic according to in-silico prediction algorithms. In addition, a rare haplogroup H associated m.7585_7586insT variant was discovered. Conclusions Among patients with a suspected mitochondrial disease, a novel MTTT variant m.15933G > A was discovered and is suggested to be pathogenic. In addition, several putatively pathogenic nonsynonymous variants and rare variants were found. These findings highlight the importance of coding region mtDNA screening among patients with clinical features suggesting a mitochondrial disease, but who lack the common mitochondrial disease mutations.
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Affiliation(s)
- Heidi K Soini
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland. .,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland. .,Department of Neurology, Oulu University Hospital, P.O. Box 20, FI-90029 OYS, Oulu, Finland. .,PEDEGO Research Unit, Pediatrics, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.
| | - Antti Väisänen
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, P.O. Box 20, FI-90029 OYS, Oulu, Finland
| | - Mikko Kärppä
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, P.O. Box 20, FI-90029 OYS, Oulu, Finland
| | - Reetta Hinttala
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,PEDEGO Research Unit, Pediatrics, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Pediatrics, Oulu University Hospital, P.O. Box 23, FI-90029 OYS, Oulu, Finland
| | - Laura Kytövuori
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, P.O. Box 20, FI-90029 OYS, Oulu, Finland
| | - Jukka S Moilanen
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Clinical Genetics, Oulu University Hospital, P.O. Box 23, FI-90029 OYS, Oulu, Finland.,PEDEGO Research Unit, Clinical Genetics, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Johanna Uusimaa
- Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,PEDEGO Research Unit, Pediatrics, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Pediatrics, Oulu University Hospital, P.O. Box 23, FI-90029 OYS, Oulu, Finland
| | - Kari Majamaa
- Research Unit of Clinical Neuroscience, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital and University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland.,Department of Neurology, Oulu University Hospital, P.O. Box 20, FI-90029 OYS, Oulu, Finland
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Peischl S, Dupanloup I, Kirkpatrick M, Excoffier L. On the accumulation of deleterious mutations during range expansions. Mol Ecol 2013; 22:5972-82. [PMID: 24102784 DOI: 10.1111/mec.12524] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 09/04/2013] [Accepted: 09/05/2013] [Indexed: 12/15/2022]
Abstract
We investigate the effect of spatial range expansions on the evolution of fitness when beneficial and deleterious mutations cosegregate. We perform individual-based simulations of 1D and 2D range expansions and complement them with analytical approximations for the evolution of mean fitness at the edge of the expansion. We find that deleterious mutations accumulate steadily on the wave front during range expansions, thus creating an expansion load. Reduced fitness due to the expansion load is not restricted to the wave front, but occurs over a large proportion of newly colonized habitats. The expansion load can persist and represent a major fraction of the total mutation load for thousands of generations after the expansion. The phenomenon of expansion load may explain growing evidence that populations that have recently expanded, including humans, show an excess of deleterious mutations. To test the predictions of our model, we analyse functional genetic diversity in humans and find patterns that are consistent with our model.
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Affiliation(s)
- S Peischl
- Institute of Ecology and Evolution, University of Berne, 3012, Berne, Switzerland; Section of Integrative Biology, University of Texas, Austin, TX, 78712, USA; Swiss Institute of Bioinformatics, 1015, Lausanne, Switzerland
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Soini HK, Moilanen JS, Vilmi-Kerälä T, Finnilä S, Majamaa K. Mitochondrial DNA variant m.15218A > G in Finnish epilepsy patients who have maternal relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus. BMC MEDICAL GENETICS 2013; 14:73. [PMID: 23870133 PMCID: PMC3726289 DOI: 10.1186/1471-2350-14-73] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 07/17/2013] [Indexed: 01/04/2023]
Abstract
BACKGROUND Mitochondrial diseases caused by mutations in mitochondrial DNA (mtDNA) affect tissues with high energy demand. Epilepsy is one of the manifestations of mitochondrial dysfunction when the brain is affected. We have studied here 79 Finnish patients with epilepsy and who have maternal first- or second-degree relatives with epilepsy, sensorineural hearing impairment or diabetes mellitus. METHODS The entire mtDNA was studied by using conformation sensitive gel electrophoresis and PCR fragments that differed in mobility were directly sequenced. RESULTS We found a common nonsynonymous variant m.15218A > G (p.T158A, MTCYB) that occurs in haplogroup U5a1 to be more frequent in patients with epilepsy. The m.15218A > G variant was present in five patients with epilepsy and in four out of 403 population controls (p = 0.0077). This variant was present in two branches in the phylogenetic network constructed on the basis of mtDNA variation among the patients. Three algorithms predicted that m.15218A > G is damaging in effect. CONCLUSIONS We suggest that the m.15218A > G variant is mildly deleterious and that mtDNA involvement should be considered in patients with epilepsy and who have a maternal history of epilepsy, sensorineural hearing impairment or diabetes mellitus.
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Affiliation(s)
- Heidi K Soini
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Jukka S Moilanen
- Department of Clinical Genetics, Oulu University Hospital and University of Oulu P.O. Box 23, FI-90029, OYS, Oulu, Finland
| | - Tiina Vilmi-Kerälä
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Saara Finnilä
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
| | - Kari Majamaa
- Department of Neurology, Oulu University Hospital, P.O. Box 20, Oulu FI-90029, OYS, Finland
- Department of Clinical Medicine, Neurology, University of Oulu, P.O. Box 5000, FI-90014, Oulu, Finland
- Clinical Research Center, Oulu University Hospital, P.O. Box 5000, FI-90014, Oulu, Finland
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Popadin KY, Nikolaev SI, Junier T, Baranova M, Antonarakis SE. Purifying selection in mammalian mitochondrial protein-coding genes is highly effective and congruent with evolution of nuclear genes. Mol Biol Evol 2012; 30:347-55. [PMID: 22983951 DOI: 10.1093/molbev/mss219] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The mammalian mitochondrial genomes differ from the nuclear genomes by maternal inheritance, absence of recombination, and higher mutation rate. All these differences decrease the effective population size of mitochondrial genome and make it more susceptible to accumulation of slightly deleterious mutations. It was hypothesized that mitochondrial genes, especially in species with low effective population size, irreversibly degrade leading to decrease of organismal fitness and even to extinction of species through the mutational meltdown. To interrogate this hypothesis, we compared the purifying selections acting on the representative set of mitochondrial (potentially degrading) and nuclear (potentially not degrading) protein-coding genes in species with different effective population size. For 21 mammalian species, we calculated the ratios of accumulation of slightly deleterious mutations approximated by Kn/Ks separately for mitochondrial and nuclear genomes. The 75% of variation in Kn/Ks is explained by two independent variables: type of a genome (mitochondrial or nuclear) and effective population size of species approximated by generation time. First, we observed that purifying selection is more effective in mitochondria than in the nucleus that implies strong evolutionary constraints of mitochondrial genome. Mitochondrial de novo nonsynonymous mutations have at least 5-fold more harmful effect when compared with nuclear. Second, Kn/Ks of mitochondrial and nuclear genomes is positively correlated with generation time of species, indicating relaxation of purifying selection with decrease of species-specific effective population size. Most importantly, the linear regression lines of mitochondrial and nuclear Kn/Ks's from generation times of species are parallel, indicating congruent relaxation of purifying selection in both genomes. Thus, our results reveal that the distribution of selection coefficients of de novo nonsynonymous mitochondrial mutations has a similar shape with the distribution of de novo nonsynonymous nuclear mutations, but its mean is five times smaller. The harmful effect of mitochondrial de novo nonsynonymous mutations triggers highly effective purifying selection, which maintains the fitness of the mammalian mitochondrial genome.
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Affiliation(s)
- Konstantin Yu Popadin
- Department of Genetic Medicine and Development, University of Geneva Medical School and iGE3 Institute of Genetics and Genomics of Geneva, Switzerland.
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