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Cosemans C, Alfano R, Sleurs H, Martens DS, Nawrot TS, Plusquin M. Exploring mitochondrial heteroplasmy in neonates: implications for growth patterns and overweight in the first years of life. Int J Obes (Lond) 2024; 48:1140-1147. [PMID: 38802661 DOI: 10.1038/s41366-024-01537-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 05/02/2024] [Accepted: 05/07/2024] [Indexed: 05/29/2024]
Abstract
BACKGROUND Mitochondrial heteroplasmy reflects genetic diversity within individuals due to the presence of varying mitochondrial DNA (mtDNA) sequences, possibly affecting mitochondrial function and energy production in cells. Rapid growth during early childhood is a critical development with long-term implications for health and well-being. In this study, we investigated if cord blood mtDNA heteroplasmy is associated with rapid growth at 6 and 12 months and overweight in childhood at 4-6 years. METHODS This study included 200 mother-child pairs of the ENVIRONAGE birth cohort. Whole mitochondrial genome sequencing was performed to determine mtDNA heteroplasmy levels (in variant allele frequency; VAF) in cord blood. Rapid growth was defined for each child as the difference between WHO-SD scores of predicted weight at either 6 or 12 months and birth weight. Logistic regression models were used to determine the association of mitochondrial heteroplasmy with rapid growth and childhood overweight. Determinants of relevant cord blood mitochondrial heteroplasmies were identified using multiple linear regression models. RESULTS One % increase in VAF of cord blood MT-D-Loop16362T > C heteroplasmy was associated with rapid growth at 6 months (OR = 1.03; 95% CI: 1.01-1.05; p = 0.001) and 12 months (OR = 1.02; 95% CI: 1.00-1.03; p = 0.02). Furthermore, this variant was associated with childhood overweight at 4-6 years (OR = 1.01; 95% CI 1.00-1.02; p = 0.05). Additionally, rapid growth at 6 months (OR = 3.00; 95% CI: 1.49-6.14; p = 0.002) and 12 months (OR = 4.05; 95% CI: 2.06-8.49; p < 0.001) was also associated with childhood overweight at 4-6 years. Furthermore, we identified maternal age, pre-pregnancy BMI, maternal education, parity, and gestational age as determinants of cord blood MT-D-Loop16362T > C heteroplasmy. CONCLUSIONS Our findings, based on mitochondrial DNA genotyping, offer insights into the molecular machinery leading to rapid growth in early life, potentially explaining a working mechanism of the development toward childhood overweight.
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Affiliation(s)
- Charlotte Cosemans
- Centre for Environmental Sciences, Hasselt University, 3590, Diepenbeek, Belgium
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, 3590, Diepenbeek, Belgium
| | - Hanne Sleurs
- Centre for Environmental Sciences, Hasselt University, 3590, Diepenbeek, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, 3590, Diepenbeek, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, 3590, Diepenbeek, Belgium
- School of Public Health, Occupational & Environmental Medicine, Leuven University, 3000, Leuven, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, 3590, Diepenbeek, Belgium.
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2
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Cosemans C, Wang C, Alfano R, Martens DS, Sleurs H, Dockx Y, Vanbrabant K, Janssen BG, Vanpoucke C, Lefebvre W, Smeets K, Nawrot TS, Plusquin M. In utero particulate matter exposure in association with newborn mitochondrial ND4L 10550A>G heteroplasmy and its role in overweight during early childhood. Environ Health 2022; 21:88. [PMID: 36117180 PMCID: PMC9484069 DOI: 10.1186/s12940-022-00899-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 09/01/2022] [Indexed: 05/26/2023]
Abstract
BACKGROUND Mitochondria play an important role in the energy metabolism and are susceptible to environmental pollution. Prenatal air pollution exposure has been linked with childhood obesity. Placental mtDNA mutations have been associated with prenatal particulate matter exposure and MT-ND4L10550A>G heteroplasmy has been associated with BMI in adults. Therefore, we hypothesized that in utero PM2.5 exposure is associated with cord blood MT-ND4L10550A>G heteroplasmy and early life growth. In addition, the role of cord blood MT-ND4L10550A>G heteroplasmy in overweight during early childhood is investigated. METHODS This study included 386 mother-newborn pairs. Outdoor PM2.5 concentrations were determined at the maternal residential address. Cord blood MT-ND4L10550A>G heteroplasmy was determined using Droplet Digital PCR. Associations were explored using logistic regression models and distributed lag linear models. Mediation analysis was performed to quantify the effects of prenatal PM2.5 exposure on childhood overweight mediated by cord blood MT-ND4L10550A>G heteroplasmy. RESULTS Prenatal PM2.5 exposure was positively associated with childhood overweight during the whole pregnancy (OR = 2.33; 95% CI: 1.20 to 4.51; p = 0.01), which was mainly driven by the second trimester. In addition, prenatal PM2.5 exposure was associated with cord blood MT-ND4L10550A>G heteroplasmy from gestational week 9 - 13. The largest effect was observed in week 10, where a 5 µg/m3 increment in PM2.5 was linked with cord blood MT-ND4L10550A>G heteroplasmy (OR = 0.93; 95% CI: 0.87 to 0.99). Cord blood MT-ND4L10550A>G heteroplasmy was also linked with childhood overweight (OR = 3.04; 95% CI: 1.15 to 7.50; p = 0.02). The effect of prenatal PM2.5 exposure on childhood overweight was mainly direct (total effect OR = 1.18; 95% CI: 0.99 to 1.36; natural direct effect OR = 1.20; 95% CI: 1.01 to 1.36)) and was not mediated by cord blood MT-ND4L10550A>G heteroplasmy. CONCLUSIONS Cord blood MT-ND4L10550A>G heteroplasmy was linked with childhood overweight. In addition, in utero exposure to PM2.5 during the first trimester of pregnancy was associated with cord blood MT-ND4L10550A>G heteroplasmy in newborns. Our analysis did not reveal any mediation of cord blood MT-ND4L10550A>G heteroplasmy in the association between PM2.5 exposure and childhood overweight.
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Affiliation(s)
- Charlotte Cosemans
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Dries S Martens
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Hanne Sleurs
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Yinthe Dockx
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Kenneth Vanbrabant
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Bram G Janssen
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | | | - Wouter Lefebvre
- Flemish Institute for Technological Research, VITO, Mol, Belgium
| | - Karen Smeets
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium
- School of Public Health, Occupational & Environmental Medicine, Leuven University, Leuven, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Diepenbeek, Belgium.
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3
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Zyla J, Kabacik S, O'Brien G, Wakil S, Al-Harbi N, Kaprio J, Badie C, Polanska J, Alsbeih G. Combining CDKN1A gene expression and genome-wide SNPs in a twin cohort to gain insight into the heritability of individual radiosensitivity. Funct Integr Genomics 2019; 19:575-585. [PMID: 30706161 PMCID: PMC6570669 DOI: 10.1007/s10142-019-00658-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 12/12/2018] [Accepted: 01/09/2019] [Indexed: 12/15/2022]
Abstract
Individual variability in response to radiation exposure is recognised and has often been reported as important in treatment planning. Despite many efforts to identify biomarkers allowing the identification of radiation sensitive patients, it is not yet possible to distinguish them with certainty before the beginning of the radiotherapy treatment. A comprehensive analysis of genome-wide single-nucleotide polymorphisms (SNPs) and a transcriptional response to ionising radiation exposure in twins have the potential to identify such an individual. In the present work, we investigated SNP profile and CDKN1A gene expression in blood T lymphocytes from 130 healthy Caucasians with a complex level of individual kinship (unrelated, mono- or dizygotic twins). It was found that genetic variation accounts for 66% (95% CI 37-82%) of CDKN1A transcriptional response to radiation exposure. We developed a novel integrative multi-kinship strategy allowing investigating the role of genome-wide polymorphisms in transcriptomic radiation response, and it revealed that rs205543 (ETV6 gene), rs2287505 and rs1263612 (KLF7 gene) are significantly associated with CDKN1A expression level. The functional analysis revealed that rs6974232 (RPA3 gene), involved in mismatch repair (p value = 9.68e-04) as well as in RNA repair (p value = 1.4e-03) might have an important role in that process. Two missense polymorphisms with possible deleterious effect in humans were identified: rs1133833 (AKIP1 gene) and rs17362588 (CCDC141 gene). In summary, the data presented here support the validity of this novel integrative data analysis strategy to provide insights into the identification of SNPs potentially influencing radiation sensitivity. Further investigations in radiation response research at the genomic level should be therefore continued to confirm these findings.
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Affiliation(s)
- Joanna Zyla
- Data Mining Division, Faculty of Automatic Control, Electronic and Computer Science, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland
| | - Sylwia Kabacik
- Cellular Biology Group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, OX11 0RQ, UK
| | - Grainne O'Brien
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, OX11 0RQ, UK
| | - Salma Wakil
- Department of Genetics, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Najla Al-Harbi
- Radiation Biology Section, Biomedical Physics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
| | - Jaakko Kaprio
- Department of Public Health and Institute for Molecular Medicine FIMM, University of Helsinki, 00140, Helsinki, Finland
| | - Christophe Badie
- Cancer Mechanisms and Biomarkers Group, Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, OX11 0RQ, UK
| | - Joanna Polanska
- Data Mining Division, Faculty of Automatic Control, Electronic and Computer Science, Silesian University of Technology, Akademicka 16, 44-100, Gliwice, Poland.
| | - Ghazi Alsbeih
- Radiation Biology Section, Biomedical Physics Department, King Faisal Specialist Hospital and Research Centre, Riyadh, 11211, Kingdom of Saudi Arabia
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Souren NYP, Gerdes LA, Kümpfel T, Lutsik P, Klopstock T, Hohlfeld R, Walter J. Mitochondrial DNA Variation and Heteroplasmy in Monozygotic Twins Clinically Discordant for Multiple Sclerosis. Hum Mutat 2016; 37:765-75. [PMID: 27119776 DOI: 10.1002/humu.23003] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Accepted: 04/10/2016] [Indexed: 12/22/2022]
Abstract
We examined the debated link between mitochondrial DNA (mtDNA) variation and multiple sclerosis (MS) using 49 monozygotic (MZ) twin pairs clinically discordant for MS, which enables to associate de novo mtDNA variants, skewed heteroplasmy, and mtDNA copy number with MS manifestation. Ultra-deep sequencing of blood-derived mtDNA revealed 25 heteroplasmic variants with potentially pathogenic features in 18 pairs. All variants were pair-specific and had low and/or similar heteroplasmy levels in both cotwins. In one pair, a confirmed pathogenic variant (m.11778G>A, heteroplasmy ∼50%) associated with Leber hereditary optic neuropathy was detected. Detailed diagnostic investigation revealed subclinical MS signs in the prior nondiseased cotwin. Moreover, neither mtDNA deletions nor copy-number variations were involved. Furthermore, the majority of heteroplasmic variants were shared among MZ twins and exhibited more similar heteroplasmy levels in the same tissue of MZ twins as compared with different tissues of the same individual. Heteroplasmy levels were also more similar within MZ twins compared with nonidentical siblings. Our analysis excludes mtDNA variation as a major driver of the discordant clinical manifestation of MS in MZ twins, and provides valuable insights into the occurrence and distribution of heteroplasmic variants within MZ twins and nonidentical siblings, and across different tissues.
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Affiliation(s)
- Nicole Y P Souren
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Lisa A Gerdes
- Institute of Clinical Neuroimmunology, Medical Campus Großhadern, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Tania Kümpfel
- Institute of Clinical Neuroimmunology, Medical Campus Großhadern, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Pavlo Lutsik
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
| | - Thomas Klopstock
- Department of Neurology, Friedrich-Baur-Institute, Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.,DZNE - German Center for Neurodegenerative Diseases, Munich, Germany
| | - Reinhard Hohlfeld
- Institute of Clinical Neuroimmunology, Medical Campus Großhadern, Ludwig-Maximilians-Universität München, Munich, Germany.,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Jörn Walter
- Department of Genetics/Epigenetics, Saarland University, Saarbrücken, Germany
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Li M, Rothwell R, Vermaat M, Wachsmuth M, Schröder R, Laros JFJ, van Oven M, de Bakker PIW, Bovenberg JA, van Duijn CM, van Ommen GJB, Slagboom PE, Swertz MA, Wijmenga C, Kayser M, Boomsma DI, Zöllner S, de Knijff P, Stoneking M. Transmission of human mtDNA heteroplasmy in the Genome of the Netherlands families: support for a variable-size bottleneck. Genome Res 2016; 26:417-26. [PMID: 26916109 PMCID: PMC4817766 DOI: 10.1101/gr.203216.115] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 01/21/2016] [Indexed: 12/17/2022]
Abstract
Although previous studies have documented a bottleneck in the transmission of mtDNA genomes from mothers to offspring, several aspects remain unclear, including the size and nature of the bottleneck. Here, we analyze the dynamics of mtDNA heteroplasmy transmission in the Genomes of the Netherlands (GoNL) data, which consists of complete mtDNA genome sequences from 228 trios, eight dizygotic (DZ) twin quartets, and 10 monozygotic (MZ) twin quartets. Using a minor allele frequency (MAF) threshold of 2%, we identified 189 heteroplasmies in the trio mothers, of which 59% were transmitted to offspring, and 159 heteroplasmies in the trio offspring, of which 70% were inherited from the mothers. MZ twin pairs exhibited greater similarity in MAF at heteroplasmic sites than DZ twin pairs, suggesting that the heteroplasmy MAF in the oocyte is the major determinant of the heteroplasmy MAF in the offspring. We used a likelihood method to estimate the effective number of mtDNA genomes transmitted to offspring under different bottleneck models; a variable bottleneck size model provided the best fit to the data, with an estimated mean of nine individual mtDNA genomes transmitted. We also found evidence for negative selection during transmission against novel heteroplasmies (in which the minor allele has never been observed in polymorphism data). These novel heteroplasmies are enhanced for tRNA and rRNA genes, and mutations associated with mtDNA diseases frequently occur in these genes. Our results thus suggest that the female germ line is able to recognize and select against deleterious heteroplasmies.
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Affiliation(s)
- Mingkun Li
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany; Fondation Mérieux, 69002 Lyon, France
| | - Rebecca Rothwell
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Martijn Vermaat
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Manja Wachsmuth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Jeroen F J Laros
- Leiden Genome Technology Center, Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Mannis van Oven
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Paul I W de Bakker
- Department of Medical Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht 3584 CG, The Netherlands; Department of Epidemiology, Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht 3584 CG, The Netherlands
| | - Jasper A Bovenberg
- Department of Biological Psychology, VU University Amsterdam, Amsterdam 1081 BT, The Netherlands
| | - Cornelia M van Duijn
- Legal Pathways Institute for Health and Bio Law, Aerdenhout 2111, The Netherlands
| | - Gert-Jan B van Ommen
- Department of Epidemiology, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - P Eline Slagboom
- Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Morris A Swertz
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, The Netherlands
| | - Cisca Wijmenga
- Section of Molecular Epidemiology, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands; Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, The Netherlands
| | | | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, Rotterdam 3000 CA, The Netherlands
| | - Dorret I Boomsma
- Genomics Coordination Center, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, The Netherlands
| | - Sebastian Zöllner
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan 48109, USA; Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden 2300 RC, The Netherlands
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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Kim H, Erlich HA, Calloway CD. Analysis of mixtures using next generation sequencing of mitochondrial DNA hypervariable regions. Croat Med J 2016; 56:208-17. [PMID: 26088845 PMCID: PMC4500979 DOI: 10.3325/cmj.2015.56.208] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Aim To apply massively parallel and clonal sequencing (next generation sequencing or NGS) to the analysis of forensic mixed samples. Methods A duplex polymerase chain reaction (PCR) assay targeting the mitochondrial DNA (mtDNA) hypervariable regions I/II (HVI/HVII) was developed for NGS analysis on the Roche 454 GS Junior instrument. Eight sets of multiplex identifier-tagged 454 fusion primers were used in a combinatorial approach for amplification and deep sequencing of up to 64 samples in parallel. Results This assay was shown to be highly sensitive for sequencing limited DNA amounts ( ~ 100 mtDNA copies) and analyzing contrived and biological mixtures with low level variants ( ~ 1%) as well as “complex” mixtures (≥3 contributors). PCR artifact “hybrid” sequences generated by jumping PCR or template switching were observed at a low level (<2%) in the analysis of mixed samples but could be eliminated by reducing the PCR cycle number. Conclusion This study demonstrates the power of NGS technologies targeting the mtDNA HVI/HVII regions for analysis of challenging forensic samples, such as mixtures and specimens with limited DNA.
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Affiliation(s)
| | | | - Cassandra D Calloway
- Cassandra D. Calloway, Children's Hospital Oakland Research Institute, Center for Genetics, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA,
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Cavadas B, Soares P, Camacho R, Brandão A, Costa MD, Fernandes V, Pereira JB, Rito T, Samuels DC, Pereira L. Fine Time Scaling of Purifying Selection on Human Nonsynonymous mtDNA Mutations Based on the Worldwide Population Tree and Mother-Child Pairs. Hum Mutat 2015; 36:1100-11. [DOI: 10.1002/humu.22849] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Accepted: 07/20/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Bruno Cavadas
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Department of Biology; CBMA (Centre of Molecular and Environmental Biology); University of Minho; Braga 4704-553 Portugal
| | - Rui Camacho
- INESC TEC; Porto 4200-465 Portugal
- Departamento de Engenharia Informática; Faculdade de Engenharia da Universidade do Porto; Porto 4200-465 Portugal
| | - Andreia Brandão
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto (ICBAS); Porto 4050-313 Portugal
| | - Marta D. Costa
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Verónica Fernandes
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Joana B. Pereira
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - Teresa Rito
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
| | - David C. Samuels
- Vanderbilt Genetics Institute; Department of Molecular Physiology and Biophysics; Vanderbilt University Medical Center; Nashville Tennessee 37232-0700
| | - Luisa Pereira
- Instituto de Investigação e Inovação em Saúde (i3S); Universidade do Porto; Porto 4200-135 Portugal
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP); Porto 4200-465 Portugal
- Faculdade de Medicina da Universidade do Porto; Porto 4200-319 Portugal
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8
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Bekaert B, Kamalandua A, Zapico SC, Van de Voorde W, Decorte R. Improved age determination of blood and teeth samples using a selected set of DNA methylation markers. Epigenetics 2015; 10:922-30. [PMID: 26280308 DOI: 10.1080/15592294.2015.1080413] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Age estimation from DNA methylation markers has seen an exponential growth of interest, not in the least from forensic scientists. The current published assays, however, can still be improved by lowering the number of markers in the assay and by providing more accurate models to predict chronological age. From the published literature we selected 4 age-associated genes (ASPA, PDE4C, ELOVL2, and EDARADD) and determined CpG methylation levels from 206 blood samples of both deceased and living individuals (age range: 0-91 years). This data was subsequently used to compare prediction accuracy with both linear and non-linear regression models. A quadratic regression model in which the methylation levels of ELOVL2 were squared showed the highest accuracy with a Mean Absolute Deviation (MAD) between chronological age and predicted age of 3.75 years and an adjusted R(2) of 0.95. No difference in accuracy was observed for samples obtained either from living and deceased individuals or between the 2 genders. In addition, 29 teeth from different individuals (age range: 19-70 years) were analyzed using the same set of markers resulting in a MAD of 4.86 years and an adjusted R(2) of 0.74. Cross validation of the results obtained from blood samples demonstrated the robustness and reproducibility of the assay. In conclusion, the set of 4 CpG DNA methylation markers is capable of producing highly accurate age predictions for blood samples from deceased and living individuals.
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Affiliation(s)
- Bram Bekaert
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium.,b KU-Leuven - University of Leuven; University Hospitals Leuven; Department of Forensic Medicine; Laboratory of Forensic Genetics and Molecular Archeology ; Leuven , Belgium
| | - Aubeline Kamalandua
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium
| | - Sara C Zapico
- c Smithsonian Institution; NMNH; MRC112 ; Anthropology Department ; Washington, DC USA
| | - Wim Van de Voorde
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium.,b KU-Leuven - University of Leuven; University Hospitals Leuven; Department of Forensic Medicine; Laboratory of Forensic Genetics and Molecular Archeology ; Leuven , Belgium
| | - Ronny Decorte
- a KU Leuven - University of Leuven ; Department of Imaging & Pathology ; Leuven , Belgium.,b KU-Leuven - University of Leuven; University Hospitals Leuven; Department of Forensic Medicine; Laboratory of Forensic Genetics and Molecular Archeology ; Leuven , Belgium
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9
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Zhang N, Zhao S, Zhang SH, Chen J, Lu D, Shen M, Li C. Intra-Monozygotic Twin Pair Discordance and Longitudinal Variation of Whole-Genome Scale DNA Methylation in Adults. PLoS One 2015; 10:e0135022. [PMID: 26248206 PMCID: PMC4527769 DOI: 10.1371/journal.pone.0135022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 07/16/2015] [Indexed: 02/04/2023] Open
Abstract
Monozygotic twins share identical genomic DNA and are indistinguishable using conventional genetic markers. Increasing evidence indicates that monozygotic twins are epigenetically distinct, suggesting that a comparison between DNA methylation patterns might be useful to approach this forensic problem. However, the extent of epigenetic discordance between healthy adult monozygotic twins and the stability of CpG loci within the same individual over a short time span at the whole-genome scale are not well understood. Here, we used Infinium HumanMethylation450 Beadchips to compare DNA methylation profiles using blood collected from 10 pairs of monozygotic twins and 8 individuals sampled at 0, 3, 6, and 9 months. Using an effective and unbiased method for calling differentially methylated (DM) CpG sites, we showed that 0.087%–1.530% of the CpG sites exhibit differential methylation in monozygotic twin pairs. We further demonstrated that, on whole-genome level, there has been no significant epigenetic drift within the same individuals for up to 9 months, including one monozygotic twin pair. However, we did identify a subset of CpG sites that vary in DNA methylation over the 9-month period. The magnitude of the intra-pair or longitudinal methylation discordance of the CpG sites inside the CpG islands is greater than those outside the CpG islands. The CpG sites located on shores appear to be more suitable for distinguishing between MZ twins.
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Affiliation(s)
- Na Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Shumin Zhao
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
| | - Su-Hua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Jinzhong Chen
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Daru Lu
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Min Shen
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
| | - Chengtao Li
- Shanghai Key Laboratory of Forensic Medicine, Institute of Forensic Sciences, Ministry of Justice, P.R. China, Shanghai, 200063, P.R. China
- * E-mail:
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10
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Mitochondrial DNA: Radically free of free-radical driven mutations. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2015; 1847:1354-61. [PMID: 26050972 DOI: 10.1016/j.bbabio.2015.06.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/08/2015] [Accepted: 06/02/2015] [Indexed: 01/31/2023]
Abstract
Mitochondrial DNA has long been posited as a likely target of oxidative damage induced mutation during the ageing process. Research over the past decades has uncovered the accumulation of mitochondrial DNA mutations in association with a mosaic pattern of cells displaying mitochondrial dysfunction in ageing individuals. Unfortunately, the underlying mechanisms are far less straightforward than originally anticipated. Recent research on mitochondria reveals that these genomes are far less helpless than originally envisioned. Additionally, new technologies have allowed us to analyze the mutational signatures of many more somatic mitochondrial DNA mutations, revealing surprising patterns that are inconsistent with a DNA-oxidative damage based hypothesis. In this review, we will discuss these recent observations and new insights into the eccentricities of mitochondrial genetics, and their impact on our understanding of mitochondrial mutations and their role in the ageing process. This article is part of a Special Issue entitled: Mitochondrial Dysfunction in Aging.
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11
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Just RS, Scheible MK, Fast SA, Sturk-Andreaggi K, Röck AW, Bush JM, Higginbotham JL, Peck MA, Ring JD, Huber GE, Xavier C, Strobl C, Lyons EA, Diegoli TM, Bodner M, Fendt L, Kralj P, Nagl S, Niederwieser D, Zimmermann B, Parson W, Irwin JA. Full mtGenome reference data: Development and characterization of 588 forensic-quality haplotypes representing three U.S. populations. Forensic Sci Int Genet 2015; 14:141-55. [DOI: 10.1016/j.fsigen.2014.09.021] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 09/08/2014] [Accepted: 09/26/2014] [Indexed: 11/26/2022]
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12
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Naue J, Hörer S, Sänger T, Strobl C, Hatzer-Grubwieser P, Parson W, Lutz-Bonengel S. Evidence for frequent and tissue-specific sequence heteroplasmy in human mitochondrial DNA. Mitochondrion 2014; 20:82-94. [PMID: 25526677 DOI: 10.1016/j.mito.2014.12.002] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/02/2014] [Accepted: 12/09/2014] [Indexed: 10/24/2022]
Abstract
Mitochondrial point heteroplasmy is a common event observed not only in patients with mitochondrial diseases but also in healthy individuals. We here report a comprehensive investigation of heteroplasmy occurrence in human including the whole mitochondrial control region from nine different tissue types of 100 individuals. Sanger sequencing was used as a standard method and results were supported by cloning, minisequencing, and massively parallel sequencing. Only 12% of all individuals showed no heteroplasmy, whereas 88% showed at least one heteroplasmic position within the investigated tissues. In 66% of individuals up to 8 positions were affected. The highest relative number of heteroplasmies was detected in muscle and liver (79%, 69%), followed by brain, hair, and heart (36.7%-30.2%). Lower percentages were observed in bone, blood, lung, and buccal cells (19.8%-16.2%). Accumulation of position-specific heteroplasmies was found in muscle (positions 64, 72, 73, 189, and 408), liver (position 72) and brain (partial deletion at position 71). Deeper analysis of these specific positions in muscle revealed a non-random appearance and position-specific dependency on age. MtDNA heteroplasmy frequency and its potential functional importance have been underestimated in the past and its occurrence is ubiquitous and dependent at least on age, tissue, and position-specific mutation rates.
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Affiliation(s)
- Jana Naue
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg, Germany.
| | - Steffen Hörer
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
| | - Timo Sänger
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
| | - Christina Strobl
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria.
| | - Petra Hatzer-Grubwieser
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria.
| | - Walther Parson
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, A-6020 Innsbruck, Austria; Penn State Eberly College of Science, University Park, PA, USA.
| | - Sabine Lutz-Bonengel
- Institute of Legal Medicine, Freiburg University Medical Center, Albertstrasse 9, D-79104 Freiburg, Germany.
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13
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Spyropoulos A, Manford M, Horvath R, Alston CL, Yu-Wai-Man P, He L, Taylor RW, Chinnery PF. Near-identical segregation of mtDNA heteroplasmy in blood, muscle, urinary epithelium, and hair follicles in twins with optic atrophy, ptosis, and intractable epilepsy. JAMA Neurol 2014; 70:1552-5. [PMID: 24126373 DOI: 10.1001/jamaneurol.2013.4111] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE Mitochondrial DNA (mtDNA) disorders have emerged as major causes of inherited neurologic disease. Despite being well recognized for more than 2 decades, the clinical presentation continues to broaden. The phenotypic heterogeneity is partly owing to different percentage levels of mutant mtDNA heteroplasmy in different tissues, but the factors influencing this are poorly understood. OBSERVATIONS This case report describes monozygotic male twins with ptosis, optic atrophy, and recent-onset intractable myoclonic epilepsy. The assessment of respiratory chain enzyme activities in the muscle from 1 twin revealed a severe and isolated defect involving mitochondrial complex I. Mitochondrial DNA sequencing revealed a pathogenic m.14487T>C MTND6 mutation, which was present at very high levels of heteroplasmy in muscle (84%) and lower levels in blood (15%), urinary epithelium (75%), and buccal mucosa (58%). Of particular interest, his identical twin was found to harbor very similar levels of the m.14487T>C mutation in his blood, urine, buccal mucosa, and hair follicle DNA samples, while the presence of low levels in the mother's tissues confirmed maternal transmission. CONCLUSIONS AND RELEVANCE It was shown that m14487T>C can also cause the unusual combination of optic atrophy, ptosis, and encephalomyopathy leading to intractable seizures. Near-identical heteroplasmy levels in different tissues in both siblings support a nuclear genetic mechanism controlling the tissue segregation of mtDNA mutations.
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Affiliation(s)
- Achilles Spyropoulos
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, England
| | - Mark Manford
- Cambridge University Hospitals NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge, England
| | - Rita Horvath
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, England
| | - Charlotte L Alston
- Wellcome Centre for Mitochondrial Research, Institute of Ageing and Health, Newcastle University, Newcastle Upon Tyne, England
| | - Patrick Yu-Wai-Man
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, England
| | - Langping He
- Wellcome Centre for Mitochondrial Research, Institute of Ageing and Health, Newcastle University, Newcastle Upon Tyne, England
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Institute of Ageing and Health, Newcastle University, Newcastle Upon Tyne, England
| | - Patrick F Chinnery
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle Upon Tyne, England
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Samuels DC, Li C, Li B, Song Z, Torstenson E, Boyd Clay H, Rokas A, Thornton-Wells TA, Moore JH, Hughes TM, Hoffman RD, Haines JL, Murdock DG, Mortlock DP, Williams SM. Recurrent tissue-specific mtDNA mutations are common in humans. PLoS Genet 2013; 9:e1003929. [PMID: 24244193 PMCID: PMC3820769 DOI: 10.1371/journal.pgen.1003929] [Citation(s) in RCA: 111] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/14/2013] [Indexed: 11/30/2022] Open
Abstract
Mitochondrial DNA (mtDNA) variation can affect phenotypic variation; therefore, knowing its distribution within and among individuals is of importance to understanding many human diseases. Intra-individual mtDNA variation (heteroplasmy) has been generally assumed to be random. We used massively parallel sequencing to assess heteroplasmy across ten tissues and demonstrate that in unrelated individuals there are tissue-specific, recurrent mutations. Certain tissues, notably kidney, liver and skeletal muscle, displayed the identical recurrent mutations that were undetectable in other tissues in the same individuals. Using RFLP analyses we validated one of the tissue-specific mutations in the two sequenced individuals and replicated the patterns in two additional individuals. These recurrent mutations all occur within or in very close proximity to sites that regulate mtDNA replication, strongly implying that these variations alter the replication dynamics of the mutated mtDNA genome. These recurrent variants are all independent of each other and do not occur in the mtDNA coding regions. The most parsimonious explanation of the data is that these frequently repeated mutations experience tissue-specific positive selection, probably through replication advantage. DNA mutations are expected to be formed randomly, thus any reproducible pattern of DNA somatic mutations across multiple individuals or even across organs within each individual is highly unexpected. Using next generation sequencing of multiple tissues from the same individuals we found several somatic mutations in mitochondrial DNA that appear in a heteroplasmic state in all individuals examined, but only in particular tissues. These mutations were only found in known regions of replication control for the mitochondrial DNA. These data imply the presence of tissue-specific positive selection for these variants.
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Affiliation(s)
- David C Samuels
- Center for Human Genetics Research, Department of Molecular Physiology & Biophysics, Vanderbilt University School of Medicine, Nashville, Tennessee, United States of America
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15
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Affiliation(s)
- Salvatore DiMauro
- Department of Neurology, Columbia University Medical Center, New York, New York
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Valdes AM, Glass D, Spector TD. Omics technologies and the study of human ageing. Nat Rev Genet 2013; 14:601-7. [PMID: 23938363 DOI: 10.1038/nrg3553] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Normal ageing is associated with diverse physiological changes in all organ systems but the rate and extent of these changes vary markedly among individuals. One aspect of ageing research focuses on the molecular profiling of the changes that occur with increasing age in humans. Such profiling has implications for disease prevention and treatment. New high-throughput 'omics' technologies (such as genomics, metabolomics, metagenomics and transcriptomics) are enabling detailed studies of these molecular changes and are thus revealing information about the biological pathways that change with age.
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Affiliation(s)
- Ana M Valdes
- 1] Department of Twin Research and Genetic Epidemiology, Kings College London, London SE1 7EH, UK. [2] Academic Rheumatology, University of Nottingham, Nottingham NG5 1PB, UK
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Krjutškov K, Koltšina M, Grand K, Võsa U, Sauk M, Tõnisson N, Salumets A. Tissue-specific mitochondrial heteroplasmy at position 16,093 within the same individual. Curr Genet 2013; 60:11-6. [PMID: 23842853 PMCID: PMC3895442 DOI: 10.1007/s00294-013-0398-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/27/2013] [Accepted: 06/29/2013] [Indexed: 11/30/2022]
Abstract
Human mitochondrial DNA (mtDNA) research has entered a massively parallel sequencing (MPS) era, providing deep insight into mtDNA genomics and molecular diagnostics. Analysis can simultaneously include coding and control regions, many samples can be studied in parallel, and even minor heteroplasmic changes can be detected. We investigated heteroplasmy using 16 different tissues from three unrelated males aged 40–54 years at the time of death. mtDNA was enriched using two independent overlapping long-range PCR amplicons and analysed by employing illumina paired-end sequencing. Point mutation heteroplasmy at position 16,093 (m.16093T > C) in the non-coding regulatory region showed great variability among one of the studied individuals; heteroplasmy extended from 5.1 % in red bone marrow to 62.0 % in the bladder. Red (5.1 %) and yellow bone marrow (8.9 %) clustered into one group and two arteries and two aortas from different locations into another (31.2–50.9 %), giving an ontogenetic explanation for the formation of somatic mitochondrial heteroplasmy. Our results demonstrate that multi-tissue screening using MPS provides surprising data even when there is a limited number (3) of study subjects and they give reason to speculate that mtDNA heteroplasmic frequency, distribution, and even its possible role in complex diseases or phenotypes seem to be underestimated.
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Affiliation(s)
- Kaarel Krjutškov
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia,
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Chen JB, Yang YH, Lee WC, Liou CW, Lin TK, Chung YH, Chuang LY, Yang CH, Chang HW. Sequence-based polymorphisms in the mitochondrial D-loop and potential SNP predictors for chronic dialysis. PLoS One 2012; 7:e41125. [PMID: 22815937 PMCID: PMC3399812 DOI: 10.1371/journal.pone.0041125] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Accepted: 06/21/2012] [Indexed: 01/12/2023] Open
Abstract
Background The mitochondrial (mt) displacement loop (D-loop) is known to accumulate structural alterations and mutations. The aim of this study was to investigate the prevalence of single nucleotide polymorphisms (SNPs) within the D-loop among chronic dialysis patients and healthy controls. Methodology and Principal Findings We enrolled 193 chronic dialysis patients and 704 healthy controls. SNPs were identified by large scale D-loop sequencing and bioinformatic analysis. Chronic dialysis patients had lower body mass index, blood thiols, and cholesterol levels than controls. A total of 77 SNPs matched with the positions in reference of the Revised Cambridge Reference Sequence (CRS) were found in the study population. Chronic dialysis patients had a significantly higher incidence of 9 SNPs compared to controls. These include SNP5 (16108Y), SNP17 (16172Y), SNP21 (16223Y), SNP34 (16274R), SNP35 (16278Y), SNP55 (16463R), SNP56 (16519Y), SNP64 (185R), and SNP65 (189R) in D-loop of CRS. Among these SNPs with genotypes, SNP55-G, SNP56-C, and SNP64-A were 4.78, 1.47, and 5.15 times more frequent in dialysis patients compared to controls (P<0.05), respectively. When adjusting the covariates of demographics and comorbidities, SNP64-A was 5.13 times more frequent in dialysis patients compared to controls (P<0.01). Furthermore, SNP64-A was found to be 35.80, 3.48, 4.69, 5,55, and 4.67 times higher in female patients and in patients without diabetes, coronary artery disease, smoking, and hypertension in an independent significance manner (P<0.05), respectively. In patients older than 50 years or with hypertension, SNP34-A and SNP17-C were found to be 7.97 and 3.71 times more frequent (P<0.05) compared to patients younger than 50 years or those without hypertension, respectively. Conclusions and Significance The results of large-scale sequencing suggest that specific SNPs in the mtDNA D-loop are significantly associated with chronic dialysis. These SNPs can be considered as potential predictors for chronic dialysis.
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Affiliation(s)
- Jin-Bor Chen
- Division of Nephrology, Department of Internal Medicine, Mitochondrial Research Unit, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yi-Hsin Yang
- School of Pharmacy, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Wen-Chin Lee
- Division of Nephrology, Department of Internal Medicine, Mitochondrial Research Unit, Kaohsiung Chang Gung Memorial Hospital, Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chia-Wei Liou
- Department of Neurology and Mitochondrial Research Unit, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Tsu-Kung Lin
- Department of Neurology and Mitochondrial Research Unit, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yueh-Hua Chung
- Institute of Biomedical Sciences, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Li-Yeh Chuang
- Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung, Taiwan
| | - Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung, Taiwan
- * E-mail: (HWC); (CHY)
| | - Hsueh-Wei Chang
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Taiwan
- Center of Excellence for Environmental Medicine, Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail: (HWC); (CHY)
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Avital G, Buchshtav M, Zhidkov I, Tuval Feder J, Dadon S, Rubin E, Glass D, Spector TD, Mishmar D. Mitochondrial DNA heteroplasmy in diabetes and normal adults: role of acquired and inherited mutational patterns in twins. Hum Mol Genet 2012; 21:4214-24. [PMID: 22736028 DOI: 10.1093/hmg/dds245] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Heteroplasmy, the mixture of mitochondrial genomes (mtDNA), varies among individuals and cells. Heteroplasmy levels alter the penetrance of pathological mtDNA mutations, and the susceptibility to age-related diseases such as Parkinson's disease. Although mitochondrial dysfunction occurs in age-related type 2 diabetes mellitus (T2DM), the involvement of heteroplasmy in diabetes is unclear. We hypothesized that the heteroplasmic mutational (HM) pattern may change in T2DM. To test this, we used next-generation sequencing, i.e. massive parallel sequencing (MPS), along with PCR-cloning-Sanger sequencing to analyze HM in blood and skeletal muscle DNA samples from monozygotic (MZ) twins either concordant or discordant for T2DM. Great variability was identified in the repertoires and amounts of HMs among individuals, with a tendency towards more mutations in skeletal muscle than in blood. Whereas many HMs were unique, many were either shared among twin pairs or among tissues of the same individual, regardless of their prevalence. This suggested a heritable influence on even low abundance HMs. We found no clear differences between T2DM and controls. However, we found ~5-fold increase of HMs in non-coding sequences implying the influence of negative selection (P < 0.001). This negative selection was evident both in moderate to highly abundant heteroplasmy (>5% of the molecules per sample) and in low abundance heteroplasmy (<5% of the molecules). Although our study found no evidence supporting the involvement of HMs in the etiology of T2DM, the twin study found clear evidence of a heritable influence on the accumulation of HMs as well as the signatures of selection in heteroplasmic mutations.
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Affiliation(s)
- Gal Avital
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
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