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Ludwig-Słomczyńska AH, Rehm M. Mitochondrial genome variations, mitochondrial-nuclear compatibility, and their association with metabolic diseases. Obesity (Silver Spring) 2022; 30:1156-1169. [PMID: 35491673 DOI: 10.1002/oby.23424] [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: 11/18/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 11/10/2022]
Abstract
Two genomes regulate the energy metabolism of eukaryotic cells: the nuclear genome, which codes for most cellular proteins, and the mitochondrial genome, which, together with the nuclear genome, coregulates cellular bioenergetics. Therefore, mitochondrial genome variations can affect, directly or indirectly, all energy-dependent cellular processes and shape the metabolic state of the organism. This review provides a current and up-to-date overview on how codependent these two genomes are, how they appear to have coevolved, and how variations within the mitochondrial genome might be associated with the manifestation of metabolic diseases. This review summarizes and structures results obtained from epidemiological studies that identified links between mitochondrial haplogroups and individual risks for developing obesity and diabetes. This is complemented by findings on the compatibility of mitochondrial and nuclear genomes and cellular bioenergetic fitness, which have been acquired from well-controlled studies in conplastic animal models. These elucidate, more mechanistically, how single-nucleotide variants can influence cellular metabolism and physiology. Overall, it seems that certain mitochondrial genome variations negatively affect mitochondrial-nuclear compatibility and are statistically linked with the onset of metabolic diseases, whereas, for others, greater uncertainty exists, and additional research into this exciting field is required.
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Affiliation(s)
| | - Markus Rehm
- Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
- Stuttgart Research Center Systems Biology, University of Stuttgart, Stuttgart, Germany
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van Rensburg D, Lindeque Z, Harvey BH, Steyn SF. Reviewing the mitochondrial dysfunction paradigm in rodent models as platforms for neuropsychiatric disease research. Mitochondrion 2022; 64:82-102. [DOI: 10.1016/j.mito.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 12/19/2022]
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Yamada M, Sato S, Ooka R, Akashi K, Nakamura A, Miyado K, Akutsu H, Tanaka M. Mitochondrial replacement by genome transfer in human oocytes: Efficacy, concerns, and legality. Reprod Med Biol 2021; 20:53-61. [PMID: 33488283 PMCID: PMC7812462 DOI: 10.1002/rmb2.12356] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Pathogenic mitochondrial (mt)DNA mutations, which often cause life-threatening disorders, are maternally inherited via the cytoplasm of oocytes. Mitochondrial replacement therapy (MRT) is expected to prevent second-generation transmission of mtDNA mutations. However, MRT may affect the function of respiratory chain complexes comprised of both nuclear and mitochondrial proteins. METHODS Based on the literature and current regulatory guidelines (especially in Japan), we analyzed and reviewed the recent developments in human models of MRT. MAIN FINDINGS MRT does not compromise pre-implantation development or stem cell isolation. Mitochondrial function in stem cells after MRT is also normal. Although mtDNA carryover is usually less than 0.5%, even low levels of heteroplasmy can affect the stability of the mtDNA genotype, and directional or stochastic mtDNA drift occurs in a subset of stem cell lines (mtDNA genetic drift). MRT could prevent serious genetic disorders from being passed on to the offspring. However, it should be noted that this technique currently poses significant risks for use in embryos designed for implantation. CONCLUSION The maternal genome is fundamentally compatible with different mitochondrial genotypes, and vertical inheritance is not required for normal mitochondrial function. Unresolved questions regarding mtDNA genetic drift can be addressed by basic research using MRT.
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Affiliation(s)
- Mitsutoshi Yamada
- Department of Obstetrics and GynecologyKeio University School of MedicineTokyoJapan
| | - Suguru Sato
- Department of Obstetrics and GynecologyKeio University School of MedicineTokyoJapan
| | - Reina Ooka
- Department of Obstetrics and GynecologyKeio University School of MedicineTokyoJapan
| | - Kazuhiro Akashi
- Department of Obstetrics and GynecologyKeio University School of MedicineTokyoJapan
| | - Akihiro Nakamura
- Department of Obstetrics and GynecologyKeio University School of MedicineTokyoJapan
- Department of Reproductive BiologyNational Research Institute for Child Health and DevelopmentTokyoJapan
| | - Kenji Miyado
- Department of Reproductive BiologyNational Research Institute for Child Health and DevelopmentTokyoJapan
| | - Hidenori Akutsu
- Department of Reproductive BiologyNational Research Institute for Child Health and DevelopmentTokyoJapan
| | - Mamoru Tanaka
- Department of Obstetrics and GynecologyKeio University School of MedicineTokyoJapan
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Aljasmi FA, Vijayan R, Sudalaimuthuasari N, Souid AK, Karuvantevida N, Almaskari R, Mohammed Abdul Kader H, Kundu B, Michel Hazzouri K, Amiri KMA. Genomic Landscape of the Mitochondrial Genome in the United Arab Emirates Native Population. Genes (Basel) 2020; 11:genes11080876. [PMID: 32752197 PMCID: PMC7464197 DOI: 10.3390/genes11080876] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Revised: 07/26/2020] [Accepted: 07/28/2020] [Indexed: 11/19/2022] Open
Abstract
In order to assess the genomic landscape of the United Arab Emirates (UAE) mitogenome, we sequenced and analyzed the complete genomes of 232 Emirate females mitochondrial DNA (mtDNA) within and compared those to Africa. We investigated the prevalence of haplogroups, genetic variation, heteroplasmy, and demography among the UAE native population with diverse ethnicity and relatively high degree of consanguinity. We identified 968 mtDNA variants and high-resolution 15 haplogroups. Our results show that the UAE population received enough gene flow from Africa represented by the haplogroups L, U6, and M1, and that 16.8% of the population has an eastern provenance, depicted by the U haplogroup and the M Indian haplogroup (12%), whereas western Eurasian and Asian haplogroups (R, J, and K) represent 11 to 15%. Interestingly, we found an ancient migration present through the descendant of L (N1 and X) and other sub-haplogroups (L2a1d and L4) and (L3x1b), which is one of the oldest evolutionary histories outside of Africa. Our demographic analysis shows no population structure among populations, with low diversity and no population differentiation. In addition, we show that the transmission of mtDNA in the UAE population is under purifying selection with hints of diversifying selection on ATP8 gene. Last, our results show a population bottleneck, which coincides with the Western European contact (1400 ybp). Our study of the UAE mitogenomes suggest that several maternal lineage migratory episodes liking African–Asian corridors occurred since the first modern human emerges out of Africa.
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Affiliation(s)
- Fatma A Aljasmi
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Ranjit Vijayan
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Abdul-Kader Souid
- Pediatric Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Raja Almaskari
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | | | - Biduth Kundu
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled Michel Hazzouri
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
| | - Khaled M A Amiri
- Biology Department, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, Abu Dhabi 15551, UAE
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Ricardo PC, Françoso E, Arias MC. Mitochondrial DNA intra-individual variation in a bumblebee species: A challenge for evolutionary studies and molecular identification. Mitochondrion 2020; 53:243-254. [PMID: 32569843 DOI: 10.1016/j.mito.2020.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2020] [Revised: 04/28/2020] [Accepted: 06/15/2020] [Indexed: 10/24/2022]
Abstract
Mitochondrial DNA (mtDNA) regions have been widely used as molecular markers in evolutionary studies and species identification. However, the presence of heteroplasmy and NUMTs may represent obstacles. Heteroplasmy is a state where an organism has different mitochondrial haplotypes. NUMTs are nuclear pseudogenes originating from mtDNA sequences transferred to nuclear DNA. Evidences of heteroplasmy were already verified in the bumblebee Bombus morio in an earlier study. The present work investigated in more detail the presence of intra-individual haplotypes variation in this species. Heteroplasmy was detected in individuals from all the ten sampled locations, with an average of six heteroplasmic haplotypes per individual. In addition, some of these heteroplasmic haplotypes were shared among individuals from different locations, suggesting the existence of stable heteroplasmy in B. morio. These results demonstrated that heteroplasmy is likely to affect inferences based on mtDNA analysis, especially in phylogenetic, phylogeographic and population genetics studies. In addition, NUMTs were also detected. These sequences showed divergence of 2.7% to 12% in relation to the mitochondrial haplotypes. These levels of divergence could mislead conclusions in evolutionary studies and affect species identification through DNA barcoding.
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Affiliation(s)
- Paulo Cseri Ricardo
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
| | - Elaine Françoso
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Maria Cristina Arias
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil.
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O'Donnell L, Blakely EL, Baty K, Alexander M, Bogdanova-Mihaylova P, Craig J, Walsh R, Brett F, Taylor RW, Murphy SM. Chronic Progressive External Ophthalmoplegia due to a Rare de novo m.12334G>A MT-TL2 Mitochondrial DNA Variant1. J Neuromuscul Dis 2020; 7:355-360. [PMID: 32310184 DOI: 10.3233/jnd-200486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
We describe a patient with chronic progressive external ophthalmoplegia (CPEO) due to a rare mitochondrial genetic variant. Muscle biopsy revealed numerous cytochrome c oxidase (COX)-deficient fibres, prompting sequencing of the entire mitochondrial genome in muscle which revealed a rare m.12334G>A variant in the mitochondrial (mt-) tRNALeu(CUN)(MT-TL2) gene. Analysis of several tissues showed this to be a de novo mutational event. Single fibre studies confirmed the segregation of high m.12334G>A heteroplasmy levels with the COX histochemical defect, confirming pathogenicity of the m.12334G>A MT-TL2 variant. This case illustrates the importance of pursuing molecular genetic analysis in clinically-affected tissues when mitochondrial disease is suspected.
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Affiliation(s)
- Luke O'Donnell
- Department of Neurology, Tallaght University Hospital, Tallaght, Dublin, Ireland
| | - Emma L Blakely
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Karen Baty
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Michael Alexander
- Department of Neurophysiology, Tallaght University Hospital, Tallaght, Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, The University of Dublin, Dublin, Ireland
| | | | - John Craig
- Department of Neurology, Belfast Health and Social Care Trust, Belfast, United Kingdom
| | - Ronan Walsh
- Department of Neurology, Hermitage Medical Clinic, Dublin, Ireland
| | - Francesca Brett
- Department of Neuropathology, Beaumont Hospital, Dublin, Ireland
| | - Robert W Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
- NHS Highly Specialised Mitochondrial Diagnostic Laboratory, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom
| | - Sinead M Murphy
- Department of Neurology, Tallaght University Hospital, Tallaght, Dublin, Ireland
- Academic Unit of Neurology, Trinity College Dublin, The University of Dublin, Dublin, Ireland
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Tranah GJ. Response: Low Heteroplasmy Rates of Pathogenic mtDNA Variants Do Not Predict Aging. J Gerontol A Biol Sci Med Sci 2019; 74:1027-1028. [PMID: 30561527 DOI: 10.1093/gerona/gly216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, California
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Tranah GJ, Katzman SM, Lauterjung K, Yaffe K, Manini TM, Kritchevsky S, Newman AB, Harris TB, Cummings SR. Mitochondrial DNA m.3243A > G heteroplasmy affects multiple aging phenotypes and risk of mortality. Sci Rep 2018; 8:11887. [PMID: 30089816 PMCID: PMC6082898 DOI: 10.1038/s41598-018-30255-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 07/20/2018] [Indexed: 12/13/2022] Open
Abstract
Mitochondria contain many copies of a circular DNA molecule (mtDNA), which has been observed as a mixture of normal and mutated states known as heteroplasmy. Elevated heteroplasmy at a single mtDNA site, m.3243A > G, leads to neurologic, sensory, movement, metabolic, and cardiopulmonary impairments. We measured leukocyte mtDNA m.3243A > G heteroplasmy in 789 elderly men and women from the bi-racial, population-based Health, Aging, and Body Composition Study to identify associations with age-related functioning and mortality. Mutation burden for the m.3243A > G ranged from 0–19% and elevated heteroplasmy was associated with reduced strength, cognitive, metabolic, and cardiovascular functioning. Risk of all-cause, dementia and stroke mortality was significantly elevated for participants in the highest tertiles of m.3243A > G heteroplasmy. These results indicate that the accumulation of a rare genetic disease mutation, m.3243A > G, manifests as several aging outcomes and that some diseases of aging may be attributed to the accumulation of mtDNA damage.
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Affiliation(s)
- Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA.
| | | | - Kevin Lauterjung
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Kristine Yaffe
- Departments of Psychiatry, Neurology, and Epidemiology, University of California, San Francisco and the San Francisco VA Medical Center, San Francisco, CA, 94121, USA
| | - Todd M Manini
- Department of Aging and Geriatric Research, University of Florida, Gainesville, FL, 32601, USA
| | - Stephen Kritchevsky
- Sticht Center on Aging, Wake Forest School of Medicine, Winston-Salem, NC, 27157, USA
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, 15213, USA
| | - Tamara B Harris
- Intramural Research Program, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD, 20892, USA
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
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Aoki K, Tanaka H, Kawahara T. Multiplexed Microsphere Suspension-Array Assay for Urine Mitochondrial DNA Typing by C-Stretch Length in Hypervariable Regions. J Clin Med Res 2018; 10:552-561. [PMID: 29904439 PMCID: PMC5997413 DOI: 10.14740/jocmr3302w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 04/10/2018] [Indexed: 11/11/2022] Open
Abstract
Background The standard method for personal identification and verification of urine samples in doping control is short tandem repeat (STR) analysis using nuclear DNA (nDNA). The DNA concentration of urine is very low and decreases under most conditions used for sample storage; therefore, the amount of DNA from cryopreserved urine samples may be insufficient for STR analysis. We aimed to establish a multiplexed assay for urine mitochondrial DNA typing containing only trace amounts of DNA, particularly for Japanese populations. Methods A multiplexed suspension-array assay using oligo-tagged microspheres (Luminex MagPlex-TAG) was developed to measure C-stretch length in hypervariable region 1 (HV1) and 2 (HV2), five single nucleotide polymorphisms (SNPs), and one polymorphic indel. Based on these SNPs and the indel, the Japanese population can be classified into five major haplogroups (D4, B, M7a, A, D5). The assay was applied to DNA samples from urine cryopreserved for 1 - 1.5 years (n = 63) and fresh blood (n = 150). Results The assay with blood DNA enabled Japanese subjects to be categorized into 62 types, exhibiting a discriminatory power of 0.960. The detection limit for cryopreserved urine was 0.005 ng of nDNA. Profiling of blood and urine pairs revealed that 5 of 63 pairs showed different C-stretch patterns in HV1 or HV2. Conclusions The assay described here yields valuable information in terms of the verification of urine sample sources employing only trace amounts of recovered DNA. However, blood cannot be used as a reference sample.
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Affiliation(s)
- Kimiko Aoki
- Anti-doping Research Laboratory, Japan Chemical Analysis Center, 6-39-4, Minami Senju, Arakawa-ku, Tokyo, 116-0003, Japan.,Nihon Pharmaceutical University, 10281, Komuro, Inamachi, Kitaadachi-gun, Saitama 362-0806, Japan
| | - Hiroyuki Tanaka
- Anti-doping Research Laboratory, Japan Chemical Analysis Center, 6-39-4, Minami Senju, Arakawa-ku, Tokyo, 116-0003, Japan
| | - Takashi Kawahara
- Anti-doping Research Laboratory, Japan Chemical Analysis Center, 6-39-4, Minami Senju, Arakawa-ku, Tokyo, 116-0003, Japan
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Human iPSC-Derived Neural Progenitors Are an Effective Drug Discovery Model for Neurological mtDNA Disorders. Cell Stem Cell 2017; 20:659-674.e9. [PMID: 28132834 DOI: 10.1016/j.stem.2016.12.013] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Revised: 11/04/2016] [Accepted: 12/19/2016] [Indexed: 01/19/2023]
Abstract
Mitochondrial DNA (mtDNA) mutations frequently cause neurological diseases. Modeling of these defects has been difficult because of the challenges associated with engineering mtDNA. We show here that neural progenitor cells (NPCs) derived from human induced pluripotent stem cells (iPSCs) retain the parental mtDNA profile and exhibit a metabolic switch toward oxidative phosphorylation. NPCs derived in this way from patients carrying a deleterious homoplasmic mutation in the mitochondrial gene MT-ATP6 (m.9185T>C) showed defective ATP production and abnormally high mitochondrial membrane potential (MMP), plus altered calcium homeostasis, which represents a potential cause of neural impairment. High-content screening of FDA-approved drugs using the MMP phenotype highlighted avanafil, which we found was able to partially rescue the calcium defect in patient NPCs and differentiated neurons. Overall, our results show that iPSC-derived NPCs provide an effective model for drug screening to target mtDNA disorders that affect the nervous system.
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Amer SAM, Al-Harthi HS, Refaat AM, Bakdash A, Kassab AC. Identification of Human Bone Remains by Autosomal STRs and Mitochondrial DNA SNPs. J HARD TISSUE BIOL 2017. [DOI: 10.2485/jhtb.26.111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Sayed AM Amer
- Biology Department, Faculty of Science, Taif University
| | - Hussam S Al-Harthi
- College of Forensic Sciences, Naif Arab University for Security Sciences
| | - Ahmed M Refaat
- College of Forensic Sciences, Naif Arab University for Security Sciences
| | | | - Ahmed Ch Kassab
- College of Forensic Sciences, Naif Arab University for Security Sciences
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Tan BG, Wellesley FC, Savery NJ, Szczelkun MD. Length heterogeneity at conserved sequence block 2 in human mitochondrial DNA acts as a rheostat for RNA polymerase POLRMT activity. Nucleic Acids Res 2016; 44:7817-29. [PMID: 27436287 PMCID: PMC5027508 DOI: 10.1093/nar/gkw648] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 07/10/2016] [Indexed: 01/21/2023] Open
Abstract
The guanine (G)-tract of conserved sequence block 2 (CSB 2) in human mitochondrial DNA can result in transcription termination due to formation of a hybrid G-quadruplex between the nascent RNA and the nontemplate DNA strand. This structure can then influence genome replication, stability and localization. Here we surveyed the frequency of variation in sequence identity and length at CSB 2 amongst human mitochondrial genomes and used in vitro transcription to assess the effects of this length heterogeneity on the activity of the mitochondrial RNA polymerase, POLRMT. In general, increased G-tract length correlated with increased termination levels. However, variation in the population favoured CSB 2 sequences which produced efficient termination while particularly weak or strong signals were avoided. For all variants examined, the 3′ end of the transcripts mapped to the same downstream sequences and were prevented from terminating by addition of the transcription factor TEFM. We propose that CSB 2 length heterogeneity allows variation in the efficiency of transcription termination without affecting the position of the products or the capacity for regulation by TEFM.
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Affiliation(s)
- Benedict G Tan
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Frederick C Wellesley
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Nigel J Savery
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol BS8 1TD, UK
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Segregation of Naturally Occurring Mitochondrial DNA Variants in a Mini-Pig Model. Genetics 2016; 202:931-44. [PMID: 26819245 DOI: 10.1534/genetics.115.181321] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 01/17/2016] [Indexed: 11/18/2022] Open
Abstract
The maternally inherited mitochondrial genome (mtDNA) is present in multimeric form within cells and harbors sequence variants (heteroplasmy). While a single mtDNA variant at high load can cause disease, naturally occurring variants likely persist at low levels across generations of healthy populations. To determine how naturally occurring variants are segregated and transmitted, we generated a mini-pig model, which originates from the same maternal ancestor. Following next-generation sequencing, we identified a series of low-level mtDNA variants in blood samples from the female founder and her daughters. Four variants, ranging from 3% to 20%, were selected for validation by high-resolution melting analysis in 12 tissues from 31 animals across three generations. All four variants were maintained in the offspring, but variant load fluctuated significantly across the generations in several tissues, with sex-specific differences in heart and liver. Moreover, variant load was persistently reduced in high-respiratory organs (heart, brain, diaphragm, and muscle), which correlated significantly with higher mtDNA copy number. However, oocytes showed increased heterogeneity in variant load, which correlated with increased mtDNA copy number during in vitro maturation. Altogether, these outcomes show that naturally occurring mtDNA variants segregate and are maintained in a tissue-specific manner across generations. This segregation likely involves the maintenance of selective mtDNA variants during organogenesis, which can be differentially regulated in oocytes and preimplantation embryos during maturation.
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Doescher A, Petershofen EK, Hertenstein B, Kraemer D, Casper J, Schmidt JP, Müller TH. Platelet recovery and survival measured in patients by quantitative polymerase chain reaction of mitochondrial DNA. Transfusion 2014; 55:55-63. [PMID: 25056505 DOI: 10.1111/trf.12778] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 05/27/2014] [Accepted: 05/31/2014] [Indexed: 12/15/2022]
Abstract
BACKGROUND Mitochondrial (mt) DNA markers have been identified as potential targets for the quantification of endogenous and allogeneic platelets (PLTs) in the blood of individuals who received transfusions. Our goal was to develop a routine polymerase chain reaction (PCR) assay for ex vivo monitoring of PLT survival in patients after transfusion. STUDY DESIGN AND METHODS Targets were selected for real-time (RT)-PCR of mt DNA based on the frequency distribution of nucleotide polymorphisms and assay sensitivity in vitro. The assays were then evaluated with ex vivo samples to measure PLT survival and recovery of therapeutic doses of apheresis PLTs in hematooncologic patients with thrombocytopenia. RESULTS Nucleotides in two positions (73/310 hypervariable region [HVR] 2) and three positions (295 HVR 2, 16069/16311 HVR 1) had allele frequencies of approximately 0.5 and 0.85, respectively, in a population of 960 Caucasian PLT donors. They provided targets for sensitive assays detecting at least 1 × 10(3) PLTs per whole blood sample with adequate reproducibility (interassay coefficient of variation <4.0%). Transfusions of single-donor PLT concentrates in patients with thrombocytopenia (n = 30) were monitored with these markers. The mean 24-hour corrected count increment was 8.3 and the mean calculated survival time was 3.3 days. Results for a second marker were available for 13 transfusions. The survival time values derived from both markers for the same transfusion were almost identical (linear regression: r(2) = 0.957, slope = 0.87). CONCLUSION This RT-PCR method detects mt DNA polymorphisms in Caucasians for a highly sensitive and reproducible quantification of endogenous and allogeneic PLT numbers in blood samples from transfused patients with thrombocytopenia.
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Affiliation(s)
- Andrea Doescher
- DRK-Blutspendedienst NSTOB, Institut Bremen-Oldenburg, Oldenburg, Germany
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15
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Frequency and pattern of heteroplasmy in the complete human mitochondrial genome. PLoS One 2013; 8:e74636. [PMID: 24098342 PMCID: PMC3788774 DOI: 10.1371/journal.pone.0074636] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 08/03/2013] [Indexed: 11/19/2022] Open
Abstract
Determining the levels of human mitochondrial heteroplasmy is of utmost importance in several fields. In spite of this, there are currently few published works that have focused on this issue. In order to increase the knowledge of mitochondrial DNA (mtDNA) heteroplasmy, the main goal of this work is to investigate the frequency and the mutational spectrum of heteroplasmy in the human mtDNA genome. To address this, a set of nine primer pairs designed to avoid co-amplification of nuclear DNA (nDNA) sequences of mitochondrial origin (NUMTs) was used to amplify the mitochondrial genome in 101 individuals. The analysed individuals represent a collection with a balanced representation of genders and mtDNA haplogroup distribution, similar to that of a Western European population. The results show that the frequency of heteroplasmic individuals exceeds 61%. The frequency of point heteroplasmy is 28.7%, with a widespread distribution across the entire mtDNA. In addition, an excess of transitions in heteroplasmy were detected, suggesting that genetic drift and/or selection may be acting to reduce its frequency at population level. In fact, heteroplasmy at highly stable positions might have a greater impact on the viability of mitochondria, suggesting that purifying selection must be operating to prevent their fixation within individuals. This study analyses the frequency of heteroplasmy in a healthy population, carrying out an evolutionary analysis of the detected changes and providing a new perspective with important consequences in medical, evolutionary and forensic fields.
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Detjen AK, Tinschert S, Kaufmann D, Algermissen B, Nürnberg P, Schuelke M. Analysis of Mitochondrial DNA in Discordant Monozygotic Twins With Neurofibromatosis Type 1. Twin Res Hum Genet 2012; 10:486-95. [PMID: 17564507 DOI: 10.1375/twin.10.3.486] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
AbstractNeurofibromatosis type 1 (NF1) is the most frequent neurocutaneous disorder with autosomal dominant inheritance. Phenotype variability is high ranging from merely several café-au-lait spots to malignant peripheral nerve sheath tumors or severe disfigurement through plexiform neurofibromas. Identification of genetic factors that modify the NF1 phenotype would contribute to the understanding of NF1 pathophysiology and improve patient counselling. As even monozygotic (MZ) twins with NF1 may differ phenotypically, we wondered whether these variations might be inherited in a non-Mendelian fashion. Mitochondrial DNA (mtDNA) is inherited extrachromosomally through the cytoplasm of the oocyte and often harbours heteroplasmic sequence variations. At the time of blastomere separation, these variants may be skewedly distributed and effect phenotypic differences. Because of their co-localization with the tumor suppressor protein neurofibromin, which is mutated in NF1, mitochondria were particular attractive candidates for investigation. MtDNA was extracted from nucleated blood cells of four pairs of discordant MZ twins with NF1 and from cutaneous neurofibromas of one twin pair. We sequenced the entire mitochondrial genome and determined the state of heteroplasmy by investigating a microsatellite region of the mitochondrial D-loop (D310-tract). The clinical diagnosis was confirmed in all patients by detection of pathogenic mutations in the NF1 gene. Monozygosity was verified by genotyping. However, we did not detect evidence for mtDNA sequence differences or for different degrees of heteroplasmy between individuals of the same twin pair. The phenotypic discordance of MZ twins with NF1 cannot be explained by skewed distribution of mtDNA mutations or polymorphisms.
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Affiliation(s)
- Anne Katrin Detjen
- Department of Neuropediatrics, Charité, University Medical Center, Berlin, Germany
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Goto H, Dickins B, Afgan E, Paul IM, Taylor J, Makova KD, Nekrutenko A. Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study. Genome Biol 2011; 12:R59. [PMID: 21699709 PMCID: PMC3218847 DOI: 10.1186/gb-2011-12-6-r59] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2010] [Revised: 05/30/2011] [Accepted: 06/23/2011] [Indexed: 12/19/2022] Open
Abstract
Background Originally believed to be a rare phenomenon, heteroplasmy - the presence of more than one mitochondrial DNA (mtDNA) variant within a cell, tissue, or individual - is emerging as an important component of eukaryotic genetic diversity. Heteroplasmies can be used as genetic markers in applications ranging from forensics to cancer diagnostics. Yet the frequency of heteroplasmic alleles may vary from generation to generation due to the bottleneck occurring during oogenesis. Therefore, to understand the alterations in allele frequencies at heteroplasmic sites, it is of critical importance to investigate the dynamics of maternal mtDNA transmission. Results Here we sequenced, at high coverage, mtDNA from blood and buccal tissues of nine individuals from three families with a total of six maternal transmission events. Using simulations and re-sequencing of clonal DNA, we devised a set of criteria for detecting polymorphic sites in heterogeneous genetic samples that is resistant to the noise originating from massively parallel sequencing technologies. Application of these criteria to nine human mtDNA samples revealed four heteroplasmic sites. Conclusions Our results suggest that the incidence of heteroplasmy may be lower than estimated in some other recent re-sequencing studies, and that mtDNA allelic frequencies differ significantly both between tissues of the same individual and between a mother and her offspring. We designed our study in such a way that the complete analysis described here can be repeated by anyone either at our site or directly on the Amazon Cloud. Our computational pipeline can be easily modified to accommodate other applications, such as viral re-sequencing.
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Affiliation(s)
- Hiroki Goto
- The Huck Institutes of Life Sciences and Department of Biology, Penn State University, 305 Wartik Lab, University Park, PA 16802, USA
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Sondheimer N, Glatz CE, Tirone JE, Deardorff MA, Krieger AM, Hakonarson H. Neutral mitochondrial heteroplasmy and the influence of aging. Hum Mol Genet 2011; 20:1653-9. [PMID: 21296868 DOI: 10.1093/hmg/ddr043] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The development and maintenance of mitochondrial heteroplasmy has important consequences for both health and heredity. Previous studies using pathogenic mutations have shown considerable variability between maternally related individuals and studies of several D-loop polymorphisms have suggested a relationship between heteroplasmy and somatic aging. To broadly explore the variation of human heteroplasmy and to clarify the dynamics of somatic heteroplasmy over the course of lifespan, we analyzed mitochondrial sequence variation across a range of ages. We utilized array-generated single-nucleotide polymorphism data that were well correlated with independent measures of heteroplasmy. Significant levels of heteroplasmy were identified at 0.24% of sites evaluated. By examining mother-child pairs, we found that heteroplasmy was inherited (30%) but could occur de novo in offspring or, conversely, be present in mothers but eliminated in their children (70%). Cumulatively, mitochondrial heteroplasmy across the genome increased significantly with advanced age (r = 0.224, P =8 × 10(-30)). Surprisingly, changes in heteroplasmy were not uniform with some sites demonstrating a loss of variation (increased homoplasmy) with aging. These data suggest that both mutation and selective pressure affect blood mitochondrial DNA sequence over the course of the human lifespan and reveal the unexpectedly dynamic nature of human heteroplasmy.
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Affiliation(s)
- Neal Sondheimer
- Department of Pediatrics, The University of Pennsylvania, Philadelphia, PA, USA.
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Chen F, Dang YH, Yan CX, Liu YL, Deng YJ, Fulton DJR, Chen T. Sequence-length variation of mtDNA HVS-I C-stretch in Chinese ethnic groups. J Zhejiang Univ Sci B 2010; 10:711-20. [PMID: 19816995 DOI: 10.1631/jzus.b0920140] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The purpose of this study was to investigate mitochondrial DNA (mtDNA) hypervariable segment-I (HVS-I) C-stretch variations and explore the significance of these variations in forensic and population genetics studies. The C-stretch sequence variation was studied in 919 unrelated individuals from 8 Chinese ethnic groups using both direct and clone sequencing approaches. Thirty eight C-stretch haplotypes were identified, and some novel and population specific haplotypes were also detected. The C-stretch genetic diversity (GD) values were relatively high, and probability (P) values were low. Additionally, C-stretch length heteroplasmy was observed in approximately 9% of individuals studied. There was a significant correlation (r=-0.961, P<0.01) between the expansion of the cytosine sequence length in the C-stretch of HVS-I and a reduction in the number of upstream adenines. These results indicate that the C-stretch could be a useful genetic maker in forensic identification of Chinese populations. The results from the Fst and dA genetic distance matrix, neighbor-joining tree, and principal component map also suggest that C-stretch could be used as a reliable genetic marker in population genetics.
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Affiliation(s)
- Feng Chen
- Department of Forensic Medicine, School of Medicine, Xi'an Jiaotong University, Xi'an 710061, China
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20
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Lutz-Bonengel S, Schmidt U, Sänger T, Heinrich M, Schneider PM, Pollak S. Analysis of mitochondrial length heteroplasmy in monozygous and non-monozygous siblings. Int J Legal Med 2008; 122:315-21. [PMID: 18478247 DOI: 10.1007/s00414-008-0240-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2008] [Accepted: 04/03/2008] [Indexed: 11/29/2022]
Abstract
The segregation of mitochondrial genomes and the inheritance of mitochondrial DNA are constant matters of debate. To obtain more information about this issue and to answer the question whether or not it is possible to distinguish mitochondrial DNA (mtDNA) samples from monozygous individuals by analysing heteroplasmic length variants, 290 monozygous and 121 dizygous twin pairs and 34 sets of multiples were studied by RFLP and partly by direct sequencing. A factor D describing the respective pattern of length variants in a given sample was also calculated. The results show that monozygous individuals exhibit a significantly lower median and closer distribution of D than non-monozygous siblings. Thus, a differentiation of mtDNA samples from monozygous twins by this trait is not possible. The high percentage of heteroplasmic individuals, the low median of the D values and the unexpectedly very similar distribution of length variants in monozygotic individuals support the existence of a relatively wide bottleneck or the assumption of a regeneration of length heteroplasmy following a tight bottleneck and agree with a random segregation of mtDNA genomes in dividing oocytes.
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Affiliation(s)
- S Lutz-Bonengel
- Institute of Legal Medicine, University of Freiburg, Albertstr. 9, 79104 Freiburg, Germany.
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21
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Rajasimha HK, Chinnery PF, Samuels DC. Selection against pathogenic mtDNA mutations in a stem cell population leads to the loss of the 3243A-->G mutation in blood. Am J Hum Genet 2008; 82:333-43. [PMID: 18252214 PMCID: PMC2427290 DOI: 10.1016/j.ajhg.2007.10.007] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Revised: 09/18/2007] [Accepted: 10/03/2007] [Indexed: 12/30/2022] Open
Abstract
The mutation 3243A-->G is the most common heteroplasmic pathogenic mitochondrial DNA (mtDNA) mutation in humans, but it is not understood why the proportion of this mutation decreases in blood during life. Changing levels of mtDNA heteroplasmy are fundamentally related to the pathophysiology of the mitochondrial disease and correlate with clinical progression. To understand this process, we simulated the segregation of mtDNA in hematopoietic stem cells and leukocyte precursors. Our observations show that the percentage of mutant mtDNA in blood decreases exponentially over time. This is consistent with the existence of a selective process acting at the stem cell level and explains why the level of mutant mtDNA in blood is almost invariably lower than in nondividing (postmitotic) tissues such as skeletal muscle. By using this approach, we derived a formula from human data to correct for the change in heteroplasmy over time. A comparison of age-corrected blood heteroplasmy levels with skeletal muscle, an embryologically distinct postmitotic tissue, provides independent confirmation of the model. These findings indicate that selection against pathogenic mtDNA mutations occurs in a stem cell population.
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Affiliation(s)
- Harsha Karur Rajasimha
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Patrick F. Chinnery
- Mitochondrial Research Group and Institute of Human Genetics, Newcastle University, The Medical School, Newcastle-upon-Tyne NE2 4HH, UK
| | - David C. Samuels
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
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Asari M, Azumi JI, Shimizu K, Shiono H. Differences in tissue distribution of HV2 length heteroplasmy in mitochondrial DNA between mothers and children. Forensic Sci Int 2007; 175:155-9. [PMID: 17646069 DOI: 10.1016/j.forsciint.2007.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2006] [Revised: 01/15/2007] [Accepted: 06/09/2007] [Indexed: 10/23/2022]
Abstract
Sequence analysis of HV2 in mitochondrial DNA has been performed as a tool for forensic identification, in addition to that of HV1. HV2 contains length heteroplasmy, which shows high variability within an individual or in maternal relatives. In this study, we used cloning analysis and PCR direct sequencing to compare, between mothers and their children, HV2 length heteroplasmic profiles in different tissues. For two mother-child pairs, different types of variant distribution were observed by cloning analysis. In pair 1, length heteroplasmic patterns in most tissues were similar (predominantly 9 and 10Cs variants), but different length heteroplasmic levels, with shifts in predominant genotype, were observed for some hairs in both mother and child. In pair 2, genotype distribution was similar for all tissues, with a predominant 8Cs genotype, but varying in the proportion of minor component. The proportion of one minor length variant (9Cs) in blood from the child was significantly higher than that from the mother, but the proportions of minor components (7 and/or 9Cs) in other tissue samples decreased from mother to child. Moreover, we could confirm that sequence types of PCR products were reflected by the distribution of length variants, which were observed especially in high proportion, in cloning analysis. Our results reveal variable changes in length heteroplasmic level in various tissues between generations. Variability between tissues, especially among hairs, within an individual would result in complicated differences in genotype distribution between maternal generations, and correlate with longer length of Cs for predominant variants.
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Affiliation(s)
- Masaru Asari
- Department of Legal Medicine, Asahikawa Medical College, 2-1 Midorigaokahigashi, Asahikawa 078-8510, Japan
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23
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Lee HY, Chung U, Park MJ, Yoo JE, Han GR, Shin KJ. Differential distribution of human mitochondrial DNA in somatic tissues and hairs. Ann Hum Genet 2006; 70:59-65. [PMID: 16441257 DOI: 10.1111/j.1529-8817.2005.00217.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To investigate mitochondrial DNA (mtDNA) distribution within tissues during life, we observed length heteroplasmy in a polycytosine tract of the mitochondrial HV2 region by size-based separation of PCR products, using a mutagenic primer which was designed to avoid stutter production. Blood, brain, heart, liver, skeletal muscle and hair shaft samples were collected during autopsies of 25 individuals. Here, we demonstrate differences in the level of mtDNA length heteroplasmy both within and between individuals and tissues. We also show that mtDNA is distributed randomly in varying proportions in various somatic tissues during growth, resulting in an imbalance in the composition of mtDNA pools among tissues. This mtDNA distribution appears not to be strictly random, and can be explained by the random somatic segregation of nucleoids. On the other hand, significant qualitative/quantitative mtDNA peak pattern variations in hair shafts are thought to be a result of the different developmental origins of hairs. Each hair shaft may have a restricted or clonal set of mtDNA molecules derived from a discrete group of stem cells.
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Affiliation(s)
- Hwan Young Lee
- Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, College of Medicine, Yonsei University, 134 Shinchon-Dong, Seodaemun-Gu, Seoul 120-752, Korea
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24
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Spikings EC, Alderson J, St John JC. Transmission of mitochondrial DNA following assisted reproduction and nuclear transfer. Hum Reprod Update 2006; 12:401-15. [PMID: 16581809 DOI: 10.1093/humupd/dml011] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Mitochondria are the organelles responsible for producing the majority of a cell's ATP and also play an essential role in gamete maturation and embryo development. ATP production within the mitochondria is dependent on proteins encoded by both the nuclear and the mitochondrial genomes, therefore co-ordination between the two genomes is vital for cell survival. To assist with this co-ordination, cells normally contain only one type of mitochondrial DNA (mtDNA) termed homoplasmy. Occasionally, however, two or more types of mtDNA are present termed heteroplasmy. This can result from a combination of mutant and wild-type mtDNA molecules or from a combination of wild-type mtDNA variants. As heteroplasmy can result in mitochondrial disease, various mechanisms exist in the natural fertilization process to ensure the maternal-only transmission of mtDNA and the maintenance of homoplasmy in future generations. However, there is now an increasing use of invasive oocyte reconstruction protocols, which tend to bypass mechanisms for the maintenance of homoplasmy, potentially resulting in the transmission of either form of mtDNA heteroplasmy. Indeed, heteroplasmy caused by combinations of wild-type variants has been reported following cytoplasmic transfer (CT) in the human and following nuclear transfer (NT) in various animal species. Other techniques, such as germinal vesicle transfer and pronuclei transfer, have been proposed as methods of preventing transmission of mitochondrial diseases to future generations. However, resulting embryos and offspring may contain mtDNA heteroplasmy, which itself could result in mitochondrial disease. It is therefore essential that uniparental transmission of mtDNA is ensured before these techniques are used therapeutically.
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Affiliation(s)
- E C Spikings
- The Mitochondrial and Reproductive Genetics Group, The Medical School, University of Birmingham, Birmingham B15 2TT, UK
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25
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Barron MJ, Chinnery PF, Howel D, Blakely EL, Schaefer AM, Taylor RW, Turnbull DM. Cytochrome c oxidase deficient muscle fibres: Substantial variation in their proportions within skeletal muscles from patients with mitochondrial myopathy. Neuromuscul Disord 2005; 15:768-74. [PMID: 16198107 DOI: 10.1016/j.nmd.2005.06.018] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2005] [Revised: 06/09/2005] [Accepted: 06/16/2005] [Indexed: 11/21/2022]
Abstract
Mitochondrial DNA (mtDNA) disease is a common cause of myopathy and the presence of histochemically demonstrated cytochrome c oxidase (COX) deficiency is an extremely useful diagnostic feature. However, there is currently no quantitative information regarding the variability of COX deficiency within or between muscles. This study addresses this issue by studying a number of skeletal muscle samples obtained at post-mortem from three patients with mitochondrial disease due to established mitochondrial DNA defects. COX deficient muscle fibres were enumerated in sections of these muscles and analysed according to patient, individual muscle, position within a particular muscle and sample size. Descriptive statistics were generated followed by an analysis of variance (ANOVA) to assess the effect of these parameters on the mean percentage of COX deficient fibres. We observed statistically significant variation in the percentage of COX deficient fibres within individual muscles from each patient for samples sizes of between 100 and 400 fibres. Our results have implications for the way in which biopsies of skeletal muscle are used for the assessment of disease severity, progression and response to treatment.
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Affiliation(s)
- M J Barron
- Mitochondrial Research Group, School of Neurology, Neuroscience and Psychiatry, The University of Newcastle upon Tyne, Newcastle upon Tyne NE2 4HH, UK
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26
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Taylor P, Manage DP, Helmle KE, Zheng Y, Glerum DM, Backhouse CJ. Analysis of mitochondrial DNA in microfluidic systems. J Chromatogr B Analyt Technol Biomed Life Sci 2005; 822:78-84. [PMID: 15990373 DOI: 10.1016/j.jchromb.2005.05.025] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2004] [Revised: 05/24/2005] [Accepted: 05/29/2005] [Indexed: 11/30/2022]
Abstract
Abnormalities in mitochondrial function play a major role in many human diseases. It is often of critical importance to ascertain what proportion of the mitochondria within a cell, or cells, bear a given mutation (the mitochondrial "demographics"). In this work, a rapid, novel, on-chip procedure was used, in which a restriction enzyme was employed to excise a mitochondrial DNA (mtDNA) sequence from plasmid DNA that acted as a prototypical mitochondrial genome. The DNA was then denatured, reassembled to form duplexes, fluorescently labelled and analysed. This method was able to differentiate between a homogeneous population and a heterogeneous population. Using a microfluidic chip, the method could be performed in about 45 min, even without robotics or multiplexed operation, whereas conventional methods of analysis require days to perform. This method may ultimately form the basis for a means of characterizing the mitochondrial demographics of a single cell.
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Affiliation(s)
- Patricia Taylor
- Department of Electrical and Computer Engineering, 2nd Floor, ECERF Building (9107-116St.), University of Alberta, Edmonton, Alta., Canada
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27
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Abstract
The mammalian mitochondrial genome encodes for 37 genes which are involved in a broad range of cellular functions. The mitochondrial DNA (mtDNA) molecule is commonly assumed to be inherited through oocyte cytoplasm in a clonal manner, and apparently species-specific mechanisms have evolved to eliminate the contribution of sperm mitochondria after natural fertilization. However, recent evidence for paternal mtDNA inheritance in embryos and offspring questions the general validity of this model, particularly in the context of assisted reproduction and embryo biotechnology. In addition to normal mt DNA haplotype variation, oocytes and spermatozoa show remarkable differences in mtDNA content and may be affected by inherited or acquired mtDNA aberrations. All these parameters have been correlated with gamete quality and reproductive success rates. Nuclear transfer (NT) technology provides experimental models for studying interactions between nuclear and mitochondrial genomes. Recent studies demonstrated (i) a significant effect of mtDNA haplotype or other maternal cytoplasmic factors on the efficiency of NT; (ii) phenotypic differences between transmitochondrial clones pointing to functionally relevant nuclear-cytoplasmic interactions; and (iii) neutral or non-neutral selection of mtDNA haplotypes in heteroplasmic conditions. Mitochondria form a dynamic reticulum, enabling complementation of mitochondrial components and possibly mixing of different mtDNA populations in heteroplasmic individuals. Future directions of research on mtDNA in the context of reproductive biotechnology range from the elimination of adverse effects of artificial heteroplasmy, e.g. created by ooplasm transfer, to engineering of optimized constellations of nuclear and cytoplasmic genes for the production of superior livestock.
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Affiliation(s)
- S Hiendleder
- Institut für Molekulare Tierzucht und Biotechnologie, Genzentrum der Ludwig-Maximilians-Universität München, Germany.
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28
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Kirches E, Mawrin C, Schneider-Stock R, Krause G, Scherlach C, Dietzmann K. Mitochondrial DNA as a clonal tumor cell marker: gliomatosis cerebri. J Neurooncol 2003; 61:1-5. [PMID: 12587789 DOI: 10.1023/a:1021296212233] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
The aim of this study was a clonal analysis of gliomatosis cerebri (GC), a rare disease characterized by diffuse, extensively infiltrating glial tumors of the central nervous system. Two females of the series were not informative in assays for X-chromosomal inactivation, and a polycytosine tract of the mitochondrial DNA (mtDNA) was tested as a clonal marker. Following fluorescent PCR, a fraction of human individuals shows several electrophoretic bands in normal tissues, some of which can be lost in corresponding glial tumors. Two male patients of our series fulfilled this prerequisite and were thus informative. In patient 1, four tumor samples from the left temporal and occipital cortex, histologically corresponding to WHO grades III and IV, showed an identical loss of bands, which was not observed in tumor-free brain and in tumors from the left cerebellum, from fornix and corpus callosum, and from the right occipital cortex, corresponding to WHO grades III and IV. Since this patient exhibited a TP53 mutation in exon 7, we sequenced this exon in all tissue samples of this individual. The mutation was found selectively in the tumor samples with a loss of mtDNA bands. In patient 2, all tumors (histologically corresponding to WHO grade II) from putamen, thalamus, midbrain and right parietal cortex exhibited an identical loss of bands in the mtDNA analysis. Taken together, these results support that even distant tumors in a patient with GC can share a common clonal origin. They demonstrate the extraordinary mobility and infiltrative power of these tumor cells.
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Affiliation(s)
- E Kirches
- Department of Neuropathology, Otto-von-Guericke-University, Magdeburg, Germany.
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