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Kim BM, Park SU, Schmelzer L, Yang SB, Lee SD, Kim MY, Naue J, Lee HY. DNA methylation-based organ tissue identification: Marker identification, SNaPshot multiplex assay development, and interlaboratory comparison. Forensic Sci Int Genet 2024; 71:103052. [PMID: 38678764 DOI: 10.1016/j.fsigen.2024.103052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/19/2024] [Accepted: 04/20/2024] [Indexed: 05/01/2024]
Abstract
Identifying body fluids and organ tissues is highly significant as they can offer crucial evidence in criminal investigations and aid the court in making informed decisions, primarily through evaluating the biological source and possibly at the activity level up to death or fatal damage. In this study, organ tissue-specific CpG markers were identified from Illumina's methylation EPIC array data of nine organ tissues, including epidermis, dermis, heart, skeletal muscle, blood, kidney, brain, lung, and liver, from autopsies of 10 Koreans. Through the validation test using 43 samples, 18 hypomethylation markers, with two markers for each organ tissue type, were selected to construct a SNaPshot assay. Two multiplex assays involving forward and reverse SBE primers were designed to help investigators accurately determine the organ origin of the analyzed tissue samples through repeated analysis of the same PCR products for markers. The developed multiplex demonstrated high accuracy, achieving 100.0 % correct detection of the presence of nine organ tissue types in 88 samples from autopsies of 10 Asians. However, two lung samples showed additional positive indications of the presence of blood. An interlaboratory comparison using 80 autopsy samples (heart, skeletal muscle, blood, kidney cortex, kidney medulla, brain, lung, and liver) from 10 individuals in Germany revealed overall comparable results with correct detection of the presence of eight organ tissue types in 92.5 % samples (74 of 80 samples). In the case of six samples, it was impossible to determine the correct tissue successfully due to drop-outs of unmethylation signals at target tissue marker loci. One of these lung samples revealed only non-intended off-target signals for blood. The observed differences might be due to differences in sample collection during routine autopsy, technical differences due to the PCR cycler, and the threshold used for signal calling. Indicating the presence of additional tissue type and off-target unmethylation signals seems alleviated by applying more stringent hypomethylation thresholds. Therefore, the developed SNaPshot multiplex assays will be valuable for forensic investigators dealing with organ tissue identification, as well as for prosecutors and defense aiming to establish the circumstances that occurred at the crime scene.
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Affiliation(s)
- Bo Min Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sang Un Park
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Laura Schmelzer
- Institute of Forensic Medicine, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Germany
| | - Soo-Bin Yang
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Soong Deok Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea
| | - Moon-Young Kim
- Laboratory of Forensic Medicine, Department of Anatomy and Cell Biology, Sungkyunkwan University School of Medicine, Suwon, Korea
| | - Jana Naue
- Institute of Forensic Medicine, Medical Center -University of Freiburg, Faculty of Medicine, University of Freiburg, Germany.
| | - Hwan Young Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea; Institute of Forensic and Anthropological Science, Seoul National University College of Medicine, Seoul, Korea.
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2
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Beecher G, Gavrilova RH, Mandrekar J, Naddaf E. Mitochondrial myopathies diagnosed in adulthood: clinico-genetic spectrum and long-term outcomes. Brain Commun 2024; 6:fcae041. [PMID: 38434220 PMCID: PMC10906953 DOI: 10.1093/braincomms/fcae041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/14/2023] [Accepted: 02/12/2024] [Indexed: 03/05/2024] Open
Abstract
Mitochondrial myopathies are frequently recognized in childhood as part of a broader multisystem disorder and often overlooked in adulthood. Herein, we describe the phenotypic and genotypic spectrum and long-term outcomes of mitochondrial myopathies diagnosed in adulthood, focusing on neuromuscular features, electrodiagnostic and myopathological findings and survival. We performed a retrospective chart review of adult patients diagnosed with mitochondrial myopathy at Mayo Clinic (2005-21). We identified 94 patients. Median time from symptom onset to diagnosis was 11 years (interquartile range 4-21 years). Median age at diagnosis was 48 years (32-63 years). Primary genetic defects were identified in mitochondrial DNA in 48 patients (10 with single large deletion, 38 with point mutations) and nuclear DNA in 29. Five patients had multiple mitochondrial DNA deletions or depletion without nuclear DNA variants. Twelve patients had histopathological features of mitochondrial myopathy without molecular diagnosis. The most common phenotypes included multisystem disorder (n = 30); mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (14); limb myopathy (13); chronic progressive external ophthalmoplegia (12); and chronic progressive external ophthalmoplegia-plus (12). Isolated skeletal muscle manifestations occurred in 27%. Sixty-nine per cent had CNS and 21% had cardiac involvement. Mutations most frequently involved MT-TL1 (27) and POLG (17); however, a wide spectrum of established and novel molecular defects, with overlapping phenotypes, was identified. Electrodiagnostic studies identified myopathy (77%), fibrillation potentials (27%) and axonal peripheral neuropathy (42%, most common with nuclear DNA variants). Among 42 muscle biopsies available, median percentage counts were highest for cytochrome C oxidase negative fibres (5.1%) then ragged blue (1.4%) and ragged red fibres (0.5%). Skeletal muscle weakness was mild and slowly progressive (decline in strength summated score of 0.01/year). Median time to gait assistance was 5.5 years from diagnosis and 17 years from symptom onset. Thirty patients died, with median survival of 33.4 years from symptom onset and 10.9 years from diagnosis. Median age at death was 55 years. Cardiac involvement was associated with increased mortality [hazard ratio 2.36 (1.05, 5.29)]. There was no difference in survival based on genotype or phenotype. Despite the wide phenotypic and genotypic spectrum, mitochondrial myopathies in adults share similar features with slowly progressive limb weakness, contrasting with common multiorgan involvement and high mortality.
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Affiliation(s)
- Grayson Beecher
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
- Division of Neurology, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
| | - Ralitza H Gavrilova
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN 55905, USA
| | - Jay Mandrekar
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
| | - Elie Naddaf
- Department of Neurology, Mayo Clinic, Rochester, MN 55905, USA
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3
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Mertens J, Belva F, van Montfoort APA, Regin M, Zambelli F, Seneca S, Couvreu de Deckersberg E, Bonduelle M, Tournaye H, Stouffs K, Barbé K, Smeets HJM, Van de Velde H, Sermon K, Blockeel C, Spits C. Children born after assisted reproduction more commonly carry a mitochondrial genotype associating with low birthweight. Nat Commun 2024; 15:1232. [PMID: 38336715 PMCID: PMC10858059 DOI: 10.1038/s41467-024-45446-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Children conceived through assisted reproductive technologies (ART) have an elevated risk of lower birthweight, yet the underlying cause remains unclear. Our study explores mitochondrial DNA (mtDNA) variants as contributors to birthweight differences by impacting mitochondrial function during prenatal development. We deep-sequenced the mtDNA of 451 ART and spontaneously conceived (SC) individuals, 157 mother-child pairs and 113 individual oocytes from either natural menstrual cycles or after ovarian stimulation (OS) and find that ART individuals carried a different mtDNA genotype than SC individuals, with more de novo non-synonymous variants. These variants, along with rRNA variants, correlate with lower birthweight percentiles, independent of conception mode. Their higher occurrence in ART individuals stems from de novo mutagenesis associated with maternal aging and OS-induced oocyte cohort size. Future research will establish the long-term health consequences of these changes and how these findings will impact the clinical practice and patient counselling in the future.
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Affiliation(s)
- Joke Mertens
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Florence Belva
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Aafke P A van Montfoort
- Department of Obstetrics & Gynaecology, GROW School for Oncology and Developmental Biology, Maastricht University Medical Center, Maastricht, The Netherlands
| | - Marius Regin
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Sara Seneca
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Edouard Couvreu de Deckersberg
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Herman Tournaye
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Research Group Biology of the Testis, Faculty of Medicine, Vrije Universiteit Brussel, Brussels, Belgium
| | - Katrien Stouffs
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
- Center for Medical Genetics, UZ Brussel, Brussels, Belgium
| | - Kurt Barbé
- Interfaculty Center Data Processing & Statistics, Vrije Universiteit Brussel, Brussels, Belgium
| | - Hubert J M Smeets
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
- MHeNs School Institute for Mental Health and Neuroscience, GROW Institute for Oncology and Developmental Biology, Maastricht University, Maastricht, The Netherlands
| | - Hilde Van de Velde
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Research Group Reproduction and Immunology, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Karen Sermon
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium
| | - Christophe Blockeel
- Brussels IVF, Center for Reproductive Medicine, UZ Brussel, Brussels, Belgium
- Department of Obstetrics and Gynaecology, School of Medicine, University of Zagreb, Šalata 3, Zagreb, 10000, Croatia
| | - Claudia Spits
- Research Group Reproduction and Genetics, Faculty of Medicine and Pharmacy, Vrije Universiteit Brussel, Brussels, Belgium.
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Korolija M, Sukser V, Vlahoviček K. Mitochondrial point heteroplasmy: insights from deep-sequencing of human replicate samples. BMC Genomics 2024; 25:48. [PMID: 38200446 PMCID: PMC10782721 DOI: 10.1186/s12864-024-09963-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 01/03/2024] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Human mitochondrial heteroplasmy is an extensively investigated phenomenon in the context of medical diagnostics, forensic identification and molecular evolution. However, technical limitations of high-throughput sequencing hinder reliable determination of point heteroplasmies (PHPs) with minor allele frequencies (MAFs) within the noise threshold. RESULTS To investigate the PHP landscape at an MAF threshold down to 0.1%, we sequenced whole mitochondrial genomes at approximately 7.700x coverage, in multiple technical and biological replicates of longitudinal blood and buccal swab samples from 11 human donors (159 libraries in total). The results obtained by two independent sequencing platforms and bioinformatics pipelines indicate distinctive PHP patterns below and above the 1% MAF cut-off. We found a high inter-individual prevalence of low-level PHPs (MAF < 1%) at polymorphic positions of the mitochondrial DNA control region (CR), their tissue preference, and a tissue-specific minor allele linkage. We also established the position-dependent potential of minor allele expansion in PHPs, and short-term PHP instability in a mitotically active tissue. We demonstrate that the increase in sensitivity of PHP detection to minor allele frequencies below 1% within a robust experimental and analytical pipeline, provides new information with potential applicative value. CONCLUSIONS Our findings reliably show different mutational loads between tissues at sub-1% allele frequencies, which may serve as an informative medical biomarker of time-dependent, tissue-specific mutational burden, or help discriminate forensically relevant tissues in a single person, close maternal relatives or unrelated individuals of similar phylogenetic background.
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Affiliation(s)
- Marina Korolija
- Biology and Fibres Department, Forensic Science Centre "Ivan Vučetić", Ministry of the Interior of the Republic of Croatia, Ilica 335, HR-10000, Zagreb, Croatia.
| | - Viktorija Sukser
- Biology and Fibres Department, Forensic Science Centre "Ivan Vučetić", Ministry of the Interior of the Republic of Croatia, Ilica 335, HR-10000, Zagreb, Croatia
| | - Kristian Vlahoviček
- Bioinformatics group, Division of Molecular Biology, Department of Biology, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000, Zagreb, Croatia
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5
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Naue J, Xavier C, Hörer S, Parson W, Lutz-Bonengel S. Assessment of mitochondrial DNA copy number variation relative to nuclear DNA quantity between different tissues. Mitochondrion 2024; 74:101823. [PMID: 38040171 DOI: 10.1016/j.mito.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/23/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mitochondrial DNA is a widely tested genetic marker in various fields of research and diagnostics. Nonetheless, there is still little understanding on its abundance and quality within different tissues. Aiming to obtain deeper knowledge about the content and quality of mtDNA, we investigated nine tissues including blood, bone, brain, hair (root and shaft), cardiac muscle, liver, lung, skeletal muscle, and buccal mucosa of 32 deceased individuals using two real-time quantitative PCR-based assays with differently sized mtDNA and nDNA targets. The results revealed that the quantity of nDNA is a weak surrogate to estimate mtDNA quantities among tissues of an individual, as well as tissues across individuals. Especially hair showed extreme variation, depicting a range of multiple magnitudes of mtDNA molecules per hair fragment. Furthermore, degradation can lead to fewer fragments being available for PCR. The results call for parallel determination of the quantity and quality of mtDNA prior to downstream genotyping assays.
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Affiliation(s)
- Jana Naue
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstrasse 9, Freiburg 79104, Germany
| | - Catarina Xavier
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, Innsbruck 6020, Austria; i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - Steffen Hörer
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstrasse 9, Freiburg 79104, Germany
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Muellerstrasse 44, Innsbruck 6020, Austria; Forensic Science Program, The Pennsylvania State University, USA.
| | - Sabine Lutz-Bonengel
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Albertstrasse 9, Freiburg 79104, Germany
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6
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Wang W, Lin L, Zhang Q, Yang J, Kamili E, Chu J, Li X, Yang S, Xu Y. Heteroplasmy and Individual Mitogene Pools: Characteristics and Potential Roles in Ecological Studies. BIOLOGY 2023; 12:1452. [PMID: 37998051 PMCID: PMC10669347 DOI: 10.3390/biology12111452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 11/25/2023]
Abstract
The mitochondrial genome (mitogenome or mtDNA), the extrachromosomal genome, is a multicopy circular DNA with high mutation rates due to replication and repair errors. A mitochondrion, cell, tissue, organ, or an individual body may hold multiple variants, both inherited and developed over a lifetime, which make up individual mitogene pools. This phenomenon is also called mtDNA heteroplasmy. MtDNA variants influence cellular and tissular functions and are consequently subjected to selection. Although it has long been recognized that only inheritable germline heteroplasmies have evolutionary significance, non-inheritable somatic heteroplasmies have been overlooked since they directly affect individual fitness and thus indirectly affect the fate of heritable germline variants. This review focuses on the characteristics, dynamics, and functions of mtDNA heteroplasmy and proposes the concept of individual mitogene pools to discuss individual genetic diversity from multiple angles. We provide a unique perspective on the relationship between individual genetic diversity and heritable genetic diversity and guide how the individual mitogene pool with novel genetic markers can be applied to ecological research.
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Affiliation(s)
| | | | | | | | | | | | | | - Shuhui Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (W.W.); (L.L.); (Q.Z.); (J.Y.); (E.K.); (J.C.); (X.L.)
| | - Yanchun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin 150040, China; (W.W.); (L.L.); (Q.Z.); (J.Y.); (E.K.); (J.C.); (X.L.)
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7
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Garcia-Gaona E, García-Gregorio A, García-Jiménez C, López-Olaiz MA, Mendoza-Ramírez P, Fernandez-Guzman D, Pillado-Sánchez RA, Soto-Pacheco AD, Yareni-Zuñiga L, Sánchez-Parada MG, González-Santiago AE, Román-Pintos LM, Castañeda-Arellano R, Hernández-Ortega LD, Mercado-Sesma AR, Orozco-Luna FDJ, Villa-Angulo C, Villa-Angulo R, Baptista-Rosas RC. mtDNA Single-Nucleotide Variants Associated with Type 2 Diabetes. Curr Issues Mol Biol 2023; 45:8716-8732. [PMID: 37998725 PMCID: PMC10670651 DOI: 10.3390/cimb45110548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 10/18/2023] [Accepted: 10/23/2023] [Indexed: 11/25/2023] Open
Abstract
Type 2 diabetes (T2D) is a chronic systemic disease with a complex etiology, characterized by insulin resistance and mitochondrial dysfunction in various cell tissues. To explore this relationship, we conducted a secondary analysis of complete mtDNA sequences from 1261 T2D patients and 1105 control individuals. Our findings revealed significant associations between certain single-nucleotide polymorphisms (SNPs) and T2D. Notably, the variants m.1438A>G (rs2001030) (controls: 32 [27.6%], T2D: 84 [72.4%]; OR: 2.46; 95%CI: 1.64-3.78; p < 0.001), m.14766C>T (rs193302980) (controls: 498 [36.9%], T2D: 853 [63.1%]; OR: 2.57, 95%CI: 2.18-3.04, p < 0.001), and m.16519T>C (rs3937033) (controls: 363 [43.4%], T2D: 474 [56.6%]; OR: 1.24, 95%CI: 1.05-1.47, p = 0.012) were significantly associated with the likelihood of developing diabetes. The variant m.16189T>C (rs28693675), which has been previously documented in several studies across diverse populations, showed no association with T2D in our analysis (controls: 148 [13.39] T2D: 171 [13.56%]; OR: 1.03; 95%CI: 0.815-1.31; p = 0.83). These results provide evidence suggesting a link between specific mtDNA polymorphisms and T2D, possibly related to association rules, topological patterns, and three-dimensional conformations associated with regions where changes occur, rather than specific point mutations in the sequence.
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Affiliation(s)
- Enrique Garcia-Gaona
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla 72420, Mexico;
| | - Alhelí García-Gregorio
- Facultad de Enfermería Región Poza Rica-Tuxpan, Universidad Veracruzana, Veracruz 91700, Mexico;
| | - Camila García-Jiménez
- Facultad de Ciencias Médicas y Biológicas “Dr. Ignacio Chávez”, Universidad Michoacana de San Nicolás de Hidalgo, Morelia 58000, Mexico;
| | | | - Paola Mendoza-Ramírez
- Facultad de Ciencias Biológicas, Benemérita Universidad Autónoma de Puebla, Puebla 72420, Mexico;
| | | | | | - Axel David Soto-Pacheco
- Facultad de Medicina Extensión Los Mochis, Universidad Autónoma de Sinaloa, Sinaloa 81223, Mexico; (R.A.P.-S.); (A.D.S.-P.)
| | - Laura Yareni-Zuñiga
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
| | - María Guadalupe Sánchez-Parada
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Ana Elizabeth González-Santiago
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Luis Miguel Román-Pintos
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Rolando Castañeda-Arellano
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Luis Daniel Hernández-Ortega
- Departamento de Ciencias Biomédicas, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (M.G.S.-P.); (A.E.G.-S.); (R.C.-A.); (L.D.H.-O.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | - Arieh Roldán Mercado-Sesma
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
| | | | - Carlos Villa-Angulo
- Laboratorio de Bioinformática y Biofotónica, Instituto de Ingeniería Universidad Autónoma de Baja California, Mexicali 21100, Mexico; (C.V.-A.); (R.V.-A.)
| | - Rafael Villa-Angulo
- Laboratorio de Bioinformática y Biofotónica, Instituto de Ingeniería Universidad Autónoma de Baja California, Mexicali 21100, Mexico; (C.V.-A.); (R.V.-A.)
| | - Raúl C. Baptista-Rosas
- Departamento de Ciencias de la Salud-Enfermedad como Proceso Individual, Centro Universitario de Tonalá, Universidad de Guadalajara, Tonalá 45425, Mexico; (L.Y.-Z.); (L.M.R.-P.); (A.R.M.-S.)
- Centro de Investigación Multidisciplinaria en Salud, Universidad de Guadalajara, Tonalá 45425, Mexico
- Hospital General de Occidente, Secretaría de Salud Jalisco, Zapopan 45170, Mexico
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8
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Liu J, Zhang S, Wen Y, Su Y, Jiang L, Li S, Shen J, Zheng X, Li X, Chen X, Wang Z. Exploring rare differences in mitochondrial genome between MZ twins using Ion Torrent semiconductor sequencing. Forensic Sci Int 2023; 348:111708. [PMID: 37119662 DOI: 10.1016/j.forsciint.2023.111708] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/15/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
Monozygotic (MZ) twins are considered to be genetically identical in that they have the same genomic DNA sequences in theory, and thus cannot be differentiated using forensic standard STR-based DNA profiling. However, a recent study employed deep sequencing to explore extremely rare mutations in the nuclear genome and reported that the mutation analysis could be applied to differentiate between MZ twins. Compared with the nuclear genome, the mitochondrial DNA (mtDNA) exhibits higher mutation rates due to fewer DNA repair mechanisms in the mitochondrial genome (mtGenome) and the lack of proofreading capability of the mtDNA polymerase. In a previous study, we used Illumina ultra-deep sequencing to describe point heteroplasmy (PHP) and nucleotide variant of the mtGenomes in venous blood samples of MZ twins. In the present study, we characterized minor differences of the mtGenomes in three tissue samples from seven sets of MZ twins using Ion Torrent semiconductor sequencing (Thermo Fisher Ion S5 XL system) and commercialized mtGenome sequencing kit (Precision ID mtDNA Whole Genome Panel). PHP was observed in blood samples from one set of MZ twins and in saliva samples from two sets of twins, but it presented in hair shaft samples from all seven sets of MZ twins. Overall, the coding region of the mtGenome exhibits more PHPs than the control region. The results of this study have further attested the competence of mtGenome sequencing in differentiating between MZ twins, and that among the three kinds of samples tested, hair shaft is more likely to accumulate minor differences in the mtGenomes of MZ twins.
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Affiliation(s)
- Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Shuyuan Zhang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Yufeng Wen
- School of Life Sciences, Jilin University, Changchun 130012, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu 610041, China
| | - Lirong Jiang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Suyu Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Jian Shen
- Anhui Hopegenerich Biotechnology, Hefei 230031, China
| | - Xinyue Zheng
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xingrui Li
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China.
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9
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Peng D, Geng J, Yang J, Liu J, Wang N, Wu R, Sun H. Whole Mitochondrial Genome Detection and Analysis of Two- to Four-Generation Maternal Pedigrees Using a New Massively Parallel Sequencing Panel. Genes (Basel) 2023; 14:genes14040912. [PMID: 37107670 PMCID: PMC10137955 DOI: 10.3390/genes14040912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 04/08/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Mitochondrial DNA (mtDNA) is an effective genetic marker in forensic practice, especially for aged bones and hair shafts. Detection of the whole mitochondrial genome (mtGenome) using traditional Sanger-type sequencing is laborious and time-consuming. Additionally, its ability to distinguish point heteroplasmy (PHP) and length heteroplasmy (LHP) is limited. The application of massively parallel sequencing in mtDNA detection helps researchers to study the mtGenome in-depth. The ForenSeq mtDNA Whole Genome Kit, which contains a total of 245 short amplicons, is one of the multiplex library preparation kits for the mtGenome. We used this system to detect the mtGenome in the blood samples and hair shafts of thirty-three individuals from eight two-generation pedigrees, one three-generation pedigree, and one four-generation pedigree. High-quality sequencing results were obtained. Ten unique mtGenome haplotypes were observed in the mothers from the ten pedigrees. A total of 26 PHPs were observed using the interpretation threshold of 6%. Eleven types of LHPs in six regions were evaluated in detail. When considering homoplasmic variants only, consistent mtGenome haplotypes were observed between the twice-sequenced libraries and between the blood and hair shafts from the same individual and among maternal relatives in the pedigrees. Four inherited PHPs were observed, and the remainder were de novo/disappearing PHPs in the pedigrees. Our results demonstrate the effective capability of the ForenSeq mtDNA Whole Genome Kit to generate the complete mtGenome in blood and hair shafts, as well as the complexity of mtDNA haplotype comparisons between different types of maternal relatives when heteroplasmy is considered.
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Affiliation(s)
- Dan Peng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiaojiao Geng
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Jiajun Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Nana Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510080, China
- Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Sun Yat-sen University, Guangzhou 510080, China
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10
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Liu Z, Simayijiang H, Wang Q, Yang J, Sun H, Wu R, Yan J. DNA and protein analyses of hair in forensic genetics. Int J Legal Med 2023; 137:613-633. [PMID: 36732435 DOI: 10.1007/s00414-023-02955-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 01/20/2023] [Indexed: 02/04/2023]
Abstract
Hair is one of the most common pieces of biological evidence found at a crime scene and plays an essential role in forensic investigation. Hairs, especially non-follicular hairs, are usually found at various crime scenes, either by natural shedding or by forcible shedding. However, the genetic material in hairs is usually highly degraded, which makes forensic analysis difficult. As a result, the value of hair has not been fully exploited in forensic investigations and trials. In recent years, with advances in molecular biology, forensic analysis of hair has achieved remarkable strides and provided crucial clues in numerous cases. This article reviews recent developments in DNA and protein analysis of hair and attempts to provide a comprehensive solution to improve forensic hair analysis.
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Affiliation(s)
- Zhiyong Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Halimureti Simayijiang
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China
| | - Qiangwei Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Jingyi Yang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Hongyu Sun
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China
| | - Riga Wu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China. .,Guangdong Province Translational Forensic Medicine Engineering Technology Research Center, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, Guangdong, 510080, People's Republic of China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, Shanxi, 030600, People's Republic of China.
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11
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Alqaisi MHM, Ekka MM, Patel BC. Forensic evaluation of mitochondrial DNA heteroplasmy in Gujarat population, India. Ann Hum Biol 2022; 49:332-341. [PMID: 36343161 DOI: 10.1080/03014460.2022.2144447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
BACKGROUND Owing to its high copy number and its small size, mtDNA analysis is the most reliable choice when biological materials from crime scenes are degraded or have mixed STR profiles. AIM To examine the occurrence of heteroplasmy along with its frequency and pattern in both HV1 and HV2 regions of the mtDNA among unrelated individuals from India. SUBJECTS AND METHODS Mitochondrial DNA control region [hypervariable region one (HV1) and hypervariable region two (HV2)] were analysed in blood and buccal tissues of 104 unrelated individuals from the Indian state of Gujarat. RESULTS A high frequency of point heteroplasmy (PH) and length heteroplasmy (LH) was revealed. PH was detected in 7.69% of the population, with a higher frequency observed in blood than in buccal samples. However, there were no statistically significant differences in PH between the two tissues (Chi-square = 0.552, p ≥ 0.05). A total of six PH positions were detected: three at HV1, and another three at HV2. The studied population showed 46.15% LH in the HV1 and HV2 regions of both tissues. The LH positions observed in the Gujarat population were the same as those previously reported at HV1 np16184-16193 and HV2 np303-315. CONCLUSIONS Our findings suggest that differences in the pattern of heteroplasmy found in different tissues can complicate the forensic analysis, on the other hand, the probability of a match between the questioned and reference samples increases when the heteroplasmy is identical in both tissues. Variability of PH among persons and even within tissues recommends analysing multiple tissue samples before drawing a conclusion in forensic mtDNA analyses.
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Affiliation(s)
- Mohammed H M Alqaisi
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
| | - Molina Madhulika Ekka
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
| | - Bhargav C Patel
- Laboratory of Forensic Biology and Biotechnology, National Forensic Sciences University (NFSU), Gandhinagar, Gujarat, India
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12
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Tostes K, dos Santos AC, Alves LO, Bechara LRG, Marascalchi R, Macabelli CH, Grejo MP, Festuccia WT, Gottlieb RA, Ferreira JCB, Chiaratti MR. Autophagy deficiency abolishes liver mitochondrial DNA segregation. Autophagy 2022; 18:2397-2408. [PMID: 35220898 PMCID: PMC9542960 DOI: 10.1080/15548627.2022.2038501] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mutations in the mitochondrial genome (mtDNA) are ubiquitous in humans and can lead to a broad spectrum of disorders. However, due to the presence of multiple mtDNA molecules in the cell, co-existence of mutant and wild-type mtDNAs (termed heteroplasmy) can mask disease phenotype unless a threshold of mutant molecules is reached. Importantly, the mutant mtDNA level can change across lifespan as mtDNA segregates in an allele- and cell-specific fashion, potentially leading to disease. Segregation of mtDNA is mainly evident in hepatic cells, resulting in an age-dependent increase of mtDNA variants, including non-synonymous potentially deleterious mutations. Here we modeled mtDNA segregation using a well-established heteroplasmic mouse line with mtDNA of NZB/BINJ and C57BL/6N origin on a C57BL/6N nuclear background. This mouse line showed a pronounced age-dependent NZB mtDNA accumulation in the liver, thus leading to enhanced respiration capacity per mtDNA molecule. Remarkably, liver-specific atg7 (autophagy related 7) knockout abolished NZB mtDNA accumulat ion, resulting in close-to-neutral mtDNA segregation through development into adulthood. prkn (parkin RBR E3 ubiquitin protein ligase) knockout also partially prevented NZB mtDNA accumulation in the liver, but to a lesser extent. Hence, we propose that age-related liver mtDNA segregation is a consequence of macroautophagic clearance of the less-fit mtDNA. Considering that NZB/BINJ and C57BL/6N mtDNAs have a level of divergence comparable to that between human Eurasian and African mtDNAs, these findings have potential implications for humans, including the safe use of mitochondrial replacement therapy.Abbreviations: Apob: apolipoprotein B; Atg1: autophagy-related 1; Atg7: autophagy related 7; Atp5a1: ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1; BL6: C57BL/6N mouse strain; BNIP3: BCL2/adenovirus E1B interacting protein 3; FCCP: carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; MAP1LC3A: microtubule-associated protein 1 light chain 3 alpha; MAP1LC3B: microtubule-associated protein 1 light chain 3 beta; mt-Atp8: mitochondrially encoded ATP synthase 8; MT-CO1: mitochondrially encoded cytochrome c oxidase I; MT-CO2: mitochondrially encoded cytochrome c oxidase II; mt-Co3: mitochondrially encoded cytochrome c oxidase III; mt-Cytb: mitochondrially encoded cytochrome b; mtDNA: mitochondrial DNA; MUL1: mitochondrial ubiquitin ligase activator of NFKB 1; nDNA: nuclear DNA; Ndufa9: NADH:ubiquinone oxireductase subunit A9; NDUFB8: NADH:ubiquinone oxireductase subunit B8; Nnt: nicotinamide nucleotide transhydrogenase; NZB: NZB/BINJ mouse strain; OXPHOS: oxidative phosphorylation; PINK1: PTEN induced putative kinase 1; Polg2: polymerase (DNA directed), gamma 2, accessory subunit; Ppara: peroxisome proliferator activated receptor alpha; Ppia: peptidylprolyl isomerase A; Prkn: parkin RBR E3 ubiquitin protein ligase; P10: post-natal day 10; P21: post-natal day 21; P100: post-natal day 100; qPCR: quantitative polymerase chain reaction; Rpl19: ribosomal protein L19; Rps18: ribosomal protein S18; SD: standard deviation; SEM: standard error of the mean; SDHB: succinate dehydrogenase complex, subunit B, iron sulfur (Ip); SQSTM1: sequestosome 1; Ssbp1: single-stranded DNA binding protein 1; TFAM: transcription factor A, mitochondrial; Tfb1m: transcription factor B1, mitochondrial; Tfb2m: transcription factor B2, mitochondrial; TOMM20: translocase of outer mitochondrial membrane 20; UQCRC2: ubiquinol cytochrome c reductase core protein 2; WT: wild-type.
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Affiliation(s)
- Katiane Tostes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Angélica C. dos Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Lindomar O. Alves
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Luiz R. G. Bechara
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Rachel Marascalchi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Carolina H. Macabelli
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Mateus P. Grejo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - William T. Festuccia
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Roberta A. Gottlieb
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Julio C. B. Ferreira
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil,Department of Chemical and Systems Biology, Stanford University School of Medicine, CA, USA
| | - Marcos R. Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil,CONTACT Marcos R. Chiaratti Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos13565-905, Brazil
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13
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Dierig L, Bamberg M, Brommer A, Klein-Unseld R, Kunz SN, Schwender M, Wiegand P. Development of a multiplex assay for detection of autosomal and Y-chromosomal STRs, assessment of the degradation state of mitochondrial DNA and presence of mitochondrial length heteroplasmies. Forensic Sci Int Genet 2022; 61:102775. [PMID: 36137414 DOI: 10.1016/j.fsigen.2022.102775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/13/2022] [Indexed: 11/04/2022]
Abstract
The current focus in most routine forensic casework is detection of autosomal or gonosomal Short Tandem Repeats (STRs). With increasing degradation, STR analysis tends to be less successful up to complete failure. For challenging samples such as telogen hair roots and shafts, touch DNA samples or skeletal remains, mitochondrial DNA (mtDNA) analysis provides a powerful tool. Determination of DNA quantity is an important part in the casework workflow. Several ready-to-use kits are commercially available for nuclear DNA targets. However, quantification of mtDNA targets requires the establishment of an in-house method. Some assays even contain assessment of degradation, which alleviates the choice of target enrichment for sequencing through medium or small amplicons. As Sanger-type Sequencing (STS) still remains the golden standard in many laboratories, identification of heteroplasmies in C-tract regions prior to the sequencing reaction is advantageous. Firstly, primer selection can be expanded with primers binding near the C-tract and secondly, determination of the dominant variant is straightforward. All those quantity (nuclear and mtDNA) and quality (degradation and length heteroplasmies) evaluations usually require at least two separate reactions. Therefore, the aim of this project was the combination of all these targets in one multiplex assay using capillary electrophoresis to spare valuable sample extract. Amplification of representative autosomal and Y-chromosomal STRs allows estimate of success of (Y-)STR analysis. Simultaneously, five length heteroplasmies in the mitochondrial control region are targeted as well as three conservative regions of differing fragment lengths for assessment of the mitochondrial degradation state. Based on the outcome of this assay, forensic examiners can decide if STR analysis may be suitable. In case of absent STR peaks, appropriate proceeding of mtDNA sequencing can be determined.
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Affiliation(s)
- Lisa Dierig
- University Ulm, Institute of Legal Medicine, Albert-Einstein-Allee 23, Ulm 89081, Germany.
| | - Malte Bamberg
- University Ulm, Institute of Legal Medicine, Albert-Einstein-Allee 23, Ulm 89081, Germany
| | - Arthur Brommer
- Ludwig-Maximilians University Munich, Geschwister-Scholl-Platz 1, München 80539, Germany
| | - Rachel Klein-Unseld
- University Ulm, Institute of Legal Medicine, Albert-Einstein-Allee 23, Ulm 89081, Germany
| | - Sebastian N Kunz
- University Ulm, Institute of Legal Medicine, Albert-Einstein-Allee 23, Ulm 89081, Germany
| | - Max Schwender
- University Ulm, Institute of Legal Medicine, Albert-Einstein-Allee 23, Ulm 89081, Germany
| | - Peter Wiegand
- University Ulm, Institute of Legal Medicine, Albert-Einstein-Allee 23, Ulm 89081, Germany
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14
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Solanky D, Fields JA, Iudicello JE, Ellis RJ, Franklin D, Clifford DB, Gelman BB, Marra CM, Morgello S, Rubin LH, Grant I, Heaton RK, Letendre SL, Mehta SR. Higher buccal mitochondrial DNA and mitochondrial common deletion number are associated with markers of neurodegeneration and inflammation in cerebrospinal fluid. J Neurovirol 2022; 28:281-290. [PMID: 35157246 PMCID: PMC9352370 DOI: 10.1007/s13365-022-01052-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Revised: 12/03/2021] [Accepted: 01/11/2022] [Indexed: 11/27/2022]
Abstract
Human immunodeficiency virus (HIV) infection is potentially associated with premature aging, but demonstrating this is difficult due to a lack of reliable biomarkers. The mitochondrial (mt) DNA "common deletion" mutation (mtCDM) is a 4977-bp deletion associated with aging and neurodegenerative diseases. We examined how mtDNA and mtCDM correlate with markers of neurodegeneration and inflammation in people with and without HIV (PWH and PWOH). Data from 149 adults were combined from two projects involving PWH (n = 124) and PWOH (n = 25). We measured buccal mtDNA and mtCDM by digital droplet PCR and compared them to disease and demographic characteristics and soluble biomarkers in cerebrospinal fluid (CSF) and blood measured by immunoassay. Participants had a median age of 52 years, with 53% white and 81% men. Median mtDNA level was 1,332 copies/cell (IQR 1,201-1,493) and median mtCDM level was 0.36 copies × 102/cell (IQR 0.31-0.42); both were higher in PWH. In the best model adjusting for HIV status and demographics, higher mtDNA levels were associated with higher CSF amyloid-β 1-42 and 8-hydroxy-2'-deoxyguanosine and higher mtCDM levels were associated with higher plasma soluble tumor necrosis factor receptor II. The differences in mtDNA markers between PWH and PWOH support potential premature aging in PWH. Our findings suggest mtDNA changes in oral tissues may reflect CNS processes, allowing the use of inexpensive and easily accessible buccal biospecimens as a screening tool for CSF inflammation and neurodegeneration. Confirmatory and mechanistic studies on mt genome alterations by HIV and ART may identify interventions to prevent or treat neurodegenerative complications.
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Affiliation(s)
- Dipesh Solanky
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
| | - Jerel A Fields
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Jennifer E Iudicello
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ronald J Ellis
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, 92093, USA
- Department of Neurosciences, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Donald Franklin
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - David B Clifford
- Division of Infectious Diseases, Washington University at St. Louis, St. Louis, MO, 63110, USA
| | - Benjamin B Gelman
- Department of Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Christina M Marra
- Deparment of Neurology, University of Washington, Seattle, WA, 98104, USA
| | - Susan Morgello
- Department of Neurology, Icahn School of Medicine at Mt, Sinai, New York, NY, 10029, USA
| | - Leah H Rubin
- Department of Neurology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Igor Grant
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Robert K Heaton
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Scott L Letendre
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Sanjay R Mehta
- Department of Medicine, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA, 92093, USA.
- Department of Medicine, VA San Diego Healthcare System, La Jolla, CA, 92161, USA.
- Infectious Diseases Division, VA San Diego Healthcare System, La Jolla, 92161, USA.
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15
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McElhoe JA, Wilton PR, Parson W, Holland MM. Exploring statistical weight estimates for mitochondrial DNA matches involving heteroplasmy. Int J Legal Med 2022; 136:671-685. [PMID: 35243529 DOI: 10.1007/s00414-022-02774-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 01/12/2022] [Indexed: 11/26/2022]
Abstract
Massively parallel sequencing (MPS) of mitochondrial (mt) DNA allows forensic laboratories to report heteroplasmy on a routine basis. Statistical approaches will be needed to determine the relative frequency of observing an mtDNA haplotype when including the presence of a heteroplasmic site. Here, we examined 1301 control region (CR) sequences, collected from individuals in four major population groups (European, African, Asian, and Latino), and covering 24 geographically distributed haplogroups, to assess the rates of point heteroplasmy (PHP) on an individual and nucleotide position (np) basis. With a minor allele frequency (MAF) threshold of 2%, the data was similar across population groups, with an overall PHP rate of 37.7%, and the majority of heteroplasmic individuals (77.3%) having only one site of heteroplasmy. The majority (75.2%) of identified PHPs had an MAF of 2-10%, and were observed at 12.6% of the nps across the CR. Both the broad and phylogenetic testing suggested that in many cases the low number of observations of heteroplasmy at any one np results in a lack of statistical association. The posterior frequency estimates, which skew conservative to a degree depending on the sample size in a given haplogroup, had a mean of 0.152 (SD 0.134) and ranged from 0.031 to 0.83. As expected, posterior frequency estimates decreased in accordance with 1/n as the sample size (n) increased. This provides a proposed conservative statistical framework for assessing haplotype/heteroplasmy matches when applying an MPS technique in forensic cases and will allow for continual refinement as more data is generated, both within the CR and across the mitochondrial genome.
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Affiliation(s)
- Jennifer A McElhoe
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA.
| | - Peter R Wilton
- Department of Integrative Biology, University of California, Berkeley, CA, 94720, USA
- 23andMe Inc, Sunnyvale, CA, 94086, USA
| | - Walther Parson
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
- Institute of Legal Medicine, Medical University of Innsbruck, Müllerstraße 44, 6020, Innsbruck, Austria
| | - Mitchell M Holland
- Department of Biochemistry & Molecular Biology, Forensic Science Program, The Pennsylvania State University, University Park, 014 Thomas Building, State College, PA, 16802, USA
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16
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LINEAGE: Label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis. Proc Natl Acad Sci U S A 2022; 119:2119767119. [PMID: 35086932 PMCID: PMC8812554 DOI: 10.1073/pnas.2119767119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/20/2021] [Indexed: 02/07/2023] Open
Abstract
Lineage analysis is an important assay for developmental biology, cancer biology, etc. Traditional tools in this field are time consuming, technically challenging, and in demand of preexisting knowledge. By integrating exogenous barcodes into cells, single-cell RNA-sequencing (scRNA-seq) can be used to conduct such tasks, but these assays required significant expertise in both wet- and dry-laboratory experiments. We developed a user-friendly algorithm to conduct cell-lineage inference solely based on endogenous markers of label-free scRNA-seq. This algorithm is able to identify lineage-informative mutations from a bunch of interfering mitochondrial RNA variants with high accuracy and efficiency. With this algorithm, we removed most of the technical hurdles of lineage analysis on scRNA-seq and will dramatically accelerate its application in biological research. Single-cell RNA-sequencing (scRNA-seq) has become a powerful tool for biomedical research by providing a variety of valuable information with the advancement of computational tools. Lineage analysis based on scRNA-seq provides key insights into the fate of individual cells in various systems. However, such analysis is limited by several technical challenges. On top of the considerable computational expertise and resources, these analyses also require specific types of matching data such as exogenous barcode information or bulk assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) data. To overcome these technical challenges, we developed a user-friendly computational algorithm called “LINEAGE” (label-free identification of endogenous informative single-cell mitochondrial RNA mutation for lineage analysis). Aiming to screen out endogenous markers of lineage located on mitochondrial reads from label-free scRNA-seq data to conduct lineage inference, LINEAGE integrates a marker selection strategy by feature subspace separation and de novo “low cross-entropy subspaces” identification. In this process, the mutation type and subspace–subspace “cross-entropy” of features were both taken into consideration. LINEAGE outperformed three other methods, which were designed for similar tasks as testified with two standard datasets in terms of biological accuracy and computational efficiency. Applied on a label-free scRNA-seq dataset of BRAF-mutated cancer cells, LINEAGE also revealed genes that contribute to BRAF inhibitor resistance. LINEAGE removes most of the technical hurdles of lineage analysis, which will remarkably accelerate the discovery of the important genes or cell-lineage clusters from scRNA-seq data.
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17
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Musson R, Gąsior Ł, Bisogno S, Ptak GE. DNA damage in preimplantation embryos and gametes: specification, clinical relevance and repair strategies. Hum Reprod Update 2022; 28:376-399. [PMID: 35021196 PMCID: PMC9071077 DOI: 10.1093/humupd/dmab046] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/13/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND DNA damage is a hazard that affects all cells of the body. DNA-damage repair (DDR) mechanisms are in place to repair damage and restore cellular function, as are other damage-induced processes such as apoptosis, autophagy and senescence. The resilience of germ cells and embryos in response to DNA damage is less well studied compared with other cell types. Given that recent studies have described links between embryonic handling techniques and an increased likelihood of disease in post-natal life, an update is needed to summarize the sources of DNA damage in embryos and their capacity to repair it. In addition, numerous recent publications have detailed novel techniques for detecting and repairing DNA damage in embryos. This information is of interest to medical or scientific personnel who wish to obtain undamaged embryos for use in offspring generation by ART. OBJECTIVE AND RATIONALE This review aims to thoroughly discuss sources of DNA damage in male and female gametes and preimplantation embryos. Special consideration is given to current knowledge and limits in DNA damage detection and screening strategies. Finally, obstacles and future perspectives in clinical diagnosis and treatment (repair) of DNA damaged embryos are discussed. SEARCH METHODS Using PubMed and Google Scholar until May 2021, a comprehensive search for peer-reviewed original English-language articles was carried out using keywords relevant to the topic with no limits placed on time. Keywords included ‘DNA damage repair’, ‘gametes’, ‘sperm’, ‘oocyte’, ‘zygote’, ‘blastocyst’ and ‘embryo’. References from retrieved articles were also used to obtain additional articles. Literature on the sources and consequences of DNA damage on germ cells and embryos was also searched. Additional papers cited by primary references were included. Results from our own studies were included where relevant. OUTCOMES DNA damage in gametes and embryos can differ greatly based on the source and severity. This damage affects the development of the embryo and can lead to long-term health effects on offspring. DDR mechanisms can repair damage to a certain extent, but the factors that play a role in this process are numerous and altogether not well characterized. In this review, we describe the multifactorial origin of DNA damage in male and female gametes and in the embryo, and suggest screening strategies for the selection of healthy gametes and embryos. Furthermore, possible therapeutic solutions to decrease the frequency of DNA damaged gametes and embryos and eventually to repair DNA and increase mitochondrial quality in embryos before their implantation is discussed. WIDER IMPLICATIONS Understanding DNA damage in gametes and embryos is essential for the improvement of techniques that could enhance embryo implantation and pregnancy success. While our knowledge about DNA damage factors and regulatory mechanisms in cells has advanced greatly, the number of feasible practical techniques to avoid or repair damaged embryos remains scarce. Our intention is therefore to focus on strategies to obtain embryos with as little DNA damage as possible, which will impact reproductive biology research with particular significance for reproductive clinicians and embryologists.
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Affiliation(s)
- Richard Musson
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Łukasz Gąsior
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Simona Bisogno
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grażyna Ewa Ptak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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18
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Cortes-Figueiredo F, Carvalho FS, Fonseca AC, Paul F, Ferro JM, Schönherr S, Weissensteiner H, Morais VA. From Forensics to Clinical Research: Expanding the Variant Calling Pipeline for the Precision ID mtDNA Whole Genome Panel. Int J Mol Sci 2021; 22:12031. [PMID: 34769461 PMCID: PMC8584537 DOI: 10.3390/ijms222112031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 10/28/2021] [Accepted: 10/29/2021] [Indexed: 02/06/2023] Open
Abstract
Despite a multitude of methods for the sample preparation, sequencing, and data analysis of mitochondrial DNA (mtDNA), the demand for innovation remains, particularly in comparison with nuclear DNA (nDNA) research. The Applied Biosystems™ Precision ID mtDNA Whole Genome Panel (Thermo Fisher Scientific, USA) is an innovative library preparation kit suitable for degraded samples and low DNA input. However, its bioinformatic processing occurs in the enterprise Ion Torrent Suite™ Software (TSS), yielding BAM files aligned to an unorthodox version of the revised Cambridge Reference Sequence (rCRS), with a heteroplasmy threshold level of 10%. Here, we present an alternative customizable pipeline, the PrecisionCallerPipeline (PCP), for processing samples with the correct rCRS output after Ion Torrent sequencing with the Precision ID library kit. Using 18 samples (3 original samples and 15 mixtures) derived from the 1000 Genomes Project, we achieved overall improved performance metrics in comparison with the proprietary TSS, with optimal performance at a 2.5% heteroplasmy threshold. We further validated our findings with 50 samples from an ongoing independent cohort of stroke patients, with PCP finding 98.31% of TSS's variants (TSS found 57.92% of PCP's variants), with a significant correlation between the variant levels of variants found with both pipelines.
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Affiliation(s)
- Filipe Cortes-Figueiredo
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
| | - Filipa S. Carvalho
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
| | - Ana Catarina Fonseca
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Friedemann Paul
- NeuroCure Clinical Research Center, Charité—Universitätsmedizin Berlin, 10117 Berlin, Germany;
- Experimental and Clinical Research Center, Charité—Universitätsmedizin Berlin and Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - José M. Ferro
- José Ferro Lab—Clinical Research in Non-communicable Neurological Diseases, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (A.C.F.); (J.M.F.)
- Serviço de Neurologia, Hospital de Santa Maria, Centro Hospitalar Universitário Lisboa Norte, 1649-035 Lisbon, Portugal
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, 6020 Innsbruck, Austria;
| | - Vanessa A. Morais
- VMorais Lab—Mitochondria Biology & Neurodegeneration, Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, 1649-028 Lisbon, Portugal; (F.C.-F.); (F.S.C.)
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19
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Fan HC, Lee HF, Yue CT, Chi CS. Clinical Characteristics of Mitochondrial Encephalomyopathy, Lactic Acidosis, and Stroke-Like Episodes. Life (Basel) 2021; 11:life11111111. [PMID: 34832987 PMCID: PMC8617702 DOI: 10.3390/life11111111] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/11/2021] [Accepted: 10/16/2021] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes (MELAS) syndrome, a maternally inherited mitochondrial disorder, is characterized by its genetic, biochemical and clinical complexity. The most common mutation associated with MELAS syndrome is the mtDNA A3243G mutation in the MT-TL1 gene encoding the mitochondrial tRNA-leu(UUR), which results in impaired mitochondrial translation and protein synthesis involving the mitochondrial electron transport chain complex subunits, leading to impaired mitochondrial energy production. Angiopathy, either alone or in combination with nitric oxide (NO) deficiency, further contributes to multi-organ involvement in MELAS syndrome. Management for MELAS syndrome is amostly symptomatic multidisciplinary approach. In this article, we review the clinical presentations, pathogenic mechanisms and options for management of MELAS syndrome.
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Affiliation(s)
- Hueng-Chuen Fan
- Department of Pediatrics, Tungs’ Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan; (H.-C.F.); (C.-T.Y.)
- Department of Medical Research, Tungs’ Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan
- Department of Rehabilitation, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 356, Taiwan
- Department of Life Sciences, Agricultural Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiu-Fen Lee
- Department of Pediatrics, Taichung Veterans General Hospital, Taichung 407, Taiwan;
| | - Chen-Tang Yue
- Department of Pediatrics, Tungs’ Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan; (H.-C.F.); (C.-T.Y.)
| | - Ching-Shiang Chi
- Department of Pediatrics, Tungs’ Taichung Metroharbor Hospital, Wuchi, Taichung 435, Taiwan; (H.-C.F.); (C.-T.Y.)
- Correspondence: ; Tel.: +886-4-26581919-4301
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20
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Kosanke M, Davenport C, Szepes M, Wiehlmann L, Kohrn T, Dorda M, Gruber J, Menge K, Sievert M, Melchert A, Gruh I, Göhring G, Martin U. iPSC culture expansion selects against putatively actionable mutations in the mitochondrial genome. Stem Cell Reports 2021; 16:2488-2502. [PMID: 34560000 PMCID: PMC8514965 DOI: 10.1016/j.stemcr.2021.08.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 01/19/2023] Open
Abstract
Therapeutic application of induced pluripotent stem cell (iPSC) derivatives requires comprehensive assessment of the integrity of their nuclear and mitochondrial DNA (mtDNA) to exclude oncogenic potential and functional deficits. It is unknown, to which extent mtDNA variants originate from their parental cells or from de novo mutagenesis, and whether dynamics in heteroplasmy levels are caused by inter- and intracellular selection or genetic drift. Sequencing of mtDNA of 26 iPSC clones did not reveal evidence for de novo mutagenesis, or for any selection processes during reprogramming or differentiation. Culture expansion, however, selected against putatively actionable mtDNA mutations. Altogether, our findings point toward a scenario in which intracellular selection of mtDNA variants during culture expansion shapes the mutational landscape of the mitochondrial genome. Our results suggest that intercellular selection and genetic drift exert minor impact and that the bottleneck effect in context of the mtDNA genetic pool might have been overestimated. Expansion culture selects against putatively actionable mtDNA mutations in iPSCs Intracellular selection on mtDNA molecules shapes the mutational landscape Random genetic drift and intercellular selection exert minor impact Selection acts during culture expansion but not during reprogramming or differentiation
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Affiliation(s)
- Maike Kosanke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Colin Davenport
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Monika Szepes
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Lutz Wiehlmann
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Tim Kohrn
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Marie Dorda
- Research Core Unit Genomics, Hannover Medical School, 30625 Hannover, Germany
| | - Jonas Gruber
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Kaja Menge
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Maike Sievert
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Anna Melchert
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Ina Gruh
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany
| | - Gudrun Göhring
- Institute of Human Genetics, Hannover Medical School, 30625 Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, REBIRTH - Research Center for Translational Regenerative Medicine, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), 30625 Hannover, Germany.
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21
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mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences. Life (Basel) 2021; 11:life11070633. [PMID: 34209862 PMCID: PMC8307225 DOI: 10.3390/life11070633] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is predominately uniparentally transmitted. This results in organisms with a single type of mtDNA (homoplasmy), but two or more mtDNA haplotypes have been observed in low frequency in several species (heteroplasmy). In this review, we aim to highlight several aspects of heteroplasmy regarding its origin and its significance on mtDNA function and evolution, which has been progressively recognized in the last several years. Heteroplasmic organisms commonly occur through somatic mutations during an individual’s lifetime. They also occur due to leakage of paternal mtDNA, which rarely happens during fertilization. Alternatively, heteroplasmy can be potentially inherited maternally if an egg is already heteroplasmic. Recent advances in sequencing techniques have increased the ability to detect and quantify heteroplasmy and have revealed that mitochondrial DNA copies in the nucleus (NUMTs) can imitate true heteroplasmy. Heteroplasmy can have significant evolutionary consequences on the survival of mtDNA from the accumulation of deleterious mutations and for its coevolution with the nuclear genome. Particularly in humans, heteroplasmy plays an important role in the emergence of mitochondrial diseases and determines the success of the mitochondrial replacement therapy, a recent method that has been developed to cure mitochondrial diseases.
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22
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Naue J, Winkelmann J, Schmidt U, Lutz-Bonengel S. Analysis of age-dependent DNA methylation changes in plucked hair samples using massive parallel sequencing. Rechtsmedizin (Berl) 2021. [DOI: 10.1007/s00194-021-00487-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
AbstractThe analysis of age-dependent DNA methylation changes is a valuable tool in epigenetic research and forensic genetics. With some exceptions, most studies in the past concentrated on the analysis of blood, buccal, and saliva samples. Another important sample type in forensic investigations is hair, where age-dependent DNA methylation has not been investigated so far. In this pilot study a deeper look was taken at the possibilities and challenges of DNA methylation analysis in hair. The DNA methylation of selected age-dependent 5’-C-phosphate-G‑3’ (CpG) sites were characterized for their potential use as a biomarker for age prediction using plucked hair samples and massive parallel sequencing. Plucked hair roots of 49 individuals were included in the study. The DNA methylation of 31 hairs was successfully analyzed. The DNA methylation pattern of 10 loci, including ELOVL2, F5, KLF14, and TRIM59, was determined by amplicon-based massive parallel sequencing. Age-dependent changes were found for several markers. The results demonstrate the possible use of already established age-dependent markers but at the same time they have tissue/cell type-specific characteristics. Special challenges such as low amounts of DNA and degraded DNA as well as the possible heterogeneous cellular composition of plucked hair samples, have to be considered.
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23
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Abstract
Mitochondria are organelles with vital functions in almost all eukaryotic cells. Often described as the cellular 'powerhouses' due to their essential role in aerobic oxidative phosphorylation, mitochondria perform many other essential functions beyond energy production. As signaling organelles, mitochondria communicate with the nucleus and other organelles to help maintain cellular homeostasis, allow cellular adaptation to diverse stresses, and help steer cell fate decisions during development. Mitochondria have taken center stage in the research of normal and pathological processes, including normal tissue homeostasis and metabolism, neurodegeneration, immunity and infectious diseases. The central role that mitochondria assume within cells is evidenced by the broad impact of mitochondrial diseases, caused by defects in either mitochondrial or nuclear genes encoding for mitochondrial proteins, on different organ systems. In this Review, we will provide the reader with a foundation of the mitochondrial 'hardware', the mitochondrion itself, with its specific dynamics, quality control mechanisms and cross-organelle communication, including its roles as a driver of an innate immune response, all with a focus on development, disease and aging. We will further discuss how mitochondrial DNA is inherited, how its mutation affects cell and organismal fitness, and current therapeutic approaches for mitochondrial diseases in both model organisms and humans.
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Affiliation(s)
- Marlies P. Rossmann
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Sonia M. Dubois
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Suneet Agarwal
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Leonard I. Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 01238, USA
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Howard Hughes Medical Institute, Boston, MA 02115, USA
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24
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Caicedo A, Zambrano K, Sanon S, Gavilanes AWD. Extracellular mitochondria in the cerebrospinal fluid (CSF): Potential types and key roles in central nervous system (CNS) physiology and pathogenesis. Mitochondrion 2021; 58:255-269. [PMID: 33662579 DOI: 10.1016/j.mito.2021.02.006] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 12/12/2022]
Abstract
The cerebrospinal fluid (CSF) has an important role in the transport of nutrients and signaling molecules to the central nervous and immune systems through its circulation along the brain and spinal cord tissues. The mitochondrial activity in the central nervous system (CNS) is essential in processes such as neuroplasticity, neural differentiation and production of neurotransmitters. Interestingly, extracellular and active mitochondria have been detected in the CSF where they act as a biomarker for the outcome of pathologies such as subarachnoid hemorrhage and delayed cerebral ischemia. Additionally, cell-free-circulating mitochondrial DNA (ccf-mtDNA) has been detected in both the CSF of healthy donors and in that of patients with neurodegenerative diseases. Key questions arise as there is still much debate regarding if ccf-mtDNA detected in CSF is associated with a diversity of active or inactive extracellular mitochondria coexisting in distinct pathologies. Additionally, it is of great scientific and medical importance to identify the role of extracellular mitochondria (active and inactive) in the CSF and the difference between them being damage associated molecular patterns (DAMPs) or factors that promote homeostasis. This review analyzes the different types of extracellular mitochondria, methods for their identification and their presence in CSF. Extracellular mitochondria in the CSF could have an important implication in health and disease, which may lead to the development of medical approaches that utilize mitochondria as therapeutic agents.
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Affiliation(s)
- Andrés Caicedo
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Sistemas Médicos SIME, Universidad San Francisco de Quito, Quito, Ecuador.
| | - Kevin Zambrano
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands; Instituto de Neurociencias, Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Serena Sanon
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; Universidad San Francisco de Quito USFQ, Instituto de Investigaciones en Biomedicina, Quito, Ecuador; Mito-Act Research Consortium, Quito, Ecuador; Cornell University, Ithaca, United States
| | - Antonio W D Gavilanes
- Universidad San Francisco de Quito USFQ, Colegio de Ciencias de la Salud, Escuela de Medicina, Quito, Ecuador; School for Mental Health and Neuroscience (MHeNs), Maastricht University, Maastricht, The Netherlands
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25
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Iannello M, Bettinazzi S, Breton S, Ghiselli F, Milani L. A Naturally Heteroplasmic Clam Provides Clues about the Effects of Genetic Bottleneck on Paternal mtDNA. Genome Biol Evol 2021; 13:6130822. [PMID: 33555290 PMCID: PMC7936021 DOI: 10.1093/gbe/evab022] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2021] [Indexed: 12/13/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is present in multiple copies within an organism. Since these copies are not identical, a single individual carries a heterogeneous population of mtDNAs, a condition known as heteroplasmy. Several factors play a role in the dynamics of the within-organism mtDNA population: among them, genetic bottlenecks, selection, and strictly maternal inheritance are known to shape the levels of heteroplasmy across mtDNAs. In Metazoa, the only evolutionarily stable exception to the strictly maternal inheritance of mitochondria is the doubly uniparental inheritance (DUI), reported in 100+ bivalve species. In DUI species, there are two highly divergent mtDNA lineages, one inherited through oocyte mitochondria (F-type) and the other through sperm mitochondria (M-type). Having both parents contributing to the mtDNA pool of the progeny makes DUI a unique system to study the dynamics of mtDNA populations. Since, in bivalves, the spermatozoon has few mitochondria (4–5), M-type mtDNA faces a tight bottleneck during embryo segregation, one of the narrowest mitochondrial bottlenecks investigated so far. Here, we analyzed the F- and M-type mtDNA variability within individuals of the DUI species Ruditapes philippinarum and investigated for the first time the effects of such a narrow bottleneck affecting mtDNA populations. As a potential consequence of this narrow bottleneck, the M-type mtDNA shows a large variability in different tissues, a condition so pronounced that it leads to genotypes from different tissues of the same individual not to cluster together. We believe that such results may help understanding the effect of low population size on mtDNA bottleneck.
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Affiliation(s)
- Mariangela Iannello
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Stefano Bettinazzi
- Department of Biological Sciences, University of Montreal, Quebec, Canada
| | - Sophie Breton
- Department of Biological Sciences, University of Montreal, Quebec, Canada
| | - Fabrizio Ghiselli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
| | - Liliana Milani
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Italy
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26
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Kargaran PK, Mosqueira D, Kozicz T. Mitochondrial Medicine: Genetic Underpinnings and Disease Modeling Using Induced Pluripotent Stem Cell Technology. Front Cardiovasc Med 2021; 7:604581. [PMID: 33585579 PMCID: PMC7874022 DOI: 10.3389/fcvm.2020.604581] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 12/22/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondrial medicine is an exciting and rapidly evolving field. While the mitochondrial genome is small and differs from the nuclear genome in that it is circular and free of histones, it has been implicated in neurodegenerative diseases, type 2 diabetes, aging and cardiovascular disorders. Currently, there is a lack of efficient treatments for mitochondrial diseases. This has promoted the need for developing an appropriate platform to investigate and target the mitochondrial genome. However, developing these therapeutics requires a model system that enables rapid and effective studying of potential candidate therapeutics. In the past decade, induced pluripotent stem cells (iPSCs) have become a promising technology for applications in basic science and clinical trials, and have the potential to be transformative for mitochondrial drug development. Engineered iPSC-derived cardiomyocytes (iPSC-CM) offer a unique tool to model mitochondrial disorders. Additionally, these cellular models enable the discovery and testing of novel therapeutics and their impact on pathogenic mtDNA variants and dysfunctional mitochondria. Herein, we review recent advances in iPSC-CM models focused on mitochondrial dysfunction often causing cardiovascular diseases. The importance of mitochondrial disease systems biology coupled with genetically encoded NAD+/NADH sensors is addressed toward developing an in vitro translational approach to establish effective therapies.
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Affiliation(s)
- Parisa K Kargaran
- Department of Cardiovascular Medicine, Center for Regenerative Medicine, Mayo Clinic, Rochester, MN, United States
| | - Diogo Mosqueira
- Division of Cancer & Stem Cells, Biodiscovery Institute, University of Nottingham, Nottingham, United Kingdom
| | - Tamas Kozicz
- Department of Clinical Genomics, Mayo Clinic, Rochester, MN, United States
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27
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Laaksonen J, Mishra PP, Seppälä I, Lyytikäinen LP, Raitoharju E, Mononen N, Lepistö M, Almusa H, Ellonen P, Hutri-Kähönen N, Juonala M, Raitakari O, Kähönen M, Salonen JT, Lehtimäki T. Examining the effect of mitochondrial DNA variants on blood pressure in two Finnish cohorts. Sci Rep 2021; 11:611. [PMID: 33436758 PMCID: PMC7804469 DOI: 10.1038/s41598-020-79931-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022] Open
Abstract
High blood pressure (BP) is a major risk factor for many noncommunicable diseases. The effect of mitochondrial DNA single-nucleotide polymorphisms (mtSNPs) on BP is less known than that of nuclear SNPs. We investigated the mitochondrial genetic determinants of systolic, diastolic, and mean arterial BP. MtSNPs were determined from peripheral blood by sequencing or with genome-wide association study SNP arrays in two independent Finnish cohorts, the Young Finns Study and the Finnish Cardiovascular Study, respectively. In total, over 4200 individuals were included. The effects of individual common mtSNPs, with an additional focus on sex-specificity, and aggregates of rare mtSNPs grouped by mitochondrial genes were evaluated by meta-analysis of linear regression and a sequence kernel association test, respectively. We accounted for the predicted pathogenicity of the rare variants within protein-encoding and the tRNA regions. In the meta-analysis of 87 common mtSNPs, we did not observe significant associations with any of the BP traits. Sex-specific and rare-variant analyses did not pinpoint any significant associations either. Our results are in agreement with several previous studies suggesting that mtDNA variation does not have a significant role in the regulation of BP. Future studies might need to reconsider the mechanisms thought to link mtDNA with hypertension.
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Affiliation(s)
- Jaakko Laaksonen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, PO Box 100, 33014, Tampere, Finland.
| | - Pashupati P Mishra
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, PO Box 100, 33014, Tampere, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, PO Box 100, 33014, Tampere, Finland
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, PO Box 100, 33014, Tampere, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, PO Box 100, 33014, Tampere, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, PO Box 100, 33014, Tampere, Finland
| | - Maija Lepistö
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Henrikki Almusa
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine (FIMM), University of Helsinki, Helsinki, Finland
| | - Nina Hutri-Kähönen
- Department of Paediatrics, Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Markus Juonala
- Department of Medicine, University of Turku, Turku, Finland.,Division of Medicine, Turku University Hospital, Turku, Finland.,Murdoch Children's Research Institute, Parkville, VIC, Australia
| | - Olli Raitakari
- Centre for Population Health Research, University of Turku and Turku University Hospital, Turku, Finland.,Research Centre for Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland.,Department of Clinical Physiology and Nuclear Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Jukka T Salonen
- Department of Public Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,MAS-Metabolic Analytical Services Oy, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories and Finnish Cardiovascular Research Center Tampere, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, PO Box 100, 33014, Tampere, Finland
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28
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Onyango IG, Bennett JP, Stokin GB. Regulation of neuronal bioenergetics as a therapeutic strategy in neurodegenerative diseases. Neural Regen Res 2021; 16:1467-1482. [PMID: 33433460 PMCID: PMC8323696 DOI: 10.4103/1673-5374.303007] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, and amyotrophic lateral sclerosis are a heterogeneous group of debilitating disorders with multifactorial etiologies and pathogeneses that manifest distinct molecular mechanisms and clinical manifestations with abnormal protein dynamics and impaired bioenergetics. Mitochondrial dysfunction is emerging as an important feature in the etiopathogenesis of these age-related neurodegenerative diseases. The prevalence and incidence of these diseases is on the rise with the increasing global population and average lifespan. Although many therapeutic approaches have been tested, there are currently no effective treatment routes for the prevention or cure of these diseases. We present the current status of our knowledge and understanding of the involvement of mitochondrial dysfunction in these diseases and highlight recent advances in novel therapeutic strategies targeting neuronal bioenergetics as potential approach for treating these diseases.
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Affiliation(s)
- Isaac G Onyango
- Center for Translational Medicine, International Clinical Research Centre (ICRC), St. Anne's University Hospital, Brno, Czech Republic
| | - James P Bennett
- Neurodegeneration Therapeutics, 3050A Berkmar Drive, Charlottesville, VA, USA
| | - Gorazd B Stokin
- Center for Translational Medicine, International Clinical Research Centre (ICRC), St. Anne's University Hospital, Brno, Czech Republic
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29
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Nguyen H, LaFramboise T. Complexities and pitfalls in analyzing and interpreting mitochondrial DNA content in human cancer. J Genet Genomics 2020; 47:349-359. [PMID: 33004308 DOI: 10.1016/j.jgg.2020.04.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 04/01/2020] [Accepted: 04/20/2020] [Indexed: 11/29/2022]
Abstract
Mutations in the human mitochondrial genome have been observed in all types of human cancer, indicating that mutations might contribute to tumorigenesis, metastasis, recurrence, or drug response. This possibility is appealing because of the known shift from oxidative metabolism to glycolysis, known as the Warburg effect, that occurs in malignancy. Mitochondrial DNA (mtDNA) mutations could either be maternally inherited and predispose to cancer (germ line mutations) or occur sporadically in the mtDNA of specific tissues (tissue- or tumor-specific somatic mutations) and contribute to the tumor initiation and progression process. High-throughput sequencing technologies now enable comprehensive detection of mtDNA variation in tissues and bodily fluids, with the potential to be used as an early detection tool that may impact the treatment of cancer. Here, we discuss insights into the roles of mtDNA mutations in carcinogenesis, highlighting the complexities involved in the analysis and interpretation of mitochondrial genomic content, technical challenges in studying their contribution to pathogenesis, and the value of mtDNA mutations in developing early detection, diagnosis, prognosis, and therapeutic strategies for cancer.
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Affiliation(s)
- Hieu Nguyen
- Vinmec Research Institute of Stem Cell and Gene Technology (VRSIG), 458 Minh Khai, Vinh Tuy, Hai Ba Trung, Hanoi, Viet Nam; Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, 10900 Euclid Avenue, Cleveland, OH, 44106, USA.
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30
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Kargaran PK, Evans JM, Bodbin SE, Smith JGW, Nelson TJ, Denning C, Mosqueira D. Mitochondrial DNA: Hotspot for Potential Gene Modifiers Regulating Hypertrophic Cardiomyopathy. J Clin Med 2020; 9:E2349. [PMID: 32718021 PMCID: PMC7463557 DOI: 10.3390/jcm9082349] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 07/17/2020] [Accepted: 07/21/2020] [Indexed: 12/16/2022] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a prevalent and untreatable cardiovascular disease with a highly complex clinical and genetic causation. HCM patients bearing similar sarcomeric mutations display variable clinical outcomes, implying the involvement of gene modifiers that regulate disease progression. As individuals exhibiting mutations in mitochondrial DNA (mtDNA) present cardiac phenotypes, the mitochondrial genome is a promising candidate to harbor gene modifiers of HCM. Herein, we sequenced the mtDNA of isogenic pluripotent stem cell-cardiomyocyte models of HCM focusing on two sarcomeric mutations. This approach was extended to unrelated patient families totaling 52 cell lines. By correlating cellular and clinical phenotypes with mtDNA sequencing, potentially HCM-protective or -aggravator mtDNA variants were identified. These novel mutations were mostly located in the non-coding control region of the mtDNA and did not overlap with those of other mitochondrial diseases. Analysis of unrelated patients highlighted family-specific mtDNA variants, while others were common in particular population haplogroups. Further validation of mtDNA variants as gene modifiers is warranted but limited by the technically challenging methods of editing the mitochondrial genome. Future molecular characterization of these mtDNA variants in the context of HCM may identify novel treatments and facilitate genetic screening in cardiomyopathy patients towards more efficient treatment options.
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Affiliation(s)
- Parisa K. Kargaran
- Department of Cardiovascular Medicine, Center for Regenerative Medicine, Mayo Clinic, Rochester, MN 55905, USA;
| | - Jared M. Evans
- Department of Health Science Research, Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA;
| | - Sara E. Bodbin
- Division of Cancer and Stem Cells, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK;
| | - James G. W. Smith
- Faculty of Medicine and Health Sciences, Norwich Medical School, University of East Anglia, Norwich NR4 7UQ, UK;
| | - Timothy J. Nelson
- Division of General Internal Medicine, Division of Pediatric Cardiology, Departments of Medicine, Molecular Pharmacology, and Experimental Therapeutics, Mayo Clinic Center for Regenerative Medicine, Rochester, MN 55905, USA;
| | - Chris Denning
- Division of Cancer and Stem Cells, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Diogo Mosqueira
- Division of Cancer and Stem Cells, Biodiscovery Institute, University of Nottingham, Nottingham NG7 2RD, UK;
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31
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Jaberi E, Tresse E, Grønbæk K, Weischenfeldt J, Issazadeh-Navikas S. Identification of unique and shared mitochondrial DNA mutations in neurodegeneration and cancer by single-cell mitochondrial DNA structural variation sequencing (MitoSV-seq). EBioMedicine 2020; 57:102868. [PMID: 32629384 PMCID: PMC7334819 DOI: 10.1016/j.ebiom.2020.102868] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/12/2020] [Accepted: 06/15/2020] [Indexed: 02/06/2023] Open
Abstract
Background Point mutations and structural variations (SVs) in mitochondrial DNA (mtDNA) contribute to many neurodegenerative diseases. Technical limitations and heteroplasmy, however, have impeded their identification, preventing these changes from being examined in neurons in healthy and disease states. Methods We have developed a high-resolution technique—Mitochondrial DNA Structural Variation Sequencing (MitoSV-seq)—that identifies all types of mtDNA SVs and single-nucleotide variations (SNVs) in single neurons and novel variations that have been undetectable with conventional techniques. Findings Using MitoSV-seq, we discovered SVs/SNVs in dopaminergic neurons in the Ifnar1−/− murine model of Parkinson disease. Further, MitoSV-seq was found to have broad applicability, delivering high-quality, full-length mtDNA sequences in a species-independent manner from human PBMCs, haematological cancers, and tumour cell lines, regardless of heteroplasmy. We characterised several common SVs in haematological cancers (AML and MDS) that were linked to the same mtDNA region, MT-ND5, using only 10 cells, indicating the power of MitoSV-seq in determining single-cancer-cell ontologies. Notably, the MT-ND5 hotspot, shared between all examined cancers and Ifnar1−/− dopaminergic neurons, suggests that its mutations have clinical value as disease biomarkers. Interpretation MitoSV-seq identifies disease-relevant mtDNA mutations in single cells with high resolution, rendering it a potential drug screening platform in neurodegenerative diseases and cancers. Funding The Lundbeck Foundation, Danish Council for Independent Research-Medicine, and European Union Horizon 2020 Research and Innovation Programme.
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Affiliation(s)
- Elham Jaberi
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Emilie Tresse
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Kirsten Grønbæk
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark; Department of Hematology, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark; The Danish Stem Cell Center (Danstem), University of Copenhagen, Faculty of Health and Medical Sciences, University of Copenhagen, Nørre Alle 14, DK-2200 Copenhagen, Denmark
| | - Joachim Weischenfeldt
- Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark
| | - Shohreh Issazadeh-Navikas
- Neuroinflammation Unit, Biotech Research and Innovation Centre, Faculty of Health and Medical Sciences, University of Copenhagen, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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32
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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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33
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Davidovic S, Malyarchuk B, Grzybowski T, Aleksic JM, Derenko M, Litvinov A, Rogalla-Ładniak U, Stevanovic M, Kovacevic-Grujicic N. Complete mitogenome data for the Serbian population: the contribution to high-quality forensic databases. Int J Legal Med 2020; 134:1581-1590. [PMID: 32504149 DOI: 10.1007/s00414-020-02324-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/28/2020] [Indexed: 11/24/2022]
Abstract
Mitochondrial genome (mtDNA) is a valuable resource in resolving various human forensic casework. The usage of variability of complete mtDNA genomes increases their discriminatory power to the maximum and enables ultimate resolution of distinct maternal lineages. However, their wider employment in forensic casework is nowadays limited by the lack of appropriate reference database. In order to fill in the gap in the reference data, which, considering Slavic-speaking populations, currently comprises only mitogenomes of East and West Slavs, we present mitogenome data for 226 Serbians, representatives of South Slavs from the Balkan Peninsula. We found 143 (sub)haplogroups among which West Eurasian ones were dominant. The percentage of unique haplotypes was 85%, and the random match probability was as low as 0.53%. We support previous findings on both high levels of genetic diversity in the Serbian population and patterns of genetic differentiation among this and ten studied European populations. However, our high-resolution data supported more pronounced genetic differentiation among Serbians and two Slavic populations (Russians and Poles) as well as expansion of the Serbian population after the Last Glacial Maximum and during the Migration period (fourth to ninth century A.D.), as inferred from the Bayesian skyline analysis. Phylogenetic analysis of haplotypes found in Serbians contributed towards the improvement of the worldwide mtDNA phylogeny, which is essential for the interpretation of the mtDNA casework.
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Affiliation(s)
- Slobodan Davidovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Department of Genetics of Populations and Ecogenotoxicology, Institute for Biological Research "Siniša Stanković", National Institute of Republic of Serbia, University of Belgrade, Bulevar despota Stefana 142, Belgrade, 11060, Serbia
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Tomasz Grzybowski
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Jelena M Aleksic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Andrey Litvinov
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya 18, Magadan, 685000, Russia
| | - Urszula Rogalla-Ładniak
- Department of Forensic Medicine, Division of Molecular and Forensic Genetics, Ludwik Rydygier Collegium Medicum, Faculty of Medicine, Nicolaus Copernicus University, Marii-Sklodowskiej-Curie Str. 9, 85-094, Bydgoszcz, Poland
| | - Milena Stevanovic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.,Faculty of Biology, University of Belgrade, Studentski Trg 16, Belgrade, 11000, Serbia.,Serbian Academy of Sciences and Arts, Kneza Mihaila 35, Belgrade, 11000, Serbia
| | - Natasa Kovacevic-Grujicic
- Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, PO Box 23, Vojvode Stepe 444a, Belgrade, 11010, Serbia.
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34
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Sauer DC, Naue J, Immel UD, Lutz-Bonengel S. Mitochondrial DNA control region variation in a population sample from Thailand. Int J Legal Med 2020; 134:1563-1568. [PMID: 32358724 PMCID: PMC7417404 DOI: 10.1007/s00414-020-02303-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/14/2020] [Indexed: 10/29/2022]
Abstract
Mitochondrial DNA (mtDNA) control region sequences from hair samples of 213 individuals from Thailand were analyzed using Sanger sequencing. A total of 170 different haplotypes were identified, of which 146 occurred only once (unique haplotypes). The dataset showed a random match probability of 0.87% and a haplotype diversity of 0.9960. The samples were assigned to 85 different haplogroups with B5a, F1a1a, and M being the most frequent ones. Pairwise FST-values between this and other Southeast and East Asian populations revealed significant but relatively low differences, indicating a close relation. Heteroplasmic positions were observed in 12.2% of hair samples confirming the frequent appearance of heteroplasmic positions in hairs. This dataset will complement existing data as an mtDNA reference for forensic investigations.
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Affiliation(s)
- Dirk Christopher Sauer
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Forensic Molecular Biology, Albertstrasse 9, 79104, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Jana Naue
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Forensic Molecular Biology, Albertstrasse 9, 79104, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Uta-Dorothee Immel
- Institute of Legal Medicine, Johannes Gutenberg-University Mainz, Am Pulverturm 3, 55131, Mainz, Germany.,Institute of Legal Medicine, Martin-Luther-University Halle-Wittenberg, Franzosenweg 1, 06114, Halle, Germany
| | - Sabine Lutz-Bonengel
- Institute of Forensic Medicine, Medical Center - University of Freiburg, Forensic Molecular Biology, Albertstrasse 9, 79104, Freiburg, Germany. .,Faculty of Medicine, University of Freiburg, Freiburg, Germany.
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35
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Klucnika A, Ma H. A battle for transmission: the cooperative and selfish animal mitochondrial genomes. Open Biol 2020; 9:180267. [PMID: 30890027 PMCID: PMC6451365 DOI: 10.1098/rsob.180267] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial genome is an evolutionarily persistent and cooperative component of metazoan cells that contributes to energy production and many other cellular processes. Despite sharing the same host as the nuclear genome, the multi-copy mitochondrial DNA (mtDNA) follows very different rules of replication and transmission, which translate into differences in the patterns of selection. On one hand, mtDNA is dependent on the host for its transmission, so selections would favour genomes that boost organismal fitness. On the other hand, genetic heterogeneity within an individual allows different mitochondrial genomes to compete for transmission. This intra-organismal competition could select for the best replicator, which does not necessarily give the fittest organisms, resulting in mito-nuclear conflict. In this review, we discuss the recent advances in our understanding of the mechanisms and opposing forces governing mtDNA transmission and selection in bilaterians, and what the implications of these are for mtDNA evolution and mitochondrial replacement therapy.
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Affiliation(s)
- Anna Klucnika
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
| | - Hansong Ma
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
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36
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Almheiri R, Bakri M, Alghafri R, Goodwin W. Whole mtGenome analysis in United Arab Emirates populations. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2019. [DOI: 10.1016/j.fsigss.2019.10.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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37
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Get it off, but keep it: Efficient cleaning of hair shafts with parallel DNA extraction of the surface stain. Forensic Sci Int Genet 2019; 45:102210. [PMID: 31812096 DOI: 10.1016/j.fsigen.2019.102210] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 01/10/2023]
Abstract
The analysis of hair samples is a common task in forensic investigations. Material transferred to the surface of a hair during a crime challenges the analysis as it has to be removed efficiently. However, the removal of the stain can also lead to a loss of information on stain contributors. DNA analysis of the stain itself might thus be helpful for the forensic investigation. The aim of this study was the examination of different methods to remove common biological surface stains completely from human hair shafts without hampering the parallel DNA extraction of the cleaned hair shaft and the isolated surface stain (blood, saliva, vaginal secretion, semen, and skin flocks). Four different methods of cleaning (water, lysis buffer, swabbing, NaClO) were compared to their cleaning efficiency as well as their success of mtDNA analysis of three hair donors and the original five stains on the hair. In order to test the suitability of this procedure for future analysis methods, a selection of samples were also sequenced with MPS. Additionally, nuclear DNA analysis of the stain DNA was performed using a screening STR assay to test the potential success for detection of a STR profile. The most efficient removal of the stain was achieved using NaClO, however compromising further analysis of the stain DNA. The best results for cleaning and parallel stain analysis were obtained using a swab moistened with 0.5 % SDS for surface cleaning. Especially water failed to remove stains efficiently, leading to a high amount of mixed mtDNA in the DNA extracts. MPS showed an increased sensitivity for detection of minute mixtures.
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38
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Kim BM, Hong SR, Chun H, Kim S, Shin KJ. Comparison of whole mitochondrial genome variants between hair shafts and reference samples using massively parallel sequencing. Int J Legal Med 2019; 134:853-861. [PMID: 31734723 DOI: 10.1007/s00414-019-02205-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Accepted: 11/07/2019] [Indexed: 10/25/2022]
Abstract
Hair shafts are one of the most common types of evidence at crime scenes, and mitochondrial DNA (mtDNA) has been analyzed as a valuable genetic marker for hair shafts in forensic casework. However, the mtDNA analysis strategy may vary according to the quantity and quality of DNA extracted from a forensic sample and the available massively parallel sequencing (MPS) platform in laboratories. Forensic practitioners often have to interpret mtDNA sequences exhibiting point heteroplasmy (PHP) that are analyzed using different analytical methods. In the present study, the whole mitochondrial genome (mtGenome) variants of hair shaft samples obtained from 20 donors, which were sampled in duplicate and stored at room temperature for > 1 year, were analyzed using the Precision ID mtDNA Whole Genome Panel and Ion S5 system. The whole mtGenome variants of 20 blood and 20 buccal swab samples (reference samples) from the hair shaft donors were analyzed using the Nextera XT DNA Library Prep Kit and MiSeq System. A total of 20 unique mtGenome haplotypes were observed, and 56 PHP variants were identified across the 4 sets of tissue. When the major nucleotide of PHP was considered, 16 of 20 haplotypes of the hair shaft samples matched those of the corresponding blood and buccal swab samples. In four donors, the major nucleotide of PHP was inverted at one nucleotide position between the hair shaft and reference samples. However, the data obtained on MPS, showing high PHP resolution, provided substantial information to avoid false exclusion when comparing two haplotypes containing PHP with inverted major nucleotides. In conclusion, the present study demonstrates the utility of MPS in forensic casework in the comparative analysis of mtGenome variants containing PHP.
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Affiliation(s)
- Bo Min Kim
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sae Rom Hong
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Hein Chun
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Sangwoo Kim
- Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.,Department of Biomedical Systems Informatics, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea. .,Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, 03722, Republic of Korea.
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Huang Y, Lu W, Ji J, Zhang X, Zhang P, Chen W. Heteroplasmy in the complete chicken mitochondrial genome. PLoS One 2019; 14:e0224677. [PMID: 31703075 PMCID: PMC6839896 DOI: 10.1371/journal.pone.0224677] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 10/19/2019] [Indexed: 12/16/2022] Open
Abstract
Chicken mitochondrial DNA is a circular molecule comprising ~16.8 kb. In this study, we used next-generation sequencing to investigate mitochondrial heteroplasmy in the whole chicken mitochondrial genome. Based on heteroplasmic detection thresholds at the 0.5% level, 178 cases of heteroplasmy were identified in the chicken mitochondrial genome, where 83% were due to nucleotide transitions. D-loop regionwas hot spot region for mtDNA heteroplasmy in the chicken since 130 cases of heteroplasmy were located in these regions. Heteroplasmy varied among intraindividual tissues with allele-specific, position-specific, and tissue-specific features. Skeletal muscle had the highest abundance of heteroplasmy. Cases of heteroplasmy at mt.G8682A and mt.G16121A were validated by PCR-restriction fragment length polymorphism analysis, which showed that both had low ratios of heteroplasmy occurrence in five natural breeds. Polymorphic sites were easy to distinguish. Based on NGS data for crureus tissues, mitochondrial mutation/heteroplasmy exhibited clear maternal inheritance features at the whole mitochondrial genomic level. Further investigations of the heterogeneity of the mt.A5694T and mt.T5718G transitions between generations using pyrosequencing based on pedigree information indicated that the degree of heteroplasmy and the occurrence ratio of heteroplasmy decreased greatly from the F0 to F1 generations in the mt.A5694T and mt.T5718G site. Thus, the intergenerational transmission of heteroplasmy in chicken mtDNA exhibited a rapid shift toward homoplasmy within a single generation. Our findings indicate that heteroplasmy is a widespread phenomenon in chicken mitochondrial genome, in which most sites exhibit low heteroplasmy and the allele frequency at heteroplasmic sites changes significantly during transmission events. It suggests that heteroplasmy may be under negative selection to some degree in the chicken.
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Affiliation(s)
- Yanqun Huang
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Weiwei Lu
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiefei Ji
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xiangli Zhang
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Pengfei Zhang
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wen Chen
- College of Livestock Husbandry and Veterinary Engineering, Henan Agricultural University, Zhengzhou, Henan, China
- * E-mail:
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40
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Desmyter S, Dognaux S, Noel F, Prieto L. Base specific variation rates at mtDNA positions 16093 and 16183 in human hairs. Forensic Sci Int Genet 2019; 43:102142. [PMID: 31437782 DOI: 10.1016/j.fsigen.2019.102142] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/25/2019] [Accepted: 08/11/2019] [Indexed: 10/26/2022]
Abstract
Small variations between haplotypes detected in different tissues from the same individual have been previously described. These differences complicate the interpretation of mtDNA results in real forensic casework. mtDNA haplotypes detected in hair strands collected at the crime scene have to be frequently compared with haplotypes of reference samples (buccal swabs) from victims or suspects. Nucleotide position 16093 is a well-known hot spot where differences can accumulate between different tissues of the same individual. Intra individual variation was also detected at positions 16182 and 16183 in haplotypes showing an uninterrupted HV1 poly-C stretch (with 16189C). In order to better characterize the type of variation in these positions between buccal cells and hair strands from the same individual, we have performed Sanger sequencing in 25-28 hair strands (411 in total) from 15 individuals showing either an uninterrupted HV1 polyC-stretch (16189C) or 16093C/Y in their buccal cells. The results have been evaluated by also taking into account our previous results published in [19]. We have found that no variation among hair strands was detected in individuals showing T16093 in buccal cells, while variation in hair strands (T16093, 16093C and 16093Y) were detected in individuals showing 16093C or 16093Y in buccal cells. Regarding nucleotide positions 16182 and 16183 in combination with an uninterrupted polyC-stretch, no variation was detected in hairs from individuals showing A16182 16183C in their buccal cells. In contrast, individuals A16182 A16183 showed hair strands with A16182 16183 M and A16182 16183C. And finally, individuals with 16182C 16183C showed some variation in a small amount of their hair strands (some hairs with 16182 M 16183C). These results can be relevant for forensic practitioners when comparing reference samples with hair strands, which is the type of sample most tested by using mtDNA analysis in forensic casework.
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Affiliation(s)
- Stijn Desmyter
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium.
| | - Sophie Dognaux
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Fabrice Noel
- NICC - Belgian Institute for Forensic Science and Criminology, Vilvoordsesteenweg 100, B-1120, Brussels, Belgium
| | - Lourdes Prieto
- Instituto de Ciencias Forenses. Grupo de Medicina Xenómica. Universidade de Santiago de Compostela, Spain; Laboratorio ADN. Comisaría General de Policía Científica, Madrid, Spain
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41
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Hübner A, Wachsmuth M, Schröder R, Li M, Eis-Hübinger AM, Madea B, Stoneking M. Sharing of heteroplasmies between human liver lobes varies across the mtDNA genome. Sci Rep 2019; 9:11219. [PMID: 31375696 PMCID: PMC6677727 DOI: 10.1038/s41598-019-47570-1] [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: 12/19/2018] [Accepted: 07/16/2019] [Indexed: 01/10/2023] Open
Abstract
Mitochondrial DNA (mtDNA) heteroplasmy (intra-individual variation) varies among different human tissues and increases with age, suggesting that the majority of mtDNA heteroplasmies are acquired, rather than inherited. However, the extent to which heteroplasmic sites are shared across a tissue remains an open question. We therefore investigated heteroplasmy in two liver samples (one from each primary lobe) from 83 Europeans, sampled at autopsy. Minor allele frequencies (MAF) at heteroplasmic sites were significantly correlated between the two liver samples from an individual, with significantly more sharing of heteroplasmic sites in the control region than in the non-control region. We show that this increased sharing for the control region cannot be explained by recent mutations at just a few specific heteroplasmic sites or by the possible presence of 7S DNA. Moreover, we carried out simulations to show that there is significantly more sharing than would be predicted from random genetic drift from a common progenitor cell. We also observe a significant excess of non-synonymous vs. synonymous heteroplasmies in the protein-coding region, but significantly more sharing of synonymous heteroplasmies. These contrasting patterns for the control vs. the non-control region, and for non-synonymous vs. synonymous heteroplasmies, suggest that selection plays a role in heteroplasmy sharing.
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Affiliation(s)
- Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
| | - Manja Wachsmuth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Roland Schröder
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany
| | - Mingkun Li
- Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, 100101, Beijing, China
| | - Anna Maria Eis-Hübinger
- Institut für Virologie, Universitätsklinikum Bonn, Sigmund-Freud-Str. 25, D-53105, Bonn, Germany
| | - Burkhard Madea
- Institut für Rechtsmedizin, Universitätsklinikum Bonn, Stiftsplatz 12, D-53111, Bonn, Germany
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103, Leipzig, Germany.
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42
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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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43
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Ramsey AJ, McCauley DE, Mandel JR. Heteroplasmy and Patterns of Cytonuclear Linkage Disequilibrium in Wild Carrot. Integr Comp Biol 2019; 59:1005-1015. [DOI: 10.1093/icb/icz102] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Abstract
Organellar genomes are considered to be strictly uniparentally-inherited. Uniparental inheritance allows for cytonuclear coevolution and the development of highly coordinated cytonuclear interactions. Yet, instances of biparental inheritance have been documented across eukaryotes. Biparental inheritance in otherwise uniparentally-inherited organelles is termed leakage (maternal or paternal) and allows for the presence of multiple variants of the same organellar genome within an individual, called heteroplasmy. It is unclear what, if any, evolutionary consequences are placed on nuclear and/or organellar genomes due to heteroplasmy. One way of accessing cytonuclear interactions and potential coevolution is through calculating cytonuclear linkage disequilibrium (cnLD), or the non-random association of alleles between nuclear and organellar genomes. Patterns of cnLD can indicate positive or negative cytonuclear selection, coevolution between the nuclear and organellar genomes, non-traditional organellar inheritance, or instances of ancestral heteroplasmy. In plants, cytonuclear interactions have been shown to play a role in cytoplasmic male sterility which occurs in gynodioecious species and is associated with leakage. We used the gynodioecious species, Daucus carota L. spp. carota, or wild carrot, to investigate cnLD. We genotyped a total of 265 individuals from two regions of the USA at 15 nuclear microsatellites, the mitochondrial genes cox1 and atp9, and an intergenic region between trnS and trnG (StoG) in the plastid genome to calculate nuclear–nuclear LD (nucLD), cnLD, and organellar LD (i.e., within the mtDNA and between mtDNA and ptDNA) within the two regions. We were further able to identify cox1 and StoG heteroplasmy and calculate some of the same LD measures within heteroplasmic and homoplasmic (non-heteroplasmic) datasets. We used a Z-transformation test to demonstrate that heteroplasmic individuals display significantly higher levels of cnLD within both regions. In spite of this, within and between organellar LD is low to moderate. Given these patterns of LD in two regions of the USA in which gene flow has been shown to occur between crop and wild carrot, we suggest that heteroplasmy is an evolutionary mechanism which permits the maintenance of cnLD while also acting to disrupt organellar LD.
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Affiliation(s)
- Adam J Ramsey
- Department of Biological Sciences, The University of Memphis, 3700 Walker Avenue, Memphis, TN 38152, USA
| | - David E McCauley
- Department of Biological Sciences, Vanderbilt University, VU Station B, Nashville, TN Box 351634, USA
| | - Jennifer R Mandel
- Department of Biological Sciences, Vanderbilt University, VU Station B, Nashville, TN Box 351634, USA
- W. Harry Feinstone Center for Genomic Research, The University of Memphis, 3774 Walker Avenue, Memphis, TN 38152, USA
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44
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Duan M, Chen L, Ge Q, Lu N, Li J, Pan X, Qiao Y, Tu J, Lu Z. Evaluating heteroplasmic variations of the mitochondrial genome from whole genome sequencing data. Gene 2019; 699:145-154. [PMID: 30876822 DOI: 10.1016/j.gene.2019.03.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 03/08/2019] [Accepted: 03/11/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Detecting heteroplasmic variations in the mitochondrial genome can help identify potential pathogenic possibilities, which is significant for disease prevention. The development of next-generation sequencing changed the quantification of mitochondrial DNA (mtDNA) heteroplasmy from scanning limited recorded points to the entire mitochondrial genome. However, due to the presence of nuclear mtDNA homologous sequences (nuMTs), maximally retaining real variations while excluding falsest heteroplasmic variations from nuMTs and sequencing errors presents a dilemma. RESULTS Herein, we used an improved method for detecting low-frequency mtDNA heteroplasmic variations from whole genome sequencing data, including point variations and short-fragment length alterations, and evaluated the effect of this method. A two-step alignment was designed and performed to accelerate data processing, to obtain and retain the true mtDNA reads and to eliminate most nuMTs reads. After analyzing whole genome sequencing data of K562 and GM12878 cells, ~90% of heteroplasmic point variations were identified in MitoMap. The results were consistent with the results of an amplification refractory mutation system qPCR. Many linkages of the detected heteroplasmy variations were also discovered. CONCLUSIONS Our improved method is a simple, efficient and accurate way to mine mitochondrial low-frequency heteroplasmic variations from whole genome sequencing data. By evaluating the highest misalignment possibility caused by the remaining nuMTs-like reads and sequencing errors, our procedure can detect mtDNA heteroplasmic variations whose heteroplasmy frequencies are as low as 0.2%.
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Affiliation(s)
- Mengqin Duan
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Liang Chen
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Qinyu Ge
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Na Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Junji Li
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xuan Pan
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing 210009, China
| | - Yi Qiao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jing Tu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China.
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45
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Nakai T, Sakurada A, Endo T, Kobayashi H, Masuda S, Makishima M, Esumi M. Caution for simple sequence repeat number variation in the mitochondrial DNA D-loop to determine cancer-specific variants. Oncol Lett 2018; 17:1883-1888. [PMID: 30675251 DOI: 10.3892/ol.2018.9809] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 11/27/2018] [Indexed: 12/11/2022] Open
Abstract
The mitochondrial DNA (mtDNA) displacement loop (D-loop) is often altered in various cancer types, including with regard to simple sequence repeat number variation (SSRNV), which includes the C-tract and CA-tract. However, because of mitochondrial heteroplasmy and slippage errors by the Taq DNA polymerase used in polymerase chain reaction (PCR) analysis, it is difficult to precisely evaluate mtDNA D-loop SSRNV experimentally. In this study, to precisely determine cancer-specific variants in mtDNA SSRNV, various microscopic portions of cancerous tissues and normal control tissues were obtained from a patient with breast cancer, followed by laser-capture microdissection of formalin-fixed paraffin-embedded specimens. Regions containing (CA)7 repeats (positions 514-523) and (C)8 repeats (positions 303-315) of the mitochondria DNA D-loop were amplified and sequenced. Variant signals of mtDNA SSRs of (CA)7 and (C)8 were observed in normal and cancerous tissues, with the content of minor alleles (CA)6 and (C)7/(C)9 differing among samples. These results were confirmed by PCR using various primers and proofreading DNA polymerases. PCR of genomic SSRs of (CA)7 in the NAALD2 gene and (C)8 in the BMP6 gene showed a simple repeat in all samples that was different from the observed mtDNA SSRNV. The present study suggests a reliable procedure for determining cancer-specific variants in mtDNA SSRNV: Using a proofreading DNA polymerase for PCR, the background of slippage by PCR is determined by PCR of the same genomic sequence as the target. Due to the varied heteroplasmy level of mtDNA SSRNV among normal tissues, the second background of polymorphic variations should be determined by several normal tissue DNA as PCR templates. Finally, the cancer-specific variant, including its variation frequency, is determined by subtracting the two background signals from the variant signals in cancer. However, care must be taken, as normal heteroplasmy drifts observed in mtDNA SSRNV may complicate such estimations.
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Affiliation(s)
- Tokiko Nakai
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nara Medical University, Kashihara, Nara 634-8521, Japan.,Department of Diagnostic Pathology, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Akihisa Sakurada
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Toshihide Endo
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Hiroko Kobayashi
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Shinobu Masuda
- Division of Oncologic Pathology, Department of Pathology and Microbiology, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Makoto Makishima
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
| | - Mariko Esumi
- Division of Biochemistry, Department of Biomedical Sciences, Nihon University School of Medicine, Tokyo 173-8610, Japan
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46
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Sylvester C, Krishna MS, Rao JS, Chandrasekar A. Allele frequencies of mitochondrial DNA HVR III 514–524 (CA)n dinucleotide repeats in the Urali Kuruman tribal population of South India. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2018. [DOI: 10.1186/s41935-018-0083-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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47
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Huber N, Parson W, Dür A. Next generation database search algorithm for forensic mitogenome analyses. Forensic Sci Int Genet 2018; 37:204-214. [PMID: 30241075 DOI: 10.1016/j.fsigen.2018.09.001] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Revised: 08/29/2018] [Accepted: 09/03/2018] [Indexed: 11/29/2022]
Abstract
Mitochondrial DNA (mtDNA) variation is being reported relative to the corrected version of the first sequenced human mitochondrial genome. A review of the existing literature across disciplines that employ mtDNA demonstrates that insertions and deletions are not reported in a standardized way. This may lead to false exclusions of identical sequences, unidentified matches in missing persons mtDNA databases, biased mtDNA database frequency estimates and overestimation of the genetic evidence. Seven years ago we introduced alignment-free database search software (SAM) and implemented it into the mtDNA database EMPOP (https://empop.online) to produce reliable and conservative frequency estimates that are required in the forensic context. However, ambiguity remained in how laboratories have been reporting mitotypes, as often more than one single alignment of a given mtDNA sequence was feasible. In order to overcome this limitation we here describe a concept and provide software for producing stable, harmonized phylogenetic alignment of mtDNA sequences for database searches. The new software SAM 2 will be made available via EMPOP and provide the user with the already established conservative frequency estimates. In addition, SAM 2 offers the rCRS-coded haplotype of a given mtDNA sequence following the established and widely accepted phylogenetic alignment. This provides the user with feedback on how mitotypes are stored in EMPOP and how they should be reported in order to harmonize nomenclature. Finally, this approach does not only permit reliable mtDNA nomenclature in forensics but invites related disciplines to take advantage of a standardized way of reporting mtDNA variation, thus closing the ranks between different genetic fields and supporting dialogue and collaboration between mtDNA scholars from various disciplines.
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Affiliation(s)
- Nicole Huber
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Walther Parson
- Institute of Legal Medicine, Medical University of Innsbruck, Innsbruck, Austria; Forensic Science Program, The Pennsylvania State University, University Park, PA, USA.
| | - Arne Dür
- Institute of Mathematics, University of Innsbruck, Austria
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48
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Sharma MA, Lee JYJ, Tam A, Sattha B, Mackenzie IR, Vallance HD, Sirrs S, Hannah-Shmouni F, Côté HCF, Mattman A. A mitochondrial DNA D loop insertion detected almost exclusively in non-replicating tissues with maternal inheritance across three generations. Mitochondrion 2018; 46:298-301. [PMID: 30114489 DOI: 10.1016/j.mito.2018.08.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 07/10/2018] [Accepted: 08/02/2018] [Indexed: 12/31/2022]
Abstract
Muscle biopsy identified a possibly pathogenic, mitochondrial DNA D-loop insertion, in each of 5 family members from two generations, that was otherwise undetectable in most other tissues. The tissue specific regulation of heteroplasmy is reflected in an age related increase in muscle heteroplasmy level, across the pedigree. This latter finding is in keeping with previous reports (e.g. T408A, C16327) but differs in having a very high muscle heteroplasmy level, and appears maternally transmitted.
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Affiliation(s)
- Mehul A Sharma
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada
| | - Ja Young J Lee
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada
| | - Andrea Tam
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada
| | - Beheroze Sattha
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada
| | - Ian R Mackenzie
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada; Division of Neuropathology, Department of Pathology and Laboratory Medicine, Vancouver General Hospital, The University of British Columbia, Canada
| | - Hilary D Vallance
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada; Biochemical Genetics, Department of Pathology and Laboratory Medicine, Children's & Women's Health Centre of BC, The University of British Columbia, Canada
| | - Sandra Sirrs
- Adult Metabolic Diseases Clinic, Vancouver General Hospital, The University of British Columbia, Canada
| | - Fady Hannah-Shmouni
- Adult Metabolic Diseases Clinic, Vancouver General Hospital, The University of British Columbia, Canada
| | - Hélène C F Côté
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada
| | - Andre Mattman
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Canada; Adult Metabolic Diseases Clinic, Vancouver General Hospital, The University of British Columbia, Canada.
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49
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Mitochondrial DNA Deletions With Low-Level Heteroplasmy in Adult-Onset Myopathy. J Clin Neuromuscul Dis 2018; 19:117-123. [PMID: 29465611 DOI: 10.1097/cnd.0000000000000200] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We report the cases of 2 patients who presented to our Myositis Center with myalgias and elevated creatine kinase levels. Muscle biopsy showed pathological features consistent with mitochondrial myopathy. In both cases, a single large deletion in mitochondrial DNA at low-level heteroplasmy was identified by next-generation sequencing in muscle tissue. In 1 case, the deletion was identified in muscle tissue but not blood. In both cases, the deletion was only identified on next-generation sequencing of muscle mitochondrial DNA and missed on array comparative genome hybridization testing. These cases demonstrate that next-generation sequencing of mitochondrial DNA in muscle tissue is the most sensitive method of molecular diagnosis for mitochondrial myopathy due to mitochondrial DNA deletions.
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50
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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] [MESH Headings] [Grants] [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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Grants
- R01-NR012459 U.S. Department of Health & Human Services | National Institutes of Health (NIH)
- R01 HL121023 NHLBI NIH HHS
- N01-AG-6-2106 U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- R01-HL121023 U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- P30 AG028740 NIA NIH HHS
- Z01A6000932 Office of Extramural Research, National Institutes of Health (OER)
- R03-AG032498 U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- R01-AG028050 U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- R01 NR012459 NINR NIH HHS
- R03 AG032498 NIA NIH HHS
- R01 AG028050 NIA NIH HHS
- This research was supported in part by the Intramural Research Program of the NIH, National Institute on Aging, Contracts N01-AG-6-2101, N01-AG-6-2103, and N01-AG-6-2106; National Institutes of Health grants R01-AG028050, R03-AG032498, R01-NR012459, Z01A6000932, R01-HL121023, and a grant from the Research and Education Leadership Committee of the CPMC Foundation and the L. K. Whittier Foundation.
- U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)
- U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)
- U.S. Department of Health & Human Services | National Institutes of Health (NIH)
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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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