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Odden MC, Li Y, Jotwani V, Dobrota S, Tan AX, Cummings SR, Shlipak MG, Scherzer R, Ix JH, Buckwalter MS, Tranah GJ. Joint and Individual Mitochondrial DNA Variation and Cognitive Outcomes in Black and White Older Adults. J Gerontol A Biol Sci Med Sci 2024; 79:glae170. [PMID: 39007867 PMCID: PMC11345514 DOI: 10.1093/gerona/glae170] [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: 02/21/2024] [Indexed: 07/16/2024] Open
Abstract
BACKGROUND Mitochondrial dysfunction manifests in neurodegenerative diseases and other age-associated disorders. In this study, we examined variation in inherited mitochondrial DNA (mtDNA) sequences in Black and White participants from 2 large aging studies to identify variants related to cognitive function. METHODS Participants included self-reported Black and White adults aged ≥70 years in the Lifestyle Interventions and Independence for Elders (LIFE; N = 1 319) and Health Aging and Body Composition (Health ABC; N = 788) studies. Cognitive function was measured by the Digit-Symbol Substitution Test (DSST), and the Modified Mini-Mental State Examination (3MSE) at baseline and over follow-up in LIFE (3.6 years) and Health ABC (10 years). We examined the joint effects of multiple variants across 16 functional mitochondrial regions with cognitive function using a sequence kernel association test. Based on these results, we prioritized meta-analysis of common variants in Black and White participants using mixed effects models. A Bonferroni-adjusted p value of <.05 was considered statistically significant. RESULTS Joint variation in subunits ND1, ND2, and ND5 of Complex I, 12S RNA, and hypervariable region (HVR) were significantly associated with DSST and 3MSE at baseline. In meta-analyses among Black participants, variant m.4216T>C, ND1 was associated with a faster decline in 3MSE, and variant m.462C>T in the HVR was associated with a slower decline in DSST. Variant m.5460G>C, ND2 was associated with slower and m.182C>T in the HVR was associated with faster decline in 3MSE in White participants. CONCLUSIONS Among Black and White adults, oxidative phosphorylation Complex I variants were associated with cognitive function.
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Affiliation(s)
- Michelle C Odden
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford, California, USA
| | - Yongmei Li
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford, California, USA
| | - Vasantha Jotwani
- Kidney Health Research Collaborative, Department of Medicine, San Francisco Veterans Affairs Health Care System, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Sylvie Dobrota
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford, California, USA
| | - Annabel X Tan
- Department of Epidemiology and Population Health, Stanford School of Medicine, Stanford, California, USA
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
| | - Michael G Shlipak
- Kidney Health Research Collaborative, Department of Medicine, San Francisco Veterans Affairs Health Care System, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Rebecca Scherzer
- Kidney Health Research Collaborative, Department of Medicine, San Francisco Veterans Affairs Health Care System, San Francisco, California, USA
- Department of Medicine, University of California San Francisco, San Francisco, California, USA
| | - Joachim H Ix
- Division of Nephrology-Hypertension, Department of Medicine, University of California San Diego, San Diego, California, USA
| | - Marion S Buckwalter
- Department of Neurology and Neurological Sciences, Stanford School of Medicine, Stanford, California, USA
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, California, USA
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, USA
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Tsai NC, Liou CW, Cheng YH, Lien HT, Lin TL, Lin TK, Lan MY, Hung PL, Wang TJ, Lee CH, Liang YC, Lan KC. The establishment of a molecular diagnostic platform for mitochondrial diseases: from conventional to next-generation sequencing. Biomed J 2024:100770. [PMID: 39048080 DOI: 10.1016/j.bj.2024.100770] [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: 03/12/2024] [Revised: 06/14/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024] Open
Abstract
BACKGROUND The aim of this study was to create a molecular diagnostic platform and establish a diagnostic pipeline for patients highly suspected of mitochondrial disorders. The effectiveness of three methods, namely, traditional restriction fragment length polymorphism-polymerase chain reaction (RFLP-PCR), Sanger sequencing for hotspot detection and whole mitochondrial DNA (mtDNA), and third-generation (Nanopore) whole mtDNA sequencing, will be compared in diagnosing patients with suspected primary mitochondrial diseases (PMDs). The strengths and limitations of different methods are also discussed. MATERIAL AND METHODS A single-center prospective cohort study was conducted to validate the diagnostic pipeline for suspected mitochondrial diseases. In the first stage, a PCR-based method with five sets of primers was used to screen for eight hotspots (m.3243A>G, m.3460G>A, m.8344A>G, m.8993T>G, m.9185T>C, m.11778G>A, m.13513G>A, and m.4977deletion) using either RFLP or direct Sanger sequencing. Sanger sequencing was also used to confirm the RFLP-positive samples. In the second stage, for samples with negative screening results for the eight hotspots, mitochondrial whole-genome sequencing was performed using Sanger sequencing or third-generation nanopore sequencing. RESULTS Between June 2020 and May 2023, 30 patients from ages 0 to 63 with clinically suspected mitochondrial disease were enrolled. The positive yield for the diagnosis of PMDs was 8/30=26.7%, and the sensitivity of the heteroplasmy level for the RFLP-based method was approximately 5%. The remaining 22 patients who tested negative at the first stage were tested using Sanger sequencing or the third-generation sequencing Nanopore, and all tested negative for pathological mtDNA mutations. Compared to the Sanger sequencing method, the results of RFLP-PCR were compromised by the limitations of incomplete RFLP enzyme digestion. For whole-genome sequencing of mtDNA, Sanger sequencing, instead of nanopore sequencing, is preferred at our institution because of its cost-effectiveness. CONCLUSIONS In our highly selective cohort, most tested positive in the first stage of the 8 hot spots screen. Sanger sequencing is a conventional and accurate method for mitochondrial disease screening, at least for the most common hot spots in the region. The results revealed that Sanger sequencing is an accurate method with the benefit of being more cost-effective. This integral platform of molecular diagnosis bears the advantages of being relatively low cost and having a shorter reporting time, facilitating crucial identification of patients with clinical evidence of such disorders. This diagnostic flowchart has also been translated into routine clinical use in the tertiary hospital.
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Affiliation(s)
- Ni-Chin Tsai
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, 100, Shih-Chuan 1st Road, Kaohsiung, 80708, Taiwan; Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan; Center for Menopause and Reproductive Medicine Research, Kaohsiung Chang Gung Memorial Hospital
| | - Chai-Wai Liou
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yin-Hua Cheng
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan; Center for Menopause and Reproductive Medicine Research, Kaohsiung Chang Gung Memorial Hospital
| | - Hao-Ting Lien
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Tzu-Ling Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Center for Menopause and Reproductive Medicine Research, Kaohsiung Chang Gung Memorial Hospital
| | - Tsu-Kung Lin
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Min-Yu Lan
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Department of Neurology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Pi-Lien Hung
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Tzu-Jou Wang
- Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Chen-Hao Lee
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Yi-Chih Liang
- Department of Pediatrics, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kuo-Chung Lan
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, 100, Shih-Chuan 1st Road, Kaohsiung, 80708, Taiwan; Center for Mitochondrial Research and Medicine, Kaohsiung Chang Gung Memorial Hospital, Kaohsiung 833, Taiwan; Department of Obstetrics and Gynecology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan; Center for Menopause and Reproductive Medicine Research, Kaohsiung Chang Gung Memorial Hospital; Department of Obstetrics and Gynecology, Jen-Ai Hospital, Taichung 412, Taiwan.
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Jeong J, Lee Y, Han J, Kang E, Kim D, Kim KS, Kim EAR, Lee BS, Jung E. Mitochondrial DNA mutations in extremely preterm infants with bronchopulmonary dysplasia. Gene 2024; 910:148337. [PMID: 38432533 DOI: 10.1016/j.gene.2024.148337] [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: 10/01/2023] [Revised: 02/21/2024] [Accepted: 02/29/2024] [Indexed: 03/05/2024]
Abstract
Bronchopulmonary dysplasia (BPD) is a serious chronic lung disease affecting extremely preterm infants. While mitochondrial dysfunction has been investigated in various medical conditions, limited research has explored mitochondrial DNA (mtDNA) gene mutations, specifically in BPD. This study aimed to evaluate mitochondrial mtDNA gene mutations in extremely preterm infants with BPD. In this prospective observational study, we enrolled a cohort of extremely preterm infants diagnosed with BPD. Clinical data were collected to provide comprehensive patient profiles. Peripheral blood mononuclear cells were isolated from whole-blood samples obtained within a defined timeframe. Subsequently, mtDNA extraction and sequencing using next-generation sequencing technology were performed to identify mtDNA gene mutations. Among the cohort of ten extremely preterm infants with BPD, mtDNA sequencing revealed the presence of mutations in seven patients, resulting in a total of twenty-one point mutations. Notably, many of these mutations were identified in loci associated with critical components of the respiratory chain complexes, vital for proper mitochondrial function and cellular energy production. This pilot study provides evidence of mtDNA point mutations in a subset of extremely preterm infants with BPD. These findings suggest a potential association between mitochondrial dysfunction and the pathogenesis of BPD. Further extensive investigations are warranted to unravel the mechanisms underlying mtDNA mutations in BPD.
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Affiliation(s)
- Jiyoon Jeong
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea.
| | - Yeonmi Lee
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea; Department of Biomedical Science, College of Life Science, CHA University, 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea.
| | - Jongsuk Han
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea; Department of Biomedical Science, College of Life Science, CHA University, 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea.
| | - Eunju Kang
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea; Department of Biomedical Science, College of Life Science, CHA University, 335, Pangyo-ro, Bundang-gu, Seongnam-si, Gyeonggi-do, Republic of Korea.
| | - Deokhoon Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea.
| | - Ki-Soo Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea.
| | - Ellen Ai-Rhan Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea.
| | - Byong Sop Lee
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea.
| | - Euiseok Jung
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, 88, Olympic-ro 43-gil, Songpa-gu, Seoul, Republic of Korea.
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Zou W, Chezhian J, Yu T, Liu W, Vu J, Slone J, Huang T. Dissecting the Roles of the Nuclear and Mitochondrial Genomes in a Mouse Model of Autoimmune Diabetes. Diabetes 2024; 73:108-119. [PMID: 37847928 DOI: 10.2337/db23-0430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 09/25/2023] [Indexed: 10/19/2023]
Abstract
Mitochondria, the organelles responsible for generating ATP in eukaryotic cells, have been previously implicated as a contributor to diabetes. However, mitochondrial proteins are encoded by both nuclear DNA (nDNA) and mtDNA. In order to better understand the relative contribution of each of these genomes to diabetes, a chimeric mitochondrial-nuclear exchange (MNX) mouse was created via pronuclear transfer carrying nDNA from a strain susceptible to type 1 diabetes (NOD/ShiLtJ) and mtDNA from nondiabetic C57BL/6J mice. Inheritance of the resulting heteroplasmic mtDNA mixture was then tracked across multiple generations, showing that offspring heteroplasmy generally followed that of the mother, with occasional large shifts consistent with an mtDNA bottleneck in the germ line. In addition, survival and incidence of diabetes in MNX mice were tracked and compared with those in unaltered NOD/ShiLtJ control mice. The results indicated improved survival and a delay in diabetes onset in the MNX mice, demonstrating that mtDNA has a critical influence on disease phenotype. Finally, enzyme activity assays showed that the NOD/ShiLtJ mice had significant hyperactivity of complex I of the electron transport chain relative to MNX mice, suggesting that a particular mtDNA variant (m.9461T>C) may be responsible for disease causation in the original NOD/ShiLtJ strain. ARTICLE HIGHLIGHTS Mitochondria have been previously implicated in diabetes, but the specific genetic factors remain unclear. To better understand the contributions of mitochondrial genes in nuclear DNA (nDNA) versus mtDNA, we created mitochondrial-nuclear exchange (MNX) mice carrying nDNA from a diabetic strain and mtDNA from nondiabetic mice. Long-term tracking of MNX mice showed occasional large shifts in heteroplasmy consistent with an mtDNA bottleneck in the germ line. In addition, the MNX mice showed improved survival and delayed incidence of diabetes relative to the unaltered diabetic mice, which appeared to be linked to the activity of respiratory complex I.
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Affiliation(s)
- Weiwei Zou
- Department of Obstetrics and Gynecology, Reproductive Medicine Center, First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, China
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
| | - Janaki Chezhian
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY
| | - Tenghui Yu
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY
- Human Aging Research Institute, School of Life Science, Nanchang University, Nanchang, Jiangxi Province, China
| | - Wensheng Liu
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY
| | - Jimmy Vu
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY
| | - Jesse Slone
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY
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Meshrkey F, Scheulin KM, Littlejohn CM, Stabach J, Saikia B, Thorat V, Huang Y, LaFramboise T, Lesnefsky EJ, Rao RR, West FD, Iyer S. Induced pluripotent stem cells derived from patients carrying mitochondrial mutations exhibit altered bioenergetics and aberrant differentiation potential. Stem Cell Res Ther 2023; 14:320. [PMID: 37936209 PMCID: PMC10631039 DOI: 10.1186/s13287-023-03546-7] [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: 05/17/2023] [Accepted: 10/25/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Human mitochondrial DNA mutations are associated with common to rare mitochondrial disorders, which are multisystemic with complex clinical pathologies. The pathologies of these diseases are poorly understood and have no FDA-approved treatments leading to symptom management. Leigh syndrome (LS) is a pediatric mitochondrial disorder that affects the central nervous system during early development and causes death in infancy. Since there are no adequate models for understanding the rapid fatality associated with LS, human-induced pluripotent stem cell (hiPSC) technology has been recognized as a useful approach to generate patient-specific stem cells for disease modeling and understanding the origins of the phenotype. METHODS hiPSCs were generated from control BJ and four disease fibroblast lines using a cocktail of non-modified reprogramming and immune evasion mRNAs and microRNAs. Expression of hiPSC-associated intracellular and cell surface markers was identified by immunofluorescence and flow cytometry. Karyotyping of hiPSCs was performed with cytogenetic analysis. Sanger and next-generation sequencing were used to detect and quantify the mutation in all hiPSCs. The mitochondrial respiration ability and glycolytic function were measured by the Seahorse Bioscience XFe96 extracellular flux analyzer. RESULTS Reprogrammed hiPSCs expressed pluripotent stem cell markers including transcription factors POU5F1, NANOG and SOX2 and cell surface markers SSEA4, TRA-1-60 and TRA-1-81 at the protein level. Sanger sequencing analysis confirmed the presence of mutations in all reprogrammed hiPSCs. Next-generation sequencing demonstrated the variable presence of mutant mtDNA in reprogrammed hiPSCs. Cytogenetic analyses confirmed the presence of normal karyotype in all reprogrammed hiPSCs. Patient-derived hiPSCs demonstrated decreased maximal mitochondrial respiration, while mitochondrial ATP production was not significantly different between the control and disease hiPSCs. In line with low maximal respiration, the spare respiratory capacity was lower in all the disease hiPSCs. The hiPSCs also demonstrated neural and cardiac differentiation potential. CONCLUSION Overall, the hiPSCs exhibited variable mitochondrial dysfunction that may alter their differentiation potential and provide key insights into clinically relevant developmental perturbations.
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Affiliation(s)
- Fibi Meshrkey
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA
- Department of Histology and Cell Biology, Faculty of Medicine, Alexandria University, Alexandria, Egypt
| | - Kelly M Scheulin
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
- Neuroscience Program, Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, USA
| | - Christopher M Littlejohn
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Joshua Stabach
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA
| | - Bibhuti Saikia
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA
| | - Vedant Thorat
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Yimin Huang
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Thomas LaFramboise
- Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Edward J Lesnefsky
- Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, VA, USA
- Cardiology Section Medical Service, McGuire Veterans Affairs Medical Center, Richmond, VA, USA
- Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, VA, USA
- Division of Cardiology, Department of Internal Medicine, Pauley Heart Center, Virginia Commonwealth University, Richmond, VA, USA
| | - Raj R Rao
- Department of Biomedical Engineering, College of Engineering, University of Arkansas, Fayetteville, AR, USA
| | - Franklin D West
- Regenerative Bioscience Center, University of Georgia, Athens, GA, USA
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
- Neuroscience Program, Biomedical and Health Sciences Institute, University of Georgia, Athens, GA, USA
| | - Shilpa Iyer
- Department of Biological Sciences, J. William Fulbright College of Arts and Sciences, University of Arkansas, Science and Engineering 601, Fayetteville, AR, 72701, USA.
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, USA.
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Satam H, Joshi K, Mangrolia U, Waghoo S, Zaidi G, Rawool S, Thakare RP, Banday S, Mishra AK, Das G, Malonia SK. Next-Generation Sequencing Technology: Current Trends and Advancements. BIOLOGY 2023; 12:997. [PMID: 37508427 PMCID: PMC10376292 DOI: 10.3390/biology12070997] [Citation(s) in RCA: 93] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023]
Abstract
The advent of next-generation sequencing (NGS) has brought about a paradigm shift in genomics research, offering unparalleled capabilities for analyzing DNA and RNA molecules in a high-throughput and cost-effective manner. This transformative technology has swiftly propelled genomics advancements across diverse domains. NGS allows for the rapid sequencing of millions of DNA fragments simultaneously, providing comprehensive insights into genome structure, genetic variations, gene expression profiles, and epigenetic modifications. The versatility of NGS platforms has expanded the scope of genomics research, facilitating studies on rare genetic diseases, cancer genomics, microbiome analysis, infectious diseases, and population genetics. Moreover, NGS has enabled the development of targeted therapies, precision medicine approaches, and improved diagnostic methods. This review provides an insightful overview of the current trends and recent advancements in NGS technology, highlighting its potential impact on diverse areas of genomic research. Moreover, the review delves into the challenges encountered and future directions of NGS technology, including endeavors to enhance the accuracy and sensitivity of sequencing data, the development of novel algorithms for data analysis, and the pursuit of more efficient, scalable, and cost-effective solutions that lie ahead.
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Affiliation(s)
- Heena Satam
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Kandarp Joshi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Upasana Mangrolia
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sanober Waghoo
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Gulnaz Zaidi
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Shravani Rawool
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Ritesh P. Thakare
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Shahid Banday
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Alok K. Mishra
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
| | - Gautam Das
- miBiome Therapeutics, Mumbai 400102, India; (H.S.); (K.J.); (U.M.); (S.W.); (G.Z.); (S.R.)
| | - Sunil K. Malonia
- Department of Molecular Cell and Cancer Biology, UMass Chan Medical School, Worcester, MA 01605, USA; (R.P.T.); (S.B.); (A.K.M.)
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7
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Li Y, Xia X, Wang Y, Zheng JC. Mitochondrial dysfunction in microglia: a novel perspective for pathogenesis of Alzheimer's disease. J Neuroinflammation 2022; 19:248. [PMID: 36203194 PMCID: PMC9535890 DOI: 10.1186/s12974-022-02613-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/28/2022] [Indexed: 11/23/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease in the elderly globally. Emerging evidence has demonstrated microglia-driven neuroinflammation as a key contributor to the onset and progression of AD, however, the mechanisms that mediate neuroinflammation remain largely unknown. Recent studies have suggested mitochondrial dysfunction including mitochondrial DNA (mtDNA) damage, metabolic defects, and quality control (QC) disorders precedes microglial activation and subsequent neuroinflammation. Therefore, an in-depth understanding of the relationship between mitochondrial dysfunction and microglial activation in AD is important to unveil the pathogenesis of AD and develop effective approaches for early AD diagnosis and treatment. In this review, we summarized current progress in the roles of mtDNA, mitochondrial metabolism, mitochondrial QC changes in microglial activation in AD, and provide comprehensive thoughts for targeting microglial mitochondria as potential therapeutic strategies of AD.
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Affiliation(s)
- Yun Li
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, 200072, China
| | - Xiaohuan Xia
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, 200072, China. .,Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai, 200331, China. .,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, 200065, China. .,Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, 200434, China.
| | - Yi Wang
- Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai, 200331, China.,Translational Research Center, Shanghai Yangzhi Rehabilitation Hospital Affiliated to Tongji University School of Medicine, Shanghai, 201613, China.,Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, 200092, China
| | - Jialin C Zheng
- Center for Translational Neurodegeneration and Regenerative Therapy, Tongji Hospital Affiliated to Tongji University School of Medicine, Shanghai, 200072, China. .,Shanghai Frontiers Science Center of Nanocatalytic Medicine, Shanghai, 200331, China. .,Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration (Tongji University), Ministry of Education, Shanghai, 200065, China. .,Translational Research Institute of Brain and Brain-Like Intelligence, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai, 200434, China. .,Collaborative Innovation Center for Brain Science, Tongji University, Shanghai, 200092, China.
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Connell JR, Benton MC, Lea RA, Sutherland HG, Haupt LM, Wright KM, Griffiths LR. Evaluating the suitability of current mitochondrial DNA interpretation guidelines for multigenerational whole mitochondrial genome comparisons. J Forensic Sci 2022; 67:1766-1775. [PMID: 35855536 PMCID: PMC9543078 DOI: 10.1111/1556-4029.15097] [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: 04/21/2022] [Revised: 06/06/2022] [Accepted: 06/30/2022] [Indexed: 12/03/2022]
Abstract
Sanger sequencing of the mitochondrial DNA (mtDNA) control region was previously the only method available for forensic casework involving degraded samples from skeletal remains. The introduction of Next Generation Sequencing (NGS) has transformed genetic data generation and human identification using mtDNA. Whole mitochondrial genome (mtGenome) analysis is now being introduced into forensic laboratories around the world to analyze historical remains. Research into large pedigrees using the mtGenome is critical to evaluate currently available interpretation guidelines for mtDNA analysis, which were developed for comparisons using the control region. This study included mtGenomes from 225 individuals from the last four generations of the Norfolk Island (NI) genetic isolate pedigree consisting of 49 distinct maternal lineages. The data from these individuals were arranged into 2339 maternally related pairs separated by up to 18 meioses. Our results show that 97.3% of maternally related pairs were concordant at all nucleotide positions, resulting in the correct interpretation of “Cannot Exclude”; 2.7% of pairs produced an “Inconclusive” result, and there were no instances of false exclusion. While these results indicate that existing guidelines are suitable for multigenerational whole mtGenome analysis, we recommend caution be taken when classifying heteroplasmic changes as differences for human identification. Our data showed the classification of heteroplasmic changes as differences increases the prevalence of inconclusive identification by 6%, with false exclusions observed in 0.34% of pairs examined. Further studies of multigenerational pedigrees, however, are needed to validate mtGenome interpretation guidelines for historical case work to more fully utilize emerging advancements.
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Affiliation(s)
- Jasmine R Connell
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Miles C Benton
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia.,Human Genomics, Kenepuru Science Centre, Institute of Environmental Science and Research, Wellington, New Zealand
| | - Rodney A Lea
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Heidi G Sutherland
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Larisa M Haupt
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
| | - Kirsty M Wright
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia.,Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Russell, ACT, Australia.,Royal Australian Air Force (RAAF), Headquarters History and Heritage, Unrecovered War Casualties-Air Force, Russell, ACT, Australia
| | - Lyn R Griffiths
- Queensland University of Technology (QUT), Centre for Genomics and Personalised Health, Genomics Research Centre, School of Biomedical Sciences, Kelvin Grove, Qld, Australia
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9
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Yang Z, Slone J, Huang T. Next-Generation Sequencing to Characterize Mitochondrial Genomic DNA Heteroplasmy. Curr Protoc 2022; 2:e412. [PMID: 35532282 DOI: 10.1002/cpz1.412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Mitochondria play a very important role in many crucial cellular functions. Each eukaryotic cell contains hundreds of mitochondria with hundreds of mitochondrial genomes. Mutant and wild-type mitochondrial DNA (mtDNA) may co-exist as heteroplasmy and cause human disease. The purpose of the protocols in this article is to simultaneously determine the mtDNA sequence and quantify the heteroplasmy level using parallel sequencing. The protocols include mitochondrial genomic DNA PCR amplification of two full-length products using two distinct sets of PCR primers. The PCR products are mixed at an equimolar ratio, and the samples are then barcoded and sequenced with high-throughput next-generation sequencing technology. This technology is highly sensitive, specific, and accurate in determining mtDNA mutations and the degree/level of heteroplasmy. © 2022 Wiley Periodicals LLC. Basic Protocol 1: PCR amplification of mitochondrial DNA Basic Protocol 2: Analysis of next-generation sequencing of mitochondrial DNA Basic Protocol 3: Mutect2 pipeline for automated sample processing and large-scale data analysis.
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Affiliation(s)
- Zeyu Yang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Jesse Slone
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
| | - Taosheng Huang
- Department of Pediatrics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York
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10
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Nuclease-Assisted, Multiplexed Minor-Allele Enrichment: Application in Liquid Biopsy of Cancer. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2394:433-451. [PMID: 35094339 DOI: 10.1007/978-1-0716-1811-0_22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The use of next-generation sequencing (NGS) to profile genomic variation of individual cancer species is revolutionizing the practice of clinical oncology. In liquid biopsy of cancer, sequencing of circulating-free DNA (cfDNA) is gradually applied to all stages of cancer diagnosis and treatment, serving as complement or replacement of tissue biopsies. However, analysis of cfDNA obtained from blood draws still faces technical obstacles due in part to an excess of wild-type DNA originating from normal tissues and hematopoietic cells. The resulting low-level mutation abundance often falls below routine NGS detection sensitivity and limits reliable mutation identification that meets clinical sensitivity and specificity standards. Despite sample preparation advances that reduce sequencing error rates via use of unique molecular identifiers (molecular barcodes) and error-suppression algorithms, excessive amounts of sequencing are still required to detect mutations at allelic frequency levels below 1%. This requirement reduces throughput and increases cost.In this chapter, we describe a sensitive multiplex mutation detection method that enriches mutation-containing DNA during sample preparation, prior to sequencing, thereby increasing signal-to-noise ratios and providing low-level mutation detection without excessive sequencing depth. We couple targeted next-generation sequencing with wild-type DNA removal using Nuclease-assisted Minor-allele Enrichment using Probe Overlap, NaME-PrO, a recently developed method to eliminate wild-type sequences from multiple targets simultaneously. A step by step guide to library preparation and data analysis are provided as well as some precautions during the sample handling.
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11
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Liu K, Xie N, Ma HJ. Next-generation sequencing reveals the mitogenomic heteroplasmy in the topmouth culter (Culter alburnus Basilewsky, 1855). Mol Biol Rep 2021; 49:943-950. [PMID: 34727288 DOI: 10.1007/s11033-021-06913-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 10/29/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND The mitogenomic heteroplasmy is the presence of multiple haplotypes in the mitochondria, which could cause genetic diseases and is also associated with many critical biological functions. The topmouth culter (Culter alburnus Basilewsky, 1855) is one of the most important freshwater fish in the family of Cyprinidae in China. At present, there are no reports on the topmouth culter's mtDNA heteroplasmy and the existence of which is not known. METHODS AND RESULTS This study aimed to analyze the mitogenomic heteroplasmy in the topmouth culter by the next-generation sequencing of the fins' total DNA. The results confirmed the existence of the heteroplasmy and indicated the presence of the extensive heteroplasmy in the topmouth culter's mitogenome. There were 38 heteroplasmic variations in the protein-coding genes from the three specimens, with 33 non-synonymous substitutions accounting for 86.84% and five synonymous substitutions accounting for 13.16%. Among them, the ND6 had the most heteroplasmic variations but only one synonymous substitution. After removing the putative nuclear mitochondrial DNA fragments, the ratio of primary haplotype in the three specimens was 43.89%, 74.72%, and 32.76%, respectively. The three specimens contained 21, 7, and 21 haplotypes of the mitogenomes, respectively. Due to the extensive heteroplasmy, we reconstructed the phylogenetic tree of the topmouth culter using the RY-coding method, which improved the performance of the phylogenetic tree to some extent. CONCLUSIONS This study reported the mitogenomic heteroplasmy in the topmouth culter and enhanced the knowledge regarding the mitogenomic heteroplasmy in phylogenetic studies. As the topmouth culter is a commercial species, the mitogenomic heteroplasmy is crucial for the fisheries management of the topmouth culter.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China.
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
| | - Heng-Jia Ma
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang, China
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12
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Park J, Kang E, Kang S, Kim D, Kim D, Park SJ, Jhang WK. Mitochondrial gene mutations in pediatric septic shock. Pediatr Res 2021; 90:1016-1022. [PMID: 33504965 DOI: 10.1038/s41390-020-01358-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 12/21/2020] [Accepted: 12/28/2020] [Indexed: 01/30/2023]
Abstract
BACKGROUND There has been a growing interest in the association between mitochondrial dysfunction and sepsis. However, most studies have focused on mitochondrial structural damage, functional aspects, or the clinical phenotypes in sepsis. The purpose of this study was to evaluate mitochondrial DNA (mtDNA) gene mutations in critically ill pediatric patients with septic shock. METHOD Thirteen patients with severe sepsis or septic shock admitted to the pediatric intensive care unit (PICU) of a tertiary children's hospital were enrolled in this prospective observational study. Clinical data from electronic medical records were obtained. Whole-blood samples were collected within 24 h of PICU admission to perform PBMC isolation, mtDNA extraction, and mtDNA sequencing using next-generation sequencing. RESULTS mtDNA sequencing revealed mutations in 9 of the 13 patients, presenting 27 point mutations overall, with 15 (55.6%) located in the locus related to adenosine triphosphate production and superoxide metabolism, including electron transport. CONCLUSION In this pilot study, significant numbers of mtDNA point mutations were detected in critically ill pediatric patients with septic shock. These mutations could provide promising evidence for mitochondrial dysfunction in sepsis and a basis for further large-scale studies. IMPACT This study is the first to examine mitochondrial DNA mutations in pediatric patients with septic shock using next-generation sequencing. A high frequency of mitochondrial DNA mutations was detected in these patients indicating an association with septic shock. This pilot study may provide a potential explanation for the association between mitochondrial dysfunction and septic shock on a genetic basis.
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Affiliation(s)
- Junsung Park
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Eunju Kang
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seoon Kang
- Department of Convergence Medicine and Stem Cell Center, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Deokhoon Kim
- Department of Pathology, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dahyun Kim
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Seong Jong Park
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Won Kyoung Jhang
- Department of Pediatrics, Asan Medical Center Children's Hospital, University of Ulsan College of Medicine, Seoul, Republic of Korea.
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13
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Yang Z, Slone J, Wang X, Zhan J, Huang Y, Namjou B, Kaufman KM, Pauciulo M, Harley JB, Muglia LJ, Chepelev I, Huang T. Validation of low-coverage whole-genome sequencing for mitochondrial DNA variants suggests mitochondrial DNA as a genetic cause of preterm birth. Hum Mutat 2021; 42:1602-1614. [PMID: 34467602 PMCID: PMC9290920 DOI: 10.1002/humu.24279] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/17/2021] [Accepted: 08/29/2021] [Indexed: 01/06/2023]
Abstract
Preterm birth (PTB), or birth that occurs earlier than 37 weeks of gestational age, is a major contributor to infant mortality and neonatal hospitalization. Mutations in the mitochondrial genome (mtDNA) have been linked to various rare mitochondrial disorders and may be a contributing factor in PTB given that maternal genetic factors have been strongly linked to PTB. However, to date, no study has found a conclusive connection between a particular mtDNA variant and PTB. Given the high mtDNA copy number per cell, an automated pipeline was developed for detecting mtDNA variants using low‐coverage whole‐genome sequencing (lcWGS) data. The pipeline was first validated against samples of known heteroplasmy, and then applied to 929 samples from a PTB cohort from diverse ethnic backgrounds with an average gestational age of 27.18 weeks (range: 21–30). Our new pipeline successfully identified haplogroups and a large number of mtDNA variants in this large PTB cohort, including 8 samples carrying known pathogenic variants and 47 samples carrying rare mtDNA variants. These results confirm that lcWGS can be utilized to reliably identify mtDNA variants. These mtDNA variants may make a contribution toward preterm birth in a small proportion of live births.
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Affiliation(s)
- Zeyu Yang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jesse Slone
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Xinjian Wang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Jack Zhan
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Yongbo Huang
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Bahram Namjou
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Kenneth M Kaufman
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Michael Pauciulo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - John B Harley
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,US Department of Veterans Affairs Medical Center, Cincinnati, Ohio, USA
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA.,Burroughs Wellcome Fund, Research Triangle Park, North Carolina, USA
| | - Iouri Chepelev
- Center for Autoimmune Genomics and Etiology (CAGE), Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center and University of Cincinnati College of Medicine, Cincinnati, Ohio, USA
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14
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Chen R, Aldred MA, Xu W, Zein J, Bazeley P, Comhair SAA, Meyers DA, Bleecker ER, Liu C, Erzurum SC, Hu B. Comparison of whole genome sequencing and targeted sequencing for mitochondrial DNA. Mitochondrion 2021; 58:303-310. [PMID: 33513442 PMCID: PMC8354572 DOI: 10.1016/j.mito.2021.01.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 10/22/2022]
Abstract
Mitochondrial dysfunction has emerged to be associated with a broad spectrum of diseases, and there is an increasing demand for accurate detection of mitochondrial DNA (mtDNA) variants. Whole genome sequencing (WGS) has been the dominant sequencing approach to identify genetic variants in recent decades, but most studies focus on variants on the nuclear genome. Whole genome sequencing is also costly and time consuming. Sequencing specifically targeted for mtDNA is commonly used in the diagnostic settings and has lower costs. However, there is a lack of pairwise comparisons between these two sequencing approaches for calling mtDNA variants on a population basis. In this study, we compared WGS and mtDNA-targeted sequencing (targeted-seq) in analyzing mitochondrial DNA from 1499 participants recruited into the Severe Asthma Research Program (SARP). Our study reveals that targeted-sequencing and WGS have comparable capacity to determine genotypes and to call haplogroups and homoplasmies on mtDNA. However, there exists a large variability in calling heteroplasmies, especially for low-frequency heteroplasmies, which indicates that investigators should be cautious about heteroplasmies acquired from different sequencing methods. Further research is highly desired to improve variant detection methods for mitochondrial DNA.
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Affiliation(s)
- Ruoying Chen
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Micheala A Aldred
- Division of Pulmonary, Critical Care, Sleep, and Occupational Medicine, Department of Medicine, Indiana University, Indianapolis, IN, USA
| | - Weiling Xu
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Joe Zein
- Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Peter Bazeley
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Suzy A A Comhair
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | | | - Chunyu Liu
- Department of Biostatistics, Boston University, Boston, MA, USA
| | - Serpil C Erzurum
- Department of Inflammation and Immunity, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA; Respiratory Institute, Cleveland Clinic, Cleveland, OH, USA.
| | - Bo Hu
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
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15
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Fazzini F, Fendt L, Schönherr S, Forer L, Schöpf B, Streiter G, Losso JL, Kloss-Brandstätter A, Kronenberg F, Weissensteiner H. Analyzing Low-Level mtDNA Heteroplasmy-Pitfalls and Challenges from Bench to Benchmarking. Int J Mol Sci 2021; 22:ijms22020935. [PMID: 33477827 PMCID: PMC7832847 DOI: 10.3390/ijms22020935] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/05/2021] [Accepted: 01/15/2021] [Indexed: 12/27/2022] Open
Abstract
Massive parallel sequencing technologies are promising a highly sensitive detection of low-level mutations, especially in mitochondrial DNA (mtDNA) studies. However, processes from DNA extraction and library construction to bioinformatic analysis include several varying tasks. Further, there is no validated recommendation for the comprehensive procedure. In this study, we examined potential pitfalls on the sequencing results based on two-person mtDNA mixtures. Therefore, we compared three DNA polymerases, six different variant callers in five mixtures between 50% and 0.5% variant allele frequencies generated with two different amplification protocols. In total, 48 samples were sequenced on Illumina MiSeq. Low-level variant calling at the 1% variant level and below was performed by comparing trimming and PCR duplicate removal as well as six different variant callers. The results indicate that sensitivity, specificity, and precision highly depend on the investigated polymerase but also vary based on the analysis tools. Our data highlight the advantage of prior standardization and validation of the individual laboratory setup with a DNA mixture model. Finally, we provide an artificial heteroplasmy benchmark dataset that can help improve somatic variant callers or pipelines, which may be of great interest for research related to cancer and aging.
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Affiliation(s)
- Federica Fazzini
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Liane Fendt
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Sebastian Schönherr
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Lukas Forer
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Bernd Schöpf
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Gertraud Streiter
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Jamie Lee Losso
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Anita Kloss-Brandstätter
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
- Carinthia University of Applied Sciences, A-9524 Villach, Austria
| | - Florian Kronenberg
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
| | - Hansi Weissensteiner
- Department of Genetics and Pharmacology, Institute of Genetic Epidemiology, Medical University of Innsbruck, A-6020 Innsbruck, Austria; (F.F.); (L.F.); (S.S.); (L.F.); (B.S.); (G.S.); (J.L.L.); (A.K.-B.); (F.K.)
- Correspondence: ; Tel.: +43-512-9003-70564
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16
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Rauf S, Zahra N, Malik SS, Zahra SAE, Sughra K, Khan MR. Extraction of Mitochondrial Genome from Whole Genome Next Generation Sequencing Data and Unveiling of Forensically Relevant Markers. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420080128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Vanlallawma A, Zami Z, Pautu JL, Bawihtlung Z, Khenglawt L, Lallawmzuali D, Chhakchhuak L, Senthil Kumar N. Pediatric leukemia could be driven predominantly by non-synonymous variants in mitochondrial complex V in Mizo population from Northeast India. Mitochondrial DNA A DNA Mapp Seq Anal 2020; 31:245-249. [PMID: 32609037 DOI: 10.1080/24701394.2020.1786545] [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: 10/23/2022]
Abstract
Leukemia is the most common childhood malignancy and studies had been carried out with promising revelations in its diagnosis and prognosis. However, majority of the studies are focused on nuclear alterations, while mitochondrial mutations are not well studied. Although there are studies of mitochondrial mutations in the adult leukemias, it does not represent the same for childhood malignancy. This is the first scientific report on the mtDNA mutational pattern of pediatric leukemic cases from a endogamous tribal population in Northeast India. ATP6 involved in the Complex V was found to be more altered with respect to the Non-synonymous variants. mtDNA variations in the non-coding region (D-Loop - g.152 T>C) and in the coding region (MT-ND2, g.4824 A>G, p.T119A) showed a maternal inheritance which could reveal a genetic predisposition with lower penetrance. D-Loop variant (g.152 T>C) could be a diagnostic marker in accordance with previous report but is in contrast to pertaining only in AML - M3 subtype rather was found across in myeloid malignancies.
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Affiliation(s)
| | - Zothan Zami
- Department of Biotechnology, Mizoram University, Aizawl, Mizoram, India
| | - Jeremy L Pautu
- Mizoram State Cancer Institute, Zemabawk, Aizawl, Mizoram, India
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18
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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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19
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Zereg E, Chaussenot A, Morel G, Bannwarth S, Sacconi S, Soriani MH, Attarian S, Cano A, Pouget J, Bellance R, Tranchant C, Lannes B, de Paula AM, Saadi Ait-El-Mkadem S, Chafino B, Berthet M, Fragaki K, Paquis-Flucklinger V, Rouzier C. Single-fiber studies for assigning pathogenicity of eight mitochondrial DNA variants associated with mitochondrial diseases. Hum Mutat 2020; 41:1394-1406. [PMID: 32419253 DOI: 10.1002/humu.24037] [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: 12/09/2019] [Revised: 03/29/2020] [Accepted: 04/19/2020] [Indexed: 12/21/2022]
Abstract
Whole mitochondrial DNA (mtDNA) sequencing is now systematically used in clinical laboratories to screen patients with a phenotype suggestive of mitochondrial disease. Next Generation Sequencing (NGS) has significantly increased the number of identified pathogenic mtDNA variants. Simultaneously, the number of variants of unknown significance (VUS) has increased even more, thus challenging their interpretation. Correct classification of the variants' pathogenicity is essential for optimal patient management, including treatment and genetic counseling. Here, we used single muscle fiber studies to characterize eight heteroplasmic mtDNA variants, among which were three novel variants. By applying the pathogenicity scoring system, we classified four variants as "definitely pathogenic" (m.590A>G, m.9166T>C, m.12293G>A, and m.15958A>T). Two variants remain "possibly pathogenic" (m.4327T>C and m.5672T>C) but should these be reported in a different family, they would be reclassified as "definitely pathogenic." We also illustrate the contribution of single-fiber studies to the diagnostic approach in patients harboring pathogenic variants with low level heteroplasmy.
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Affiliation(s)
- Elamine Zereg
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France
| | - Annabelle Chaussenot
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Godelieve Morel
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France
| | - Sylvie Bannwarth
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Sabrina Sacconi
- Department of Clinical Neurosciences, Neuromuscular Diseases Centre, Nice Teaching Hospital, Nice, France
| | - Marie-Hélène Soriani
- Department of Clinical Neurosciences, Neuromuscular Diseases Centre, Nice Teaching Hospital, Nice, France
| | - Shahram Attarian
- Neurology Department, Referral Center for ALS and Neuromuscular Diseases, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Aline Cano
- Pediatric Neurology Department, Reference Center for Inherited Metabolic Diseases, Timone Hospital, Marseille, France
| | - Jean Pouget
- Neurology Department, Referral Center for ALS and Neuromuscular Diseases, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Rémi Bellance
- Neuromyology Department, Neuromuscular Reference Center, Fort-de-France Teaching Hospital, Fort-de-France, France
| | - Christine Tranchant
- Department of Movement Pathology, Strasbourg Teaching Hospital, Strasbourg, France
| | - Béatrice Lannes
- Pathology Department, Hôpitaux Universitaires de Strasbourg, Hôpital de Hautepierre, Strasbourg, France
| | - André Maues de Paula
- Pathology Department, Timone University Hospital, Aix-Marseille University, Marseille, France
| | - Samira Saadi Ait-El-Mkadem
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Bernadette Chafino
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France
| | - Mathieu Berthet
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France
| | - Konstantina Fragaki
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Véronique Paquis-Flucklinger
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
| | - Cécile Rouzier
- Department of Medical Genetics, National Center for Mitochondrial Diseases, Nice Teaching Hospital, Nice, France.,Inserm U1081, CNRS UMR7284, IRCAN, Université Côte d'Azur, Nice, France
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20
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Salas A, Schönherr S, Bandelt HJ, Gómez-Carballa A, Weissensteiner H. Extraordinary claims require extraordinary evidence in asserted mtDNA biparental inheritance. Forensic Sci Int Genet 2020; 47:102274. [PMID: 32330850 DOI: 10.1016/j.fsigen.2020.102274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Revised: 03/08/2020] [Accepted: 03/11/2020] [Indexed: 01/26/2023]
Abstract
A breakthrough article published in PNAS by Luo et al. challenges a central dogma in biology which states that the mitochondrial DNA (mtDNA) in humans is inherited exclusively from the mother. We re-analyzed original FASTQ files and results reported by Luo et al. to investigate methodological issues (e.g. nuclear mitochondrial DNA or NUMTs, DNA rearrangements) that could lead to biological misinterpretations. A comprehensive analysis of their data reveals several methodological and analytical issues that must be carefully addressed before challenging the current paradigm. We first show that the probability of the findings described by the authors is extremely small (most likely below 10-37). The sequencing replicates from the same donors show aberrations in the variants detected that need further investigation to exclude contributions from other sources or methodological artifacts. Applying the principle of reductio ad absurdum, we demonstrate that the nuclear factor invoked by the authors to explain the phenomenon would need to be extraordinarily complex and precise to preclude linear accumulation of mtDNA lineages across generations, which would make the appearance of mixed haplotypes a much more frequent event in the population. We discuss alternate scenarios that explain findings of the same nature as reported by Luo et al., in the context of in-vitro fertilization and therapeutic mtDNA replacement ooplasmic transplantation.
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Affiliation(s)
- Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain.
| | - Sebastian Schönherr
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, 6020, Austria
| | | | - Alberto Gómez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, and GenPoB Research Group, Instituto de Investigaciones Sanitarias (IDIS), Hospital Clínico Universitario de Santiago (SERGAS), Galicia, Spain
| | - Hansi Weissensteiner
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, 6020, Austria
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21
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The special considerations of gene therapy for mitochondrial diseases. NPJ Genom Med 2020; 5:7. [PMID: 32140258 PMCID: PMC7051955 DOI: 10.1038/s41525-020-0116-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 12/30/2019] [Indexed: 12/21/2022] Open
Abstract
The recent success of gene therapy across multiple clinical trials has inspired a great deal of hope regarding the treatment of previously intractable genetic diseases. This optimism has been extended to the prospect of gene therapy for mitochondrial disorders, which are not only particularly severe but also difficult to treat. However, this hope must be tempered by the reality of the mitochondrial organelle, which possesses specific biological properties that complicate genetic manipulation. In this perspective, we will discuss some of these complicating factors, including the unique pathways used to express and import mitochondrial proteins. We will also present some ways in which these challenges can be overcome by genetic manipulation strategies tailored specifically for mitochondrial diseases.
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22
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Liu Y, Guo S, Yin C, Guo X, Liu M, Yuan Z, Zhao Z, Jia Y, Xing J. Optimized PCR-Based Enrichment Improves Coverage Uniformity and Mutation Detection in Mitochondrial DNA Next-Generation Sequencing. J Mol Diagn 2020; 22:503-512. [PMID: 32036083 DOI: 10.1016/j.jmoldx.2020.01.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/03/2019] [Accepted: 01/11/2020] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing-based methods have been commonly used for detecting mutations of mitochondrial genome (mtDNA). PCR amplification is a highly effective method of mtDNA enrichment before sequencing. However, it has been observed that highly variable sequencing depth within PCR amplicons severely reduces the coverage uniformity and accuracy of mutation calling. Therefore, it is necessary to develop an optimized PCR-based strategy for mtDNA sequencing. Herein, the effect of DNA quality on the efficiency of PCR amplification was analyzed and the effects of different primer-design methods, including the number of primer pairs, overlap length of amplicons, and modification of primers, on coverage uniformity and mutation calling in mtDNA sequencing were assessed. Results showed that DNA quality significantly affected the efficiency of PCR amplification. Importantly, over- and under-representation of coverage depth at overlap regions of amplicons were observed when amplicons were not modified and overlap was shorter than two sequencing fragment sizes (800 bp). Then, under-representation was overcome by increasing the overlap length of the amplicons, and over-representation was effectively reduced by 5'-block modification of primers and sticky-end ligation of amplicons. Moreover, findings indicated that these two optimized PCR-based sequencing strategies effectively improved mutation calling in primer-binding regions. Optimized PCR-based mtDNA enrichment and sequencing approaches have been established, which laid a foundation for accurate mutation detection of mtDNA in diseases.
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Affiliation(s)
- Yang Liu
- Department of Pathology, Basic Medical College, Inner Mongolia Medical University, Huhhot, People's Republic of China
| | - Shanshan Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Chun Yin
- Department of Cardiovascular Medicine, the 902nd Hospital of PLA Joint Service Support Force, Bengbu, People's Republic of China
| | - Xu Guo
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Manling Liu
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Zhidong Yuan
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China
| | - Zheng Zhao
- Third Department of Medical Oncology, Shanxi Provincial Cancer Hospital, Xi'an, People's Republic of China
| | - Yongfeng Jia
- Department of Pathology, Basic Medical College, Inner Mongolia Medical University, Huhhot, People's Republic of China.
| | - Jinliang Xing
- State Key Laboratory of Cancer Biology and Department of Physiology and Pathophysiology, Fourth Military Medical University, Xi'an, People's Republic of China.
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23
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Sensitivity of mitochondrial DNA heteroplasmy detection using Next Generation Sequencing. Mitochondrion 2020; 50:88-93. [DOI: 10.1016/j.mito.2019.10.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 10/10/2019] [Indexed: 01/03/2023]
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24
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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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25
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Dierckxsens N, Mardulyn P, Smits G. Unraveling heteroplasmy patterns with NOVOPlasty. NAR Genom Bioinform 2019; 2:lqz011. [PMID: 33575563 PMCID: PMC7671380 DOI: 10.1093/nargab/lqz011] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 09/16/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022] Open
Abstract
Heteroplasmy, the existence of multiple mitochondrial haplotypes within an individual, has been studied across different scientific fields. Mitochondrial genome polymorphisms have been linked to multiple severe disorders and are of interest to evolutionary studies and forensic science. Before the development of massive parallel sequencing (MPS), most studies of mitochondrial genome variation were limited to short fragments and to heteroplasmic variants associated with a relatively high frequency (>10%). By utilizing ultra-deep sequencing, it has now become possible to uncover previously undiscovered patterns of intra-individual polymorphisms. Despite these technological advances, it is still challenging to determine the origin of the observed intra-individual polymorphisms. We therefore developed a new method that not only detects intra-individual polymorphisms within mitochondrial and chloroplast genomes more accurately, but also looks for linkage among polymorphic sites by assembling the sequence around each detected polymorphic site. Our benchmark study shows that this method is capable of detecting heteroplasmy more accurately than any method previously available and is the first tool that is able to completely or partially reconstruct the sequence for each mitochondrial haplotype (allele). The method is implemented in our open source software NOVOPlasty that can be downloaded at https://github.com/ndierckx/NOVOPlasty.
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Affiliation(s)
- Nicolas Dierckxsens
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles and Vrije Universiteit Brussel, Triomflaan CP 263, 1050 Brussels, Belgium
| | - Patrick Mardulyn
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles and Vrije Universiteit Brussel, Triomflaan CP 263, 1050 Brussels, Belgium.,Evolutionary Biology and Ecology, CP 160/12, Université Libre de Bruxelles, Av. F. D. Roosevelt 50, B-1050 Brussels, Belgium
| | - Guillaume Smits
- Interuniversity Institute of Bioinformatics in Brussels (IB2), Université Libre de Bruxelles and Vrije Universiteit Brussel, Triomflaan CP 263, 1050 Brussels, Belgium.,Genetics, Hôpital Universitaire des Enfants Reine Fabiola, Université Libre de Bruxelles, 1020 Brussels, Belgium.,Center for Human Genetics, Hôpital Erasme, Université Libre de Bruxelles, Route de Lennik 808, 1070 Brussels, Belgium
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26
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Németh K, Darvasi O, Likó I, Szücs N, Czirják S, Reiniger L, Szabó B, Kurucz PA, Krokker L, Igaz P, Patócs A, Butz H. Next-generation sequencing identifies novel mitochondrial variants in pituitary adenomas. J Endocrinol Invest 2019; 42:931-940. [PMID: 30684245 PMCID: PMC6647476 DOI: 10.1007/s40618-019-1005-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/08/2019] [Indexed: 12/30/2022]
Abstract
PURPOSE Disrupted mitochondrial functions and genetic variants of mitochondrial DNA (mtDNA) have been observed in different human neoplasms. Next-generation sequencing (NGS) can be used to detect even low heteroplasmy-level mtDNA variants. We aimed to investigate the mitochondrial genome in pituitary adenomas by NGS. METHODS We analysed 11 growth hormone producing and 33 non-functioning [22 gonadotroph and 11 hormone immunonegative] pituitary adenomas using VariantPro™ Mitochondrion Panel on Illumina MiSeq instrument. Revised Cambridge Reference Sequence (rCRS) of the mtDNA was used as reference. Heteroplasmy was determined using a 3% cutoff. RESULTS 496 variants were identified in pituitary adenomas with overall low level of heteroplasmy (7.22%). On average, 35 variants were detected per sample. Samples harbouring the highest number of variants had the highest Ki-67 indices independently of histological subtypes. We identified eight variants (A11251G, T4216C, T16126C, C15452A, T14798C, A188G, G185A, and T16093C) with different prevalences among different histological groups. T16189C was found in 40% of non-recurrent adenomas, while it was not present in the recurrent ones. T14798C and T4216C were confirmed by Sanger sequencing in all 44 samples. 100% concordance was found between NGS and Sanger method. CONCLUSIONS NGS is a reliable method for investigating mitochondrial genome and heteroplasmy in pituitary adenomas. Out of the 496 detected variants, 414 have not been previously reported in pituitary adenoma. The high number of mtDNA variants may contribute to adenoma genesis, and some variants (i.e., T16189C) might associate with benign behaviour.
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Affiliation(s)
- K Németh
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - O Darvasi
- "Lendulet" Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, 46 Szentkiralyi Street, Budapest, H-1088, Hungary
| | - I Likó
- "Lendulet" Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, 46 Szentkiralyi Street, Budapest, H-1088, Hungary
| | - N Szücs
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - S Czirják
- National Institute of Clinical Neurosciences, Budapest, Hungary
| | - L Reiniger
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - B Szabó
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - P A Kurucz
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - L Krokker
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
| | - P Igaz
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
- Molecular Medicine Research Group, Hungarian Academy of Sciences and Semmelweis University, Budapest, Hungary
| | - A Patócs
- "Lendulet" Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, 46 Szentkiralyi Street, Budapest, H-1088, Hungary
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary
| | - H Butz
- "Lendulet" Hereditary Endocrine Tumours Research Group, Hungarian Academy of Sciences and Semmelweis University, 46 Szentkiralyi Street, Budapest, H-1088, Hungary.
- Department of Laboratory Medicine, Semmelweis University, Budapest, Hungary.
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27
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Grace HE, Galdun P, Lesnefsky EJ, West FD, Iyer S. mRNA Reprogramming of T8993G Leigh's Syndrome Fibroblast Cells to Create Induced Pluripotent Stem Cell Models for Mitochondrial Disorders. Stem Cells Dev 2019; 28:846-859. [PMID: 31017045 DOI: 10.1089/scd.2019.0045] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Early molecular and developmental events impacting many incurable mitochondrial disorders are not fully understood and require generation of relevant patient- and disease-specific stem cell models. In this study, we focus on the ability of a nonviral and integration-free reprogramming method for deriving clinical-grade induced pluripotent stem cells (iPSCs) specific to Leigh's syndrome (LS), a fatal neurodegenerative mitochondrial disorder of infants. The cause of fatality could be due to the presence of high abundance of mutant mitochondrial DNA (mtDNA) or decline in respiration levels, thus affecting early molecular and developmental events in energy-intensive tissues. LS patient fibroblasts (designated LS1 in this study), carrying a high percentage of mutant T8993G mtDNA, were reprogrammed using a combined mRNA-miRNA nonviral approach to generate human iPSCs (hiPSCs). The LS1-hiPSCs were evaluated for their self-renewal, embryoid body (EB) formation, and differentiation potential, using immunocytochemistry and gene expression profiling methods. Sanger sequencing and next-generation sequencing approaches were used to detect the mutation and quantify the percentage of mutant mtDNA in the LS1-hiPSCs and differentiated derivatives. Reprogrammed LS-hiPSCs expressed pluripotent stem cell markers including transcription factors OCT4, NANOG, and SOX2 and cell surface markers SSEA4, TRA-1-60, and TRA-1-81 at the RNA and protein level. LS1-hiPSCs also demonstrated the capacity for self-renewal and multilineage differentiation into all three embryonic germ layers. EB analysis demonstrated impaired differentiation potential in cells carrying high percentage of mutant mtDNA. Next-generation sequencing analysis confirmed the presence of high abundance of T8993G mutant mtDNA in the patient fibroblasts and their reprogrammed and differentiated derivatives. These results represent for the first time the derivation and characterization of a stable nonviral hiPSC line reprogrammed from a LS patient fibroblast carrying a high abundance of mutant mtDNA. These outcomes are important steps toward understanding disease origins and developing personalized therapies for patients suffering from mitochondrial diseases.
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Affiliation(s)
- Harrison E Grace
- 1 Regenerative Bioscience Center, University of Georgia, Athens, Georgia.,2 Department of Animal and Dairy Science, University of Georgia, Athens, Georgia
| | - Patrick Galdun
- 3 Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia
| | - Edward J Lesnefsky
- 3 Department of Physiology and Biophysics, Virginia Commonwealth University, Richmond, Virginia.,4 Cardiology Section Medical Service, McGuire Veterans Affairs Medical Center, Richmond, Virginia.,5 Department of Biochemistry and Molecular Biology, Virginia Commonwealth University, Richmond, Virginia.,6 Division of Cardiology, Pauley Heart Center, Department of Internal Medicine, Virginia Commonwealth University, Richmond, Virginia
| | - Franklin D West
- 1 Regenerative Bioscience Center, University of Georgia, Athens, Georgia.,2 Department of Animal and Dairy Science, University of Georgia, Athens, Georgia
| | - Shilpa Iyer
- 7 Department of Biological Sciences, Fulbright College of Arts and Sciences, University of Arkansas, Fayetteville, Arkansas
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28
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Kim MY, Cho S, Lee JH, Seo HJ, Lee SD. Detection of Innate and Artificial Mitochondrial DNA Heteroplasmy by Massively Parallel Sequencing: Considerations for Analysis. J Korean Med Sci 2018; 33:e337. [PMID: 30584415 PMCID: PMC6300661 DOI: 10.3346/jkms.2018.33.e337] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 10/02/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Mitochondrial heteroplasmy, the co-existence of different mitochondrial polymorphisms within an individual, has various forensic and clinical implications. But there is still no guideline on the application of massively parallel sequencing (MPS) in heteroplasmy detection. We present here some critical issues that should be considered in heteroplasmy studies using MPS. METHODS Among five samples with known innate heteroplasmies, two pairs of mixture were generated for artificial heteroplasmies with target minor allele frequencies (MAFs) ranging from 50% to 1%. Each sample was amplified by two-amplicon method and sequenced by Ion Torrent system. The outcomes of two different analysis tools, Torrent Suite Variant Caller (TVC) and mtDNA-Server (mDS), were compared. RESULTS All the innate heteroplasmies were detected correctly by both analysis tools. Average MAFs of artificial heteroplasmies correlated well to the target values. The detection rates were almost 90% for high-level heteroplasmies, but decreased for low-level heteroplasmies. TVC generally showed lower detection rates than mDS, which seems to be due to their own computation algorithms which drop out some reference-dominant heteroplasmies. Meanwhile, mDS reported several unintended low-level heteroplasmies which were suggested as nuclear mitochondrial DNA sequences. The average coverage depth of each sample placed on the same chip showed considerable variation. The increase of coverage depth had no effect on the detection rates. CONCLUSION In addition to the general accuracy of the MPS application on detecting heteroplasmy, our study indicates that the understanding of the nature of mitochondrial DNA and analysis algorithm would be crucial for appropriate interpretation of MPS results.
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Affiliation(s)
- Moon-Young Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Sohee Cho
- Institute of Forensic Science, Seoul National University College of Medicine, Seoul, Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Hee Jin Seo
- 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 Science, Seoul National University College of Medicine, Seoul, Korea
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29
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Abstract
Although there has been considerable debate about whether paternal mitochondrial DNA (mtDNA) transmission may coexist with maternal transmission of mtDNA, it is generally believed that mitochondria and mtDNA are exclusively maternally inherited in humans. Here, we identified three unrelated multigeneration families with a high level of mtDNA heteroplasmy (ranging from 24 to 76%) in a total of 17 individuals. Heteroplasmy of mtDNA was independently examined by high-depth whole mtDNA sequencing analysis in our research laboratory and in two Clinical Laboratory Improvement Amendments and College of American Pathologists-accredited laboratories using multiple approaches. A comprehensive exploration of mtDNA segregation in these families shows biparental mtDNA transmission with an autosomal dominantlike inheritance mode. Our results suggest that, although the central dogma of maternal inheritance of mtDNA remains valid, there are some exceptional cases where paternal mtDNA could be passed to the offspring. Elucidating the molecular mechanism for this unusual mode of inheritance will provide new insights into how mtDNA is passed on from parent to offspring and may even lead to the development of new avenues for the therapeutic treatment for pathogenic mtDNA transmission.
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30
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Current and emerging tools for the recovery of genetic information from post mortem samples: New directions for disaster victim identification. Forensic Sci Int Genet 2018; 37:270-282. [DOI: 10.1016/j.fsigen.2018.08.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 08/27/2018] [Accepted: 08/27/2018] [Indexed: 01/14/2023]
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31
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Manini TM, Buford TW, Kairalla JA, McDermott MM, Vaz Fragoso CA, Fielding RA, Hsu FC, Johannsen N, Kritchevsky S, Harris TB, Newman AB, Cummings SR, King AC, Pahor M, Santanasto AJ, Tranah GJ. Meta-analysis identifies mitochondrial DNA sequence variants associated with walking speed. GeroScience 2018; 40:497-511. [PMID: 30338417 DOI: 10.1007/s11357-018-0043-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/06/2018] [Indexed: 12/25/2022] Open
Abstract
Declines in walking speed are associated with a variety of poor health outcomes including disability, comorbidity, and mortality. While genetic factors are putative contributors to variability in walking, few genetic loci have been identified for this trait. We examined the role of mitochondrial genomic variation on walking speed by sequencing the entire mitochondrial DNA (mtDNA). Data were meta-analyzed from 1758 Lifestyle Interventions and Independence for Elders (LIFE) Study and replication data from 730 Health, Aging, and Body Composition (HABC) Study participants with baseline walking speed information. Participants were 69+ years old of diverse racial backgrounds (African, European, and other race/ethnic groups) and had a wide range of mean walking speeds [4-6 m (0.78-1.09 m/s) and 400 m (0.83-1.24 m/s)]. Meta-analysis across studies and racial groups showed that m.12705C>T, ND5 variant was significantly associated (p < 0.0001) with walking speed at both short and long distances. Replication and meta-analysis also identified statistically significant walking speed associations (p < 0.0001) between the m.5460.G>A, ND2 and m.309C>CT, HV2 variants at short and long distances, respectively. All results remained statistically significant after multiple comparisons adjustment for 499 mtDNA variants. The m.12705C>T variant can be traced to the beginnings of human global migration and that cells carrying this variant display altered tRNA expression. Significant pooled effects related to stopping during the long-distance walk test were observed across OXPHOS complexes I (p = 0.0017) and III (p = 0.0048). These results suggest that mtDNA-encoded variants are associated with differences in walking speed among older adults, potentially identifying those at risk of developing mobility impairments.
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Affiliation(s)
- Todd M Manini
- Department of Aging and Geriatric Research, University of Florida, 2004 Mowry Rd., Gainesville, FL, 32611, USA.
| | - Thomas W Buford
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - John A Kairalla
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Mary M McDermott
- General Internal Medicine and Geriatrics and Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Carlos A Vaz Fragoso
- Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Roger A Fielding
- Gerald J. and Dorothy R. Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, USA
| | - Fang-Chi Hsu
- The Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Neil Johannsen
- Preventive Medicine Department, Pennington Biomedical Research Center, Baton Rouge, LA, USA
| | - Stephen Kritchevsky
- Sticht Center on Aging, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Tamara B Harris
- Intramural Research Program, Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, MD, USA
| | - Anne B Newman
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA
| | - Abby C King
- Department of Health Research and Policy - Epidemiology, Stanford University School of Medicine, Stanford, CA, USA
| | - Marco Pahor
- Department of Aging and Geriatric Research, University of Florida, 2004 Mowry Rd., Gainesville, FL, 32611, USA
| | - Adam J Santanasto
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, 94107, USA.
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32
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Theunissen TEJ, Nguyen M, Kamps R, Hendrickx AT, Sallevelt SCEH, Gottschalk RWH, Calis CM, Stassen APM, de Koning B, Mulder-Den Hartog ENM, Schoonderwoerd K, Fuchs SA, Hilhorst-Hofstee Y, de Visser M, Vanoevelen J, Szklarczyk R, Gerards M, de Coo IFM, Hellebrekers DMEI, Smeets HJM. Whole Exome Sequencing Is the Preferred Strategy to Identify the Genetic Defect in Patients With a Probable or Possible Mitochondrial Cause. Front Genet 2018; 9:400. [PMID: 30369941 PMCID: PMC6194163 DOI: 10.3389/fgene.2018.00400] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 09/03/2018] [Indexed: 01/03/2023] Open
Abstract
Mitochondrial disorders, characterized by clinical symptoms and/or OXPHOS deficiencies, are caused by pathogenic variants in mitochondrial genes. However, pathogenic variants in some of these genes can lead to clinical manifestations which overlap with other neuromuscular diseases, which can be caused by pathogenic variants in non-mitochondrial genes as well. Mitochondrial pathogenic variants can be found in the mitochondrial DNA (mtDNA) or in any of the 1,500 nuclear genes with a mitochondrial function. We have performed a two-step next-generation sequencing approach in a cohort of 117 patients, mostly children, in whom a mitochondrial disease-cause could likely or possibly explain the phenotype. A total of 86 patients had a mitochondrial disorder, according to established clinical and biochemical criteria. The other 31 patients had neuromuscular symptoms, where in a minority a mitochondrial genetic cause is present, but a non-mitochondrial genetic cause is more likely. All patients were screened for pathogenic variants in the mtDNA and, if excluded, analyzed by whole exome sequencing (WES). Variants were filtered for being pathogenic and compatible with an autosomal or X-linked recessive mode of inheritance in families with multiple affected siblings and/or consanguineous parents. Non-consanguineous families with a single patient were additionally screened for autosomal and X-linked dominant mutations in a predefined gene-set. We identified causative pathogenic variants in the mtDNA in 20% of the patient-cohort, and in nuclear genes in 49%, implying an overall yield of 68%. We identified pathogenic variants in mitochondrial and non-mitochondrial genes in both groups with, obviously, a higher number of mitochondrial genes affected in mitochondrial disease patients. Furthermore, we show that 31% of the disease-causing genes in the mitochondrial patient group were not included in the MitoCarta database, and therefore would have been missed with MitoCarta based gene-panels. We conclude that WES is preferable to panel-based approaches for both groups of patients, as the mitochondrial gene-list is not complete and mitochondrial symptoms can be secondary. Also, clinically and genetically heterogeneous disorders would require sequential use of multiple different gene panels. We conclude that WES is a comprehensive and unbiased approach to establish a genetic diagnosis in these patients, able to resolve multi-genic disease-causes.
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Affiliation(s)
- Tom E J Theunissen
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Minh Nguyen
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Rick Kamps
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Alexandra T Hendrickx
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Suzanne C E H Sallevelt
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Ralph W H Gottschalk
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Chantal M Calis
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Alphons P M Stassen
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Bart de Koning
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | | | | | - Sabine A Fuchs
- Department of Metabolic Disorders, University Medical Centre Utrecht, Utrecht, Netherlands
| | | | - Marianne de Visser
- Department of Neurology, Academic Medical Centre Amsterdam, Amsterdam, Netherlands
| | - Jo Vanoevelen
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Radek Szklarczyk
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Mike Gerards
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Maastricht Center for Systems Biology (MaCSBio), Maastricht University Medical Centre, Maastricht, Netherlands
| | - Irenaeus F M de Coo
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Department of Pediatric Neurology, Erasmus MC Sophia Children's Hospital, Rotterdam, Netherlands
| | - Debby M E I Hellebrekers
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Hubert J M Smeets
- Department of Genetics and Cell Biology, Maastricht University Medical Centre, Maastricht, Netherlands.,Research Institute GROW, Maastricht University Medical Centre, Maastricht, Netherlands
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33
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Palodhi A, Ghosh S, Biswas NK, Basu A, Majumder PP, Maitra A. Profiling of genomic alterations of mitochondrial DNA in gingivobuccal oral squamous cell carcinoma: Implications for disease progress. Mitochondrion 2018; 46:361-369. [PMID: 30261279 DOI: 10.1016/j.mito.2018.09.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 08/08/2018] [Accepted: 09/14/2018] [Indexed: 01/31/2023]
Abstract
We have identified 164 somatic mutations in mitochondrial DNA in gingivobuccal oral cancer by deep sequencing the mitochondrial genome from paired tumor and blood DNA samples from 89 patients. We have found evidence of positive selection of somatic nonsynonymous mutations. Non-synonymous mutations in mitochondrial respiratory genes were found to increase the risk of lymph node metastasis (P = 0.0028). We have observed a significant reduction in mitochondrial DNA copy number in tumor DNA of these patients compared to the DNA from adjacent normal tissue samples (P < 1 × 10-6). Analysis of transcriptome data of tumor and adjacent normal tissue revealed patients harboring mutations in mitochondrial protein-coding genes exhibited reduced expression of mitochondrial transcripts.
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Affiliation(s)
- Arindam Palodhi
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Nidhan K Biswas
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | - Analabha Basu
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
| | | | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India.
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34
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Kesäniemi J, Boratyński Z, Danforth J, Itam P, Jernfors T, Lavrinienko A, Mappes T, Møller AP, Mousseau TA, Watts PC. Analysis of heteroplasmy in bank voles inhabiting the Chernobyl exclusion zone: A commentary on Baker et al. (2017) "Elevated mitochondrial genome variation after 50 generations of radiation exposure in a wild rodent.". Evol Appl 2018; 11:820-826. [PMID: 29875822 PMCID: PMC5978973 DOI: 10.1111/eva.12578] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 11/03/2017] [Indexed: 12/19/2022] Open
Affiliation(s)
- Jenni Kesäniemi
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Zbyszek Boratyński
- CIBIO/InBIO, Research Center in Biodiversity and Genetic ResourcesUniversity of PortoVairãoPortugal
| | - John Danforth
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Prince Itam
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | - Toni Jernfors
- Department of Ecology and GeneticsUniversity of OuluOuluFinland
| | | | - Tapio Mappes
- Department of Biological and Environmental ScienceUniversity of JyväskyläJyväskyläFinland
| | - Anders Pape Møller
- Ecologie Systématique EvolutionUniversité Paris‐Sud, CNRS, AgroParisTechUniversité Paris‐SaclayOrsay CedexFrance
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35
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Hefti E, Blanco JG. Mitochondrial DNA heteroplasmy in cardiac tissue from individuals with and without coronary artery disease. Mitochondrial DNA A DNA Mapp Seq Anal 2018; 29:587-593. [PMID: 28521548 PMCID: PMC5694712 DOI: 10.1080/24701394.2017.1325480] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2017] [Revised: 04/19/2017] [Accepted: 04/27/2017] [Indexed: 01/11/2023]
Abstract
The cellular environment associated with coronary artery disease (CAD) can lead to mitochondrial DNA (mtDNA) damage. Mitochondrial variants in some copies of mtDNA (heteroplasmy) and mtDNA content are potential genetic biomarkers for CAD-associated disease states. Massively parallel sequencing and qRT-PCR techniques were used to measure heteroplasmic variants and mtDNA content in heart samples from donors with (n = 8) and without (n = 7) documented CAD. Both groups showed increased numbers of heteroplasmic mtDNA variants in the control region (CR) (p < .0010, ANOVA). The donors with CAD displayed a 41.07% increase in heteroplasmic mtDNA variant number in the CR (p = .043), an 87.50% increase in the number of heteroplasmic mtDNA deletions (p = .12), and a 48.76% increase in the number of heteroplasmic mtDNA single nucleotide variants (p = .029). These data suggest potential trends towards higher cardiac mtDNA heteroplasmy levels in heart samples from donors with CAD.
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Affiliation(s)
- Erik Hefti
- Department of Pharmaceutical Sciences, The School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, New York, United States of America
| | - Javier G. Blanco
- Department of Pharmaceutical Sciences, The School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, New York, United States of America
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36
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Langdahl J, Larsen M, Frost M, Andersen P, Yderstraede K, Vissing J, Dunø M, Thomassen M, Frederiksen A. Lecocytes mutation load declines with age in carriers of the m.3243A>G mutation: A 10-year Prospective Cohort. Clin Genet 2018; 93:925-928. [DOI: 10.1111/cge.13201] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Revised: 12/14/2017] [Accepted: 12/15/2017] [Indexed: 01/30/2023]
Affiliation(s)
- J.H. Langdahl
- Department of Clinical Genetics; Odense University Hospital; Odense Denmark
- Institute of Clinical Research; University of Southern Denmark; Odense Denmark
- Department of Endocrinology; Hospital of Southwest Jutland; Esbjerg Denmark
| | - M. Larsen
- Department of Clinical Genetics; Odense University Hospital; Odense Denmark
- Institute of Clinical Research; University of Southern Denmark; Odense Denmark
| | - M. Frost
- Institute of Clinical Research; University of Southern Denmark; Odense Denmark
- Department of Internal Medicine; Kolding Hospital; Kolding Denmark
| | - P.H. Andersen
- Department of Endocrinology; Hospital of Southwest Jutland; Esbjerg Denmark
| | - K.B. Yderstraede
- Department of Endocrinology; Odense University Hospital; Odense Denmark
| | - J. Vissing
- Copenhagen Neuromuscular Center; Rigshospitalet; Copenhagen Denmark
| | - M. Dunø
- Department of Clinical Genetics; Rigshospitalet; Copenhagen Denmark
| | - M. Thomassen
- Department of Clinical Genetics; Odense University Hospital; Odense Denmark
- Institute of Clinical Research; University of Southern Denmark; Odense Denmark
| | - A.L. Frederiksen
- Department of Clinical Genetics; Odense University Hospital; Odense Denmark
- Institute of Clinical Research; University of Southern Denmark; Odense Denmark
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37
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Recent Advances in Detecting Mitochondrial DNA Heteroplasmic Variations. Molecules 2018; 23:molecules23020323. [PMID: 29401641 PMCID: PMC6017848 DOI: 10.3390/molecules23020323] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 01/27/2018] [Accepted: 01/31/2018] [Indexed: 12/31/2022] Open
Abstract
The co-existence of wild-type and mutated mitochondrial DNA (mtDNA) molecules termed heteroplasmy becomes a research hot point of mitochondria. In this review, we listed several methods of mtDNA heteroplasmy research, including the enrichment of mtDNA and the way of calling heteroplasmic variations. At the present, while calling the novel ultra-low level heteroplasmy, high-throughput sequencing method is dominant while the detection limit of recorded mutations is accurate to 0.01% using the other quantitative approaches. In the future, the studies of mtDNA heteroplasmy may pay more attention to the single-cell level and focus on the linkage of mutations.
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38
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Cho S, Kim MY, Lee JH, Lee SD. Assessment of mitochondrial DNA heteroplasmy detected on commercial panel using MPS system with artificial mixture samples. Int J Legal Med 2017; 132:1049-1056. [PMID: 29279961 DOI: 10.1007/s00414-017-1755-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 11/30/2017] [Indexed: 01/05/2023]
Abstract
Mitochondrial DNA (mtDNA) heteroplasmy is a potential genetic marker for forensic mtDNA analysis as well as phylogenic studies. Frequency of mtDNA heteroplasmy has been investigated in different populations through massively parallel sequencing (MPS) analysis, revealing various levels of frequency based on different MPS systems. For accurate heteroplasmy identification, it is essential to explore reliable detection threshold on various MPS systems. In addition, software solutions and pipelines need to be evaluated to analyze data effectively. In this study, heteroplasmy analysis was conducted on a commercially available mtDNA analysis system developed for forensic caseworks with artificially mixed DNA samples known for ratios and variant positions for assessment. mtDNA heteroplasmy > 10% was detectable with Torrent Variant Caller (TVC) while lower levels were identified using GeneMarker® HTS specialized software for minor variant detection. This study implies that analytical parameters and tools need to be optimized and evaluated for low-level heteroplasmy identification. Automated system with simple and efficient workflow is needed for forensic caseworks.
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Affiliation(s)
- Sohee Cho
- Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Moon Young Kim
- Department of Forensic Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Ji Hyun Lee
- Department of Forensic Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea
| | - Soong Deok Lee
- Institute of Forensic Science, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea. .,Department of Forensic Medicine, Seoul National University College of Medicine, 103 Daehak-ro, Jongno-gu, Seoul, 03080, South Korea.
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39
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Live birth derived from oocyte spindle transfer to prevent mitochondrial disease. Reprod Biomed Online 2017; 34:361-368. [PMID: 28385334 DOI: 10.1016/j.rbmo.2017.01.013] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2016] [Revised: 01/23/2017] [Accepted: 01/31/2017] [Indexed: 12/31/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) are maternally inherited and can cause fatal or debilitating mitochondrial disorders. The severity of clinical symptoms is often associated with the level of mtDNA mutation load or degree of heteroplasmy. Current clinical options to prevent transmission of mtDNA mutations to offspring are limited. Experimental spindle transfer in metaphase II oocytes, also called mitochondrial replacement therapy, is a novel technology for preventing mtDNA transmission from oocytes to pre-implantation embryos. Here, we report a female carrier of Leigh syndrome (mtDNA mutation 8993T > G), with a long history of multiple undiagnosed pregnancy losses and deaths of offspring as a result of this disease, who underwent IVF after reconstitution of her oocytes by spindle transfer into the cytoplasm of enucleated donor oocytes. A male euploid blastocyst wasobtained from the reconstituted oocytes, which had only a 5.7% mtDNA mutation load. Transfer of the embryo resulted in a pregnancy with delivery of a boy with neonatal mtDNA mutation load of 2.36-9.23% in his tested tissues. The boy is currently healthy at 7 months of age, although long-term follow-up of the child's longitudinal development remains crucial.
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40
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Ishiya K, Ueda S. MitoSuite: a graphical tool for human mitochondrial genome profiling in massive parallel sequencing. PeerJ 2017; 5:e3406. [PMID: 28584729 PMCID: PMC5452969 DOI: 10.7717/peerj.3406] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Accepted: 05/11/2017] [Indexed: 11/20/2022] Open
Abstract
Recent rapid advances in high-throughput, next-generation sequencing (NGS) technologies have promoted mitochondrial genome studies in the fields of human evolution, medical genetics, and forensic casework. However, scientists unfamiliar with computer programming often find it difficult to handle the massive volumes of data that are generated by NGS. To address this limitation, we developed MitoSuite, a user-friendly graphical tool for analysis of data from high-throughput sequencing of the human mitochondrial genome. MitoSuite generates a visual report on NGS data with simple mouse operations. Moreover, it analyzes high-coverage sequencing data but runs on a stand-alone computer, without the need for file upload. Therefore, MitoSuite offers outstanding usability for handling massive NGS data, and is ideal for evolutionary, clinical, and forensic studies on the human mitochondrial genome variations. It is freely available for download from the website https://mitosuite.com.
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Affiliation(s)
- Koji Ishiya
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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41
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Clima R, Preste R, Calabrese C, Diroma MA, Santorsola M, Scioscia G, Simone D, Shen L, Gasparre G, Attimonelli M. HmtDB 2016: data update, a better performing query system and human mitochondrial DNA haplogroup predictor. Nucleic Acids Res 2016; 45:D698-D706. [PMID: 27899581 PMCID: PMC5210550 DOI: 10.1093/nar/gkw1066] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Revised: 10/20/2016] [Accepted: 11/04/2016] [Indexed: 11/14/2022] Open
Abstract
The HmtDB resource hosts a database of human mitochondrial genome sequences from individuals with healthy and disease phenotypes. The database is intended to support both population geneticists as well as clinicians undertaking the task to assess the pathogenicity of specific mtDNA mutations. The wide application of next-generation sequencing (NGS) has provided an enormous volume of high-resolution data at a low price, increasing the availability of human mitochondrial sequencing data, which called for a cogent and significant expansion of HmtDB data content that has more than tripled in the current release. We here describe additional novel features, including: (i) a complete, user-friendly restyling of the web interface, (ii) links to the command-line stand-alone and web versions of the MToolBox package, an up-to-date tool to reconstruct and analyze human mitochondrial DNA from NGS data and (iii) the implementation of the Reconstructed Sapiens Reference Sequence (RSRS) as mitochondrial reference sequence. The overall update renders HmtDB an even more handy and useful resource as it enables a more rapid data access, processing and analysis. HmtDB is accessible at http://www.hmtdb.uniba.it/.
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Affiliation(s)
- Rosanna Clima
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy.,Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, 40126 Bologna, Italy
| | - Roberto Preste
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
| | - Claudia Calabrese
- European Bioinformatics Institute EMBL Outstation - Hinxton, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK
| | - Maria Angela Diroma
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
| | - Mariangela Santorsola
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
| | - Gaetano Scioscia
- IBM Italia S.p.A., GBS BAO Advanced Analytics Services and MBLab Bari, Italy
| | - Domenico Simone
- Department of Biology and Environmental Science, Centre for Ecology and Evolution in Microbial model Systems (EEMiS), Linnaeus University, Barlastgatan 11, Kalmar, Sweden
| | - Lishuang Shen
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, California, CA 90027, USA
| | - Giuseppe Gasparre
- Department of Medical and Surgical Sciences-DIMEC, Medical Genetics Unit, University of Bologna, 40126 Bologna, Italy
| | - Marcella Attimonelli
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari, 70126 Bari, Italy
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42
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Hefti E, Bard J, Blanco JG. Analysis of Heteroplasmic Variants in the Cardiac Mitochondrial Genome of Individuals with Down Syndrome. Hum Mutat 2016; 38:48-54. [PMID: 27594409 DOI: 10.1002/humu.23071] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 08/29/2016] [Indexed: 11/08/2022]
Abstract
Individuals with Down syndrome (DS, trisomy 21) exhibit a pro-oxidative cellular environment as well as mitochondrial dysfunction. Increased oxidative stress may damage the mitochondrial DNA (mtDNA). The coexistence of mtDNA variants in a cell or tissue (i.e., heteroplasmy) may contribute to mitochondrial dysfunction. Given the evidence on mitochondrial dysfunction and the relatively high incidence of multiorganic disorders associated with DS, we hypothesized that cardiac tissue from subjects with DS may exhibit higher frequencies of mtDNA variants in comparison to cardiac tissue from donors without DS. This study documents the analysis of mtDNA variants in heart tissue samples from donors with (n = 12) and without DS (n = 33) using massively parallel sequencing. Contrary to the original hypothesis, the study's findings suggest that the cardiac mitochondrial genomes from individuals with and without DS exhibit many similarities in terms of (1) total number of mtDNA variants per sample, (2) the frequency of mtDNA variants, (3) the type of mtDNA variants, and (4) the patterns of distribution of mtDNA variants. In both groups of samples, the mtDNA control region showed significantly more heteroplasmic variants in comparison to the number of variants in protein- and RNA-coding genes (P < 1.00×10-4 , ANOVA).
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Affiliation(s)
- Erik Hefti
- Department of Pharmaceutical Sciences, The School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, New York
| | - Jonathan Bard
- University at Buffalo Genomics and Bioinformatics Core, New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York
| | - Javier G Blanco
- Department of Pharmaceutical Sciences, The School of Pharmacy and Pharmaceutical Sciences, The State University of New York at Buffalo, Buffalo, New York
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43
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Wang J, Chen GJ. Mitochondria as a therapeutic target in Alzheimer's disease. Genes Dis 2016; 3:220-227. [PMID: 30258891 PMCID: PMC6150105 DOI: 10.1016/j.gendis.2016.05.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2016] [Accepted: 05/30/2016] [Indexed: 11/29/2022] Open
Abstract
Alzheimer's disease (AD) remains the most common neurodegenerative disease characterized by β-amyloid protein (Aβ) deposition and memory loss. Studies have shown that mitochondrial dysfunction plays a crucial role in AD, which involves oxidative stress-induced respiratory chain dysfunction, loss of mitochondrial biogenesis, defects of mitochondrial dynamics and mtDNA mutations. Thus mitochondria might serve as drug therapy target for AD. In this article, we first briefly discussed mitochondrial theory in the development of AD, and then we summarized recent advances of mitochondrial abnormalities in AD pathology and introduced a series of drugs and techniques targeting mitochondria. We think that maintaining mitochondrial function may provide a new way of thinking in the treatment of AD.
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Affiliation(s)
| | - Guo-Jun Chen
- Department of Neurology, The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Neurology, 1 Youyi Road, Chongqing 400016, China
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Targeted sequencing with enrichment PCR: a novel diagnostic method for the detection of EGFR mutations. Oncotarget 2016; 6:13742-9. [PMID: 25915533 PMCID: PMC4537046 DOI: 10.18632/oncotarget.3807] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Accepted: 03/18/2015] [Indexed: 01/01/2023] Open
Abstract
Epidermal growth factor receptor (EGFR) is an important mediator of tumor cell survival and proliferation. The detection of EGFR mutations can predict prognoses and indicate when treatment with EGFR tyrosine kinase inhibitors should be used. As such, the development of highly sensitive methods for detecting EGFR mutations is important. Targeted next-generation sequencing is an effective method for diagnosing mutations. We compared the abilities of enrichment PCR followed by ultra-deep pyrosequencing (UDP), UDP alone, and PNA-mediated RT-PCR clamping to detect low-frequency EGFR mutations in tumor cell lines and tissue samples. Using enrichment PCR-UDP, we were able to detect the E19del and L858R mutations at minimum frequencies of 0.01% and 0.05%, respectively, in the PC-9 and H197 tumor cell lines. We also confirmed the sensitivity of detecting the E19del mutation by performing a titration analysis in FFPE tumor samples. The lowest mutation frequency detected was 0.0692% in tissue samples. EGFR mutations with frequencies as low as 0.01% were detected using enrichment PCR-UDP, suggesting that this method is a valuable tool for detecting rare mutations, especially in scarce tissue samples or those with small quantities of DNA.
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Kang E, Wang X, Tippner-Hedges R, Ma H, Folmes CDL, Gutierrez NM, Lee Y, Van Dyken C, Ahmed R, Li Y, Koski A, Hayama T, Luo S, Harding CO, Amato P, Jensen J, Battaglia D, Lee D, Wu D, Terzic A, Wolf DP, Huang T, Mitalipov S. Age-Related Accumulation of Somatic Mitochondrial DNA Mutations in Adult-Derived Human iPSCs. Cell Stem Cell 2016; 18:625-36. [PMID: 27151456 DOI: 10.1016/j.stem.2016.02.005] [Citation(s) in RCA: 168] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 01/05/2016] [Accepted: 02/15/2016] [Indexed: 12/21/2022]
Abstract
The genetic integrity of iPSCs is an important consideration for therapeutic application. In this study, we examine the accumulation of somatic mitochondrial genome (mtDNA) mutations in skin fibroblasts, blood, and iPSCs derived from young and elderly subjects (24-72 years). We found that pooled skin and blood mtDNA contained low heteroplasmic point mutations, but a panel of ten individual iPSC lines from each tissue or clonally expanded fibroblasts carried an elevated load of heteroplasmic or homoplasmic mutations, suggesting that somatic mutations randomly arise within individual cells but are not detectable in whole tissues. The frequency of mtDNA defects in iPSCs increased with age, and many mutations were non-synonymous or resided in RNA coding genes and thus can lead to respiratory defects. Our results highlight a need to monitor mtDNA mutations in iPSCs, especially those generated from older patients, and to examine the metabolic status of iPSCs destined for clinical applications.
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Affiliation(s)
- Eunju Kang
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Xinjian Wang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Rebecca Tippner-Hedges
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Hong Ma
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Clifford D L Folmes
- Department of Medicine, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Nuria Marti Gutierrez
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Yeonmi Lee
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Crystal Van Dyken
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Riffat Ahmed
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Ying Li
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Amy Koski
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Tomonari Hayama
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Shiyu Luo
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA
| | - Cary O Harding
- Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Paula Amato
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Jeffrey Jensen
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - David Battaglia
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - David Lee
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Diana Wu
- Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA
| | - Andre Terzic
- Department of Medicine, Division of Cardiovascular Diseases, Mayo Clinic, Rochester, MN 55905, USA
| | - Don P Wolf
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA
| | - Taosheng Huang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, Cincinnati, OH 45229, USA.
| | - Shoukhrat Mitalipov
- Center for Embryonic Cell and Gene Therapy, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA; Division of Reproductive and Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, 505 NW 185th Avenue, Beaverton, OR 97006, USA; Department of Molecular and Medical Genetics, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Division of Reproductive Endocrinology, Department of Obstetrics and Gynecology, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Knight Cardiovascular Institute, Oregon Health & Science University, 3181 SW Sam Jackson Park Road, Portland, OR 97239, USA; Department of Biomedical Engineering, Oregon Health & Science University, 3303 SW Bond Avenue, Portland, OR 97239, USA.
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Zhang P, Samuels DC, Lehmann B, Stricker T, Pietenpol J, Shyr Y, Guo Y. Mitochondria sequence mapping strategies and practicability of mitochondria variant detection from exome and RNA sequencing data. Brief Bioinform 2016; 17:224-32. [PMID: 26249222 PMCID: PMC5974936 DOI: 10.1093/bib/bbv057] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/23/2015] [Indexed: 12/30/2022] Open
Abstract
The rapid progress in high-throughput sequencing has significantly enriched our capacity for studying the mitochondrial DNA (mtDNA). In addition to performing specific mitochondrial targeted sequencing, an increasingly popular alternative approach is using the off-target reads from exome sequencing to infer mtDNA variants, including single nucleotide polymorphisms (SNPs) and heteroplasmy. However, the effectiveness and practicality of this approach have not been tested. Recently, RNAseq data have also been suggested as a good source for alternative data mining, but whether mitochondrial variants can be detected from RNAseq data has not been validated. We designed a study to evaluate the practicability of mtDNA variant detection using exome and RNA sequencing data. Five breast cancer cell lines were sequenced through mitochondrial targeted, exome, and RNA sequencing. Mitochondrial targeted sequencing was used as the gold standard to compute the validation and false discovery rates of SNP and heteroplasmy detection in exome and RNAseq data. We found that exome and RNA sequencing can accurately detect mitochondrial SNPs. However, the lower false discovery rate makes exome sequencing a better choice for heteroplasmy detection than RNAseq. Furthermore, we examined three alignment strategies and found that aligning reads directly to the mitochondrial reference genome or aligning reads to the nuclear and mitochondrial references genomes simultaneously produced the best results, and that aligning to the nuclear genome first and afterwards to the mitochondrial genome performed poorly. In conclusion, our study provides important guidelines for future studies that intend to use either exome sequencing or RNAseq data to infer mitochondrial SNPs and heteroplasmy.
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Hammond ER, Green MP, Shelling AN, Berg MC, Peek JC, Cree LM. Oocyte mitochondrial deletions and heteroplasmy in a bovine model of ageing and ovarian stimulation. Mol Hum Reprod 2016; 22:261-71. [PMID: 26792869 DOI: 10.1093/molehr/gaw003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 01/11/2016] [Indexed: 01/07/2023] Open
Abstract
STUDY HYPOTHESIS Maternal ageing and ovarian stimulation result in the accumulation of mitochondrial DNA (mtDNA) deletions and heteroplasmy in individual oocytes from a novel bovine model for human assisted reproductive technology (ART). STUDY FINDING The levels of mtDNA deletions detected in oocytes increased with ovarian ageing. Low levels of mtDNA heteroplasmy were apparent across oocytes and no relationship was identified with respect to ovarian ageing or ovarian stimulation. WHAT IS KNOWN ALREADY Oocyte quality decreases with ovarian ageing and it is postulated that the mtDNA may have a role in this decline. The impact of ovarian stimulation on oocyte quality is poorly understood. Human studies investigating these effects are often limited by the use of low quality oocytes and embryos, variation in age and ovarian stimulation regimens within the patients studied, as well as genetic and environmental variability. Further, no study has investigated mtDNA heteroplasmy in individual oocytes using next-generation sequencing (NGS), and little is known about whether the oocyte accumulates heteroplasmic mtDNA mutations following ageing or ovarian stimulation. STUDY DESIGN, SAMPLES/MATERIALS, METHODS A novel bovine model for the effect of stimulation and age in human ART was undertaken using cows generated by somatic cell nuclear transfer (SCNT) from one founder, to produce a homogeneous population with reduced genetic and environmental variability. Oocytes and somatic tissues were collected from young (3 years of age; n = 4 females) and old (10 years of age; n = 5 females) cow clones following multiple natural ovarian cycles, as well as oocytes following multiple mild (FSH only) and standard (based on human a long GnRH agonist protocol) ovarian stimulation cycles. In addition, oocytes were recovered in a natural cycle from naturally conceived cows aged 4-13.5 years (n = 10) to provide a heterogeneous cohort for mtDNA deletion studies. The presence or absence of mtDNA deletions were investigated using long-range PCR in individual oocytes (n = 62). To determine the detection threshold for mtDNA heteroplasmy levels in individual oocytes, a novel NGS methodology was validated; artificial mixtures of the Bos taurus and Bos indicus mitochondrial genome were generated at 1, 2, 5, 15 and 50% ratios to experimentally mimic different levels of heteroplasmy. This NGS methodology was then employed to determine mtDNA heteroplasmy levels in single oocytes (n = 24). Oocyte mtDNA deletion and heteroplasmy data were analysed by binary logistic regression with respect to the effects of ovarian ageing and ovarian stimulation regimens. MAIN RESULTS AND THE ROLE OF CHANCE Ovarian ageing, but not ovarian stimulation, increased the number of oocytes exhibiting mtDNA deletions (P = 0.04). A minimum mtDNA heteroplasmy level of 2% was validated as a sensitive (97-100%) threshold for variant detection in individual oocytes using NGS. Few mtDNA heteroplasmies were detected across the individual oocytes, with only 15 oocyte-specific variants confined to two of the 24 oocytes studied. There was no relationship (P > 0.05) evident between ovarian ageing or ovarian stimulation and the presence of mtDNA heteroplasmies. LIMITATIONS, REASON FOR CAUTION The low number of oocytes collected from the natural ovarian cycles limited the analysis. Fertilization and developmental potential of the oocytes was not assessed as the oocytes were destroyed for mtDNA deletion and heteroplasmy analysis. WIDER IMPLICATIONS OF THE FINDINGS If the findings of this model apply to the human, this study suggests that the incidence of mtDNA deletions increases with age, but not with degree of ovarian stimulation, while the frequency of mtDNA heteroplasmies may be low regardless of ovarian ageing or level of ovarian stimulation. STUDY FUNDING AND COMPETING INTERESTS Funding was provided by Fertility Associates, the Nurture Foundation for Reproductive Research, the Fertility Society of Australia, and the Auckland Medical Research Foundation. J.C.P. is a shareholder of Fertility Associates and M.P.G. received a fellowship from Fertility Associates. The other authors of this manuscript declare no conflict of interest that could be perceived as prejudicing the impartiality of the reported research.
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Affiliation(s)
- Elizabeth R Hammond
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand
| | - Mark P Green
- AgResearch Ltd, Ruakura Research Centre, Hamilton 3240, New Zealand The Liggins Institute, University of Auckland, Auckland 1023, New Zealand School of BioSciences, University of Melbourne, Parkville, Melbourne 3010, VIC, Australia
| | - Andrew N Shelling
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand
| | - Martin C Berg
- AgResearch Ltd, Ruakura Research Centre, Hamilton 3240, New Zealand
| | - John C Peek
- Fertility Associates, Greenlane, Auckland 1051, New Zealand
| | - Lynsey M Cree
- Department of Obstetrics and Gynaecology, Faculty of Medical and Health Sciences, University of Auckland, Auckland 1023, New Zealand Fertility Associates, Greenlane, Auckland 1051, New Zealand
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Rollins LA, Woolnough AP, Fanson BG, Cummins ML, Crowley TM, Wilton AN, Sinclair R, Butler A, Sherwin WB. Selection on Mitochondrial Variants Occurs between and within Individuals in an Expanding Invasion. Mol Biol Evol 2016; 33:995-1007. [DOI: 10.1093/molbev/msv343] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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49
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Magalhães S, Marques S, Alves C, Amorim A, Alvarez L, Goios A. Evaluation of heteroplasmy detection in the Ion Torrent PGM. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2015. [DOI: 10.1016/j.fsigss.2015.09.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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50
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Hagen CM, Aidt FH, Havndrup O, Hedley PL, Jensen MK, Kanters JK, Pham TT, Bundgaard H, Christiansen M. Private mitochondrial DNA variants in danish patients with hypertrophic cardiomyopathy. PLoS One 2015; 10:e0124540. [PMID: 25923817 PMCID: PMC4414448 DOI: 10.1371/journal.pone.0124540] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 02/19/2015] [Indexed: 02/02/2023] Open
Abstract
Hypertrophic cardiomyopathy (HCM) is a genetic cardiac disease primarily caused by mutations in genes coding for sarcomeric proteins. A molecular-genetic etiology can be established in ~60% of cases. Evolutionarily conserved mitochondrial DNA (mtDNA) haplogroups are susceptibility factors for HCM. Several polymorphic mtDNA variants are associated with a variety of late-onset degenerative diseases and affect mitochondrial function. We examined the role of private, non-haplogroup associated, mitochondrial variants in the etiology of HCM. In 87 Danish HCM patients, full mtDNA sequencing revealed 446 variants. After elimination of 312 (69.9%) non-coding and synonymous variants, a further 109 (24.4%) with a global prevalence > 0.1%, three (0.7%) haplogroup associated and 19 (2.0%) variants with a low predicted in silico likelihood of pathogenicity, three variants: MT-TC: m.5772G>A, MT-TF: m.644A>G, and MT-CYB: m.15024G>A, p.C93Y remained. A detailed analysis of these variants indicated that none of them are likely to cause HCM. In conclusion, private mtDNA mutations are frequent, but they are rarely, if ever, associated with HCM.
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Affiliation(s)
- Christian M. Hagen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Frederik H. Aidt
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Havndrup
- Department of Cardiology, Roskilde Hospital, Roskilde, Denmark
| | - Paula L. Hedley
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Morten K. Jensen
- Department of Medicine B, The Heart Center, Rigshospitalet, Copenhagen, Denmark
| | - Jørgen K. Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tam T. Pham
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Henning Bundgaard
- Department of Medicine B, The Heart Center, Rigshospitalet, Copenhagen, Denmark
| | - Michael Christiansen
- Department of Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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