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Lan X, Ao WL, Li J. Preimplantation genetic testing as a preventive strategy for the transmission of mitochondrial DNA disorders. Syst Biol Reprod Med 2024; 70:38-51. [PMID: 38323618 DOI: 10.1080/19396368.2024.2306389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/07/2024] [Indexed: 02/08/2024]
Abstract
Mitochondrial diseases are distinct types of metabolic and/or neurologic abnormalities that occur as a consequence of dysfunction in oxidative phosphorylation, affecting several systems in the body. There is no effective treatment modality for mitochondrial disorders so far, emphasizing the clinical significance of preventing the inheritance of these disorders. Various reproductive options are available to reduce the probability of inheriting mitochondrial disorders, including in vitro fertilization (IVF) using donated oocytes, preimplantation genetic testing (PGT), and prenatal diagnosis (PND), among which PGT not only makes it possible for families to have genetically-owned children but also PGT has the advantage that couples do not have to decide to terminate the pregnancy if a mutation is detected in the fetus. PGT for mitochondrial diseases originating from nuclear DNA includes analyzing the nuclear genome for the presence or absence of corresponding mutations. However, PGT for mitochondrial disorders arising from mutations in mitochondrial DNA (mtDNA) is more intricate, due to the specific characteristics of mtDNA such as multicopy nature, heteroplasmy phenomenon, and exclusive maternal inheritance. Therefore, the present review aims to discuss the utility and challenges of PGT as a preventive approach to inherited mitochondrial diseases caused by mtDNA mutations.
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Affiliation(s)
- Xinpeng Lan
- College of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, Heilongjiang, China
| | - Wu Liji Ao
- College of Mongolian Medicine and Pharmacy, Inner Mongolia University for Nationalities, Tongliao, Inner Mongolia, China
| | - Ji Li
- College of Basic Medical Sciences, Heilongjiang University of Chinese Medicine, Harbin, China
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2
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Veeraragavan S, Johansen M, Johnston IG. Evolution and maintenance of mtDNA gene content across eukaryotes. Biochem J 2024; 481:1015-1042. [PMID: 39101615 DOI: 10.1042/bcj20230415] [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: 04/08/2024] [Revised: 06/26/2024] [Accepted: 07/18/2024] [Indexed: 08/06/2024]
Abstract
Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.
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Affiliation(s)
| | - Maria Johansen
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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3
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Zhou G, Li T, Du J, Wu M, Lin D, Pu W, Zhang J, Gu Z. Harnessing HetHydrogel: A Universal Platform to Dropletize Single-Cell Multiomics. SMALL METHODS 2024; 8:e2301631. [PMID: 38419597 DOI: 10.1002/smtd.202301631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/12/2024] [Indexed: 03/02/2024]
Abstract
A universal platform is developed for dropletizing single cell plate-based multiomic assays, consisting of three main pillars: a miniaturized open Heterogeneous Hydrogel reactor (abbreviated HetHydrogel) for multi-step biochemistry, its tunable permeability that allows Tn5 tagmentation, and single cell droplet barcoding. Through optimizing the HetHydrogel manufacturing procedure, the chemical composition, and cell permeation conditions, simultaneous high-throughput mitochondrial DNA genotyping and chromatin profiling at the single-cell level are demonstrated using a mixed-species experiment. This platform offers a powerful way to investigate the genotype-phenotype relationships of various mtDNA mutations in biological processes. The HetHydrogel platform is believed to have the potential to democratize droplet technologies, upgrading a whole range of plate-based single cell assays to high throughput format.
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Affiliation(s)
- Guoqiang Zhou
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Ting Li
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
| | - Jingjing Du
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Mengying Wu
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Deng Lin
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Weilin Pu
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
| | - Jingwei Zhang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Human Phenome Institute, Fudan University, Shanghai, 200438, China
- Zhejiang Lab, Hangzhou, 310000, China
| | - Zhenglong Gu
- Center for Mitochondrial Genetics and Health, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, 511458, China
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4
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Jin X, Zhang R, Fu Y, Zhu Q, Hong L, Wu A, Wang H. Unveiling aging dynamics in the hematopoietic system insights from single-cell technologies. Brief Funct Genomics 2024:elae019. [PMID: 38688725 DOI: 10.1093/bfgp/elae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/10/2024] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
As the demographic structure shifts towards an aging society, strategies aimed at slowing down or reversing the aging process become increasingly essential. Aging is a major predisposing factor for many chronic diseases in humans. The hematopoietic system, comprising blood cells and their associated bone marrow microenvironment, intricately participates in hematopoiesis, coagulation, immune regulation and other physiological phenomena. The aging process triggers various alterations within the hematopoietic system, serving as a spectrum of risk factors for hematopoietic disorders, including clonal hematopoiesis, immune senescence, myeloproliferative neoplasms and leukemia. The emerging single-cell technologies provide novel insights into age-related changes in the hematopoietic system. In this review, we summarize recent studies dissecting hematopoietic system aging using single-cell technologies. We discuss cellular changes occurring during aging in the hematopoietic system at the levels of the genomics, transcriptomics, epigenomics, proteomics, metabolomics and spatial multi-omics. Finally, we contemplate the future prospects of single-cell technologies, emphasizing the impact they may bring to the field of hematopoietic system aging research.
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Affiliation(s)
- Xinrong Jin
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Ruohan Zhang
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Yunqi Fu
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Qiunan Zhu
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Liquan Hong
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Aiwei Wu
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
| | - Hu Wang
- Zhejiang Key Laboratory of Medical Epigenetics, School of Basic Medical Sciences, The Third People's Hospital of Deqing, Deqing Hospital of Hangzhou Normal University, Hangzhou Normal University, Hangzhou 311121, China
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Gao Y, Guo L, Wang F, Wang Y, Li P, Zhang D. Development of mitochondrial gene-editing strategies and their potential applications in mitochondrial hereditary diseases: a review. Cytotherapy 2024; 26:11-24. [PMID: 37930294 DOI: 10.1016/j.jcyt.2023.10.004] [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: 06/08/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/07/2023]
Abstract
Mitochondrial DNA (mtDNA) is a critical genome contained within the mitochondria of eukaryotic cells, with many copies present in each mitochondrion. Mutations in mtDNA often are inherited and can lead to severe health problems, including various inherited diseases and premature aging. The lack of efficient repair mechanisms and the susceptibility of mtDNA to damage exacerbate the threat to human health. Heteroplasmy, the presence of different mtDNA genotypes within a single cell, increases the complexity of these diseases and requires an effective editing method for correction. Recently, gene-editing techniques, including programmable nucleases such as restriction endonuclease, zinc finger nuclease, transcription activator-like effector nuclease, clustered regularly interspaced short palindromic repeats/clustered regularly interspaced short palindromic repeats-associated 9 and base editors, have provided new tools for editing mtDNA in mammalian cells. Base editors are particularly promising because of their high efficiency and precision in correcting mtDNA mutations. In this review, we discuss the application of these techniques in mitochondrial gene editing and their limitations. We also explore the potential of base editors for mtDNA modification and discuss the opportunities and challenges associated with their application in mitochondrial gene editing. In conclusion, this review highlights the advancements, limitations and opportunities in current mitochondrial gene-editing technologies and approaches. Our insights aim to stimulate the development of new editing strategies that can ultimately alleviate the adverse effects of mitochondrial hereditary diseases.
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Affiliation(s)
- Yanyan Gao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Linlin Guo
- The Affiliated Cardiovascular Hospital of Qingdao University, Qingdao University, Qingdao, China
| | - Fei Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Dejiu Zhang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China.
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6
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Fleischmann Z, Cote-L'Heureux A, Franco M, Oreshkov S, Annis S, Khrapko M, Aidlen D, Popadin K, Woods DC, Tilly JL, Khrapko K. Reanalysis of mtDNA mutations of human primordial germ cells (PGCs) reveals NUMT contamination and suggests that selection in PGCs may be positive. Mitochondrion 2024; 74:101817. [PMID: 37914096 DOI: 10.1016/j.mito.2023.10.005] [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: 04/20/2023] [Revised: 10/19/2023] [Accepted: 10/28/2023] [Indexed: 11/03/2023]
Abstract
The resilience of the mitochondrial genome (mtDNA) to a high mutational pressure depends, in part, on negative purifying selection in the germline. A paradigm in the field has been that such selection, at least in part, takes place in primordial germ cells (PGCs). Specifically, Floros et al. (Nature Cell Biology 20: 144-51) reported an increase in the synonymity of mtDNA mutations (a sign of purifying selection) between early-stage and late-stage PGCs. We re-analyzed Floros' et al. data and determined that their mutational dataset was significantly contaminated with single nucleotide variants (SNVs) derived from a nuclear sequence of mtDNA origin (NUMT) located on chromosome 5. Contamination was caused by co-amplification of the NUMT sequence by cross-specific PCR primers. Importantly, when we removed NUMT-derived SNVs, the evidence of purifying selection was abolished. In addition to bulk PGCs, Floros et al. reported the analysis of single-cell late-stage PGCs, which were amplified with different sets of PCR primers that cannot amplify the NUMT sequence. Accordingly, there were no NUMT-derived SNVs among single PGC mutations. Interestingly, single PGC mutations show adecreaseof synonymity with increased intracellular mutant fraction. More specifically, nonsynonymous mutations show faster intracellular genetic drift towards higher mutant fraction than synonymous ones. This pattern is incompatible with predominantly negative selection. This suggests that germline selection of mtDNA mutations is a complex phenomenon and that the part of this process that takes place in PGCs may be predominantly positive. However counterintuitive, positive germline selection of detrimental mtDNA mutations has been reported previously andpotentially may be evolutionarily advantageous.
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Affiliation(s)
- Zoë Fleischmann
- Department of Biology, Northeastern University, Boston, MA, USA
| | | | - Melissa Franco
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Sergey Oreshkov
- Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia
| | - Sofia Annis
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Mark Khrapko
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Dylan Aidlen
- Department of Biology, Northeastern University, Boston, MA, USA
| | - Konstantin Popadin
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia
| | - Dori C Woods
- Department of Biology, Northeastern University, Boston, MA, USA
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Ji D, Zhang N, Zou W, Zhang Z, Marley JL, Liu Z, Liang C, Shen L, Liu Y, Liang D, Su T, Du Y, Cao Y. Modeling-based prediction tools for preimplantation genetic testing of mitochondrial DNA diseases: estimating symptomatic thresholds, risk, and chance of success. J Assist Reprod Genet 2023; 40:2185-2196. [PMID: 37439868 PMCID: PMC10440331 DOI: 10.1007/s10815-023-02880-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 06/30/2023] [Indexed: 07/14/2023] Open
Abstract
PURPOSE Preimplantation genetic testing (PGT) has become a reliable tool for preventing the germline transmission of mitochondrial DNA (mtDNA) variants. However, procedures are not standardized across mtDNA variants. In this study, we aim to estimate symptomatic thresholds, risk, and chance of success for PGT for mtDNA pathogenic variant carriers. METHODS We performed a systematic analysis of heteroplasmy data including 455 individuals from 187 familial pedigrees with the common m.3243A>G, m.8344A>G, or m.8993T>G pathogenic variants. We applied binary logistic regression for estimating symptomatic thresholds of heteroplasmy, simplified Sewell-Wright formula and Kimura equations for predicting the risk of disease transmission, and binomial distribution for predicting minimum oocyte numbers. RESULTS We estimated the symptomatic thresholds of m.8993T>G and m.8344A>G as 29.86% and 16.15%, respectively. We could not determine a threshold for m.3243A>G. We established models for mothers harboring common and rare mtDNA pathogenic variants to predict the risk of disease transmission and the number of oocytes required to produce an embryo with sufficiently low variant load. In addition, we provide a table allowing the prediction of transmission risk and the minimum required oocytes for PGT patients with different variant levels. CONCLUSION We have established models that can determine the symptomatic thresholds of common mtDNA pathogenic variants. We also constructed universal models applicable to nearly all mtDNA pathogenic variants which can predict risk and minimum numbers for PGT patients. These models have advanced our understanding of mtDNA disease pathogenesis and will enable more effective prevention of disease transmission using PGT.
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Affiliation(s)
- Dongmei Ji
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui, China
| | - Ning Zhang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Weiwei Zou
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui, China
| | - Zhikang Zhang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Jordan Lee Marley
- Wellcome Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Zhuoli Liu
- Department of Electronic Engineering and Information Science, University of Science and Technology of China, Hefei, Anhui, China
| | - Chunmei Liang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui, China
| | - Lingchao Shen
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
- First School of Clinical Medicine, Anhui Medical University, Hefei, Anhui, China
| | - Yajing Liu
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui, China
| | - Dan Liang
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui, China
| | - Tianhong Su
- Division of Gastroenterology and Hepatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
- Baoshan Branch, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China.
| | - Yinan Du
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China.
| | - Yunxia Cao
- Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, China.
- NHC Key Laboratory of Study on Abnormal Gametes and Reproductive Tract (Anhui Medical University), Hefei, Anhui, China.
- Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, Hefei, Anhui, China.
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Giannakis K, Broz AK, Sloan DB, Johnston IG. Avoiding misleading estimates using mtDNA heteroplasmy statistics to study bottleneck size and selection. G3 (BETHESDA, MD.) 2023; 13:jkad068. [PMID: 36951404 PMCID: PMC10234379 DOI: 10.1093/g3journal/jkad068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 10/18/2022] [Accepted: 03/10/2023] [Indexed: 03/24/2023]
Abstract
Mitochondrial DNA heteroplasmy samples can shed light on vital developmental and genetic processes shaping mitochondrial DNA populations. The sample means and sample variance of a set of heteroplasmy observations are typically used both to estimate bottleneck sizes and to perform fits to the theoretical "Kimura" distribution in seeking evidence for mitochondrial DNA selection. However, each of these applications raises problems. Sample statistics do not generally provide optimal fits to the Kimura distribution and so can give misleading results in hypothesis testing, including false positive signals of selection. Using sample variance can give misleading results for bottleneck size estimates, particularly for small samples. These issues can and do lead to false positive results for mitochondrial DNA mechanisms-all published experimental datasets we re-analyzed, reported as displaying departures from the Kimura model, do not in fact give evidence for such departures. Here we outline a maximum likelihood approach that is simple to implement computationally and addresses all of these issues. We advocate the use of maximum likelihood fits and explicit hypothesis tests, not fits and Kolmogorov-Smirnov tests via summary statistics, for ongoing work with mitochondrial DNA heteroplasmy.
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Affiliation(s)
| | - Amanda K Broz
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Iain G Johnston
- Department of Mathematics, University of Bergen, 5007 Bergen, Norway
- Computational Biology Unit, University of Bergen, 5008 Bergen, Norway
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9
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Abstract
Mitochondrial diseases require customized approaches for reproductive counseling, addressing differences in recurrence risks and reproductive options. The majority of mitochondrial diseases is caused by mutations in nuclear genes and segregate in a Mendelian way. Prenatal diagnosis (PND) or preimplantation genetic testing (PGT) are available to prevent the birth of another severely affected child. In at least 15%-25% of cases, mitochondrial diseases are caused by mitochondrial DNA (mtDNA) mutations, which can occur de novo (25%) or be maternally inherited. For de novo mtDNA mutations, the recurrence risk is low and PND can be offered for reassurance. For maternally inherited, heteroplasmic mtDNA mutations, the recurrence risk is often unpredictable, due to the mitochondrial bottleneck. PND for mtDNA mutations is technically possible, but often not applicable given limitations in predicting the phenotype. Another option for preventing the transmission of mtDNA diseases is PGT. Embryos with mutant load below the expression threshold are being transferred. Oocyte donation is another safe option to prevent the transmission of mtDNA disease to a future child for couples who reject PGT. Recently, mitochondrial replacement therapy (MRT) became available for clinical application as an alternative to prevent the transmission of heteroplasmic and homoplasmic mtDNA mutations.
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10
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High-frequency and functional mitochondrial DNA mutations at the single-cell level. Proc Natl Acad Sci U S A 2023; 120:e2201518120. [PMID: 36577067 PMCID: PMC9910596 DOI: 10.1073/pnas.2201518120] [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] [Indexed: 12/29/2022] Open
Abstract
Decline in mitochondrial function underlies aging and age-related diseases, but the role of mitochondrial DNA (mtDNA) mutations in these processes remains elusive. To investigate patterns of mtDNA mutations, it is particularly important to quantify mtDNA mutations and their associated pathogenic effects at the single-cell level. However, existing single-cell mtDNA sequencing approaches remain inefficient due to high cost and low mtDNA on-target rates. In this study, we developed a cost-effective mtDNA targeted-sequencing protocol called single-cell sequencing by targeted amplification of multiplex probes (scSTAMP) and experimentally validated its reliability. We then applied our method to assess single-cell mtDNA mutations in 768 B lymphocytes and 768 monocytes from a 76-y-old female. Across 632 B lymphocyte and 617 monocytes with medium mtDNA coverage over >100×, our results indicated that over 50% of cells carried at least one mtDNA mutation with variant allele frequencies (VAFs) over 20%, and that cells carried an average of 0.658 and 0.712 such mutation for B lymphocytes and monocytes, respectively. Surprisingly, more than 20% of the observed mutations had VAFs of over 90% in either cell population. In addition, over 60% of the mutations were in protein-coding genes, of which over 70% were nonsynonymous, and more than 50% of the nonsynonymous mutations were predicted to be highly pathogenic. Interestingly, about 80% of the observed mutations were singletons in the respective cell populations. Our results revealed mtDNA mutations with functional significance might be prevalent at advanced age, calling further investigation on age-related mtDNA mutation dynamics at the single-cell level.
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11
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Chiaratti MR, Chinnery PF. Modulating mitochondrial DNA mutations: factors shaping heteroplasmy in the germ line and somatic cells. Pharmacol Res 2022; 185:106466. [PMID: 36174964 DOI: 10.1016/j.phrs.2022.106466] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
Until recently it was thought that most humans only harbor one type of mitochondrial DNA (mtDNA), however, deep sequencing and single-cell analysis has shown the converse - that mixed populations of mtDNA (heteroplasmy) are the norm. This is important because heteroplasmy levels can change dramatically during transmission in the female germ line, leading to high levels causing severe mitochondrial diseases. There is also emerging evidence that low level mtDNA mutations contribute to common late onset diseases such as neurodegenerative disorders and cardiometabolic diseases because the inherited mutation levels can change within developing organs and non-dividing cells over time. Initial predictions suggested that the segregation of mtDNA heteroplasmy was largely stochastic, with an equal tendency for levels to increase or decrease. However, transgenic animal work and single-cell analysis have shown this not to be the case during germ-line transmission and in somatic tissues during life. Mutation levels in specific mtDNA regions can increase or decrease in different contexts and the underlying molecular mechanisms are starting to be unraveled. In this review we provide a synthesis of recent literature on the mechanisms of selection for and against mtDNA variants. We identify the most pertinent gaps in our understanding and suggest ways these could be addressed using state of the art techniques.
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Affiliation(s)
- Marcos R Chiaratti
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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12
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Franco M, Pickett SJ, Fleischmann Z, Khrapko M, Cote-L'Heureux A, Aidlen D, Stein D, Markuzon N, Popadin K, Braverman M, Woods DC, Tilly JL, Turnbull DM, Khrapko K. Dynamics of the most common pathogenic mtDNA variant m.3243A > G demonstrate frequency-dependency in blood and positive selection in the germline. Hum Mol Genet 2022; 31:4075-4086. [PMID: 35849052 DOI: 10.1093/hmg/ddac149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 06/29/2022] [Accepted: 06/29/2022] [Indexed: 11/14/2022] Open
Abstract
The A-to-G point mutation at position 3243 in the human mitochondrial genome (m.3243A > G) is the most common pathogenic mtDNA variant responsible for disease in humans. It is widely accepted that m.3243A > G levels decrease in blood with age, and an age correction representing ~ 2% annual decline is often applied to account for this change in mutation level. Here we report that recent data indicate that the dynamics of m.3243A > G are more complex and depend on the mutation level in blood in a bi-phasic way. Consequently, the traditional 2% correction, which is adequate 'on average', creates opposite predictive biases at high and low mutation levels. Unbiased age correction is needed to circumvent these drawbacks of the standard model. We propose to eliminate both biases by using an approach where age correction depends on mutation level in a biphasic way to account for the dynamics of m.3243A > G in blood. The utility of this approach was further tested in estimating germline selection of m.3243A > G. The biphasic approach permitted us to uncover patterns consistent with the possibility of positive selection for m.3243A > G. Germline selection of m.3243A > G shows an 'arching' profile by which selection is positive at intermediate mutant fractions and declines at high and low mutant fractions. We conclude that use of this biphasic approach will greatly improve the accuracy of modelling changes in mtDNA mutation frequencies in the germline and in somatic cells during aging.
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Affiliation(s)
- Melissa Franco
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research and Institute for Translational and Clinical Research, Newcastle University and Newcastle Medical School, Newcastle-upon-Tyne, United Kingdom
| | - Zoe Fleischmann
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Mark Khrapko
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | | | - Dylan Aidlen
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - David Stein
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | | | - Konstantin Popadin
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Center for Mitochondrial Functional Genomics, Institute of Living Systems, Immanuel Kant Baltic Federal University, 236040 Kaliningrad, Russia
| | - Maxim Braverman
- Department of Mathematics, Northeastern University, Boston, Massachusetts, USA
| | - Dori C Woods
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Jonathan L Tilly
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research and Institute for Translational and Clinical Research, Newcastle University and Newcastle Medical School, Newcastle-upon-Tyne, United Kingdom
| | - Konstantin Khrapko
- Department of Biology, Northeastern University, Boston, Massachusetts, USA
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13
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Zhang H, Esposito M, Pezet MG, Aryaman J, Wei W, Klimm F, Calabrese C, Burr SP, Macabelli CH, Viscomi C, Saitou M, Chiaratti MR, Stewart JB, Jones N, Chinnery PF. Mitochondrial DNA heteroplasmy is modulated during oocyte development propagating mutation transmission. SCIENCE ADVANCES 2021; 7:eabi5657. [PMID: 34878831 PMCID: PMC8654302 DOI: 10.1126/sciadv.abi5657] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 10/15/2021] [Indexed: 05/02/2023]
Abstract
Heteroplasmic mitochondrial DNA (mtDNA) mutations are a common cause of inherited disease, but a few recurrent mutations account for the vast majority of new families. The reasons for this are not known. We studied heteroplasmic mice transmitting m.5024C>T corresponding to a human pathogenic mutation. Analyzing 1167 mother-pup pairs, we show that m.5024C>T is preferentially transmitted from low to higher levels but does not reach homoplasmy. Single-cell analysis of the developing mouse oocytes showed the preferential increase in mutant over wild-type mtDNA in the absence of cell division. A similar inheritance pattern is seen in human pedigrees transmitting several pathogenic mtDNA mutations. In m.5024C>T mice, this can be explained by the preferential propagation of mtDNA during oocyte maturation, counterbalanced by purifying selection against high heteroplasmy levels. This could explain how a disadvantageous mutation in a carrier increases to levels that cause disease but fails to fixate, causing multigenerational heteroplasmic mtDNA disorders.
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Affiliation(s)
- Haixin Zhang
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Marco Esposito
- EPSRC Centre for the Mathematics of Precision Healthcare, Department of Mathematics, Imperial College, London, UK
- Leverhulme Centre for Cellular Bionics, Imperial College, London, UK
| | - Mikael G. Pezet
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Juvid Aryaman
- EPSRC Centre for the Mathematics of Precision Healthcare, Department of Mathematics, Imperial College, London, UK
| | - Wei Wei
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Florian Klimm
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- EPSRC Centre for the Mathematics of Precision Healthcare, Department of Mathematics, Imperial College, London, UK
| | - Claudia Calabrese
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Stephen P. Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Carolina H. Macabelli
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil
| | - Carlo Viscomi
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Mitinori Saitou
- Department of Anatomy and Cell Biology, Graduate School of Medicine, Kyoto University, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
- JST, ERATO, Yoshida-Konoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Marcos R. Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos 13565-905, Brazil
| | - James B. Stewart
- Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
- Biosciences Institute, Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Nick Jones
- EPSRC Centre for the Mathematics of Precision Healthcare, Department of Mathematics, Imperial College, London, UK
- Leverhulme Centre for Cellular Bionics, Imperial College, London, UK
| | - Patrick F. Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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14
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Ji D, Li X, Pan J, Zong K, Chen D, Marley JL, Zou W, Deng X, Cao Y, Zhang Z, Zhou P, Sha H, Cao Y. Preimplantation genetic diagnosis for a carrier with m.3697G > A mitochondrial DNA mutation. J Assist Reprod Genet 2021; 38:3251-3260. [PMID: 34802141 DOI: 10.1007/s10815-021-02354-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/08/2021] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVE To explore inheritance of the m.3697G > A mitochondrial DNA (mtDNA) mutation and the effectiveness of preimplantation genetic diagnosis (PGD) for the carrier. METHODS The study encompassed a pedigree of m.3697G > A mtDNA mutation, including one asymptomatic patient who pursued for PGD treatment. Twelve cumulus oocyte complexes (COCs) were collected in the first PGD cycle and 11 COCs in the second cycle. The efficiency of cumulus cells, polar bodies, and trophectoderm (TE) in predicting the m.3697G > A heteroplasmy of embryos was analyzed. RESULTS From 23 COCs, 20 oocytes were fertilized successfully. On day 5 and 6 post-fertilization, 15 blastocysts were biopsied. The m.3697G > A mutation load of TE biopsies ranged from 15.2 to 100%. In the first cycle, a blastocyst with mutation load of 31.7% and chromosomal mosaicism was transferred, but failed to yield a clinical pregnancy. In the second cycle, a euploid blastocyst with mutation load of 53.9% was transferred, which gave rise to a clinical pregnancy. However, the pregnancy was terminated due to fetal cleft lip and palate. The mutation loads of different tissues (47.7 ± 1.8%) from the induced fetus were comparable to that of the biopsied TE and amniotic fluid cell (49.7%). The mutation load of neither cumulus cells (R2 = 0.02, p = 0.58) nor polar bodies (R2 = 0.33, p = 0.13) correlated with TE mutation load which was regarded as a gold standard. CONCLUSIONS The m.3697G > A mutation showed a random pattern of inheritance. PGD could be used to reduce the risk of inheritance of a high mutation load. Cumulus cells are not a suitable predictor of blastocyst mutation load.
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Affiliation(s)
- Dongmei Ji
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Xinyuan Li
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China.,Obstetrics and Gynecology Hospital, Institute of Reproduction and Development, Fudan University, Shanghai, China
| | - Jianxin Pan
- Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China.,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Kai Zong
- Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China.,China Technical Center of Hefei Customs District, No. 329 Tunxi Road, Hefei, 230022, Anhui, China
| | - Dawei Chen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Jordan Lee Marley
- Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China.,Biosciences Institute, Tyne and Wear, Newcastle University,, Newcastle Upon Tyne, NE1 8PB, UK
| | - Weiwei Zou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Xiaohong Deng
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Yu Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Zhiguo Zhang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Ping Zhou
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China.,NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No. 81 Meishan Road, Hefei, 230032, Anhui, China.,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China
| | - Hongying Sha
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China. .,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China. .,State Key Laboratory of Medical Neurobiology, Institutes of Brain Science, Shanghai Medical College, Fudan University, Shanghai, 200032, China.
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No. 218 Jixi Road, Hefei, 230022, Anhui, China. .,NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract (Anhui Medical University), No. 81 Meishan Road, Hefei, 230032, Anhui, China. .,Key Laboratory of Population Health Across Life Cycle (Anhui Medical University), Ministry of Education of the People's Republic of China, No. 81 Meishan Road, Hefei, 230032, Anhui, China. .,Reproductive Medicine Center, No. 120 Wanshui Road, Shushan District, the First Affiliated Hospital of Anhui Medical University, Hefei City, Anhui Province, China.
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15
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Dziadek MA, Sue CM. Mitochondrial donation: is Australia ready? Med J Aust 2021; 216:118-121. [PMID: 34719038 PMCID: PMC9297849 DOI: 10.5694/mja2.51309] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 11/29/2022]
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16
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Moreira JD, Gopal DM, Kotton DN, Fetterman JL. Gaining Insight into Mitochondrial Genetic Variation and Downstream Pathophysiology: What Can i(PSCs) Do? Genes (Basel) 2021; 12:1668. [PMID: 34828274 PMCID: PMC8624338 DOI: 10.3390/genes12111668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized organelles involved in energy production that have retained their own genome throughout evolutionary history. The mitochondrial genome (mtDNA) is maternally inherited and requires coordinated regulation with nuclear genes to produce functional enzyme complexes that drive energy production. Each mitochondrion contains 5-10 copies of mtDNA and consequently, each cell has several hundreds to thousands of mtDNAs. Due to the presence of multiple copies of mtDNA in a mitochondrion, mtDNAs with different variants may co-exist, a condition called heteroplasmy. Heteroplasmic variants can be clonally expanded, even in post-mitotic cells, as replication of mtDNA is not tied to the cell-division cycle. Heteroplasmic variants can also segregate during germ cell formation, underlying the inheritance of some mitochondrial mutations. Moreover, the uneven segregation of heteroplasmic variants is thought to underlie the heterogeneity of mitochondrial variation across adult tissues and resultant differences in the clinical presentation of mitochondrial disease. Until recently, however, the mechanisms mediating the relation between mitochondrial genetic variation and disease remained a mystery, largely due to difficulties in modeling human mitochondrial genetic variation and diseases. The advent of induced pluripotent stem cells (iPSCs) and targeted gene editing of the nuclear, and more recently mitochondrial, genomes now provides the ability to dissect how genetic variation in mitochondrial genes alter cellular function across a variety of human tissue types. This review will examine the origins of mitochondrial heteroplasmic variation and propagation, and the tools used to model mitochondrial genetic diseases. Additionally, we discuss how iPSC technologies represent an opportunity to advance our understanding of human mitochondrial genetics in disease.
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Affiliation(s)
- Jesse D. Moreira
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
| | - Deepa M. Gopal
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
- Cardiovascular Medicine Section, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Boston Medical Center, Center for Regenerative Medicine of Boston University, Boston, MA 02118, USA;
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jessica L. Fetterman
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
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17
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Bernardino Gomes TM, Ng YS, Pickett SJ, Turnbull DM, Vincent AE. Mitochondrial DNA disorders: From pathogenic variants to preventing transmission. Hum Mol Genet 2021; 30:R245-R253. [PMID: 34169319 PMCID: PMC8490015 DOI: 10.1093/hmg/ddab156] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/28/2021] [Accepted: 06/01/2021] [Indexed: 11/27/2022] Open
Abstract
Mitochondrial DNA (mtDNA) disorders are recognized as one of the most common causes of inherited metabolic disorders. The mitochondrial genome occurs in multiple copies resulting in both homoplasmic and heteroplasmic pathogenic mtDNA variants. A biochemical defect arises when the pathogenic variant level reaches a threshold, which differs between variants. Moreover, variants can segregate, clonally expand, or be lost from cellular populations resulting in a dynamic and tissue-specific mosaic pattern of oxidative deficiency. MtDNA is maternally inherited but transmission patterns of heteroplasmic pathogenic variants are complex. During oogenesis, a mitochondrial bottleneck results in offspring with widely differing variant levels to their mother, whilst highly deleterious variants, such as deletions, are not transmitted. Complemented by a complex interplay between mitochondrial and nuclear genomes, these peculiar genetics produce marked phenotypic variation, posing challenges to the diagnosis and clinical management of patients. Novel therapeutic compounds and several genetic therapies are currently under investigation, but proven disease-modifying therapies remain elusive. Women who carry pathogenic mtDNA variants require bespoke genetic counselling to determine their reproductive options. Recent advances in in vitro fertilization techniques, have greatly improved reproductive choices, but are not without their challenges. Since the first pathogenic mtDNA variants were identified over 30 years ago, there has been remarkable progress in our understanding of these diseases. However, many questions remain unanswered and future studies are required to investigate the mechanisms of disease progression and to identify new disease-specific therapeutic targets.
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Affiliation(s)
- Tiago M Bernardino Gomes
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE2 4HH, UK
| | - Yi Shiau Ng
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK.,NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, NE2 4HH, UK
| | - Sarah J Pickett
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Amy E Vincent
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
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18
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Jeedigunta SP, Minenkova AV, Palozzi JM, Hurd TR. Avoiding Extinction: Recent Advances in Understanding Mechanisms of Mitochondrial DNA Purifying Selection in the Germline. Annu Rev Genomics Hum Genet 2021; 22:55-80. [PMID: 34038145 DOI: 10.1146/annurev-genom-121420-081805] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mitochondria are unusual organelles in that they contain their own genomes, which are kept apart from the rest of the DNA in the cell. While mitochondrial DNA (mtDNA) is essential for respiration and most multicellular life, maintaining a genome outside the nucleus brings with it a number of challenges. Chief among these is preserving mtDNA genomic integrity from one generation to the next. In this review, we discuss what is known about negative (purifying) selection mechanisms that prevent deleterious mutations from accumulating in mtDNA in the germline. Throughout, we focus on the female germline, as it is the tissue through which mtDNA is inherited in most organisms and, therefore, the tissue that most profoundly shapes the genome. We discuss recent progress in uncovering the mechanisms of germline mtDNA selection, from humans to invertebrates.
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Affiliation(s)
- Swathi P Jeedigunta
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| | - Anastasia V Minenkova
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| | - Jonathan M Palozzi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
| | - Thomas R Hurd
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5G 1M1, Canada;
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19
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Spath K, Babariya D, Konstantinidis M, Lowndes J, Child T, Grifo JA, Poulton J, Wells D. Clinical application of sequencing-based methods for parallel preimplantation genetic testing for mitochondrial DNA disease and aneuploidy. Fertil Steril 2021; 115:1521-1532. [PMID: 33745725 DOI: 10.1016/j.fertnstert.2021.01.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE To validate and apply a strategy permitting parallel preimplantation genetic testing (PGT) for mitochondrial DNA (mtDNA) disease and aneuploidy (PGT-A). DESIGN Preclinical test validation and case reports. SETTING Fertility centers. Diagnostics laboratory. PATIENTS Four patients at risk of transmitting mtDNA disease caused by m.8993T>G (Patients A and B), m.10191T>G (Patient C), and m.3243A>G (Patient D). Patients A, B, and C had affected children. Patients A and D displayed somatic heteroplasmy for mtDNA mutations. INTERVENTIONS Embryo biopsy, genetic testing, and uterine transfer of embryos predicted to be euploid and mutation-free. MAIN OUTCOME MEASURES Test accuracy, treatment outcomes, and mutation segregation. RESULTS Accuracy of mtDNA mutation quantification was confirmed. The test was compatible with PGT-A, and half of the embryos tested were shown to be aneuploid (16/33). Mutations were detected in approximately 40% of embryo biopsies from Patients A and D (10/24) but in none from Patients B and C (n = 29). Patients B and C had healthy children following PGT and natural conception, respectively. The m.8993T>G mutation displayed skewed segregation, whereas m.3243A>G mutation levels were relatively low and potentially impacted embryo development. CONCLUSIONS Considering the high aneuploidy rate, strategies providing a combination of PGT for mtDNA disease and aneuploidy may be advantageous compared with approaches that consider only mtDNA. Heteroplasmic women had a higher incidence of affected embryos than those with undetectable somatic mutant mtDNA but were still able to produce mutation-free embryos. While not conclusive, the results are consistent with the existence of mutation-specific segregation mechanisms occurring during oogenesis and possibly embryogenesis.
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Affiliation(s)
- Katharina Spath
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, United Kingdom; Juno Genetics, Oxford, United Kingdom.
| | - Dhruti Babariya
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, United Kingdom; Juno Genetics, Oxford, United Kingdom
| | | | - Jo Lowndes
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Nuffield Orthopaedic Centre, Oxford, United Kingdom
| | - Tim Child
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, United Kingdom; Oxford Fertility, Fertility Partnership, Oxford, United Kingdom
| | | | - Joanna Poulton
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, United Kingdom
| | - Dagan Wells
- Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, United Kingdom; Juno Genetics, Oxford, United Kingdom
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20
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Elesela S, Lukacs NW. Role of Mitochondria in Viral Infections. Life (Basel) 2021; 11:life11030232. [PMID: 33799853 PMCID: PMC7998235 DOI: 10.3390/life11030232] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022] Open
Abstract
Viral diseases account for an increasing proportion of deaths worldwide. Viruses maneuver host cell machinery in an attempt to subvert the intracellular environment favorable for their replication. The mitochondrial network is highly susceptible to physiological and environmental insults, including viral infections. Viruses affect mitochondrial functions and impact mitochondrial metabolism, and innate immune signaling. Resurgence of host-virus interactions in recent literature emphasizes the key role of mitochondria and host metabolism on viral life processes. Mitochondrial dysfunction leads to damage of mitochondria that generate toxic compounds, importantly mitochondrial DNA, inducing systemic toxicity, leading to damage of multiple organs in the body. Mitochondrial dynamics and mitophagy are essential for the maintenance of mitochondrial quality control and homeostasis. Therefore, metabolic antagonists may be essential to gain a better understanding of viral diseases and develop effective antiviral therapeutics. This review briefly discusses how viruses exploit mitochondrial dynamics for virus proliferation and induce associated diseases.
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Affiliation(s)
- Srikanth Elesela
- Department of Pathology, Michigan Medicine, Ann Arbor, MI 48109, USA
- Correspondence:
| | - Nicholas W. Lukacs
- Mary H. Weiser Food Allergy Center, Michigan Medicine, Ann Arbor, MI 48109, USA;
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21
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Mitochondrial DNA mutations do not impact early human embryonic development. Mitochondrion 2021; 58:59-63. [PMID: 33639270 DOI: 10.1016/j.mito.2021.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 02/08/2021] [Accepted: 02/12/2021] [Indexed: 11/20/2022]
Abstract
Mitochondrial DNA (mtDNA) mutations cause severe maternally inherited disorders, although mechanisms regulating mother-to-offspring transmission have not yet been elucidated. To investigate if mtDNA mutations affect embryonic development, we compared morphology, viability and mtDNA content in control (n = 165) and mitochondrial (n = 16) human embryos at the cleavage-stage. mtDNA copy number (CN) was assessed in one or two embryonic cells, by real-time PCR. The presence of a maternal or embryonic mtDNA mutation did not impact on either embryonic quality or viability. mtDNA CN was not altered by mtDNA mutations, suggesting that mtDNA defects do not modify mtDNA metabolism at this early stage.
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22
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Steffann J, Monnot S, Magen M, Assouline Z, Gigarel N, Ville Y, Salomon L, Bessiere B, Martinovic J, Rötig A, Bengoa J, Borghèse R, Munnich A, Barcia G, Bonnefont JP. A retrospective study on the efficacy of prenatal diagnosis for pregnancies at risk of mitochondrial DNA disorders. Genet Med 2020; 23:720-731. [PMID: 33303968 DOI: 10.1038/s41436-020-01043-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 11/11/2020] [Accepted: 11/11/2020] [Indexed: 11/09/2022] Open
Abstract
PURPOSE Prenatal diagnosis of mitochondrial DNA (mtDNA) disorders is challenging due to potential instability of fetal mutant loads and paucity of data connecting prenatal mutant loads to postnatal observations. Retrospective study of our prenatal cohort aims to examine the efficacy of prenatal diagnosis to improve counseling and reproductive options for those with pregnancies at risk of mtDNA disorders. METHODS We report on a retrospective review of 20 years of prenatal diagnosis of pathogenic mtDNA variants in 80 pregnant women and 120 fetuses. RESULTS Patients with undetectable pathogenic variants (n = 29) consistently had fetuses free of variants, while heteroplasmic women (n = 51) were very likely to transmit their variant (57/78 fetuses, 73%). In the latter case, 26 pregnancies were terminated because fetal mutant loads were >40%. Of the 84 children born, 27 were heteroplasmic (mutant load <65%). To date, no medical problems related to mitochondrial dysfunction have been reported. CONCLUSION Placental heterogeneity of mutant loads questioned the reliability of chorionic villous testing. Fetal mutant load stability, however, suggests the reliability of a single analysis of amniotic fluid at any stage of pregnancy for prenatal diagnosis of mtDNA disorders. Mutant loads under 40% reliably predict lack of symptoms in the progeny of heteroplasmic women.
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Affiliation(s)
- Julie Steffann
- Université de Paris-Sorbonne Paris Cité, Imagine Institute, INSERM UMR1163, Paris, France. .,Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France.
| | - Sophie Monnot
- Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Maryse Magen
- Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Zahra Assouline
- Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Nadine Gigarel
- Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Yves Ville
- Université de Paris-Sorbonne Paris Cité, Imagine Institute, INSERM UMR1163, Paris, France.,Service d'Obstétrique - Maternité, chirurgie médecine et imagerie fœtale, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Laurent Salomon
- Université de Paris-Sorbonne Paris Cité, Imagine Institute, INSERM UMR1163, Paris, France.,Service d'Obstétrique - Maternité, chirurgie médecine et imagerie fœtale, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Bettina Bessiere
- Service d'histo-embryologie et fœtopathologie, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Jelena Martinovic
- Unité de Foetopathologie, Hôpital Antoine Béclère, GHU Paris Saclay, AP-HP, Clamart, France
| | - Agnès Rötig
- Université de Paris-Sorbonne Paris Cité, Imagine Institute, INSERM UMR1163, Paris, France
| | - Joana Bengoa
- Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Roxana Borghèse
- Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Arnold Munnich
- Université de Paris-Sorbonne Paris Cité, Imagine Institute, INSERM UMR1163, Paris, France.,Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Giulia Barcia
- Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
| | - Jean-Paul Bonnefont
- Université de Paris-Sorbonne Paris Cité, Imagine Institute, INSERM UMR1163, Paris, France.,Service de Génétique Moléculaire, Groupe hospitalier Necker-Enfants Malades, AP-HP, Paris, France
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23
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Possible A2E Mutagenic Effects on RPE Mitochondrial DNA from Innovative RNA-Seq Bioinformatics Pipeline. Antioxidants (Basel) 2020; 9:antiox9111158. [PMID: 33233726 PMCID: PMC7699917 DOI: 10.3390/antiox9111158] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/12/2020] [Accepted: 11/18/2020] [Indexed: 01/10/2023] Open
Abstract
Mitochondria are subject to continuous oxidative stress stimuli that, over time, can impair their genome and lead to several pathologies, like retinal degenerations. Our main purpose was the identification of mtDNA variants that might be induced by intense oxidative stress determined by N-retinylidene-N-retinylethanolamine (A2E), together with molecular pathways involving the genes carrying them, possibly linked to retinal degeneration. We performed a variant analysis comparison between transcriptome profiles of human retinal pigment epithelial (RPE) cells exposed to A2E and untreated ones, hypothesizing that it might act as a mutagenic compound towards mtDNA. To optimize analysis, we proposed an integrated approach that foresaw the complementary use of the most recent algorithms applied to mtDNA data, characterized by a mixed output coming from several tools and databases. An increased number of variants emerged following treatment. Variants mainly occurred within mtDNA coding sequences, corresponding with either the polypeptide-encoding genes or the RNA. Time-dependent impairments foresaw the involvement of all oxidative phosphorylation complexes, suggesting a serious damage to adenosine triphosphate (ATP) biosynthesis, that can result in cell death. The obtained results could be incorporated into clinical diagnostic settings, as they are hypothesized to modulate the phenotypic expression of mtDNA pathogenic variants, drastically improving the field of precision molecular medicine.
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24
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Babich R, Hamlin H, Thayer L, Dorr M, Wei Z, Neilson A, Jayasundara N. Mitochondrial response and resilience to anthropogenic chemicals during embryonic development. Comp Biochem Physiol C Toxicol Pharmacol 2020; 233:108759. [PMID: 32259593 DOI: 10.1016/j.cbpc.2020.108759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 03/27/2020] [Accepted: 03/31/2020] [Indexed: 12/28/2022]
Abstract
Mitochondria are integral to maintaining cellular homeostasis. Optimum mitochondrial function is critical during embryonic development, as they play a key role in early signaling cascades and epigenetic programming, in addition to sustaining an adequate energy production. Mitochondria are sensitive targets of environmental toxins, potentially even at levels considered safe under current regulatory limits. Most mitochondrial analyses have focused only on chemical exposure effects in vitro or in isolated mitochondria. However, comparatively little is known about mitochondrial effects of chemical exposure during vertebrate embryogenesis, especially during the recovery phase following a chemical insult. Here, we used the zebrafish (Danio rerio), in a 96-well plate system, to examine mitochondrial effects of 24 chemicals including pharmaceuticals, industrial chemicals, and agrochemicals. We used oxygen consumption rate (OCR) during embryogenesis as a proxy for mitochondrial function. Embryonic OCR (eOCR) was measured in clean egg water immediately following 24 h of chemical exposure and subsequently for an additional 8 h. Each chemical, dependent upon the concentration, resulted in a unique eOCR response profile. While some eOCR effects were persistent or recoverable over time, some effects were only detected several hours after being removed from the exposure. Non-monotonic dose response effects as well as mitochondrial hormesis were also detected following exposure to some chemicals. Collectively, our study shows that mitochondrial response to chemicals are highly dynamic and warrant careful consideration when determining mitochondrial toxicity of a given chemical.
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Affiliation(s)
- Remy Babich
- The School of Marine Sciences, University of Maine, Orono, ME 04469, USA.
| | - Heather Hamlin
- The School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - LeeAnne Thayer
- The School of Marine Sciences, University of Maine, Orono, ME 04469, USA
| | - Madeline Dorr
- The Department of Mathematics and Statistics, University of Maine, Orono, ME, 04469, USA
| | - Zheng Wei
- The Department of Mathematics and Statistics, University of Maine, Orono, ME, 04469, USA
| | | | - Nishad Jayasundara
- The School of Marine Sciences, University of Maine, Orono, ME 04469, USA
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25
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Wei W, Chinnery PF. Inheritance of mitochondrial DNA in humans: implications for rare and common diseases. J Intern Med 2020; 287:634-644. [PMID: 32187761 PMCID: PMC8641369 DOI: 10.1111/joim.13047] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 11/01/2019] [Accepted: 12/10/2019] [Indexed: 12/27/2022]
Abstract
The first draft human mitochondrial DNA (mtDNA) sequence was published in 1981, paving the way for two decades of discovery linking mtDNA variation with human disease. Severe pathogenic mutations cause sporadic and inherited rare disorders that often involve the nervous system. However, some mutations cause mild organ-specific phenotypes that have a reduced clinical penetrance, and polymorphic variation of mtDNA is associated with an altered risk of developing several late-onset common human diseases including Parkinson's disease. mtDNA mutations also accumulate during human life and are enriched in affected organs in a number of age-related diseases. Thus, mtDNA contributes to a wide range of human pathologies. For many decades, it has generally been accepted that mtDNA is inherited exclusively down the maternal line in humans. Although recent evidence has challenged this dogma, whole-genome sequencing has identified nuclear-encoded mitochondrial sequences (NUMTs) that can give the false impression of paternally inherited mtDNA. This provides a more likely explanation for recent reports of 'bi-parental inheritance', where the paternal alleles are actually transmitted through the nuclear genome. The presence of both mutated and wild-type variant alleles within the same individual (heteroplasmy) and rapid shifts in allele frequency can lead to offspring with variable severity of disease. In addition, there is emerging evidence that selection can act for and against specific mtDNA variants within the developing germ line, and possibly within developing tissues. Thus, understanding how mtDNA is inherited has far-reaching implications across medicine. There is emerging evidence that this highly dynamic system is amenable to therapeutic manipulation, raising the possibility that we can harness new understanding to prevent and treat rare and common human diseases where mtDNA mutations play a key role.
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Affiliation(s)
- W Wei
- From the, Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - P F Chinnery
- From the, Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge, UK.,Medical Research Council Mitochondrial Biology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
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26
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Harvey AJ. Mitochondria in early development: linking the microenvironment, metabolism and the epigenome. Reproduction 2020; 157:R159-R179. [PMID: 30870807 DOI: 10.1530/rep-18-0431] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 02/04/2019] [Indexed: 12/24/2022]
Abstract
Mitochondria, originally of bacterial origin, are highly dynamic organelles that have evolved a symbiotic relationship within eukaryotic cells. Mitochondria undergo dynamic, stage-specific restructuring and redistribution during oocyte maturation and preimplantation embryo development, necessary to support key developmental events. Mitochondria also fulfil a wide range of functions beyond ATP synthesis, including the production of intracellular reactive oxygen species and calcium regulation, and are active participants in the regulation of signal transduction pathways. Communication between not only mitochondria and the nucleus, but also with other organelles, is emerging as a critical function which regulates preimplantation development. Significantly, perturbations and deficits in mitochondrial function manifest not only as reduced quality and/or poor oocyte and embryo development but contribute to post-implantation failure, long-term cell function and adult disease. A growing body of evidence indicates that altered availability of metabolic co-factors modulate the activity of epigenetic modifiers, such that oocyte and embryo mitochondrial activity and dynamics have the capacity to establish long-lasting alterations to the epigenetic landscape. It is proposed that preimplantation embryo development may represent a sensitive window during which epigenetic regulation by mitochondria is likely to have significant short- and long-term effects on embryo, and offspring, health. Hence, mitochondrial integrity, communication and metabolism are critical links between the environment, the epigenome and the regulation of embryo development.
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Affiliation(s)
- Alexandra J Harvey
- School of BioSciences, University of Melbourne, Parkville, Victoria, Australia
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27
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Abstract
Mitochondrial genomes are present in hundreds of copies per cell. Recent work now reports the levels of inheritance of mtDNA heteroplasmy in humans and also explores mechanisms that restrict the inheritance of deleterious mtDNA variants in the Drosophila female germline.
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Affiliation(s)
- Carlos T Moraes
- Departments of Neurology and Cell Biology, University of Miami Miller School of Medicine, Miami, FL, USA.
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28
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Oliveira MT, Pontes CDB, Ciesielski GL. Roles of the mitochondrial replisome in mitochondrial DNA deletion formation. Genet Mol Biol 2020; 43:e20190069. [PMID: 32141473 PMCID: PMC7197994 DOI: 10.1590/1678-4685-gmb-2019-0069] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 08/12/2019] [Indexed: 01/07/2023] Open
Abstract
Mitochondrial DNA (mtDNA) deletions are a common cause of human mitochondrial
diseases. Mutations in the genes encoding components of the mitochondrial
replisome, such as DNA polymerase gamma (Pol γ) and the mtDNA helicase Twinkle,
have been associated with the accumulation of such deletions and the development
of pathological conditions in humans. Recently, we demonstrated that changes in
the level of wild-type Twinkle promote mtDNA deletions, which implies that not
only mutations in, but also dysregulation of the stoichiometry between the
replisome components is potentially pathogenic. The mechanism(s) by which
alterations to the replisome function generate mtDNA deletions is(are) currently
under debate. It is commonly accepted that stalling of the replication fork at
sites likely to form secondary structures precedes the deletion formation. The
secondary structural elements can be bypassed by the replication-slippage
mechanism. Otherwise, stalling of the replication fork can generate single- and
double-strand breaks, which can be repaired through recombination leading to the
elimination of segments between the recombination sites. Here, we discuss
aberrances of the replisome in the context of the two debated outcomes, and
suggest new mechanistic explanations based on replication restart and template
switching that could account for all the deletion types reported for
patients.
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Affiliation(s)
- Marcos T Oliveira
- Universidade Estadual Paulista Júlio de Mesquita Filho, Faculdade de Ciências Agrárias e Veterinárias, Departamento de Tecnologia, Jaboticabal, SP, Brazil
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29
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Evolving mtDNA populations within cells. Biochem Soc Trans 2020; 47:1367-1382. [PMID: 31484687 PMCID: PMC6824680 DOI: 10.1042/bst20190238] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/14/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes vital respiratory machinery. Populations of mtDNA molecules exist in most eukaryotic cells, subject to replication, degradation, mutation, and other population processes. These processes affect the genetic makeup of cellular mtDNA populations, changing cell-to-cell distributions, means, and variances of mutant mtDNA load over time. As mtDNA mutant load has nonlinear effects on cell functionality, and cell functionality has nonlinear effects on tissue performance, these statistics of cellular mtDNA populations play vital roles in health, disease, and inheritance. This mini review will describe some of the better-known ways in which these populations change over time in different organisms, highlighting the importance of quantitatively understanding both mutant load mean and variance. Due to length constraints, we cannot attempt to be comprehensive but hope to provide useful links to some of the many excellent studies on these topics.
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30
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Latorre-Pellicer A, Lechuga-Vieco AV, Johnston IG, Hämäläinen RH, Pellico J, Justo-Méndez R, Fernández-Toro JM, Clavería C, Guaras A, Sierra R, Llop J, Torres M, Criado LM, Suomalainen A, Jones NS, Ruíz-Cabello J, Enríquez JA. Regulation of Mother-to-Offspring Transmission of mtDNA Heteroplasmy. Cell Metab 2019; 30:1120-1130.e5. [PMID: 31588014 PMCID: PMC6899444 DOI: 10.1016/j.cmet.2019.09.007] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 06/12/2019] [Accepted: 09/10/2019] [Indexed: 01/05/2023]
Abstract
mtDNA is present in multiple copies in each cell derived from the expansions of those in the oocyte. Heteroplasmy, more than one mtDNA variant, may be generated by mutagenesis, paternal mtDNA leakage, and novel medical technologies aiming to prevent inheritance of mtDNA-linked diseases. Heteroplasmy phenotypic impact remains poorly understood. Mouse studies led to contradictory models of random drift or haplotype selection for mother-to-offspring transmission of mtDNA heteroplasmy. Here, we show that mtDNA heteroplasmy affects embryo metabolism, cell fitness, and induced pluripotent stem cell (iPSC) generation. Thus, genetic and pharmacological interventions affecting oxidative phosphorylation (OXPHOS) modify competition among mtDNA haplotypes during oocyte development and/or at early embryonic stages. We show that heteroplasmy behavior can fall on a spectrum from random drift to strong selection, depending on mito-nuclear interactions and metabolic factors. Understanding heteroplasmy dynamics and its mechanisms provide novel knowledge of a fundamental biological process and enhance our ability to mitigate risks in clinical applications affecting mtDNA transmission.
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Affiliation(s)
- Ana Latorre-Pellicer
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, ISS-Aragon, 50009 Zaragoza, Spain
| | - Ana Victoria Lechuga-Vieco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; CIBERES: C/ Melchor Fernández-Almagro 3, 28029 Madrid, Spain
| | - Iain G Johnston
- School of Biosciences, University of Birmingham, Birmingham, UK
| | - Riikka H Hämäläinen
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland; Research Program of Molecular Neurology, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Juan Pellico
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; CIBERES: C/ Melchor Fernández-Almagro 3, 28029 Madrid, Spain
| | - Raquel Justo-Méndez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | | | - Cristina Clavería
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Adela Guaras
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Rocío Sierra
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Jordi Llop
- CIC biomaGUNE, Paseo Miramón No 182, San Sebastián, 20014 Guipúzcoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Miguel Torres
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Luis Miguel Criado
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Anu Suomalainen
- Research Program of Molecular Neurology, Biomedicum, University of Helsinki, Helsinki, Finland
| | - Nick S Jones
- Department of Mathematics, Imperial College London, London SW7 2BB, UK
| | - Jesús Ruíz-Cabello
- CIBERES: C/ Melchor Fernández-Almagro 3, 28029 Madrid, Spain; CIC biomaGUNE, Paseo Miramón No 182, San Sebastián, 20014 Guipúzcoa, Spain; IKERBASQUE, Basque Foundation for Science, Bilbao, Spain; Universidad Complutense de Madrid, Madrid 28606, Spain
| | - José Antonio Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; CIBERFES: C/ Melchor Fernández-Almagro 3, 28029 Madrid, Spain.
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31
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Koolkarnkhai P, Intakham C, Sangthong P, Surat W, Wonnapinij P. Portunus pelagicus mtDNA heteroplasmy inheritance and its effect on the use of mtCR and mtCOI sequence data. Mitochondrial DNA A DNA Mapp Seq Anal 2019; 30:848-860. [PMID: 31766903 DOI: 10.1080/24701394.2019.1693549] [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: 10/25/2022]
Abstract
Mitochondrial DNA (mtDNA) sequences, especially mitochondrial control region (mtCR) and mitochondrial cytochrome c oxidase subunit I (mtCOI), have been widely used in population and evolutionary genetic analyses of metazoan. The presence of mtDNA heteroplasmy - a mixture of mtDNA haplotypes - possibly affects these analyses. This study aimed to reveal mtDNA heteroplasmy in mtCR, mtCOI, and mtND2 (mitochondrial NADH dehydrogenase subunit 2) of Portunus pelagicus, and examine its effect on the use of mtCR and mtCOI sequences. The screening result showed that the probability of observing mtDNA heteroplasmy was approximately 8%. Across the three targeted regions, 92 heteroplasmic variants were observed from seven samples comprising three mothers and four offspring. Most inherited heteroplasmy presented transition and silence mutation. By comparing the proportion of shared variants among maternal relatives to that among non-relatives, the result suggested that most heteroplasmic variants observed in an individual are inherited. Statistical analyses carried out on the inter-generational differences suggested that random drift and purifying selection play roles in determining the offspring's heteroplasmy level. The size of the random shift varies according to the location of variants and the mothers. The phylogenetic analysis showed that the presence of mtDNA heteroplasmy in mtCR and mtCOI does not affect familial and species identification, respectively. This study firstly reported the mtDNA heteroplasmy in P. pelagicus, its inheritance pattern, and its effect on the use of mtDNA sequence data. This basic knowledge would be useful for the study based on mtDNA sequence data, especially in other invertebrates.
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Affiliation(s)
| | - Chidchanok Intakham
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pradit Sangthong
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
| | - Wunrada Surat
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, Thailand.,Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok, Thailand
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32
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Johnston IG. Varied Mechanisms and Models for the Varying Mitochondrial Bottleneck. Front Cell Dev Biol 2019; 7:294. [PMID: 31824946 PMCID: PMC6879659 DOI: 10.3389/fcell.2019.00294] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA (mtDNA) molecules exist in populations within cells, and may carry mutations. Different cells within an organism, and organisms within a family, may have different proportions of mutant mtDNA in these cellular populations. This diversity is often thought of as arising from a “genetic bottleneck.” This article surveys approaches to characterize and model the generation of this genetic diversity, aiming to provide an introduction to the range of concepts involved, and to highlight some recent advances in understanding. In particular, differences between the statistical “genetic bottleneck” (mutant proportion spread) and the physical mtDNA bottleneck and other cellular processes are highlighted. Particular attention is paid to the quantitative analysis of the “genetic bottleneck,” estimation of its magnitude from observed data, and inference of its underlying mechanisms. Evidence that the “genetic bottleneck” (mutant proportion spread) varies with age, between individuals and species, and across mtDNA sequences, is described. The interpretation issues that arise from sampling errors, selection, and different quantitative definitions are also discussed.
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Affiliation(s)
- Iain G Johnston
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
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33
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Lledo B, Ortiz JA, Morales R, García-Hernández E, Ten J, Bernabeu A, Llácer J, Bernabeu R. Comprehensive mitochondrial DNA analysis and IVF outcome. Hum Reprod Open 2018; 2018:hoy023. [PMID: 30895263 PMCID: PMC6396640 DOI: 10.1093/hropen/hoy023] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/31/2018] [Accepted: 11/15/2018] [Indexed: 12/21/2022] Open
Abstract
STUDY QUESTION Do mitochondrial DNA (mtDNA) copy number and heteroplasmy in human embryos affect the ongoing pregnancy rate? SUMMARY ANSWER Our study suggests that mtDNA copy number above a specific threshold is associated with the ongoing pregnancy rate. WHAT IS KNOWN ALREADY Mitochondria play a vital role in cell function. Recently, there has been increasing research on mtDNA as a biomarker of embryo implantation. Although reports showed that high levels of mtDNA in the blastocyst are associated with low implantation potential, other publications were unable to confirm this. Confounding factors may influence the mtDNA copy number in euploid embryos. On the other hand it has been speculated that both mtDNA heteroplasmy and copy number contribute to mitochondrial function. Next generation sequencing (NGS) allows us to study in depth mtDNA heteroplasmy and copy number simultaneously. STUDY DESIGN, SIZE, DURATION A prospective non-selection study was performed. We included 159 blastocyst biopsies from 142 couples who attended our clinic for preimplantation genetic testing for aneuploidies (PGT-A), from January 2017 to December 2017. All embryos were biopsied on Day 5 or Day 6. The aneuploid testing was performed by NGS. All blastocysts were diagnosed as euploid non-mosaic and were transferred. The mtDNA analysis was performed once the embryo diagnosis was known. PARTICIPANTS/MATERIALS, SETTING, METHODS Sequencing reads mapping to the mtDNA genome were extracted from indexed bam files to identify copy number and heteroplasmy. The relative measure of mtDNA copy number was calculated by dividing the mtDNA reads by the nuclear DNA value to normalize for technical variants and the number of cells collected at the biopsy. All the results were subjected to a mathematical correction factor according to the embryo genome. Heteroplasmy was assigned by MitoSeek. MAIN RESULTS AND THE ROLE OF CHANCE The mean average copy number and SD of mtDNA per genome was 0.0016 ± 0.0012. Regarding heteroplasmy, 40 embryos were heteroplasmy carriers (26.32%). MtDNA variants were detected in coding and non-coding regions and the highest number of variants in an embryo was eight. With respect to IVF outcome for mtDNA copy number analysis, we set a threshold of 0.003 for the following analysis. The vast majority of the embryos were below the threshold (142/159, 89.31%) and 17 embryos were classified as having higher mtDNA levels. We showed a reduction in ongoing pregnancy rate associated with elevated mtDNA copy number (42.96% versus 17.65%, P < 0.05). This result was independent of maternal age and day of the biopsy: these factors were included as confounding factors because mtDNA copy number was negatively correlated with female age (25 –30 y: 0.0017 ± 0.0011, 30 –35 y: 0.0012 ± 0.0007, 35 –40 y: 0.0016 ± 0.0009, over 40 y: 0.0024 + 0.0017, P < 0.05). Embryos biopsied on Day 5 were more likely to have higher quantities of mtDNA compared with those biopsied on Day 6 (0.0017 versus 0.0009, P < 0.001). According to IVF outcome and heteroplasmy, a lower ongoing pregnancy rate was reported for embryos that carried more than two variants. However, this did not reach statistical significance when we compared embryos with a number of variants lower or higher than two (39.15 versus 20.0, P = 0.188). Finally, a clear positive association between the mtDNA variants and copy number was reported when we compare embryos with or without heteroplasmy (0.0013 ± 0.0009 versus 0.0025 ± 0.0014, P < 0.001) and among different numbers of variants (0:0.0013 ± 0.0009, 1–2:0.0023 ± 0.0012, >2:0.0043 ± 0.0014, P < 0.05). LIMITATIONS, REASONS FOR CAUTION A limitation may be the size of the sample and the high-throughput sequencing technology that might not have detected heteroplasmy levels below 2% which requires high sequence depth A clinical randomized trial comparing the clinical outcome after the transfer of embryos selected according to mtDNA levels or only by morphological evaluation will be necessary. More research into the impact of mtDNA heteroplasmy and copy number on IVF outcome is needed. WIDER IMPLICATIONS OF THE FINDINGS Our results demonstrate that embryos with elevated mtDNA copy number have a lower chance of producing an ongoing pregnancy. MtDNA copy number is higher in older women and is dependent upon the number of cell divisions that preceded biopsy. Moreover, our data suggest that mitochondrial activity could be a balance between functional capacity and relative mtDNA copy number. STUDY FUNDING/COMPETING INTEREST(S) There are no conflicts of interest or sources of funding to declare. Trial registration number Not applicable.
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Affiliation(s)
- B Lledo
- Instituto Bernabeu Biotech, 03016 Alicante, Spain
| | - J A Ortiz
- Instituto Bernabeu Biotech, 03016 Alicante, Spain
| | - R Morales
- Instituto Bernabeu Biotech, 03016 Alicante, Spain
| | | | - J Ten
- Instituto Bernabeu of Fertility and Gynecology, Alicante, Spain
| | - A Bernabeu
- Instituto Bernabeu Biotech, 03016 Alicante, Spain
| | - J Llácer
- Instituto Bernabeu of Fertility and Gynecology, Alicante, Spain
| | - R Bernabeu
- Instituto Bernabeu Biotech, 03016 Alicante, Spain.,Instituto Bernabeu of Fertility and Gynecology, Alicante, Spain
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