1
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Bernardino Gomes TM, Vincent AE, Menger KE, Stewart JB, Nicholls TJ. Mechanisms and pathologies of human mitochondrial DNA replication and deletion formation. Biochem J 2024; 481:683-715. [PMID: 38804971 DOI: 10.1042/bcj20230262] [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: 03/22/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Human mitochondria possess a multi-copy circular genome, mitochondrial DNA (mtDNA), that is essential for cellular energy metabolism. The number of copies of mtDNA per cell, and their integrity, are maintained by nuclear-encoded mtDNA replication and repair machineries. Aberrant mtDNA replication and mtDNA breakage are believed to cause deletions within mtDNA. The genomic location and breakpoint sequences of these deletions show similar patterns across various inherited and acquired diseases, and are also observed during normal ageing, suggesting a common mechanism of deletion formation. However, an ongoing debate over the mechanism by which mtDNA replicates has made it difficult to develop clear and testable models for how mtDNA rearrangements arise and propagate at a molecular and cellular level. These deletions may impair energy metabolism if present in a high proportion of the mtDNA copies within the cell, and can be seen in primary mitochondrial diseases, either in sporadic cases or caused by autosomal variants in nuclear-encoded mtDNA maintenance genes. These mitochondrial diseases have diverse genetic causes and multiple modes of inheritance, and show notoriously broad clinical heterogeneity with complex tissue specificities, which further makes establishing genotype-phenotype relationships challenging. In this review, we aim to cover our current understanding of how the human mitochondrial genome is replicated, the mechanisms by which mtDNA replication and repair can lead to mtDNA instability in the form of large-scale rearrangements, how rearranged mtDNAs subsequently accumulate within cells, and the pathological consequences when this occurs.
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Affiliation(s)
- Tiago M Bernardino Gomes
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- NHS England Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, U.K
| | - Amy E Vincent
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Katja E Menger
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - James B Stewart
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
| | - Thomas J Nicholls
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
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2
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Yu C, Asadian S, Tigano M. Molecular and cellular consequences of mitochondrial DNA double-stranded breaks. Hum Mol Genet 2024; 33:R12-R18. [PMID: 38779775 PMCID: PMC11112379 DOI: 10.1093/hmg/ddae048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 05/25/2024] Open
Abstract
Mitochondria are subcellular organelles essential for life. Beyond their role in producing energy, mitochondria govern various physiological mechanisms, encompassing energy generation, metabolic processes, apoptotic events, and immune responses. Mitochondria also contain genetic material that is susceptible to various forms of damage. Mitochondrial double-stranded breaks (DSB) are toxic lesions that the nucleus repairs promptly. Nevertheless, the significance of DSB repair in mammalian mitochondria is controversial. This review presents an updated view of the available research on the consequences of mitochondrial DNA DSB from the molecular to the cellular level. We discuss the crucial function of mitochondrial DNA damage in regulating processes such as senescence, integrated stress response, and innate immunity. Lastly, we discuss the potential role of mitochondrial DNA DSB in mediating the cellular consequences of ionizing radiations, the standard of care in treating solid tumors.
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Affiliation(s)
- Chenxiao Yu
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia 19107, United States
- Department of Radiotherapy and Oncology, The Second Affiliated Hospital of Soochow University, 199 Renai Road, Suzhou 215123, China
| | - Samieh Asadian
- Tehran University of Medical Sciences, Pour Sina St, Tehran 1416634793, Iran
| | - Marco Tigano
- Department of Pathology and Genomic Medicine, Thomas Jefferson University, 1020 Locust Street, Philadelphia 19107, United States
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3
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Moraes CT. Tools for editing the mammalian mitochondrial genome. Hum Mol Genet 2024; 33:R92-R99. [PMID: 38779768 DOI: 10.1093/hmg/ddae037] [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: 01/17/2024] [Revised: 02/28/2024] [Accepted: 03/03/2024] [Indexed: 05/25/2024] Open
Abstract
The manipulation of animal mitochondrial genomes has long been a challenge due to the lack of an effective transformation method. With the discovery of specific gene editing enzymes, designed to target pathogenic mitochondrial DNA mutations (often heteroplasmic), the selective removal or modification of mutant variants has become a reality. Because mitochondria cannot efficiently import RNAs, CRISPR has not been the first choice for editing mitochondrial genes. However, the last few years witnessed an explosion in novel and optimized non-CRISPR approaches to promote double-strand breaks or base-edit of mtDNA in vivo. Engineered forms of specific nucleases and cytidine/adenine deaminases form the basis for these techniques. I will review the newest developments that constitute the current toolbox for animal mtDNA gene editing in vivo, bringing these approaches not only to the exploration of mitochondrial function, but also closer to clinical use.
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Affiliation(s)
- Carlos T Moraes
- Miller School of Medicine, University of Miami, 1600 NW 10th Ave, room 7044, Miami, FL 33136, United States
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4
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Fragkoulis G, Hangas A, Fekete Z, Michell C, Moraes C, Willcox S, Griffith JD, Goffart S, Pohjoismäki JO. Linear DNA-driven recombination in mammalian mitochondria. Nucleic Acids Res 2024; 52:3088-3105. [PMID: 38300793 PMCID: PMC11014290 DOI: 10.1093/nar/gkae040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 01/11/2024] [Indexed: 02/03/2024] Open
Abstract
Mitochondrial DNA (mtDNA) recombination in animals has remained enigmatic due to its uniparental inheritance and subsequent homoplasmic state, which excludes the biological need for genetic recombination, as well as limits tools to study it. However, molecular recombination is an important genome maintenance mechanism for all organisms, most notably being required for double-strand break repair. To demonstrate the existence of mtDNA recombination, we took advantage of a cell model with two different types of mitochondrial genomes and impaired its ability to degrade broken mtDNA. The resulting excess of linear DNA fragments caused increased formation of cruciform mtDNA, appearance of heterodimeric mtDNA complexes and recombinant mtDNA genomes, detectable by Southern blot and by long range PacBio® HiFi sequencing approach. Besides utilizing different electrophoretic methods, we also directly observed molecular complexes between different mtDNA haplotypes and recombination intermediates using transmission electron microscopy. We propose that the known copy-choice recombination by mitochondrial replisome could be sufficient for the needs of the small genome, thus removing the requirement for a specialized mitochondrial recombinase. The error-proneness of this system is likely to contribute to the formation of pathological mtDNA rearrangements.
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Affiliation(s)
- Georgios Fragkoulis
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Anu Hangas
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Zsófia Fekete
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
- Department of Genetics and Genomics, Institute of Genetics and Biotechnology, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
- Doctoral School of Animal Biotechnology and Animal Science, Hungarian University of Agriculture and Life Sciences, Gödöllő, Hungary
| | - Craig Michell
- Red Sea Research Center, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami,FL, USA
| | - Smaranda Willcox
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, USA
| | - Jack D Griffith
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, USA
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, PO Box 111, 80101 Joensuu, Finland
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5
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Lim K. Mitochondrial genome editing: strategies, challenges, and applications. BMB Rep 2024; 57:19-29. [PMID: 38178652 PMCID: PMC10828433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/12/2023] [Accepted: 12/21/2023] [Indexed: 01/06/2024] Open
Abstract
Mitochondrial DNA (mtDNA), a multicopy genome found in mitochondria, is crucial for oxidative phosphorylation. Mutations in mtDNA can lead to severe mitochondrial dysfunction in tissues and organs with high energy demand. MtDNA mutations are closely associated with mitochondrial and age-related disease. To better understand the functional role of mtDNA and work toward developing therapeutics, it is essential to advance technology that is capable of manipulating the mitochondrial genome. This review discusses ongoing efforts in mitochondrial genome editing with mtDNA nucleases and base editors, including the tools, delivery strategies, and applications. Future advances in mitochondrial genome editing to address challenges regarding their efficiency and specificity can achieve the promise of therapeutic genome editing. [BMB Reports 2024; 57(1): 19-29].
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Affiliation(s)
- Kayeong Lim
- Brain Science Institute, Korea Institute of Science and Technology (KIST), Seoul 02792, Korea
- Division of Bio-Medical Science & Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Korea
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6
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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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7
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Shoop WK, Lape J, Trum M, Powell A, Sevigny E, Mischler A, Bacman SR, Fontanesi F, Smith J, Jantz D, Gorsuch CL, Moraes CT. Efficient elimination of MELAS-associated m.3243G mutant mitochondrial DNA by an engineered mitoARCUS nuclease. Nat Metab 2023; 5:2169-2183. [PMID: 38036771 PMCID: PMC10730414 DOI: 10.1038/s42255-023-00932-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/16/2023] [Indexed: 12/02/2023]
Abstract
Nuclease-mediated editing of heteroplasmic mitochondrial DNA (mtDNA) seeks to preferentially cleave and eliminate mutant mtDNA, leaving wild-type genomes to repopulate the cell and shift mtDNA heteroplasmy. Various technologies are available, but many suffer from limitations based on size and/or specificity. The use of ARCUS nucleases, derived from naturally occurring I-CreI, avoids these pitfalls due to their small size, single-component protein structure and high specificity resulting from a robust protein-engineering process. Here we describe the development of a mitochondrial-targeted ARCUS (mitoARCUS) nuclease designed to target one of the most common pathogenic mtDNA mutations, m.3243A>G. mitoARCUS robustly eliminated mutant mtDNA without cutting wild-type mtDNA, allowing for shifts in heteroplasmy and concomitant improvements in mitochondrial protein steady-state levels and respiration. In vivo efficacy was demonstrated using a m.3243A>G xenograft mouse model with mitoARCUS delivered systemically by adeno-associated virus. Together, these data support the development of mitoARCUS as an in vivo gene-editing therapeutic for m.3243A>G-associated diseases.
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Affiliation(s)
- Wendy K Shoop
- Precision BioSciences, Durham, NC, USA
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | | | | | | | - Sandra R Bacman
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Flavia Fontanesi
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Miami, FL, USA
| | | | | | | | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA.
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8
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Fu Y, Sacco O, DeBitetto E, Kanshin E, Ueberheide B, Sfeir A. Mitochondrial DNA breaks activate an integrated stress response to reestablish homeostasis. Mol Cell 2023; 83:3740-3753.e9. [PMID: 37832546 PMCID: PMC11229056 DOI: 10.1016/j.molcel.2023.09.026] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 08/10/2023] [Accepted: 09/21/2023] [Indexed: 10/15/2023]
Abstract
Mitochondrial DNA double-strand breaks (mtDSBs) lead to the degradation of circular genomes and a reduction in copy number; yet, the cellular response in human cells remains elusive. Here, using mitochondrial-targeted restriction enzymes, we show that a subset of cells with mtDSBs exhibited defective mitochondrial protein import, reduced respiratory complexes, and loss of membrane potential. Electron microscopy confirmed the altered mitochondrial membrane and cristae ultrastructure. Intriguingly, mtDSBs triggered the integrated stress response (ISR) via the phosphorylation of eukaryotic translation initiation factor 2α (eIF2α) by DELE1 and heme-regulated eIF2α kinase (HRI). When ISR was inhibited, the cells experienced intensified mitochondrial defects and slower mtDNA recovery post-breakage. Lastly, through proteomics, we identified ATAD3A-a membrane-bound protein interacting with nucleoids-as potentially pivotal in relaying signals from impaired genomes to the inner mitochondrial membrane. In summary, our study delineates the cascade connecting damaged mitochondrial genomes to the cytoplasm and highlights the significance of the ISR in maintaining mitochondrial homeostasis amid genome instability.
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Affiliation(s)
- Yi Fu
- Skirball Institute of Biomolecular Medicine, Cell Biology Department, NYU School of Medicine, New York, NY 10016, USA; Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Olivia Sacco
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Emily DeBitetto
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Evgeny Kanshin
- Proteomics Laboratory, NYU School of Medicine, New York, NY 10016, USA; Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, NYU School of Medicine, New York, NY 10016, USA; Biochemistry and Molecular Pharmacology, NYU School of Medicine, New York, NY 10016, USA; Department of Neurology, NYU School of Medicine, New York, NY 10016, USA; Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Agnel Sfeir
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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9
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Doimo M, Chaudhari N, Abrahamsson S, L’Hôte V, Nguyen TH, Berner A, Ndi M, Abrahamsson A, Das R, Aasumets K, Goffart S, Pohjoismäki JLO, López MD, Chorell E, Wanrooij S. Enhanced mitochondrial G-quadruplex formation impedes replication fork progression leading to mtDNA loss in human cells. Nucleic Acids Res 2023; 51:7392-7408. [PMID: 37351621 PMCID: PMC10415151 DOI: 10.1093/nar/gkad535] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Accepted: 06/09/2023] [Indexed: 06/24/2023] Open
Abstract
Mitochondrial DNA (mtDNA) replication stalling is considered an initial step in the formation of mtDNA deletions that associate with genetic inherited disorders and aging. However, the molecular details of how stalled replication forks lead to mtDNA deletions accumulation are still unclear. Mitochondrial DNA deletion breakpoints preferentially occur at sequence motifs predicted to form G-quadruplexes (G4s), four-stranded nucleic acid structures that can fold in guanine-rich regions. Whether mtDNA G4s form in vivo and their potential implication for mtDNA instability is still under debate. In here, we developed new tools to map G4s in the mtDNA of living cells. We engineered a G4-binding protein targeted to the mitochondrial matrix of a human cell line and established the mtG4-ChIP method, enabling the determination of mtDNA G4s under different cellular conditions. Our results are indicative of transient mtDNA G4 formation in human cells. We demonstrate that mtDNA-specific replication stalling increases formation of G4s, particularly in the major arc. Moreover, elevated levels of G4 block the progression of the mtDNA replication fork and cause mtDNA loss. We conclude that stalling of the mtDNA replisome enhances mtDNA G4 occurrence, and that G4s not resolved in a timely manner can have a negative impact on mtDNA integrity.
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Affiliation(s)
- Mara Doimo
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
- Department of Women and Children Health, University of Padova, 35128 Padova, Italy
| | - Namrata Chaudhari
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Sanna Abrahamsson
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Valentin L’Hôte
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Tran V H Nguyen
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Andreas Berner
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | - Mama Ndi
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
| | | | | | - Koit Aasumets
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Steffi Goffart
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Jaakko L O Pohjoismäki
- Department of Environmental and Biological Sciences, University of Eastern Finland, FI-80101 Joensuu, Finland
| | - Marcela Dávila López
- Bioinformatics and Data Centre, Sahlgrenska Academy, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Erik Chorell
- Department of Chemistry, Umeå University, 90187 Umeå, Sweden
| | - Sjoerd Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187 Umeå, Sweden
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10
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Phan HTL, Lee H, Kim K. Trends and prospects in mitochondrial genome editing. Exp Mol Med 2023:10.1038/s12276-023-00973-7. [PMID: 37121968 DOI: 10.1038/s12276-023-00973-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 11/20/2022] [Accepted: 01/05/2023] [Indexed: 05/02/2023] Open
Abstract
Mitochondria are of fundamental importance in programmed cell death, cellular metabolism, and intracellular calcium concentration modulation, and inheritable mitochondrial disorders via mitochondrial DNA (mtDNA) mutation cause several diseases in various organs and systems. Nevertheless, mtDNA editing, which plays an essential role in the treatment of mitochondrial disorders, still faces several challenges. Recently, programmable editing tools for mtDNA base editing, such as cytosine base editors derived from DddA (DdCBEs), transcription activator-like effector (TALE)-linked deaminase (TALED), and zinc finger deaminase (ZFD), have emerged with considerable potential for correcting pathogenic mtDNA variants. In this review, we depict recent advances in the field, including structural biology and repair mechanisms, and discuss the prospects of using base editing tools on mtDNA to broaden insight into their medical applicability for treating mitochondrial diseases.
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Affiliation(s)
- Hong Thi Lam Phan
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Hyunji Lee
- Laboratory Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, 28116, Cheongju, Republic of Korea.
- School of Medicine, Sungkyunkwan University, Suwon, 16419, Republic of Korea.
| | - Kyoungmi Kim
- Department of Physiology, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
- Department of Biomedical Sciences, Korea University College of Medicine, Seoul, 02841, Republic of Korea.
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11
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Kar B, Castillo SR, Sabharwal A, Clark KJ, Ekker SC. Mitochondrial Base Editing: Recent Advances towards Therapeutic Opportunities. Int J Mol Sci 2023; 24:ijms24065798. [PMID: 36982871 PMCID: PMC10056815 DOI: 10.3390/ijms24065798] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/06/2023] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
Mitochondria are critical organelles that form networks within our cells, generate energy dynamically, contribute to diverse cell and organ function, and produce a variety of critical signaling molecules, such as cortisol. This intracellular microbiome can differ between cells, tissues, and organs. Mitochondria can change with disease, age, and in response to the environment. Single nucleotide variants in the circular genomes of human mitochondrial DNA are associated with many different life-threatening diseases. Mitochondrial DNA base editing tools have established novel disease models and represent a new possibility toward personalized gene therapies for the treatment of mtDNA-based disorders.
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Affiliation(s)
- Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Santiago R Castillo
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
- Mayo Clinic Graduate School of Biomedical Sciences, Virology and Gene Therapy Track, Mayo Clinic, Rochester, MN 55905, USA
| | - Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl J Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Stephen C Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
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12
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Rahman MM, Tumpa MAA, Rahaman MS, Islam F, Sutradhar PR, Ahmed M, Alghamdi BS, Hafeez A, Alexiou A, Perveen A, Ashraf GM. Emerging Promise of Therapeutic Approaches Targeting Mitochondria in Neurodegenerative Disorders. Curr Neuropharmacol 2023; 21:1081-1099. [PMID: 36927428 PMCID: PMC10286587 DOI: 10.2174/1570159x21666230316150559] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 12/05/2022] [Accepted: 12/06/2022] [Indexed: 03/18/2023] Open
Abstract
Mitochondria are critical for homeostasis and metabolism in all cellular eukaryotes. Brain mitochondria are the primary source of fuel that supports many brain functions, including intracellular energy supply, cellular calcium regulation, regulation of limited cellular oxidative capacity, and control of cell death. Much evidence suggests that mitochondria play a central role in neurodegenerative disorders (NDDs) such as Parkinson's disease, Alzheimer's disease, Huntington's disease, and amyotrophic lateral sclerosis. Ongoing studies of NDDs have revealed that mitochondrial pathology is mainly found in inherited or irregular NDDs and is thought to be associated with the pathophysiological cycle of these disorders. Typical mitochondrial disturbances in NDDs include increased free radical production, decreased ATP synthesis, alterations in mitochondrial permeability, and mitochondrial DNA damage. The main objective of this review is to highlight the basic mitochondrial problems that occur in NDDs and discuss the use mitochondrial drugs, especially mitochondrial antioxidants, mitochondrial permeability transition blockade, and mitochondrial gene therapy, for the treatment and control of NDDs.
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Affiliation(s)
- Md. Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Mst. Afroza Alam Tumpa
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Md. Saidur Rahaman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Fahadul Islam
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Popy Rani Sutradhar
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Muniruddin Ahmed
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, Bangladesh
| | - Badrah S. Alghamdi
- Department of Physiology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- Pre-Clinical Research Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah, Saudi Arabia
- The Neuroscience Research Unit, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Abdul Hafeez
- Glocal School of Pharmacy, Glocal University, Mirzapur Pole, Saharanpur, Uttar Pradesh, India
| | - Athanasios Alexiou
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, Australia
- AFNP Med Austria, Wien, Austria
| | - Asma Perveen
- Glocal School of Life Sciences, Glocal University, Mirzapur Pole, Saharanpur, Uttar Pradesh, India
| | - Ghulam Md. Ashraf
- Department of Medical Laboratory Sciences, College of Health Sciences, and Sharjah Institute for Medical Research, University of Sharjah, Sharjah, 27272, United Arab Emirates
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13
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Silva-Pinheiro P, Mutti CD, Van Haute L, Powell CA, Nash PA, Turner K, Minczuk M. A library of base editors for the precise ablation of all protein-coding genes in the mouse mitochondrial genome. Nat Biomed Eng 2022; 7:692-703. [PMID: 36470976 DOI: 10.1038/s41551-022-00968-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 10/20/2022] [Indexed: 12/07/2022]
Abstract
The development of curative treatments for mitochondrial diseases, which are often caused by mutations in mitochondrial DNA (mtDNA) that impair energy metabolism and other aspects of cellular homoeostasis, is hindered by an incomplete understanding of the underlying biology and a scarcity of cellular and animal models. Here we report the design and application of a library of double-stranded-DNA deaminase-derived cytosine base editors optimized for the precise ablation of every mtDNA protein-coding gene in the mouse mitochondrial genome. We used the library, which we named MitoKO, to produce near-homoplasmic knockout cells in vitro and to generate a mouse knockout with high heteroplasmy levels and no off-target edits. MitoKO should facilitate systematic and comprehensive investigations of mtDNA-related pathways and their impact on organismal homoeostasis, and aid the generation of clinically meaningful in vivo models of mtDNA dysfunction.
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Affiliation(s)
| | - Christian D Mutti
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | | | - Pavel A Nash
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Keira Turner
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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14
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Soldatov VO, Kubekina MV, Skorkina MY, Belykh AE, Egorova TV, Korokin MV, Pokrovskiy MV, Deykin AV, Angelova PR. Current advances in gene therapy of mitochondrial diseases. J Transl Med 2022; 20:562. [PMID: 36471396 PMCID: PMC9724384 DOI: 10.1186/s12967-022-03685-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 10/04/2022] [Indexed: 12/12/2022] Open
Abstract
Mitochondrial diseases (MD) are a heterogeneous group of multisystem disorders involving metabolic errors. MD are characterized by extremely heterogeneous symptoms, ranging from organ-specific to multisystem dysfunction with different clinical courses. Most primary MD are autosomal recessive but maternal inheritance (from mtDNA), autosomal dominant, and X-linked inheritance is also known. Mitochondria are unique energy-generating cellular organelles designed to survive and contain their own unique genetic coding material, a circular mtDNA fragment of approximately 16,000 base pairs. The mitochondrial genetic system incorporates closely interacting bi-genomic factors encoded by the nuclear and mitochondrial genomes. Understanding the dynamics of mitochondrial genetics supporting mitochondrial biogenesis is especially important for the development of strategies for the treatment of rare and difficult-to-diagnose diseases. Gene therapy is one of the methods for correcting mitochondrial disorders.
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Affiliation(s)
- Vladislav O. Soldatov
- grid.4886.20000 0001 2192 9124Core Facility Centre, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia ,grid.445984.00000 0001 2224 0652Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod, Russia ,grid.445984.00000 0001 2224 0652Laboratory of Genome Editing for Biomedicine and Animal Health, Belgorod State National Research University, Belgorod, Russia ,grid.465470.4Laboratory of Biophysics of Cell Membranes under Critical State, V.A. Negovsky Scientific Research Institute of General Reanimatology, Russian Academy of Sciences, Moscow, Russia
| | - Marina V. Kubekina
- grid.4886.20000 0001 2192 9124Core Facility Centre, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Marina Yu. Skorkina
- grid.445984.00000 0001 2224 0652Department of Biochemistry, Belgorod State National Research University, Belgorod, Russia ,grid.445984.00000 0001 2224 0652Laboratory of Genome Editing for Biomedicine and Animal Health, Belgorod State National Research University, Belgorod, Russia
| | - Andrei E. Belykh
- grid.419305.a0000 0001 1943 2944Dioscuri Centre for Metabolic Diseases, Nencki Institute of Experimental Biology, Polish Academy of Sciences, Warsaw, Poland
| | - Tatiana V. Egorova
- grid.4886.20000 0001 2192 9124Laboratory of Modeling and Gene Therapy of Hereditary Diseases, Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia
| | - Mikhail V. Korokin
- grid.445984.00000 0001 2224 0652Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod, Russia
| | - Mikhail V. Pokrovskiy
- grid.445984.00000 0001 2224 0652Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod, Russia
| | - Alexey V. Deykin
- grid.445984.00000 0001 2224 0652Department of Pharmacology and Clinical Pharmacology, Belgorod State National Research University, Belgorod, Russia ,grid.445984.00000 0001 2224 0652Laboratory of Genome Editing for Biomedicine and Animal Health, Belgorod State National Research University, Belgorod, Russia
| | - Plamena R. Angelova
- grid.83440.3b0000000121901201Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
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15
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Kim M, Mahmood M, Reznik E, Gammage PA. Mitochondrial DNA is a major source of driver mutations in cancer. Trends Cancer 2022; 8:1046-1059. [PMID: 36041967 PMCID: PMC9671861 DOI: 10.1016/j.trecan.2022.08.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 07/29/2022] [Accepted: 08/02/2022] [Indexed: 12/24/2022]
Abstract
Mitochondrial DNA (mtDNA) mutations are among the most common genetic events in all tumors and directly impact metabolic homeostasis. Despite the central role mitochondria play in energy metabolism and cellular physiology, the role of mutations in the mitochondrial genomes of tumors has been contentious. Until recently, genomic and functional studies of mtDNA variants were impeded by a lack of adequate tumor mtDNA sequencing data and available methods for mitochondrial genome engineering. These barriers and a conceptual fog surrounding the functional impact of mtDNA mutations in tumors have begun to lift, revealing a path to understanding the role of this essential metabolic genome in cancer initiation and progression. Here we discuss the history, recent developments, and challenges that remain for mitochondrial oncogenetics as the impact of a major new class of cancer-associated mutations is unveiled.
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Affiliation(s)
- Minsoo Kim
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | | | - Ed Reznik
- Computational Oncology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Urology Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
| | - Payam A Gammage
- CRUK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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16
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Falabella M, Minczuk M, Hanna MG, Viscomi C, Pitceathly RDS. Gene therapy for primary mitochondrial diseases: experimental advances and clinical challenges. Nat Rev Neurol 2022; 18:689-698. [PMID: 36257993 DOI: 10.1038/s41582-022-00715-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/25/2022] [Indexed: 11/09/2022]
Abstract
The variable clinical and biochemical manifestations of primary mitochondrial diseases (PMDs), and the complexity of mitochondrial genetics, have proven to be a substantial barrier to the development of effective disease-modifying therapies. Encouraging data from gene therapy trials in patients with Leber hereditary optic neuropathy and advances in DNA editing techniques have raised expectations that successful clinical transition of genetic therapies for PMDs is feasible. However, obstacles to the clinical application of genetic therapies in PMDs remain; the development of innovative, safe and effective genome editing technologies and vectors will be crucial to their future success and clinical approval. In this Perspective, we review progress towards the genetic treatment of nuclear and mitochondrial DNA-related PMDs. We discuss advances in mitochondrial DNA editing technologies alongside the unique challenges to targeting mitochondrial genomes. Last, we consider ongoing trials and regulatory requirements.
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Affiliation(s)
- Micol Falabella
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Michael G Hanna
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK
| | - Carlo Viscomi
- Department of Biomedical Sciences, University of Padova, Padova, Italy
- CESNE - Center for the Study of Neurodegeneration, University of Padova, Padova, Italy
| | - Robert D S Pitceathly
- Department of Neuromuscular Diseases, UCL Queen Square Institute of Neurology, London, UK.
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Queen Square Centre for Neuromuscular Diseases, The National Hospital for Neurology and Neurosurgery, London, UK.
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17
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Sabharwal A, Campbell JM, Schwab TL, WareJoncas Z, Wishman MD, Ata H, Liu W, Ichino N, Hunter DE, Bergren JD, Urban MD, Urban RM, Holmberg SR, Kar B, Cook A, Ding Y, Xu X, Clark KJ, Ekker SC. A Primer Genetic Toolkit for Exploring Mitochondrial Biology and Disease Using Zebrafish. Genes (Basel) 2022; 13:1317. [PMID: 35893052 PMCID: PMC9331066 DOI: 10.3390/genes13081317] [Citation(s) in RCA: 2] [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: 06/25/2022] [Revised: 07/14/2022] [Accepted: 07/19/2022] [Indexed: 02/04/2023] Open
Abstract
Mitochondria are a dynamic eukaryotic innovation that play diverse roles in biology and disease. The mitochondrial genome is remarkably conserved in all vertebrates, encoding the same 37-gene set and overall genomic structure, ranging from 16,596 base pairs (bp) in the teleost zebrafish (Danio rerio) to 16,569 bp in humans. Mitochondrial disorders are amongst the most prevalent inherited diseases, affecting roughly 1 in every 5000 individuals. Currently, few effective treatments exist for those with mitochondrial ailments, representing a major unmet patient need. Mitochondrial dysfunction is also a common component of a wide variety of other human illnesses, ranging from neurodegenerative disorders such as Huntington's disease and Parkinson's disease to autoimmune illnesses such as multiple sclerosis and rheumatoid arthritis. The electron transport chain (ETC) component of mitochondria is critical for mitochondrial biology and defects can lead to many mitochondrial disease symptoms. Here, we present a publicly available collection of genetic mutants created in highly conserved, nuclear-encoded mitochondrial genes in Danio rerio. The zebrafish system represents a potentially powerful new opportunity for the study of mitochondrial biology and disease due to the large number of orthologous genes shared with humans and the many advanced features of this model system, from genetics to imaging. This collection includes 15 mutant lines in 13 different genes created through locus-specific gene editing to induce frameshift or splice acceptor mutations, leading to predicted protein truncation during translation. Additionally, included are 11 lines created by the random insertion of the gene-breaking transposon (GBT) protein trap cassette. All these targeted mutant alleles truncate conserved domains of genes critical to the proper function of the ETC or genes that have been implicated in human mitochondrial disease. This collection is designed to accelerate the use of zebrafish to study many different aspects of mitochondrial function to widen our understanding of their role in biology and human disease.
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Affiliation(s)
- Ankit Sabharwal
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Jarryd M. Campbell
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Tanya L. Schwab
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Zachary WareJoncas
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Mark D. Wishman
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Hirotaka Ata
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Wiebin Liu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
- Division of Cardiovascular Diseases, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Noriko Ichino
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Danielle E. Hunter
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Jake D. Bergren
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Mark D. Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Rhianna M. Urban
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Shannon R. Holmberg
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Bibekananda Kar
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Alex Cook
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Yonghe Ding
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
- Division of Cardiovascular Diseases, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xiaolei Xu
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
- Division of Cardiovascular Diseases, Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA
| | - Karl J. Clark
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
| | - Stephen C. Ekker
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA; (A.S.); (J.M.C.); (T.L.S.); (Z.W.); (M.D.W.); (H.A.); (W.L.); (N.I.); (D.E.H.); (J.D.B.); (M.D.U.); (R.M.U.); (S.R.H.); (B.K.); (A.C.); (Y.D.); (X.X.); (K.J.C.)
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18
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Gene Therapy for Mitochondrial Diseases: Current Status and Future Perspective. Pharmaceutics 2022; 14:pharmaceutics14061287. [PMID: 35745859 PMCID: PMC9231068 DOI: 10.3390/pharmaceutics14061287] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/09/2022] [Accepted: 06/15/2022] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial diseases (MDs) are a group of severe genetic disorders caused by mutations in the nuclear or mitochondrial genome encoding proteins involved in the oxidative phosphorylation (OXPHOS) system. MDs have a wide range of symptoms, ranging from organ-specific to multisystemic dysfunctions, with different clinical outcomes. The lack of natural history information, the limits of currently available preclinical models, and the wide range of phenotypic presentations seen in MD patients have all hampered the development of effective therapies. The growing number of pre-clinical and clinical trials over the last decade has shown that gene therapy is a viable precision medicine option for treating MD. However, several obstacles must be overcome, including vector design, targeted tissue tropism and efficient delivery, transgene expression, and immunotoxicity. This manuscript offers a comprehensive overview of the state of the art of gene therapy in MD, addressing the main challenges, the most feasible solutions, and the future perspectives of the field.
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19
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Barrera-Paez JD, Moraes CT. Mitochondrial genome engineering coming-of-age. Trends Genet 2022; 38:869-880. [PMID: 35599021 PMCID: PMC9283244 DOI: 10.1016/j.tig.2022.04.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/11/2022] [Accepted: 04/27/2022] [Indexed: 12/16/2022]
Abstract
The mitochondrial genome has been difficult to manipulate because it is shielded by the organelle double membranes, preventing efficient nucleic acid entry. Moreover, mitochondrial DNA (mtDNA) recombination is not a robust system in most species. This limitation has forced investigators to rely on naturally occurring alterations to study both mitochondrial function and pathobiology. Because most pathogenic mtDNA mutations are heteroplasmic, the development of specific nucleases has allowed us to selectively eliminate mutant species. Several 'protein only' gene-editing platforms have been successfully used for this purpose. More recently, a DNA double-strand cytidine deaminase has been identified and adapted to edit mtDNA. This enzyme was also used as a component to adapt a DNA single-strand deoxyadenosine deaminase to mtDNA editing. These are major advances in our ability to precisely alter the mtDNA in animal cells.
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20
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Silva-Pinheiro P, Minczuk M. The potential of mitochondrial genome engineering. Nat Rev Genet 2022; 23:199-214. [PMID: 34857922 DOI: 10.1038/s41576-021-00432-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2021] [Indexed: 12/19/2022]
Abstract
Mitochondria are subject to unique genetic control by both nuclear DNA and their own genome, mitochondrial DNA (mtDNA), of which each mitochondrion contains multiple copies. In humans, mutations in mtDNA can lead to devastating, heritable, multi-system diseases that display different tissue-specific presentation at any stage of life. Despite rapid advances in nuclear genome engineering, for years, mammalian mtDNA has remained resistant to genetic manipulation, hampering our ability to understand the mechanisms that underpin mitochondrial disease. Recent developments in the genetic modification of mammalian mtDNA raise the possibility of using genome editing technologies, such as programmable nucleases and base editors, for the treatment of hereditary mitochondrial disease.
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Affiliation(s)
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK.
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21
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The Mitochondrial Genome in Aging and Disease and the Future of Mitochondrial Therapeutics. Biomedicines 2022; 10:biomedicines10020490. [PMID: 35203698 PMCID: PMC8962324 DOI: 10.3390/biomedicines10020490] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/10/2022] [Accepted: 02/16/2022] [Indexed: 11/29/2022] Open
Abstract
Mitochondria are intracellular organelles that utilize nutrients to generate energy in the form of ATP by oxidative phosphorylation. Mitochondrial DNA (mtDNA) in humans is a 16,569 base pair double-stranded circular DNA that encodes for 13 vital proteins of the electron transport chain. Our understanding of the mitochondrial genome’s transcription, translation, and maintenance is still emerging, and human pathologies caused by mtDNA dysfunction are widely observed. Additionally, a correlation between declining mitochondrial DNA quality and copy number with organelle dysfunction in aging is well-documented in the literature. Despite tremendous advancements in nuclear gene-editing technologies and their value in translational avenues, our ability to edit mitochondrial DNA is still limited. In this review, we discuss the current therapeutic landscape in addressing the various pathologies that result from mtDNA mutations. We further evaluate existing gene therapy efforts, particularly allotopic expression and its potential to become an indispensable tool for restoring mitochondrial health in disease and aging.
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22
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In vivo mitochondrial base editing via adeno-associated viral delivery to mouse post-mitotic tissue. Nat Commun 2022; 13:750. [PMID: 35136065 PMCID: PMC8825850 DOI: 10.1038/s41467-022-28358-w] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 01/21/2022] [Indexed: 01/01/2023] Open
Abstract
Mitochondria host key metabolic processes vital for cellular energy provision and are central to cell fate decisions. They are subjected to unique genetic control by both nuclear DNA and their own multi-copy genome - mitochondrial DNA (mtDNA). Mutations in mtDNA often lead to clinically heterogeneous, maternally inherited diseases that display different organ-specific presentation at any stage of life. For a long time, genetic manipulation of mammalian mtDNA has posed a major challenge, impeding our ability to understand the basic mitochondrial biology and mechanisms underpinning mitochondrial disease. However, an important new tool for mtDNA mutagenesis has emerged recently, namely double-stranded DNA deaminase (DddA)-derived cytosine base editor (DdCBE). Here, we test this emerging tool for in vivo use, by delivering DdCBEs into mouse heart using adeno-associated virus (AAV) vectors and show that it can install desired mtDNA edits in adult and neonatal mice. This work provides proof-of-concept for use of DdCBEs to mutagenize mtDNA in vivo in post-mitotic tissues and provides crucial insights into potential translation to human somatic gene correction therapies to treat primary mitochondrial disease phenotypes. Mutations in mitochondrial DNA can lead to clinically heterogeneous disease. Here the authors demonstrate in vivo base editing of mouse mitochondrial DNA in a post-mitotic tissue by AAV delivery of DddA-derived cytosine base editor (DdCBE).
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23
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Mitochondrial Genome Editing to Treat Human Osteoarthritis-A Narrative Review. Int J Mol Sci 2022; 23:ijms23031467. [PMID: 35163384 PMCID: PMC8835930 DOI: 10.3390/ijms23031467] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 01/24/2022] [Accepted: 01/26/2022] [Indexed: 12/27/2022] Open
Abstract
Osteoarthritis (OA) is a severe, common chronic orthopaedic disorder characterised by a degradation of the articular cartilage with an incidence that increases over years. Despite the availability of various clinical options, none can stop the irreversible progression of the disease to definitely cure OA. Various mutations have been evidenced in the mitochondrial DNA (mtDNA) of cartilage cells (chondrocytes) in OA, leading to a dysfunction of the mitochondrial oxidative phosphorylation processes that significantly contributes to OA cartilage degeneration. The mitochondrial genome, therefore, represents a central, attractive target for therapy in OA, especially using genome editing procedures. In this narrative review article, we present and discuss the current advances and breakthroughs in mitochondrial genome editing as a potential, novel treatment to overcome mtDNA-related disorders such as OA. While still in its infancy and despite a number of challenges that need to be addressed (barriers to effective and site-specific mtDNA editing and repair), such a strategy has strong value to treat human OA in the future, especially using the groundbreaking clustered regularly interspaced short palindromic repeats (CRIPSR)/CRISPR-associated 9 (CRISPR/Cas9) technology and mitochondrial transplantation approaches.
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24
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Wu Z, Sainz AG, Shadel GS. Mitochondrial DNA: cellular genotoxic stress sentinel. Trends Biochem Sci 2021; 46:812-821. [PMID: 34088564 PMCID: PMC9809014 DOI: 10.1016/j.tibs.2021.05.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/24/2021] [Accepted: 05/08/2021] [Indexed: 02/08/2023]
Abstract
High copy number, damage prone, and lean on repair mechanisms are unique features of mitochondrial DNA (mtDNA) that are hard to reconcile with its essentiality for oxidative phosphorylation, the primary function ascribed to this maternally inherited component of our genome. We propose that mtDNA is also a genotoxic stress sentinel, as well as a direct second messenger of this type of cellular stress. Here, we discuss existing evidence for this sentinel/effector role through the ability of mtDNA to escape the confines of the mitochondrial matrix and activate nuclear DNA damage/repair responses via interferon-stimulated gene products and other downstream effectors. However, this arrangement may come at a cost, leading to cancer chemoresistance and contributing to inflammation, disease pathology, and aging.
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Affiliation(s)
- Zheng Wu
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA,Graduate Program in Genetics, Yale School of Medicine, New Haven, CT 06437, USA,These authors contributed equally to this work
| | - Alva G. Sainz
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA,Graduate Program in Experimental Pathology, Yale School of Medicine, New Haven, CT 06437, USA,These authors contributed equally to this work
| | - Gerald S. Shadel
- Salk Institute for Biological Studies, La Jolla, CA 92037, USA,Correspondence: (G.S. Shadel)
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25
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Targeted elimination of mutated mitochondrial DNA by a multi-functional conjugate capable of sequence-specific adenine alkylation. Cell Chem Biol 2021; 29:690-695.e5. [PMID: 34450110 DOI: 10.1016/j.chembiol.2021.08.003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 06/07/2021] [Accepted: 08/06/2021] [Indexed: 11/21/2022]
Abstract
Mutations in mitochondrial DNA (mtDNA) cause mitochondrial diseases, characterized by abnormal mitochondrial function. Although eliminating mutated mtDNA has potential to cure mitochondrial diseases, no chemical-based drugs in clinical trials are capable of selective modulation of mtDNA mutations. Here, we construct a class of compounds encompassing pyrrole-imidazole polyamides (PIPs), mitochondria-penetrating peptide, and chlorambucil, an adenine-specific DNA-alkylating reagent. The sequence-selective DNA binding of PIPs allows chlorambucil to alkylate mutant adenine more efficiently than other sites in mtDNA. In vitro DNA alkylation assay shows that our compound 8950A-Chb(Cl/OH) targeting a nonpathogenic point mutation in HeLa S3 cells (m.8950G>A) can specifically alkylate the mutant adenine. Furthermore, the compound reduces the mtDNA possessing the target mutation in cultured HeLa S3 cells. The programmability of PIPs to target different sequences could allow this class of compounds to be developed as designer drugs targeting pathogenic mutations associated with mitochondrial diseases in future studies.
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26
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Arora A, Behl T, Sehgal A, Singh S, Sharma N, Mathew B, Bungau S. Targeting cellular batteries for the therapy of neurological diseases. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:41517-41532. [PMID: 34080116 DOI: 10.1007/s11356-021-14665-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 05/27/2021] [Indexed: 06/12/2023]
Abstract
The mitochondria, apart from being known as the cell's "powerhouse," are crucial in the viability of nerve cells. Any damage to these cellular organelles can result in their cellular level dysfunction which includes rapidly multiplying reactive oxygen species (ROS) from the mitochondrial membrane, impaired calcium ion homeostasis, and disturbed mitochondrial dynamics by the formation of permeability transition pore in mitochondria. All these impaired biochemical changes lead to various neurological disorders such as progressive supranuclear palsy (PSP), Parkinson's disease (PD), and Alzheimer's disease (AD). Moreover, impaired mitochondrial functions are particularly prone to damage owing to prolonged lifespan and stretched length of the neurons. At the same time, neurons are highly dependent on ATP, and thus, the mitochondria play a central role in the pathogenesis pertaining to neuronal disorders. Dysfunction in the mitochondria is an early pathological hallmark of neurological disorders, and its early detection with the help of suitable biomarkers can lead to promising treatment in this area. Thus, the drugs which are targeting mitochondrial dysfunctions are the emerging area of research in connection with neurological disorders. This can be evidenced by the great opportunities for mitigation, diagnosis, and treatment of numerous human disorders that entail mitochondrial dysfunction at the nexus of their pathogenesis. Here, we throw light at the mitochondrial pathologies and indications of dysfunctional mitochondria in PD, AD, and PSP. There is also an insight into the possible therapeutic strategies highlighting the need for mitochondria-based medicine and made an attempt for claiming the prerequisite for the therapy of neurological diseases.
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Affiliation(s)
- Arpita Arora
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Tapan Behl
- Chitkara College of Pharmacy, Chitkara University, Punjab, India.
| | - Aayush Sehgal
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Sukhbir Singh
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Neelam Sharma
- Chitkara College of Pharmacy, Chitkara University, Punjab, India
| | - Bijo Mathew
- Department of Pharmaceutical Chemistry, Amrita School of Pharmacy, Amrita Vishwa Vidyapeetham, AIMS Health Science Campus, Kochi, India
| | - Simona Bungau
- Department of Pharmacy, Faculty of Medicine and Pharmacy, University of Oradea, Oradea, Romania
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27
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Mitochondrial Heteroplasmy Shifting as a Potential Biomarker of Cancer Progression. Int J Mol Sci 2021; 22:ijms22147369. [PMID: 34298989 PMCID: PMC8304746 DOI: 10.3390/ijms22147369] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/25/2021] [Accepted: 06/28/2021] [Indexed: 02/07/2023] Open
Abstract
Cancer is a serious health problem with a high mortality rate worldwide. Given the relevance of mitochondria in numerous physiological and pathological mechanisms, such as adenosine triphosphate (ATP) synthesis, apoptosis, metabolism, cancer progression and drug resistance, mitochondrial genome (mtDNA) analysis has become of great interest in the study of human diseases, including cancer. To date, a high number of variants and mutations have been identified in different types of tumors, which coexist with normal alleles, a phenomenon named heteroplasmy. This mechanism is considered an intermediate state between the fixation or elimination of the acquired mutations. It is suggested that mutations, which confer adaptive advantages to tumor growth and invasion, are enriched in malignant cells. Notably, many recent studies have reported a heteroplasmy-shifting phenomenon as a potential shaper in tumor progression and treatment response, and we suggest that each cancer type also has a unique mitochondrial heteroplasmy-shifting profile. So far, a plethora of data evidencing correlations among heteroplasmy and cancer-related phenotypes are available, but still, not authentic demonstrations, and whether the heteroplasmy or the variation in mtDNA copy number (mtCNV) in cancer are cause or consequence remained unknown. Further studies are needed to support these findings and decipher their clinical implications and impact in the field of drug discovery aimed at treating human cancer.
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28
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Ji MH, Kreymerman A, Belle K, Ghiam BK, Muscat SR, Mahajan VB, Enns GM, Mercola M, Wood EH. The Present and Future of Mitochondrial-Based Therapeutics for Eye Disease. Transl Vis Sci Technol 2021; 10:4. [PMID: 34232272 PMCID: PMC8267180 DOI: 10.1167/tvst.10.8.4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Translational Relevance Mitochondria are viable therapeutic targets for a broad spectrum of ocular diseases.
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Affiliation(s)
- Marco H Ji
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Alexander Kreymerman
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Kinsley Belle
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Benjamin K Ghiam
- Department of Ophthalmology and Visual Sciences, Case Western Reserve University, Cleveland, OH, USA
| | - Stephanie R Muscat
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Vinit B Mahajan
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Gregory M Enns
- Department of Pediatrics, Division of Medical Genetics, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Mark Mercola
- Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Edward H Wood
- Department of Ophthalmology, Byers Eye Institute, Stanford University School of Medicine, Palo Alto, CA, USA.,Stanford Cardiovascular Institute, Stanford University School of Medicine, Palo Alto, CA, USA
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29
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Mitochondrial targeted meganuclease as a platform to eliminate mutant mtDNA in vivo. Nat Commun 2021; 12:3210. [PMID: 34050192 PMCID: PMC8163834 DOI: 10.1038/s41467-021-23561-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Accepted: 04/26/2021] [Indexed: 11/24/2022] Open
Abstract
Diseases caused by heteroplasmic mitochondrial DNA mutations have no effective treatment or cure. In recent years, DNA editing enzymes were tested as tools to eliminate mutant mtDNA in heteroplasmic cells and tissues. Mitochondrial-targeted restriction endonucleases, ZFNs, and TALENs have been successful in shifting mtDNA heteroplasmy, but they all have drawbacks as gene therapy reagents, including: large size, heterodimeric nature, inability to distinguish single base changes, or low flexibility and effectiveness. Here we report the adaptation of a gene editing platform based on the I-CreI meganuclease known as ARCUS®. These mitochondrial-targeted meganucleases (mitoARCUS) have a relatively small size, are monomeric, and can recognize sequences differing by as little as one base pair. We show the development of a mitoARCUS specific for the mouse m.5024C>T mutation in the mt-tRNAAla gene and its delivery to mice intravenously using AAV9 as a vector. Liver and skeletal muscle show robust elimination of mutant mtDNA with concomitant restoration of mt-tRNAAla levels. We conclude that mitoARCUS is a potential powerful tool for the elimination of mutant mtDNA. Heteroplasmic mitochondrial DNA mutations lack effective treatments. Here the authors adapt I-CreI meganuclease to target the mitochondria and specifically-eliminate mtDNA with a m.5024C>T mutation in the mttRNA Ala gene.
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30
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Stewart JB. Current progress with mammalian models of mitochondrial DNA disease. J Inherit Metab Dis 2021; 44:325-342. [PMID: 33099782 DOI: 10.1002/jimd.12324] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 12/16/2022]
Abstract
Mitochondrial disorders make up a large class of heritable diseases that cause a broad array of different human pathologies. They can affect many different organ systems, or display very specific tissue presentation, and can lead to illness either in childhood or later in life. While the over 1200 genes encoded in the nuclear DNA play an important role in human mitochondrial disease, it has been known for over 30 years that mutations of the mitochondria's own small, multicopy DNA chromosome (mtDNA) can lead to heritable human diseases. Unfortunately, animal mtDNA has resisted transgenic and directed genome editing technologies until quite recently. As such, animal models to aid in our understanding of these diseases, and to explore preclinical therapeutic research have been quite rare. This review will discuss the unusual properties of animal mitochondria that have hindered the generation of animal models. It will also discuss the existing mammalian models of human mtDNA disease, describe the methods employed in their generation, and will discuss recent advances in the targeting of DNA-manipulating enzymes to the mitochondria and how these may be employed to generate new models.
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Affiliation(s)
- James Bruce Stewart
- Max Planck Institute for Biology of Ageing, Cologne, Germany
- Wellcome Centre for Mitochondrial Research, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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31
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Effects of mitoTALENs-Directed Double-Strand Breaks on Plant Mitochondrial Genomes. Genes (Basel) 2021; 12:genes12020153. [PMID: 33503806 PMCID: PMC7911708 DOI: 10.3390/genes12020153] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/22/2021] [Accepted: 01/22/2021] [Indexed: 11/17/2022] Open
Abstract
Mitochondrial genomes in flowering plants differ from those in animals and yeasts in several ways, including having large and variable sizes, circular, linear and branched structures, long repeat sequences that participate in homologous recombinations, and variable genes orders, even within a species. Understanding these differences has been hampered by a lack of genetic methods for transforming plant mitochondrial genomes. We recently succeeded in disrupting targeted genes in mitochondrial genomes by mitochondria-targeted transcription activator-like effector nucleases (mitoTALENs) in rice, rapeseed, and Arabidopsis. Double-strand breaks created by mitoTALENs were repaired not by non-homologous end-joining (NHEJ) but by homologous recombination (HR) between repeats near and far from the target sites, resulting in new genomic structures with large deletions and different configurations. On the other hand, in mammals, TALENs-induced DSBs cause small insertions or deletions in nuclear genomes and degradation of mitochondrial genomes. These results suggest that the mitochondrial and nuclear genomes of plants and mammals have distinct mechanisms for responding to naturally occurring DSBs. The different responses appear to be well suited to differences in size and copy numbers of each genome.
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32
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Amore G, Romagnoli M, Carbonelli M, Barboni P, Carelli V, La Morgia C. Therapeutic Options in Hereditary Optic Neuropathies. Drugs 2021; 81:57-86. [PMID: 33159657 PMCID: PMC7843467 DOI: 10.1007/s40265-020-01428-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Options for the effective treatment of hereditary optic neuropathies have been a long time coming. The successful launch of the antioxidant idebenone for Leber's Hereditary Optic Neuropathy (LHON), followed by its introduction into clinical practice across Europe, was an important step forward. Nevertheless, other options, especially for a variety of mitochondrial optic neuropathies such as dominant optic atrophy (DOA), are needed, and a number of pharmaceutical agents, acting on different molecular pathways, are currently under development. These include gene therapy, which has reached Phase III development for LHON, but is expected to be developed also for DOA, whilst most of the other agents (other antioxidants, anti-apoptotic drugs, activators of mitobiogenesis, etc.) are almost all at Phase II or at preclinical stage of research. Here, we review proposed target mechanisms, preclinical evidence, available clinical trials with primary endpoints and results, of a wide range of tested molecules, to give an overview of the field, also providing the landscape of future scenarios, including gene therapy, gene editing, and reproductive options to prevent transmission of mitochondrial DNA mutations.
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Affiliation(s)
- Giulia Amore
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Martina Romagnoli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Via Altura 3, 40139, Bologna, Italy
| | - Michele Carbonelli
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Via Altura 3, 40139, Bologna, Italy
| | | | - Valerio Carelli
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Via Altura 3, 40139, Bologna, Italy
| | - Chiara La Morgia
- IRCCS Istituto delle Scienze Neurologiche di Bologna, UOC Clinica Neurologica, Bologna, Via Altura 3, 40139, Bologna, Italy.
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33
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Filograna R, Mennuni M, Alsina D, Larsson NG. Mitochondrial DNA copy number in human disease: the more the better? FEBS Lett 2020; 595:976-1002. [PMID: 33314045 PMCID: PMC8247411 DOI: 10.1002/1873-3468.14021] [Citation(s) in RCA: 209] [Impact Index Per Article: 52.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/02/2020] [Accepted: 11/26/2020] [Indexed: 12/19/2022]
Abstract
Most of the genetic information has been lost or transferred to the nucleus during the evolution of mitochondria. Nevertheless, mitochondria have retained their own genome that is essential for oxidative phosphorylation (OXPHOS). In mammals, a gene‐dense circular mitochondrial DNA (mtDNA) of about 16.5 kb encodes 13 proteins, which constitute only 1% of the mitochondrial proteome. Mammalian mtDNA is present in thousands of copies per cell and mutations often affect only a fraction of them. Most pathogenic human mtDNA mutations are recessive and only cause OXPHOS defects if present above a certain critical threshold. However, emerging evidence strongly suggests that the proportion of mutated mtDNA copies is not the only determinant of disease but that also the absolute copy number matters. In this review, we critically discuss current knowledge of the role of mtDNA copy number regulation in various types of human diseases, including mitochondrial disorders, neurodegenerative disorders and cancer, and during ageing. We also provide an overview of new exciting therapeutic strategies to directly manipulate mtDNA to restore OXPHOS in mitochondrial diseases.
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Affiliation(s)
- Roberta Filograna
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Mara Mennuni
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - David Alsina
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
| | - Nils-Göran Larsson
- Division of Molecular Metabolism, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Max Planck Institute for Biology of Ageing - Karolinska Institutet Laboratory, Karolinska Institutet, Stockholm, Sweden
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34
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Ishikawa K, Nakada K. Attempts to understand the mechanisms of mitochondrial diseases: The reverse genetics of mouse models for mitochondrial disease. Biochim Biophys Acta Gen Subj 2020; 1865:129835. [PMID: 33358867 DOI: 10.1016/j.bbagen.2020.129835] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 08/25/2020] [Accepted: 12/18/2020] [Indexed: 11/16/2022]
Abstract
BACKGROUND Mitochondrial disease is a general term for a disease caused by a decline in mitochondrial function. The pathology of this disease is extremely diverse and complex, and the mechanism of its pathogenesis is still unknown. Using mouse models that develop the disease via the same processes as in humans is the easiest path to understanding the underlying mechanism. However, creating a mouse model is extremely difficult due to the lack of technologies that enable editing of mitochondrial DNA (mtDNA). SCOPE OF REVIEW This paper outlines the complex pathogenesis of mitochondrial disease, and the difficulties in producing relevant mouse models. Then, the paper provides a detailed discussion on several mice created with mutations in mtDNA. The paper also introduces the pathology of mouse models with mutations including knockouts of nuclear genes that directly affect mitochondrial function. MAJOR CONCLUSIONS Several mice with mtDNA mutations and those with nuclear DNA mutations have been established. Although these models help elucidate the pathological mechanism of mitochondrial disease, they lack sufficient diversity to enable a complete understanding. Considering the variety of factors that affect the cause and mechanism of mitochondrial disease, it is necessary to account for this background diversity in mouse models as well. GENERAL SIGNIFICANCE Mouse models are indispensable for understanding the pathological mechanism of mitochondrial disease, as well as for searching new treatments. There is a need for the creation and examination of mouse models with more diverse mutations and altered nuclear backgrounds and breeding environments.
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Affiliation(s)
- Kaori Ishikawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan
| | - Kazuto Nakada
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan; Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
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35
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Koňaříková E, Marković A, Korandová Z, Houštěk J, Mráček T. Current progress in the therapeutic options for mitochondrial disorders. Physiol Res 2020; 69:967-994. [PMID: 33129249 PMCID: PMC8549882 DOI: 10.33549/physiolres.934529] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 10/02/2020] [Indexed: 12/20/2022] Open
Abstract
Mitochondrial disorders manifest enormous genetic and clinical heterogeneity - they can appear at any age, present with various phenotypes affecting any organ, and display any mode of inheritance. What mitochondrial diseases do have in common, is impairment of respiratory chain activity, which is responsible for more than 90% of energy production within cells. While diagnostics of mitochondrial disorders has been accelerated by introducing Next-Generation Sequencing techniques in recent years, the treatment options are still very limited. For many patients only a supportive or symptomatic therapy is available at the moment. However, decades of basic and preclinical research have uncovered potential target points and numerous compounds or interventions are now subjects of clinical trials. In this review, we focus on current and emerging therapeutic approaches towards the treatment of mitochondrial disorders. We focus on small compounds, metabolic interference, such as endurance training or ketogenic diet and also on genomic approaches.
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Affiliation(s)
- E Koňaříková
- Laboratory of Bioenergetics, Institute of Physiology Czech Acad. Sci., Prague, Czech Republic. ,
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36
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Antón Z, Mullally G, Ford HC, van der Kamp MW, Szczelkun MD, Lane JD. Mitochondrial import, health and mtDNA copy number variability seen when using type II and type V CRISPR effectors. J Cell Sci 2020; 133:jcs.248468. [PMID: 32843580 DOI: 10.1242/jcs.248468] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022] Open
Abstract
Current methodologies for targeting the mitochondrial genome for research and/or therapy development in mitochondrial diseases are restricted by practical limitations and technical inflexibility. A molecular toolbox for CRISPR-mediated mitochondrial genome editing is desirable, as this could enable targeting of mtDNA haplotypes using the precision and tuneability of CRISPR enzymes. Such 'MitoCRISPR' systems described to date lack reproducibility and independent corroboration. We have explored the requirements for MitoCRISPR in human cells by CRISPR nuclease engineering, including the use of alternative mitochondrial protein targeting sequences and smaller paralogues, and the application of guide (g)RNA modifications for mitochondrial import. We demonstrate varied mitochondrial targeting efficiencies and effects on mitochondrial dynamics/function of different CRISPR nucleases, with Lachnospiraceae bacterium ND2006 (Lb) Cas12a being better targeted and tolerated than Cas9 variants. We also provide evidence of Cas9 gRNA association with mitochondria in HeLa cells and isolated yeast mitochondria, even in the absence of a targeting RNA aptamer. Our data link mitochondrial-targeted LbCas12a/crRNA with increased mtDNA copy number dependent upon DNA binding and cleavage activity. We discuss reproducibility issues and the future steps necessary for MitoCRISPR.
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Affiliation(s)
- Zuriñe Antón
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Grace Mullally
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Holly C Ford
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK
| | - Marc W van der Kamp
- School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK.,Centre for Computational Chemistry, School of Chemistry, Faculty of Science, University of Bristol, Bristol BS8 1TD, UK.,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK .,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
| | - Jon D Lane
- Cell Biology Laboratories, School of Biochemistry, Faculty of Life Sciences, University of Bristol, Bristol BS8 1TD, UK .,BrisSynBio, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol BS8 1TQ, UK
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37
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Naeem MM, Maheshan R, Costford SR, Wahedi A, Trajkovski M, Plavec J, Yatsunyk LA, Ciesielski GL, Kaufman BA, Sondheimer N. G-quadruplex-mediated reduction of a pathogenic mitochondrial heteroplasmy. Hum Mol Genet 2020; 28:3163-3174. [PMID: 31261379 DOI: 10.1093/hmg/ddz153] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/28/2019] [Accepted: 06/21/2019] [Indexed: 12/18/2022] Open
Abstract
Disease-associated variants in mitochondrial DNA (mtDNA) are frequently heteroplasmic, a state of co-existence with the wild-type genome. Because heteroplasmy correlates with the severity and penetrance of disease, improvement in the ratio between these genomes in favor of the wild-type, known as heteroplasmy shifting, is potentially therapeutic. We evaluated known pathogenic mtDNA variants and identified those with the potential for allele-specific differences in the formation of non-Watson-Crick G-quadruplex (GQ) structures. We found that the Leigh syndrome (LS)-associated m.10191C variant promotes GQ formation within local sequence in vitro. Interaction of this sequence with a small molecule GQ-binding agent, berberine hydrochloride, further increased GQ stability. The GQ formed at m.10191C differentially impeded the processivity of the mitochondrial DNA polymerase gamma (Pol γ) in vitro, providing a potential means to favor replication of the wild-type allele. We tested the potential for shifting heteroplasmy through the cyclical application of two different mitochondria-targeted GQ binding compounds in primary fibroblasts from patients with m.10191T>C heteroplasmy. Treatment induced alternating mtDNA depletion and repopulation and was effective in shifting heteroplasmy towards the non-pathogenic allele. Similar treatment of pathogenic heteroplasmies that do not affect GQ formation did not induce heteroplasmy shift. Following treatment, heteroplasmic m.10191T>C cells had persistent improvements and heteroplasmy and a corresponding increase in maximal mitochondrial oxygen consumption. This study demonstrates the potential for using small-molecule GQ-binding agents to induce genetic and functional improvements in m.10191T>C heteroplasmy.
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Affiliation(s)
| | - Rathena Maheshan
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Sheila R Costford
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Azizia Wahedi
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Marko Trajkovski
- National Institute of Chemistry, Slovenian NMR Center, Ljubljana, Slovenia
| | - Janez Plavec
- National Institute of Chemistry, Slovenian NMR Center, Ljubljana, Slovenia
| | - Liliya A Yatsunyk
- Department of Chemistry and Biochemistry, Swarthmore College, Swarthmore PA, USA
| | | | - Brett A Kaufman
- Center for Metabolism and Mitochondrial Medicine, Division of Cardiology, Vascular Medicine Institute, Department of Medicine, University of Pittsburgh Medical School, Pittsburgh, PA, USA
| | - Neal Sondheimer
- Institute of Medical Science.,Departments of Paediatrics and Molecular Genetics, The University of Toronto, Toronto, ON, Canada.,Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada
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38
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Jackson CB, Turnbull DM, Minczuk M, Gammage PA. Therapeutic Manipulation of mtDNA Heteroplasmy: A Shifting Perspective. Trends Mol Med 2020; 26:698-709. [PMID: 32589937 DOI: 10.1016/j.molmed.2020.02.006] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/19/2020] [Accepted: 02/21/2020] [Indexed: 12/23/2022]
Abstract
Mutations of mitochondrial DNA (mtDNA) often underlie mitochondrial disease, one of the most common inherited metabolic disorders. Since the sequencing of the human mitochondrial genome and the discovery of pathogenic mutations in mtDNA more than 30 years ago, a movement towards generating methods for robust manipulation of mtDNA has ensued, although with relatively few advances and some controversy. While developments in the transformation of mammalian mtDNA have stood still for some time, recent demonstrations of programmable nuclease-based technology suggest that clinical manipulation of mtDNA heteroplasmy may be on the horizon for these largely untreatable disorders. Here we review historical and recent developments in mitochondrially targeted nuclease technology and the clinical outlook for treatment of hereditary mitochondrial disease.
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Affiliation(s)
- Christopher B Jackson
- Stem Cells and Metabolism, Biomedicum Helsinki, University of Helsinki, Helsinki, Finland
| | - Doug M Turnbull
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Payam A Gammage
- CRUK Beatson Institute, Glasgow, UK; Institute of Cancer Sciences, University of Glasgow, Glasgow, UK.
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39
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Nissanka N, Moraes CT. Mitochondrial DNA heteroplasmy in disease and targeted nuclease-based therapeutic approaches. EMBO Rep 2020; 21:e49612. [PMID: 32073748 DOI: 10.15252/embr.201949612] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Revised: 12/11/2019] [Accepted: 01/29/2020] [Indexed: 12/31/2022] Open
Abstract
Mitochondrial DNA (mtDNA) encodes a subset of the genes which are responsible for oxidative phosphorylation. Pathogenic mutations in the human mtDNA are often heteroplasmic, where wild-type mtDNA species co-exist with the pathogenic mtDNA and a bioenergetic defect is only seen when the pathogenic mtDNA percentage surpasses a threshold for biochemical manifestations. mtDNA segregation during germline development can explain some of the extreme variation in heteroplasmy from one generation to the next. Patients with high heteroplasmy for deleterious mtDNA species will likely suffer from bona-fide mitochondrial diseases, which currently have no cure. Shifting mtDNA heteroplasmy toward the wild-type mtDNA species could provide a therapeutic option to patients. Mitochondrially targeted engineered nucleases, such as mitoTALENs and mitoZFNs, have been used in vitro in human cells harboring pathogenic patient-derived mtDNA mutations and more recently in vivo in a mouse model of a pathogenic mtDNA point mutation. These gene therapy tools for shifting mtDNA heteroplasmy can also be used in conjunction with other therapies aimed at eliminating and/or preventing the transfer of pathogenic mtDNA from mother to child.
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Affiliation(s)
- Nadee Nissanka
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
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40
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van den Ameele J, Li AY, Ma H, Chinnery PF. Mitochondrial heteroplasmy beyond the oocyte bottleneck. Semin Cell Dev Biol 2020; 97:156-166. [DOI: 10.1016/j.semcdb.2019.10.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 09/17/2019] [Accepted: 10/01/2019] [Indexed: 12/31/2022]
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41
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Bacman SR, Gammage P, Minczuk M, Moraes CT. Manipulation of mitochondrial genes and mtDNA heteroplasmy. Methods Cell Biol 2020; 155:441-487. [DOI: 10.1016/bs.mcb.2019.12.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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42
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Wallis CP, Scott LH, Filipovska A, Rackham O. Manipulating and elucidating mitochondrial gene expression with engineered proteins. Philos Trans R Soc Lond B Biol Sci 2019; 375:20190185. [PMID: 31787043 DOI: 10.1098/rstb.2019.0185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many conventional, modern genome engineering tools cannot be used to study mitochondrial genetics due to the unusual structure and physiology of the mitochondrial genome. Here, we review a number of newly developed, synthetic biology-based approaches for altering levels of mutant mammalian mitochondrial DNA and mitochondrial RNAs, including transcription activator-like effector nucleases, zinc finger nucleases and engineered RNA-binding proteins. These approaches allow researchers to manipulate and visualize mitochondrial processes and may provide future therapeutics. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Christopher P Wallis
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia
| | - Louis H Scott
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia
| | - Aleksandra Filipovska
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,The University of Western Australia Centre for Medical Research, Crawley, Western Australia 6009, Australia.,School of Molecular Sciences, The University of Western Australia, Crawley, Western Australia 6009, Australia
| | - Oliver Rackham
- Harry Perkins Institute of Medical Research, Nedlands, Western Australia 6009, Australia.,School of Pharmacy and Biomedical Sciences, Curtin University, Bentley, Western Australia 6102, Australia.,Curtin Health Innovation Research Institute, Curtin University, Bentley, Western Australia 6102, Australia
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43
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Klucnika A, Ma H. Mapping and editing animal mitochondrial genomes: can we overcome the challenges? Philos Trans R Soc Lond B Biol Sci 2019; 375:20190187. [PMID: 31787046 DOI: 10.1098/rstb.2019.0187] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The animal mitochondrial genome, although small, can have a big impact on health and disease. Non-pathogenic sequence variation among mitochondrial DNA (mtDNA) haplotypes influences traits including fertility, healthspan and lifespan, whereas pathogenic mutations are linked to incurable mitochondrial diseases and other complex conditions like ageing, diabetes, cancer and neurodegeneration. However, we know very little about how mtDNA genetic variation contributes to phenotypic differences. Infrequent recombination, the multicopy nature and nucleic acid-impenetrable membranes present significant challenges that hamper our ability to precisely map mtDNA variants responsible for traits, and to genetically modify mtDNA so that we can isolate specific mutants and characterize their biochemical and physiological consequences. Here, we summarize the past struggles and efforts in developing systems to map and edit mtDNA. We also assess the future of performing forward and reverse genetic studies on animal mitochondrial genomes. This article is part of the theme issue 'Linking the mitochondrial genotype to phenotype: a complex endeavour'.
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Affiliation(s)
- Anna Klucnika
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
| | - Hansong Ma
- Wellcome Trust/Cancer Research UK Gurdon Institute, Tennis Court Road, Cambridge CB2 1QN, UK.,Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK
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44
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Al Khatib I, Shutt TE. Advances Towards Therapeutic Approaches for mtDNA Disease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:217-246. [PMID: 31452143 DOI: 10.1007/978-981-13-8367-0_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mitochondria maintain and express their own genome, referred to as mtDNA, which is required for proper mitochondrial function. While mutations in mtDNA can cause a heterogeneous array of disease phenotypes, there is currently no cure for this collection of diseases. Here, we will cover characteristics of the mitochondrial genome important for understanding the pathology associated with mtDNA mutations, and review recent approaches that are being developed to treat and prevent mtDNA disease. First, we will discuss mitochondrial replacement therapy (MRT), where mitochondria from a healthy donor replace maternal mitochondria harbouring mutant mtDNA. In addition to ethical concerns surrounding this procedure, MRT is only applicable in cases where the mother is known or suspected to carry mtDNA mutations. Thus, there remains a need for other strategies to treat patients with mtDNA disease. To this end, we will also discuss several alternative means to reduce the amount of mutant mtDNA present in cells. Such methods, referred to as heteroplasmy shifting, have proven successful in animal models. In particular, we will focus on the approach of targeting engineered endonucleases to specifically cleave mutant mtDNA. Together, these approaches offer hope to prevent the transmission of mtDNA disease and potentially reduce the impact of mtDNA mutations.
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Affiliation(s)
- Iman Al Khatib
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada
| | - Timothy E Shutt
- Deparments of Medical Genetics and Biochemistry & Molecular Biology, Cumming School of Medicine, Alberta Children's Hospital Research Institute, Hotchkiss Brain Institute, University of Calgary, Calgary, Alberta, Canada.
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45
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Pereira CV, Bacman SR, Arguello T, Zekonyte U, Williams SL, Edgell DR, Moraes CT. mitoTev-TALE: a monomeric DNA editing enzyme to reduce mutant mitochondrial DNA levels. EMBO Mol Med 2019; 10:emmm.201708084. [PMID: 30012581 PMCID: PMC6127889 DOI: 10.15252/emmm.201708084] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Pathogenic mitochondrial DNA (mtDNA) mutations often co‐exist with wild‐type molecules (mtDNA heteroplasmy). Phenotypes manifest when the percentage of mutant mtDNA is high (70–90%). Previously, our laboratory showed that mitochondria‐targeted transcription activator‐like effector nucleases (mitoTALENs) can eliminate mutant mtDNA from heteroplasmic cells. However, mitoTALENs are dimeric and relatively large, making it difficult to package their coding genes into viral vectors, limiting their clinical application. The smaller monomeric GIY‐YIG homing nuclease from T4 phage (I‐TevI) provides a potential alternative. We tested whether molecular hybrids (mitoTev‐TALEs) could specifically bind and cleave mtDNA of patient‐derived cybrids harboring different levels of the m.8344A>G mtDNA point mutation, associated with myoclonic epilepsy with ragged‐red fibers (MERRF). We tested two mitoTev‐TALE designs, one of which robustly shifted the mtDNA ratio toward the wild type. When this mitoTev‐TALE was tested in a clone with high levels of the MERRF mutation (91% mutant), the shift in heteroplasmy resulted in an improvement of oxidative phosphorylation function. mitoTev‐TALE provides an effective architecture for mtDNA editing that could facilitate therapeutic delivery of mtDNA editing enzymes to affected tissues.
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Affiliation(s)
- Claudia V Pereira
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sandra R Bacman
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Tania Arguello
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Ugne Zekonyte
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sion L Williams
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry University of Western Ontario, London, ON, Canada
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, FL, USA
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46
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Yan C, Duanmu X, Zeng L, Liu B, Song Z. Mitochondrial DNA: Distribution, Mutations, and Elimination. Cells 2019; 8:E379. [PMID: 31027297 PMCID: PMC6523345 DOI: 10.3390/cells8040379] [Citation(s) in RCA: 133] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/17/2019] [Accepted: 04/20/2019] [Indexed: 12/21/2022] Open
Abstract
Mitochondrion harbors its own DNA (mtDNA), which encodes many critical proteins for the assembly and activity of mitochondrial respiratory complexes. mtDNA is packed by many proteins to form a nucleoid that uniformly distributes within the mitochondrial matrix, which is essential for mitochondrial functions. Defects or mutations of mtDNA result in a range of diseases. Damaged mtDNA could be eliminated by mitophagy, and all paternal mtDNA are degraded by endonuclease G or mitophagy during fertilization. In this review, we describe the role and mechanism of mtDNA distribution and elimination. In particular, we focus on the regulation of paternal mtDNA elimination in the process of fertilization.
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Affiliation(s)
- Chaojun Yan
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Xiaoying Duanmu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Ling Zeng
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Bing Liu
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
| | - Zhiyin Song
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan 430072, China.
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47
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Chen Z, Zhang F, Xu H. Human mitochondrial DNA diseases and Drosophila models. J Genet Genomics 2019; 46:201-212. [DOI: 10.1016/j.jgg.2019.03.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Revised: 03/05/2019] [Accepted: 03/25/2019] [Indexed: 01/06/2023]
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48
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Nissanka N, Minczuk M, Moraes CT. Mechanisms of Mitochondrial DNA Deletion Formation. Trends Genet 2019; 35:235-244. [PMID: 30691869 DOI: 10.1016/j.tig.2019.01.001] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/07/2019] [Accepted: 01/08/2019] [Indexed: 02/02/2023]
Abstract
Mitochondrial DNA (mtDNA) encodes a subset of genes which are essential for oxidative phosphorylation. Deletions in the mtDNA can ablate a number of these genes and result in mitochondrial dysfunction, which is associated with bona fide mitochondrial disorders. Although mtDNA deletions are thought to occur as a result of replication errors or following double-strand breaks, the exact mechanism(s) behind deletion formation have yet to be determined. In this review we discuss the current knowledge about the fate of mtDNA following double-strand breaks, including the molecular players which mediate the degradation of linear mtDNA fragments and possible mechanisms of recircularization. We propose that mtDNA deletions formed from replication errors versus following double-strand breaks can be mediated by separate pathways.
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Affiliation(s)
- Nadee Nissanka
- Department of Neurology, University of Miami, Miller School of Medicine, FL 33136, USA
| | - Michal Minczuk
- Medical Research Council (MRC) Mitochondrial Biology Unit, University of Cambridge, Cambridge, UK
| | - Carlos T Moraes
- Department of Neurology, University of Miami, Miller School of Medicine, FL 33136, USA.
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49
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Naeem MM, Sondheimer N. Heteroplasmy Shifting as Therapy for Mitochondrial Disorders. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1158:257-267. [PMID: 31452145 DOI: 10.1007/978-981-13-8367-0_14] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Mitochondrial disease can arise due to pathogenic sequence variants in the mitochondrial DNA (mtDNA) that prevent cells from meeting their energy demands. Mitochondrial diseases are often fatal and currently there are no treatments directed towards the underlying cause of disease. Pathogenic variants in mtDNA often exist in a state of heteroplasmy, with coexistence of pathogenic and wild type mtDNA. The load of heteroplasmy, defined as the relative amount of pathogenic mtDNA to wild type mtDNA, corresponds to timing and symptom severity. Thus, changing the heteroplasmy load may lead to a shift in disease onset and symptom severity. Here we review techniques aimed at preventing inheritance of pathogenic mtDNA via mitochondrial replacement therapy (MRT) and strategies geared toward shifting of heteroplasmy in individuals with active mitochondrial disease. MRT strategies seek to create embryos with the nuclear genetic makeup of the intended parents and wild type mtDNA from a donor in order to avoid known maternal pathogenic variants. Heteroplasmy shift approaches in patients are of two categories: nuclease dependent and nuclease independent strategies. Despite initial success in mouse models and patient cells, these techniques have not reached clinical use. Translational attempts in this area are urgently needed to improve therapies for a currently untreatable set of disorders.
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Affiliation(s)
- Mansur M Naeem
- Institute of Medical Science, The University of Toronto, Toronto, ON, Canada
| | - Neal Sondheimer
- Institute of Medical Science, The University of Toronto, Toronto, ON, Canada.
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50
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Emerging therapies for mitochondrial diseases. Essays Biochem 2018; 62:467-481. [PMID: 29980632 DOI: 10.1042/ebc20170114] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 05/20/2018] [Accepted: 05/23/2018] [Indexed: 12/25/2022]
Abstract
For the vast majority of patients with mitochondrial diseases, only supportive and symptomatic therapies are available. However, in the last decade, due to extraordinary advances in defining the causes and pathomechanisms of these diverse disorders, new therapies are being developed in the laboratory and are entering human clinical trials. In this review, we highlight the current use of dietary supplement and exercise therapies as well as emerging therapies that may be broadly applicable across multiple mitochondrial diseases or tailored for specific disorders. Examples of non-tailored therapeutic targets include: activation of mitochondrial biogenesis, regulation of mitophagy and mitochondrial dynamics, bypass of biochemical defects, mitochondrial replacement therapy, and hypoxia. In contrast, tailored therapies are: scavenging of toxic compounds, deoxynucleoside and deoxynucleotide treatments, cell replacement therapies, gene therapy, shifting mitochondrial DNA mutation heteroplasmy, and stabilization of mutant mitochondrial transfer RNAs.
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