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Mikhailov N, Hämäläinen RH. Modulating Mitochondrial DNA Heteroplasmy with Mitochondrially Targeted Endonucleases. Ann Biomed Eng 2024; 52:2627-2640. [PMID: 36001180 PMCID: PMC11329604 DOI: 10.1007/s10439-022-03051-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 08/09/2022] [Indexed: 11/01/2022]
Abstract
Mitochondria, mainly known as energy factories of eukaryotic cells, also exert several additional signaling and metabolic functions and are today recognized as major cellular biosynthetic and signaling hubs. Mitochondria possess their own genome (mitochondrial DNA-mtDNA), that encodes proteins essential for oxidative phosphorylation, and mutations in it are an important contributor to human disease. The mtDNA mutations often exist in heteroplasmic conditions, with both healthy and mutant versions of the mtDNA residing in patients' cells and the level of mutant mtDNA may vary between different tissues and organs and affect the clinical outcome of the disease. Thus, shifting the ratio between healthy and mutant mtDNA in patients' cells provides an intriguing therapeutic option for mtDNA diseases. In this review we describe current strategies for modulating mitochondrial heteroplasmy levels with engineered endonucleases including mitochondrially targeted TALENs and Zinc finger nucleases (ZFNs) and discuss their therapeutic potential. These gene therapy tools could in the future provide therapeutic help both for patients with mitochondrial disease as well as in preventing the transfer of pathogenic mtDNA mutations from a mother to her offspring.
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Affiliation(s)
- Nikita Mikhailov
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland
| | - Riikka H Hämäläinen
- A.I.Virtanen Institute for Molecular Sciences, University of Eastern Finland, 70211, Kuopio, Finland.
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2
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Wang Y, Yang JS, Zhao M, Chen JQ, Xie HX, Yu HY, Liu NH, Yi ZJ, Liang HL, Xing L, Jiang HL. Mitochondrial endogenous substance transport-inspired nanomaterials for mitochondria-targeted gene delivery. Adv Drug Deliv Rev 2024; 211:115355. [PMID: 38849004 DOI: 10.1016/j.addr.2024.115355] [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: 03/18/2024] [Revised: 05/16/2024] [Accepted: 06/04/2024] [Indexed: 06/09/2024]
Abstract
Mitochondrial genome (mtDNA) independent of nuclear gene is a set of double-stranded circular DNA that encodes 13 proteins, 2 ribosomal RNAs and 22 mitochondrial transfer RNAs, all of which play vital roles in functions as well as behaviors of mitochondria. Mutations in mtDNA result in various mitochondrial disorders without available cures. However, the manipulation of mtDNA via the mitochondria-targeted gene delivery faces formidable barriers, particularly owing to the mitochondrial double membrane. Given the fact that there are various transport channels on the mitochondrial membrane used to transfer a variety of endogenous substances to maintain the normal functions of mitochondria, mitochondrial endogenous substance transport-inspired nanomaterials have been proposed for mitochondria-targeted gene delivery. In this review, we summarize mitochondria-targeted gene delivery systems based on different mitochondrial endogenous substance transport pathways. These are categorized into mitochondrial steroid hormones import pathways-inspired nanomaterials, protein import pathways-inspired nanomaterials and other mitochondria-targeted gene delivery nanomaterials. We also review the applications and challenges involved in current mitochondrial gene editing systems. This review delves into the approaches of mitochondria-targeted gene delivery, providing details on the design of mitochondria-targeted delivery systems and the limitations regarding the various technologies. Despite the progress in this field is currently slow, the ongoing exploration of mitochondrial endogenous substance transport and mitochondrial biological phenomena may act as a crucial breakthrough in the targeted delivery of gene into mitochondria and even the manipulation of mtDNA.
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Affiliation(s)
- Yi Wang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Jing-Song Yang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Min Zhao
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Jia-Qi Chen
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hai-Xin Xie
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hao-Yuan Yu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Na-Hui Liu
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Zi-Juan Yi
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hui-Lin Liang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Lei Xing
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China
| | - Hu-Lin Jiang
- State Key Laboratory of Natural Medicines, Department of Pharmaceutics, China Pharmaceutical University, Nanjing 210009, China; College of Pharmacy, Yanbian University, Yanji 133002, China.
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Waneka G, Stewart J, Anderson JR, Li W, Wilusz J, Argueso JL, Sloan DB. UV damage induces production of mitochondrial DNA fragments with specific length profiles. Genetics 2024; 227:iyae070. [PMID: 38722894 PMCID: PMC11228841 DOI: 10.1093/genetics/iyae070] [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: 02/08/2024] [Revised: 02/08/2024] [Accepted: 04/22/2024] [Indexed: 05/21/2024] Open
Abstract
UV light is a potent mutagen that induces bulky DNA damage in the form of cyclobutane pyrimidine dimers (CPDs). Photodamage and other bulky lesions occurring in nuclear genomes can be repaired through nucleotide excision repair (NER), where incisions on both sides of a damaged site precede the removal of a single-stranded oligonucleotide containing the damage. Mitochondrial genomes (mtDNAs) are also susceptible to damage from UV light, but current evidence suggests that the only way to eliminate bulky mtDNA damage is through mtDNA degradation. Damage-containing oligonucleotides excised during NER can be captured with antidamage antibodies and sequenced (XR-seq) to produce high-resolution maps of active repair locations following UV exposure. We analyzed previously published datasets from Arabidopsis thaliana, Saccharomyces cerevisiae, and Drosophila melanogaster to identify reads originating from the mtDNA (and plastid genome in A. thaliana). In A. thaliana and S. cerevisiae, the mtDNA-mapping reads have unique length distributions compared to the nuclear-mapping reads. The dominant fragment size was 26 nt in S. cerevisiae and 28 nt in A. thaliana with distinct secondary peaks occurring in regular intervals. These reads also show a nonrandom distribution of di-pyrimidines (the substrate for CPD formation) with TT enrichment at positions 7-8 of the reads. Therefore, UV damage to mtDNA appears to result in production of DNA fragments of characteristic lengths and positions relative to the damaged location. The mechanisms producing these fragments are unclear, but we hypothesize that they result from a previously uncharacterized DNA degradation pathway or repair mechanism in mitochondria.
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Affiliation(s)
- Gus Waneka
- Department of Biology, Colorado State University, Fort Collins 80521, CO, USA
| | - Joseph Stewart
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins 80521, CO, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins 80521, CO, USA
| | - John R Anderson
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins 80521, CO, USA
| | - Wentao Li
- Department of Environmental Health Science, University of Georgia, Athens 30602, GA, USA
| | - Jeffrey Wilusz
- Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins 80521, CO, USA
| | - Juan Lucas Argueso
- Department of Environmental and Radiological Health Sciences, Colorado State University, Fort Collins 80521, CO, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins 80521, CO, USA
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins 80521, CO, USA
- Cell and Molecular Biology Graduate Program, Colorado State University, Fort Collins 80521, CO, USA
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4
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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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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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6
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Eghbalsaied S, Lawler C, Petersen B, Hajiyev RA, Bischoff SR, Frankenberg S. CRISPR/Cas9-mediated base editors and their prospects for mitochondrial genome engineering. Gene Ther 2024; 31:209-223. [PMID: 38177342 DOI: 10.1038/s41434-023-00434-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024]
Abstract
Base editors are a type of double-stranded break (DSB)-free gene editing technology that has opened up new possibilities for precise manipulation of mitochondrial DNA (mtDNA). This includes cytosine and adenosine base editors and more recently guanosine base editors. Because of having low off-target and indel rates, there is a growing interest in developing and evolving this research field. Here, we provide a detailed update on DNA base editors. While base editing has widely been used for nuclear genome engineering, the growing interest in applying this technology to mitochondrial DNA has been faced with several challenges. While Cas9 protein has been shown to enter mitochondria, use of smaller Cas proteins, such as Cas12a, has higher import efficiency. However, sgRNA transfer into mitochondria is the most challenging step. sgRNA structure and ratio of Cas protein to sgRNA are both important factors for efficient sgRNA entry into mitochondria. In conclusion, while there are still several challenges to be addressed, ongoing research in this field holds the potential for new treatments and therapies for mitochondrial disorders.
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Affiliation(s)
- Shahin Eghbalsaied
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
- Department of Animal Science, Isfahan Branch, Islamic Azad University (IAU), Isfahan, Iran.
- Department of Cardiology and Pneumology, University Medical Center Göttingen, Göttingen, Germany.
| | - Clancy Lawler
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia
| | - Björn Petersen
- Department of Biotechnology, Institute of Farm Animal Genetics, Friedrich-Loeffler-Institute (FLI), Mariensee, Germany
- eGenesis, 2706 HWY E, 53572, Mount Horeb, WI, USA
| | - Raul A Hajiyev
- Department of Genome Engineering, NovoHelix, Miami, FL, USA
- Department of Computer Science, Kent State University, Kent, OH, USA
| | - Steve R Bischoff
- Department of Genome Engineering, NovoHelix, Miami, FL, USA
- Foundry for Genome Engineering & Reproductive Medicine (FGERM), Miami, FL, USA
| | - Stephen Frankenberg
- School of BioSciences, The University of Melbourne, Parkville, VIC, Australia.
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Song M, Ye L, Yan Y, Li X, Han X, Hu S, Yu M. Mitochondrial diseases and mtDNA editing. Genes Dis 2024; 11:101057. [PMID: 38292200 PMCID: PMC10825299 DOI: 10.1016/j.gendis.2023.06.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 06/22/2023] [Accepted: 06/27/2023] [Indexed: 02/01/2024] Open
Abstract
Mitochondrial diseases are a heterogeneous group of inherited disorders characterized by mitochondrial dysfunction, and these diseases are often severe or even fatal. Mitochondrial diseases are often caused by mitochondrial DNA mutations. Currently, there is no curative treatment for patients with pathogenic mitochondrial DNA mutations. With the rapid development of traditional gene editing technologies, such as zinc finger nucleases and transcription activator-like effector nucleases methods, there has been a search for a mitochondrial gene editing technology that can edit mutated mitochondrial DNA; however, there are still some problems hindering the application of these methods. The discovery of the DddA-derived cytosine base editor has provided hope for mitochondrial gene editing. In this paper, we will review the progress in the research on several mitochondrial gene editing technologies with the hope that this review will be useful for further research on mitochondrial gene editing technologies to optimize the treatment of mitochondrial diseases in the future.
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Affiliation(s)
- Min Song
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215000, China
| | - Lingqun Ye
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215000, China
| | - Yongjin Yan
- Hai'an People's Hospital, Nantong, Jiangsu 226600, China
| | - Xuechun Li
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215000, China
| | - Xinglong Han
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215000, China
| | - Shijun Hu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215000, China
| | - Miao Yu
- Department of Cardiovascular Surgery of the First Affiliated Hospital & Institute for Cardiovascular Science, Collaborative Innovation Center of Hematology, State Key Laboratory of Radiation Medicine and Protection, Suzhou Medical College, Soochow University, Suzhou, Jiangsu 215000, China
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8
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Mao EYC, Yen HY, Wu CC. Structural basis of how MGME1 processes DNA 5' ends to maintain mitochondrial genome integrity. Nucleic Acids Res 2024; 52:4067-4078. [PMID: 38471810 DOI: 10.1093/nar/gkae186] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024] Open
Abstract
Mitochondrial genome maintenance exonuclease 1 (MGME1) helps to ensure mitochondrial DNA (mtDNA) integrity by serving as an ancillary 5'-exonuclease for DNA polymerase γ. Curiously, MGME1 exhibits unique bidirectionality in vitro, being capable of degrading DNA from either the 5' or 3' end. The structural basis of this bidirectionally and, particularly, how it processes DNA from the 5' end to assist in mtDNA maintenance remain unclear. Here, we present a crystal structure of human MGME1 in complex with a 5'-overhang DNA, revealing that MGME1 functions as a rigid DNA clamp equipped with a single-strand (ss)-selective arch, allowing it to slide on single-stranded DNA in either the 5'-to-3' or 3'-to-5' direction. Using a nuclease activity assay, we have dissected the structural basis of MGME1-derived DNA cleavage patterns in which the arch serves as a ruler to determine the cleavage site. We also reveal that MGME1 displays partial DNA-unwinding ability that helps it to better resolve 5'-DNA flaps, providing insights into MGME1-mediated 5'-end processing of nascent mtDNA. Our study builds on previously solved MGME1-DNA complex structures, finally providing the comprehensive functional mechanism of this bidirectional, ss-specific exonuclease.
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Affiliation(s)
- Eric Y C Mao
- Department of Chemistry, College of Science, National Cheng Kung University, Tainan City 701, Taiwan
| | - Han-Yi Yen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan City 701, Taiwan
| | - Chyuan-Chuan Wu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan City 701, Taiwan
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Gonzalez CD, Nissanka N, Van Booven D, Griswold AJ, Moraes CT. Absence of both MGME1 and POLG EXO abolishes mtDNA whereas absence of either creates unique mtDNA duplications. J Biol Chem 2024; 300:107128. [PMID: 38432635 PMCID: PMC11002302 DOI: 10.1016/j.jbc.2024.107128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 02/21/2024] [Accepted: 02/23/2024] [Indexed: 03/05/2024] Open
Abstract
Both POLG and MGME1 are needed for mitochondrial DNA (mtDNA) maintenance in animal cells. POLG, the primary replicative polymerase of the mitochondria, has an exonuclease activity (3'→5') that corrects for the misincorporation of bases. MGME1 serves as an exonuclease (5'→3'), producing ligatable DNA ends. Although both have a critical role in mtDNA replication and elimination of linear fragments, these mechanisms are still not fully understood. Using digital PCR to evaluate and compare mtDNA integrity, we show that Mgme1 knock out (Mgme1 KK) tissue mtDNA is more fragmented than POLG exonuclease-deficient "Mutator" (Polg MM) or WT tissue. In addition, next generation sequencing of mutant hearts showed abundant duplications in/nearby the D-loop region and unique 100 bp duplications evenly spaced throughout the genome only in Mgme1 KK hearts. However, despite these unique mtDNA features at steady-state, we observed a similar delay in the degradation of mtDNA after an induced double strand DNA break in both Mgme1 KK and Polg MM models. Lastly, we characterized double mutant (Polg MM/Mgme1 KK) cells and show that mtDNA cannot be maintained without at least one of these enzymatic activities. We propose a model for the generation of these genomic abnormalities which suggests a role for MGME1 outside of nascent mtDNA end ligation. Our results highlight the role of MGME1 in and outside of the D-loop region during replication, support the involvement of MGME1 in dsDNA degradation, and demonstrate that POLG EXO and MGME1 can partially compensate for each other in maintaining mtDNA.
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Affiliation(s)
- Christian D Gonzalez
- MSTP and MCDB Programs, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Nadee Nissanka
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Derek Van Booven
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Anthony J Griswold
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Carlos T Moraes
- Department of Neurology, University of Miami Miller School of Medicine, Miami, Florida, USA.
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Basei FL, E Silva IR, Dias PRF, Ferezin CC, Peres de Oliveira A, Issayama LK, Moura LAR, da Silva FR, Kobarg J. The Mitochondrial Connection: The Nek Kinases' New Functional Axis in Mitochondrial Homeostasis. Cells 2024; 13:473. [PMID: 38534317 DOI: 10.3390/cells13060473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/28/2024] [Accepted: 02/29/2024] [Indexed: 03/28/2024] Open
Abstract
Mitochondria provide energy for all cellular processes, including reactions associated with cell cycle progression, DNA damage repair, and cilia formation. Moreover, mitochondria participate in cell fate decisions between death and survival. Nek family members have already been implicated in DNA damage response, cilia formation, cell death, and cell cycle control. Here, we discuss the role of several Nek family members, namely Nek1, Nek4, Nek5, Nek6, and Nek10, which are not exclusively dedicated to cell cycle-related functions, in controlling mitochondrial functions. Specifically, we review the function of these Neks in mitochondrial respiration and dynamics, mtDNA maintenance, stress response, and cell death. Finally, we discuss the interplay of other cell cycle kinases in mitochondrial function and vice versa. Nek1, Nek5, and Nek6 are connected to the stress response, including ROS control, mtDNA repair, autophagy, and apoptosis. Nek4, in turn, seems to be related to mitochondrial dynamics, while Nek10 is involved with mitochondrial metabolism. Here, we propose that the participation of Neks in mitochondrial roles is a new functional axis for the Nek family.
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Affiliation(s)
- Fernanda L Basei
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Ivan Rosa E Silva
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Pedro R Firmino Dias
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Camila C Ferezin
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | | | - Luidy K Issayama
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | - Livia A R Moura
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
| | | | - Jörg Kobarg
- Faculty of Pharmaceutical Sciences, University of Campinas, Campinas 13083-871, Brazil
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11
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Afshari N, Koturbash I, Boerma M, Newhauser W, Kratz M, Willey J, Williams J, Chancellor J. A Review of Numerical Models of Radiation Injury and Repair Considering Subcellular Targets and the Extracellular Microenvironment. Int J Mol Sci 2024; 25:1015. [PMID: 38256089 PMCID: PMC10816679 DOI: 10.3390/ijms25021015] [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: 11/16/2023] [Revised: 01/10/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Astronauts in space are subject to continuous exposure to ionizing radiation. There is concern about the acute and late-occurring adverse health effects that astronauts could incur following a protracted exposure to the space radiation environment. Therefore, it is vital to consider the current tools and models used to describe and study the organic consequences of ionizing radiation exposure. It is equally important to see where these models could be improved. Historically, radiobiological models focused on how radiation damages nuclear deoxyribonucleic acid (DNA) and the role DNA repair mechanisms play in resulting biological effects, building on the hypotheses of Crowther and Lea from the 1940s and 1960s, and they neglected other subcellular targets outside of nuclear DNA. The development of these models and the current state of knowledge about radiation effects impacting astronauts in orbit, as well as how the radiation environment and cellular microenvironment are incorporated into these radiobiological models, aid our understanding of the influence space travel may have on astronaut health. It is vital to consider the current tools and models used to describe the organic consequences of ionizing radiation exposure and identify where they can be further improved.
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Affiliation(s)
- Nousha Afshari
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA; (N.A.); (W.N.)
| | - Igor Koturbash
- Department of Environmental Health Sciences, Fay W. Boozman College of Public Health, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Marjan Boerma
- Division of Radiation Health, Department of Pharmaceutical Sciences, College of Pharmacy, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA;
| | - Wayne Newhauser
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA; (N.A.); (W.N.)
| | - Maria Kratz
- Department of Biological and Agricultural Engineering, Louisiana State University, Baton Rouge, LA 70803, USA;
| | - Jeffrey Willey
- Department of Radiation Oncology, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA;
| | - Jacqueline Williams
- School of Medicine and Dentistry, University of Rochester Medical Center, Rochester, NY 14642, USA;
| | - Jeffery Chancellor
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA; (N.A.); (W.N.)
- Department of Preventive Medicine and Population Health, University of Texas Medical Branch, Galveston, TX 77555, USA
- Outer Space Institute, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
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12
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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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13
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Wangh LJ, Rice JE, Sanchez JA. Recent Applications of FastFish-ID. Methods Mol Biol 2024; 2744:503-514. [PMID: 38683338 DOI: 10.1007/978-1-0716-3581-0_30] [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] [Indexed: 05/01/2024]
Abstract
FastFish-ID via Closed-Tube barcoding is a portable platform for rapid and accurate identification of fish species that was conceived at Brandeis University, commercialized at Thermagenix, Inc., and further improved at Ecologenix, LLC (see Chap. 17 in this volume). This chapter focuses on the use of FastFish-ID for (1) identification of intraspecies variants, (2) quantitative use of FastFish-ID to measure the decay of fresh fish, and (3) use of FastFish-ID for the identification of dried and processed shark fins.
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Affiliation(s)
- Lawrence J Wangh
- Department of Biology (Emeritus), Brandeis University, Waltham, MA, USA.
- Founder of Ecologenix, LLC, Auburndale, MA, USA.
| | - John E Rice
- Consult to Ecologenix, LLC, Auburndale, MA, USA
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14
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Sack T, Dhavarasa P, Szames D, O'Brien S, Angers S, Kelley SO. CRISPR Screening in Tandem with Targeted mtDNA Damage Reveals WRNIP1 Essentiality. ACS Chem Biol 2023; 18:2599-2609. [PMID: 38054633 DOI: 10.1021/acschembio.3c00620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
A major impediment to the characterization of mtDNA repair mechanisms in comparison to nuclear DNA repair mechanisms is the difficulty of specifically addressing mitochondrial damage. Using a mitochondria-penetrating peptide, we can deliver DNA-damaging agents directly to mitochondria, bypassing the nuclear compartment. Here, we describe the use of an mtDNA-damaging agent in tandem with CRISPR/Cas9 screening for the genome-wide discovery of factors essential for mtDNA damage response. Using mitochondria-targeted doxorubicin (mtDox), we generate mtDNA double-strand breaks (mtDSBs) specifically in this organelle. Combined with an untargeted doxorubicin (Dox) screen, we identify genes with significantly greater essentiality during mitochondrial versus nuclear DNA damage. We characterize the essentiality of our top hit, WRNIP1─observed here for the first time to respond to mtDNA damage. We further investigate the mitochondrial role of WRNIP1 in innate immune signaling and nuclear genome maintenance, outlining a model that experimentally supports mitochondrial turnover in response to mtDSBs.
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Affiliation(s)
- Tanja Sack
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Piriththiv Dhavarasa
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Daniel Szames
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Siobhan O'Brien
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Stephane Angers
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Terrence Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Toronto, Ontario M5S 3E1, Canada
| | - Shana O Kelley
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- Department of Chemistry, Faculty of Arts and Science, University of Toronto, Toronto, Ontario M5S 3H6, Canada
- Department of Chemistry, Weinberg College of Arts & Sciences, Northwestern University, Evanston, Illinois 60208, United States
- Chan Zuckerberg Biohub Chicago, Chicago, Illinois 60607, United States
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15
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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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16
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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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17
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Sack T, Dhavarasa P, Szames D, O'Brien S, Angers S, Kelley SO. CRISPR Screening in Tandem with Targeted mtDNA Damage Reveals WRNIP1 Essentiality. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.03.560559. [PMID: 37873237 PMCID: PMC10592966 DOI: 10.1101/2023.10.03.560559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
A major impediment to the characterization of mtDNA repair mechanisms, in comparison to nuclear DNA repair mechanisms, is the difficulty of specifically addressing mitochondrial damage. Using a mitochondria-penetrating peptide, we can deliver DNA-damaging agents directly to mitochondria, bypassing the nuclear compartment. Here, we describe the use of a mtDNA-damaging agent in tandem with CRISPR/Cas9 screening for the genome-wide discovery of factors essential for mtDNA damage response. Using mitochondria-targeted doxorubicin (mtDox) we generate mtDNA double-strand breaks (mtDSBs) specifically in this organelle. Combined with an untargeted Dox screen, we identify genes with significantly greater essentiality during mitochondrial versus nuclear DNA damage. We characterize the essentially of our top hit - WRNIP1 - observed here for the first time to respond to mtDNA damage. We further investigate the mitochondrial role of WRNIP1 in innate immune signaling and nuclear genome maintenance, outlining a model that experimentally supports mitochondrial turnover in response to mtDSBs.
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18
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Czarny P, Ziółkowska S, Kołodziej Ł, Watała C, Wigner-Jeziorska P, Bliźniewska-Kowalska K, Wachowska K, Gałecka M, Synowiec E, Gałecki P, Bijak M, Szemraj J, Śliwiński T. Single-Nucleotide Polymorphisms in Genes Maintaining the Stability of Mitochondrial DNA Affect the Occurrence, Onset, Severity and Treatment of Major Depressive Disorder. Int J Mol Sci 2023; 24:14752. [PMID: 37834200 PMCID: PMC10573273 DOI: 10.3390/ijms241914752] [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: 09/02/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
One of the key features of major depressive disorder (MDD, depression) is increased oxidative stress manifested by elevated levels of mtROS, a hallmark of mitochondrial dysfunction, which can arise from mitochondrial DNA (mtDNA) damage. Thus, the current study explores possibility that the single-nucleotide polymorphisms (SNPs) of genes encoding the three enzymes that are thought to be implicated in the replication, repair or degradation of mtDNA, i.e., POLG, ENDOG and EXOG, have an impact on the occurrence, onset, severity and treatment of MDD. Five SNPs were selected: EXOG c.-188T > G (rs9838614), EXOG c.*627G > A (rs1065800), POLG c.-1370T > A (rs1054875), ENDOG c.-394T > C (rs2977998) and ENDOG c.-220C > T (rs2997922), while genotyping was performed on 538 DNA samples (277 cases and 261 controls) using TaqMan probes. All SNPs of EXOG and ENDOG modulated the risk of depression, but the strongest effect was observed for rs1065800, while rs9838614 and rs2977998 indicate that they might influence the severity of symptoms, and, to a lesser extent, treatment effectiveness. Although the SNP located in POLG did not affect occurrence of the disease, the result suggests that it may influence the onset and treatment outcome. These findings further support the hypothesis that mtDNA damage and impairment in its metabolism play a crucial role not only in the development, but also in the treatment of depression.
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Affiliation(s)
- Piotr Czarny
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (S.Z.); (J.S.)
| | - Sylwia Ziółkowska
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (S.Z.); (J.S.)
| | - Łukasz Kołodziej
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 92-215 Lodz, Poland; (Ł.K.)
| | - Cezary Watała
- Department of Haemostatic Disorders, Medical University of Lodz, 92-215 Lodz, Poland;
| | - Paulina Wigner-Jeziorska
- Department of General Biochemistry, Faculty of Biology and Environmental Protection, University of Lodz, 90-136 Lodz, Poland;
| | | | - Katarzyna Wachowska
- Department of Adult Psychiatry, Medical University of Lodz, 91-229 Lodz, Poland; (K.B.-K.); (K.W.); (P.G.)
| | - Małgorzata Gałecka
- Department of Psychotherapy, Medical University of Lodz, 91-229 Lodz, Poland;
| | - Ewelina Synowiec
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 92-215 Lodz, Poland; (Ł.K.)
| | - Piotr Gałecki
- Department of Adult Psychiatry, Medical University of Lodz, 91-229 Lodz, Poland; (K.B.-K.); (K.W.); (P.G.)
| | - Michał Bijak
- Biohazard Prevention Centre, Faculty of Biology and Environmental Protection, University of Lodz, 90-136 Lodz, Poland;
| | - Janusz Szemraj
- Department of Medical Biochemistry, Medical University of Lodz, 92-215 Lodz, Poland; (S.Z.); (J.S.)
| | - Tomasz Śliwiński
- Laboratory of Medical Genetics, Faculty of Biology and Environmental Protection, University of Lodz, 92-215 Lodz, Poland; (Ł.K.)
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19
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Caston RA, Fortini P, Chen K, Bauer J, Dogliotti E, Yin YW, Demple B. Maintenance of Flap Endonucleases for Long-Patch Base Excision DNA Repair in Mouse Muscle and Neuronal Cells Differentiated In Vitro. Int J Mol Sci 2023; 24:12715. [PMID: 37628896 PMCID: PMC10454756 DOI: 10.3390/ijms241612715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/02/2023] [Accepted: 08/03/2023] [Indexed: 08/27/2023] Open
Abstract
After cellular differentiation, nuclear DNA is no longer replicated, and many of the associated proteins are downregulated accordingly. These include the structure-specific endonucleases Fen1 and DNA2, which are implicated in repairing mitochondrial DNA (mtDNA). Two more such endonucleases, named MGME1 and ExoG, have been discovered in mitochondria. This category of nuclease is required for so-called "long-patch" (multinucleotide) base excision DNA repair (BER), which is necessary to process certain oxidative lesions, prompting the question of how differentiation affects the availability and use of these enzymes in mitochondria. In this study, we demonstrate that Fen1 and DNA2 are indeed strongly downregulated after differentiation of neuronal precursors (Cath.a-differentiated cells) or mouse myotubes, while the expression levels of MGME1 and ExoG showed minimal changes. The total flap excision activity in mitochondrial extracts of these cells was moderately decreased upon differentiation, with MGME1 as the predominant flap endonuclease and ExoG playing a lesser role. Unexpectedly, both differentiated cell types appeared to accumulate less oxidative or alkylation damage in mtDNA than did their proliferating progenitors. Finally, the overall rate of mtDNA repair was not significantly different between proliferating and differentiated cells. Taken together, these results indicate that neuronal cells maintain mtDNA repair upon differentiation, evidently relying on mitochondria-specific enzymes for long-patch BER.
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Affiliation(s)
- Rachel A. Caston
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Paola Fortini
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.F.)
| | - Kevin Chen
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Jack Bauer
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Eugenia Dogliotti
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy; (P.F.)
| | - Y. Whitney Yin
- Department of Pharmacology and Toxicology, Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Bruce Demple
- Department of Pharmacological Sciences, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
- Department of Radiation Oncology, Renaissance School of Medicine, Stony Brook University, Stony Brook, NY 11794, USA
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20
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Yang L, Han Y, Zhou T, Lacko LA, Saeed M, Tan C, Danziger R, Zhu J, Zhao Z, Cahir C, Giani AM, Li Y, Dong X, Moroziewicz D, Paull D, Chen Z, Zhong A, Noggle SA, Rice CM, Qi Q, Evans T, Chen S. Isogenic human trophectoderm cells demonstrate the role of NDUFA4 and associated variants in ZIKV infection. iScience 2023; 26:107001. [PMID: 37534130 PMCID: PMC10391681 DOI: 10.1016/j.isci.2023.107001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 03/17/2023] [Accepted: 05/25/2023] [Indexed: 08/04/2023] Open
Abstract
Population-based genome-wide association studies (GWAS) normally require a large sample size, which can be labor intensive and costly. Recently, we reported a human induced pluripotent stem cell (hiPSC) array-based GWAS method, identifying NDUFA4 as a host factor for Zika virus (ZIKV) infection. In this study, we extended our analysis to trophectoderm cells, which constitute one of the major routes of mother-to-fetus transmission of ZIKV during pregnancy. We differentiated hiPSCs from various donors into trophectoderm cells. We then infected cells carrying loss of function mutations in NDUFA4, harboring risk versus non-risk alleles of SNPs (rs917172 and rs12386620) or having deletions in the NDUFA4 cis-regulatory region with ZIKV. We found that loss/reduction of NDUFA4 suppressed ZIKV infection in trophectoderm cells. This study validated our published hiPSC array-based system as a useful platform for GWAS and confirmed the role of NDUFA4 as a susceptibility locus for ZIKV in disease-relevant trophectoderm cells.
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Affiliation(s)
- Liuliu Yang
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Yuling Han
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Ting Zhou
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Lauretta A. Lacko
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
- Department of Biochemistry & Cell Biology, Boston University Chobanian and Avedisian School of Medicine, Boston, MA 02118, USA
- National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Christina Tan
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Ron Danziger
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Jiajun Zhu
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Zeping Zhao
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Clare Cahir
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Alice Maria Giani
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Yang Li
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Xue Dong
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Dorota Moroziewicz
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3Road Floor, New York, NY 10019, USA
| | | | - Daniel Paull
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3Road Floor, New York, NY 10019, USA
| | - Zhengming Chen
- Department of Population Health Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Aaron Zhong
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Scott A. Noggle
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3Road Floor, New York, NY 10019, USA
| | - Charles M. Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
- Center for Genomic Health, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
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21
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Tanriover C, Copur S, Ucku D, Cakir AB, Hasbal NB, Soler MJ, Kanbay M. The Mitochondrion: A Promising Target for Kidney Disease. Pharmaceutics 2023; 15:pharmaceutics15020570. [PMID: 36839892 PMCID: PMC9960839 DOI: 10.3390/pharmaceutics15020570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 01/28/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Mitochondrial dysfunction is important in the pathogenesis of various kidney diseases and the mitochondria potentially serve as therapeutic targets necessitating further investigation. Alterations in mitochondrial biogenesis, imbalance between fusion and fission processes leading to mitochondrial fragmentation, oxidative stress, release of cytochrome c and mitochondrial DNA resulting in apoptosis, mitophagy, and defects in energy metabolism are the key pathophysiological mechanisms underlying the role of mitochondrial dysfunction in kidney diseases. Currently, various strategies target the mitochondria to improve kidney function and kidney treatment. The agents used in these strategies can be classified as biogenesis activators, fission inhibitors, antioxidants, mPTP inhibitors, and agents which enhance mitophagy and cardiolipin-protective drugs. Several glucose-lowering drugs, such as glucagon-like peptide-1 receptor agonists (GLP-1-RA) and sodium glucose co-transporter-2 (SGLT-2) inhibitors are also known to have influences on these mechanisms. In this review, we delineate the role of mitochondrial dysfunction in kidney disease, the current mitochondria-targeting treatment options affecting the kidneys and the future role of mitochondria in kidney pathology.
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Affiliation(s)
- Cem Tanriover
- Department of Medicine, Koc University School of Medicine, 34010 Istanbul, Turkey
| | - Sidar Copur
- Department of Medicine, Koc University School of Medicine, 34010 Istanbul, Turkey
| | - Duygu Ucku
- Department of Medicine, Koc University School of Medicine, 34010 Istanbul, Turkey
| | - Ahmet B. Cakir
- Department of Medicine, Koc University School of Medicine, 34010 Istanbul, Turkey
| | - Nuri B. Hasbal
- Department of Medicine, Division of Nephrology, Koc University School of Medicine, 34010 Istanbul, Turkey
| | - Maria Jose Soler
- Nephrology and Kidney Transplant Research Group, Vall d’Hebron Research Institute (VHIR), 08035 Barcelona, Spain
| | - Mehmet Kanbay
- Department of Medicine, Division of Nephrology, Koc University School of Medicine, 34010 Istanbul, Turkey
- Correspondence: or ; Tel.: +90-212-2508250
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22
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Shang D, Huang M, Wang B, Yan X, Wu Z, Zhang X. mtDNA Maintenance and Alterations in the Pathogenesis of Neurodegenerative Diseases. Curr Neuropharmacol 2023; 21:578-598. [PMID: 35950246 PMCID: PMC10207910 DOI: 10.2174/1570159x20666220810114644] [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: 03/17/2022] [Revised: 06/13/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
Abstract
Considerable evidence indicates that the semiautonomous organelles mitochondria play key roles in the progression of many neurodegenerative disorders. Mitochondrial DNA (mtDNA) encodes components of the OXPHOS complex but mutated mtDNA accumulates in cells with aging, which mirrors the increased prevalence of neurodegenerative diseases. This accumulation stems not only from the misreplication of mtDNA and the highly oxidative environment but also from defective mitophagy after fission. In this review, we focus on several pivotal mitochondrial proteins related to mtDNA maintenance (such as ATAD3A and TFAM), mtDNA alterations including mtDNA mutations, mtDNA elimination, and mtDNA release-activated inflammation to understand the crucial role played by mtDNA in the pathogenesis of neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease. Our work outlines novel therapeutic strategies for targeting mtDNA.
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Affiliation(s)
- Dehao Shang
- Center of Implant Dentistry, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Minghao Huang
- Center of Implant Dentistry, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Biyao Wang
- The VIP Department, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Xu Yan
- The VIP Department, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
| | - Zhou Wu
- Department of Aging Science and Pharmacology, Faculty of Dental Science, Kyushu University, Fukuoka 812-8582, Japan
- OBT Research Center, Faculty of Dental Science, Kyushu University, Fukuoka 812-8582, Japan
| | - Xinwen Zhang
- Center of Implant Dentistry, School and Hospital of Stomatology, China Medical University, Liaoning Provincial Key Laboratory of Oral Diseases, Shenyang, China
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23
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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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24
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Chatgilialoglu C, Krokidis MG, Masi A, Barata-Vallejo S, Ferreri C, Pascucci B, D’Errico M. Assessing the Formation of Purine Lesions in Mitochondrial DNA of Cockayne Syndrome Cells. Biomolecules 2022; 12:1630. [PMID: 36358980 PMCID: PMC9687895 DOI: 10.3390/biom12111630] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/27/2022] [Accepted: 10/30/2022] [Indexed: 11/06/2022] Open
Abstract
Mitochondrial (mt) DNA and nuclear (n) DNA have known structures and roles in cells; however, they are rarely compared under specific conditions such as oxidative or degenerative environments that can create damage to the DNA base moieties. Six purine lesions were ascertained in the mtDNA of wild type (wt) CSA (CS3BE-wtCSA) and wtCSB (CS1AN-wtCSB) cells and defective counterparts CS3BE and CS1AN in comparison with the corresponding total (t) DNA (t = n + mt). In particular, the four 5',8-cyclopurine (cPu) and the two 8-oxo-purine (8-oxo-Pu) lesions were accurately quantified by LC-MS/MS analysis using isotopomeric internal standards after an enzymatic digestion procedure. The 8-oxo-Pu levels were found to be in the range of 25-50 lesions/107 nucleotides in both the mtDNA and tDNA. The four cPu were undetectable in the mtDNA both in defective cells and in the wt counterparts (CSA and CSB), contrary to their detection in tDNA, indicating a nonappearance of hydroxyl radical (HO•) reactivity within the mtDNA. In order to assess the HO• reactivity towards purine nucleobases in the two genetic materials, we performed γ-radiolysis experiments coupled with the 8-oxo-Pu and cPu quantifications on isolated mtDNA and tDNA from wtCSB cells. In the latter experiments, all six purine lesions were detected in both of the DNA, showing a higher resistance to HO• attack in the case of mtDNA compared with tDNA, likely due to their different DNA helical topology influencing the relative abundance of the lesions.
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Affiliation(s)
- Chryssostomos Chatgilialoglu
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
- Center for Advanced Technologies, Adam Mickiewicz University, 61–614 Poznań, Poland
| | - Marios G. Krokidis
- Institute of Nanoscience and Nanotechnology, N.C.S.R. “Demokritos”, Agia Paraskevi Attikis, 15310 Athens, Greece
| | - Annalisa Masi
- Institute of Crystallography, Consiglio Nazionale delle Ricerche, Monterotondo Stazione, 00015 Rome, Italy
| | - Sebastian Barata-Vallejo
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
- Departamento de Ciencias Químicas, Facultad de Farmacia y Bioquimíca, Universidad de Buenos Aires, Junin 954, Buenos Aires CP 1113, Argentina
| | - Carla Ferreri
- Istituto per la Sintesi Organica e la Fotoreattività, Consiglio Nazionale delle Ricerche, Via P. Gobetti 101, 40129 Bologna, Italy
| | - Barbara Pascucci
- Institute of Crystallography, Consiglio Nazionale delle Ricerche, Monterotondo Stazione, 00015 Rome, Italy
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
| | - Mariarosaria D’Errico
- Department of Environment and Health, Istituto Superiore di Sanità, Viale Regina Elena 299, 00161 Rome, Italy
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25
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Han Y, Tan L, Zhou T, Yang L, Carrau L, Lacko LA, Saeed M, Zhu J, Zhao Z, Nilsson-Payant BE, Lira Neto FT, Cahir C, Giani AM, Chai JC, Li Y, Dong X, Moroziewicz D, Paull D, Zhang T, Koo S, Tan C, Danziger R, Ba Q, Feng L, Chen Z, Zhong A, Wise GJ, Xiang JZ, Wang H, Schwartz RE, tenOever BR, Noggle SA, Rice CM, Qi Q, Evans T, Chen S. A human iPSC-array-based GWAS identifies a virus susceptibility locus in the NDUFA4 gene and functional variants. Cell Stem Cell 2022; 29:1475-1490.e6. [PMID: 36206731 PMCID: PMC9550219 DOI: 10.1016/j.stem.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 06/09/2022] [Accepted: 09/16/2022] [Indexed: 11/16/2022]
Abstract
Population-based studies to identify disease-associated risk alleles typically require samples from a large number of individuals. Here, we report a human-induced pluripotent stem cell (hiPSC)-based screening strategy to link human genetics with viral infectivity. A genome-wide association study (GWAS) identified a cluster of single-nucleotide polymorphisms (SNPs) in a cis-regulatory region of the NDUFA4 gene, which was associated with susceptibility to Zika virus (ZIKV) infection. Loss of NDUFA4 led to decreased sensitivity to ZIKV, dengue virus, and SARS-CoV-2 infection. Isogenic hiPSC lines carrying non-risk alleles of SNPs or deletion of the cis-regulatory region lower sensitivity to viral infection. Mechanistic studies indicated that loss/reduction of NDUFA4 causes mitochondrial stress, which leads to the leakage of mtDNA and thereby upregulation of type I interferon signaling. This study provides proof-of-principle for the application of iPSC arrays in GWAS and identifies NDUFA4 as a previously unknown susceptibility locus for viral infection.
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Affiliation(s)
- Yuling Han
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Lei Tan
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Center for Energy Metabolism and Reproduction, Institute of Biomedicine and Biotechnology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Ting Zhou
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Liuliu Yang
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Lucia Carrau
- Department of Microbiology, New York University, 430 E 29th Street, New York, NY 10016, USA
| | - Lauretta A Lacko
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Mohsan Saeed
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA; Department of Biochemistry, Boston University School of Medicine, Boston, MA 02118, USA; National Emerging Infectious Diseases Laboratories (NEIDL), Boston University, Boston, MA 02118, USA
| | - Jiajun Zhu
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Zeping Zhao
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | | | | | - Clare Cahir
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; The Tri-Institutional PhD Program in Chemical Biology, New York, NY, USA
| | - Alice Maria Giani
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Jin Chou Chai
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Yang Li
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Xue Dong
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Dorota Moroziewicz
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019, USA
| | - Daniel Paull
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019, USA
| | - Tuo Zhang
- Genomic Resource Core Facility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Soyeon Koo
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Weill Cornell Neuroscience PhD Program, New York, NY, USA
| | - Christina Tan
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Ron Danziger
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Qian Ba
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Lingling Feng
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA; Key Laboratory of Pesticide and Chemical Biology (CCNU), Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, China
| | - Zhengming Chen
- Department of Population Health Sciences, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Aaron Zhong
- Stem Cell Research Facility, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Gilbert J Wise
- Department of Urology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Jenny Z Xiang
- Genomic Resource Core Facility, Weill Cornell Medical College, New York, NY 10065, USA
| | - Hui Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Robert E Schwartz
- Division of Gastroenterology and Hepatology, Department of Medicine, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA; Department of Physiology, Biophysics, and Systems Biology, Weill Cornell Medicine, 1300 York Avenue, New York, NY 10065, USA
| | - Benjamin R tenOever
- Department of Microbiology, New York University, 430 E 29th Street, New York, NY 10016, USA
| | - Scott A Noggle
- The New York Stem Cell Foundation Research Institute, 619 West 54th Street, 3rd Floor, New York, NY 10019, USA
| | - Charles M Rice
- Laboratory of Virology and Infectious Disease, The Rockefeller University, New York, NY 10065, USA
| | - Qibin Qi
- Department of Epidemiology & Population Health, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, NY 10461, USA
| | - Todd Evans
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA
| | - Shuibing Chen
- Department of Surgery, Weill Cornell Medical College, 1300 York Avenue, New York, NY 10065, USA.
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26
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Mitochondrial DNA Repair in Neurodegenerative Diseases and Ageing. Int J Mol Sci 2022; 23:ijms231911391. [PMID: 36232693 PMCID: PMC9569545 DOI: 10.3390/ijms231911391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/20/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022] Open
Abstract
Mitochondria are the only organelles, along with the nucleus, that have their own DNA. Mitochondrial DNA (mtDNA) is a double-stranded circular molecule of ~16.5 kbp that can exist in multiple copies within the organelle. Both strands are translated and encode for 22 tRNAs, 2 rRNAs, and 13 proteins. mtDNA molecules are anchored to the inner mitochondrial membrane and, in association with proteins, form a structure called nucleoid, which exerts a structural and protective function. Indeed, mitochondria have evolved mechanisms necessary to protect their DNA from chemical and physical lesions such as DNA repair pathways similar to those present in the nucleus. However, there are mitochondria-specific mechanisms such as rapid mtDNA turnover, fission, fusion, and mitophagy. Nevertheless, mtDNA mutations may be abundant in somatic tissue due mainly to the proximity of the mtDNA to the oxidative phosphorylation (OXPHOS) system and, consequently, to the reactive oxygen species (ROS) formed during ATP production. In this review, we summarise the most common types of mtDNA lesions and mitochondria repair mechanisms. The second part of the review focuses on the physiological role of mtDNA damage in ageing and the effect of mtDNA mutations in neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease. Considering the central role of mitochondria in maintaining cellular homeostasis, the analysis of mitochondrial function is a central point for developing personalised medicine.
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27
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Akbari M, Nilsen HL, Montaldo NP. Dynamic features of human mitochondrial DNA maintenance and transcription. Front Cell Dev Biol 2022; 10:984245. [PMID: 36158192 PMCID: PMC9491825 DOI: 10.3389/fcell.2022.984245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022] Open
Abstract
Mitochondria are the primary sites for cellular energy production and are required for many essential cellular processes. Mitochondrial DNA (mtDNA) is a 16.6 kb circular DNA molecule that encodes only 13 gene products of the approximately 90 different proteins of the respiratory chain complexes and an estimated 1,200 mitochondrial proteins. MtDNA is, however, crucial for organismal development, normal function, and survival. MtDNA maintenance requires mitochondrially targeted nuclear DNA repair enzymes, a mtDNA replisome that is unique to mitochondria, and systems that control mitochondrial morphology and quality control. Here, we provide an overview of the current literature on mtDNA repair and transcription machineries and discuss how dynamic functional interactions between the components of these systems regulate mtDNA maintenance and transcription. A profound understanding of the molecular mechanisms that control mtDNA maintenance and transcription is important as loss of mtDNA integrity is implicated in normal process of aging, inflammation, and the etiology and pathogenesis of a number of diseases.
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Affiliation(s)
- Mansour Akbari
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Hilde Loge Nilsen
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- Unit for precision medicine, Akershus University Hospital, Nordbyhagen, Norway
- Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Nicola Pietro Montaldo
- Department of Clinical Molecular Biology, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
- *Correspondence: Nicola Pietro Montaldo,
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28
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Oanh N, Lee HS, Kim YH, Min S, Park YJ, Heo J, Park YY, Lim WC, Cho H. Regulation of nuclear DNA damage response by mitochondrial morphofunctional pathway. Nucleic Acids Res 2022; 50:9247-9259. [PMID: 35979947 PMCID: PMC9458461 DOI: 10.1093/nar/gkac690] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 07/22/2022] [Accepted: 08/03/2022] [Indexed: 12/24/2022] Open
Abstract
Cells are constantly challenged by genotoxic stresses that can lead to genome instability. The integrity of the nuclear genome is preserved by the DNA damage response (DDR) and repair. Additionally, these stresses can induce mitochondria to transiently hyperfuse; however, it remains unclear whether canonical DDR is linked to these mitochondrial morphological changes. Here, we report that the abolition of mitochondrial fusion causes a substantial defect in the ATM-mediated DDR signaling. This deficiency is overcome by the restoration of mitochondria fusion. In cells with fragmented mitochondria, genotoxic stress-induced activation of JNK and its translocation to DNA lesion are lost. Importantly, the mitochondrial fusion machinery of MFN1/MFN2 associates with Sab (SH3BP5) and JNK, and these interactions are indispensable for the Sab-mediated activation of JNK and the ATM-mediated DDR signaling. Accordingly, the formation of BRCA1 and 53BP1 foci, as well as homology and end-joining repair are impaired in cells with fragmented mitochondria. Together, these data show that mitochondrial fusion-dependent JNK signaling is essential for the DDR, providing vital insight into the integration of nuclear and cytoplasmic stress signals.
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Affiliation(s)
| | | | - Yong-Hyun Kim
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea,Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, Republic of Korea
| | - Sunwoo Min
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Yeon-Ji Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - June Heo
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea,Department of Biomedical Sciences, Graduate School of Ajou University, Suwon, Republic of Korea
| | - Yong-Yea Park
- Department of Biochemistry and Molecular Biology, Ajou University School of Medicine, Suwon, Republic of Korea
| | - Won-Chung Lim
- Correspondence may also be addressed to Won-Chung Lim.
| | - Hyeseong Cho
- To whom correspondence should be addressed. Tel: +82 312195052; Fax: +82 312195059;
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29
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Roy A, Kandettu A, Ray S, Chakrabarty S. Mitochondrial DNA replication and repair defects: Clinical phenotypes and therapeutic interventions. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148554. [PMID: 35341749 DOI: 10.1016/j.bbabio.2022.148554] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 03/06/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022]
Abstract
Mitochondria is a unique cellular organelle involved in multiple cellular processes and is critical for maintaining cellular homeostasis. This semi-autonomous organelle contains its circular genome - mtDNA (mitochondrial DNA), that undergoes continuous cycles of replication and repair to maintain the mitochondrial genome integrity. The majority of the mitochondrial genes, including mitochondrial replisome and repair genes, are nuclear-encoded. Although the repair machinery of mitochondria is quite efficient, the mitochondrial genome is highly susceptible to oxidative damage and other types of exogenous and endogenous agent-induced DNA damage, due to the absence of protective histones and their proximity to the main ROS production sites. Mutations in replication and repair genes of mitochondria can result in mtDNA depletion and deletions subsequently leading to mitochondrial genome instability. The combined action of mutations and deletions can result in compromised mitochondrial genome maintenance and lead to various mitochondrial disorders. Here, we review the mechanism of mitochondrial DNA replication and repair process, key proteins involved, and their altered function in mitochondrial disorders. The focus of this review will be on the key genes of mitochondrial DNA replication and repair machinery and the clinical phenotypes associated with mutations in these genes.
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Affiliation(s)
- Abhipsa Roy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Amoolya Kandettu
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Swagat Ray
- Department of Life Sciences, School of Life and Environmental Sciences, University of Lincoln, Lincoln LN6 7TS, United Kingdom
| | - Sanjiban Chakrabarty
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, Karnataka, India.
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30
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Wada KI, Hosokawa K, Ito Y, Mizuo M, Harada Y, Yonemitsu Y. Generation of transmitochondrial cybrids using a microfluidic device. Exp Cell Res 2022; 418:113233. [PMID: 35659971 DOI: 10.1016/j.yexcr.2022.113233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 05/26/2022] [Accepted: 05/28/2022] [Indexed: 11/04/2022]
Abstract
Mitochondrial cloning is a promising approach to achieve homoplasmic mitochondrial DNA (mtDNA) mutations. We previously developed a microfluidic device that performs single mitochondrion transfer from a mtDNA-intact cell to a mtDNA-less (ρ0) cell by promoting cytoplasmic connection through a microtunnel between them. In the present study, we described a method for generating transmitochondrial cybrids using the microfluidic device. After achieving mitochondrial transfer between HeLa cells and thymidine kinase-deficient ρ0143B cells using the microfluidic device, selective culture was carried out using a pyruvate and uridine (PU)-absent and 5-bromo-2'-deoxyuridine-supplemented culture medium. The resulting cells contained HeLa mtDNA and 143B nuclei, but both 143B mtDNA and HeLa nuclei were absent in these cells. Additionally, these cells showed lower lactate production than parent ρ0143B cells and disappearance of PU auxotrophy for cell growth. These results suggest successful generation of transmitochondrial cybrids using the microfluidic device. Furthermore, we succeeded in selective harvest of generated transmitochondrial cybrids under a PU-supplemented condition by removing unfused ρ0 cells with puromycin-based selection in the microfluidic device.
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Affiliation(s)
- Ken-Ichi Wada
- R&D Laboratory for Innovative Biotherapeutics, Graduate School of Pharmaceutical Sciences, Kyushu Univ., 3-1-1 Maidasi, Higashi, Fukuoka, 8112-8582, Japan; Bioengineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan; Nano Medical Engineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.
| | - Kazuo Hosokawa
- Bioengineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yoshihiro Ito
- Nano Medical Engineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Maeda Mizuo
- Bioengineering Laboratory, Cluster for Pioneering Research, RIKEN, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
| | - Yui Harada
- R&D Laboratory for Innovative Biotherapeutics, Graduate School of Pharmaceutical Sciences, Kyushu Univ., 3-1-1 Maidasi, Higashi, Fukuoka, 8112-8582, Japan
| | - Yoshikazu Yonemitsu
- R&D Laboratory for Innovative Biotherapeutics, Graduate School of Pharmaceutical Sciences, Kyushu Univ., 3-1-1 Maidasi, Higashi, Fukuoka, 8112-8582, Japan
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31
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Schreier HK, Wiehe RS, Ricchetti M, Wiesmüller L. Polymerase ζ is Involved in Mitochondrial DNA Maintenance Processes in Concert with APE1 Activity. Genes (Basel) 2022; 13:genes13050879. [PMID: 35627264 PMCID: PMC9141751 DOI: 10.3390/genes13050879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 05/10/2022] [Accepted: 05/11/2022] [Indexed: 01/25/2023] Open
Abstract
Mitochondrial DNA (mtDNA) damaged by reactive oxygen species (ROS) triggers so far poorly understood processes of mtDNA maintenance that are coordinated by a complex interplay among DNA repair, DNA degradation, and DNA replication. This study was designed to identify the proteins involved in mtDNA maintenance by applying a special long-range PCR, reflecting mtDNA integrity in the minor arc. A siRNA screening of literature-based candidates was performed under conditions of enforced oxidative phosphorylation revealing the functional group of polymerases and therein polymerase ζ (POLZ) as top hits. Thus, POLZ knockdown caused mtDNA accumulation, which required the activity of the base excision repair (BER) nuclease APE1, and was followed by compensatory mtDNA replication determined by the single-cell mitochondrial in situ hybridization protocol (mTRIP). Quenching reactive oxygen species (ROS) in mitochondria unveiled an additional, ROS-independent involvement of POLZ in the formation of a typical deletion in the minor arc region. Together with data demonstrating the localization of POLZ in mitochondria, we suggest that POLZ plays a significant role in mtDNA turnover, particularly under conditions of oxidative stress.
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Affiliation(s)
- Heike Katrin Schreier
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
| | - Rahel Stefanie Wiehe
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
| | - Miria Ricchetti
- Department of Developmental and Stem Cell Biology, Institute Pasteur, CEDEX 15, 75724 Paris, France;
| | - Lisa Wiesmüller
- Department of Obstetrics and Gynecology, Ulm University, 89075 Ulm, Germany; (H.K.S.); (R.S.W.)
- Correspondence:
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Radiation-induced non-targeted effect of immunity provoked by mitochondrial DNA damage triggered cGAS/ AIM2 pathways. RADIATION MEDICINE AND PROTECTION 2022. [DOI: 10.1016/j.radmp.2022.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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The fate of damaged mitochondrial DNA in the cell. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119233. [PMID: 35131372 DOI: 10.1016/j.bbamcr.2022.119233] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 01/25/2022] [Accepted: 01/31/2022] [Indexed: 12/12/2022]
Abstract
Mitochondrion is a double membrane organelle that is responsible for cellular respiration and production of most of the ATP in eukaryotic cells. Mitochondrial DNA (mtDNA) is the genetic material carried by mitochondria, which encodes some essential subunits of respiratory complexes independent of nuclear DNA. Normally, mtDNA binds to certain proteins to form a nucleoid that is stable in mitochondria. Nevertheless, a variety of physiological or pathological stresses can cause mtDNA damage, and the accumulation of damaged mtDNA in mitochondria leads to mitochondrial dysfunction, which triggers the occurrence of mitochondrial diseases in vivo. In response to mtDNA damage, cell initiates multiple pathways including mtDNA repair, degradation, clearance and release, to recover mtDNA, and maintain mitochondrial quality and cell homeostasis. In this review, we provide our current understanding of the fate of damaged mtDNA, focus on the pathways and mechanisms of removing damaged mtDNA in the cell.
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Abstract
Significance: The small, multicopy mitochondrial genome (mitochondrial DNA [mtDNA]) is essential for efficient energy production, as alterations in its coding information or a decrease in its copy number disrupt mitochondrial ATP synthesis. However, the mitochondrial replication machinery encounters numerous challenges that may limit its ability to duplicate this important genome and that jeopardize mtDNA stability, including various lesions in the DNA template, topological stress, and an insufficient nucleotide supply. Recent Advances: An ever-growing array of DNA repair or maintenance factors are being reported to localize to the mitochondria. We review current knowledge regarding the mitochondrial factors that may contribute to the tolerance or repair of various types of changes in the mitochondrial genome, such as base damage, incorporated ribonucleotides, and strand breaks. We also discuss the newly discovered link between mtDNA instability and activation of the innate immune response. Critical Issues: By which mechanisms do mitochondria respond to challenges that threaten mtDNA maintenance? What types of mtDNA damage are repaired, and when are the affected molecules degraded instead? And, finally, which forms of mtDNA instability trigger an immune response, and how? Future Directions: Further work is required to understand the contribution of the DNA repair and damage-tolerance factors present in the mitochondrial compartment, as well as the balance between mtDNA repair and degradation. Finally, efforts to understand the events underlying mtDNA release into the cytosol are warranted. Pursuing these and many related avenues can improve our understanding of what goes wrong in mitochondrial disease. Antioxid. Redox Signal. 36, 885-905.
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Affiliation(s)
- Gustavo Carvalho
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Bruno Marçal Repolês
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Isabela Mendes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Paulina H Wanrooij
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
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Kussainova A, Bulgakova O, Aripova A, Khalid Z, Bersimbaev R, Izzotti A. The Role of Mitochondrial miRNAs in the Development of Radon-Induced Lung Cancer. Biomedicines 2022; 10:428. [PMID: 35203638 PMCID: PMC8962319 DOI: 10.3390/biomedicines10020428] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 02/07/2022] [Accepted: 02/07/2022] [Indexed: 12/07/2022] Open
Abstract
MicroRNAs are short, non-coding RNA molecules regulating gene expression by inhibiting the translation of messenger RNA (mRNA) or leading to degradation. The miRNAs are encoded in the nuclear genome and exported to the cytosol. However, miRNAs have been found in mitochondria and are probably derived from mitochondrial DNA. These miRNAs are able to directly regulate mitochondrial genes and mitochondrial activity. Mitochondrial dysfunction is the cause of many diseases, including cancer. In this review, we consider the role of mitochondrial miRNAs in the pathogenesis of lung cancer with particular reference to radon exposure.
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Affiliation(s)
- Assiya Kussainova
- Department of Health Sciences, University of Genova, Via Pastore 1, 16132 Genoa, Italy; (A.K.); (Z.K.)
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Nur-Sultan, Akmola 010008, Kazakhstan; (O.B.); (A.A.)
| | - Olga Bulgakova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Nur-Sultan, Akmola 010008, Kazakhstan; (O.B.); (A.A.)
| | - Akmaral Aripova
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Nur-Sultan, Akmola 010008, Kazakhstan; (O.B.); (A.A.)
| | - Zumama Khalid
- Department of Health Sciences, University of Genova, Via Pastore 1, 16132 Genoa, Italy; (A.K.); (Z.K.)
| | - Rakhmetkazhi Bersimbaev
- Department of General Biology and Genomics, Institute of Cell Biology and Biotechnology, L.N. Gumilyov Eurasian National University, Nur-Sultan, Akmola 010008, Kazakhstan; (O.B.); (A.A.)
| | - Alberto Izzotti
- Department of Experimental Medicine, University of Genoa, 16132 Genoa, Italy
- IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
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Nadalutti CA, Ayala-Peña S, Santos JH. Mitochondrial DNA damage as driver of cellular outcomes. Am J Physiol Cell Physiol 2022; 322:C136-C150. [PMID: 34936503 PMCID: PMC8799395 DOI: 10.1152/ajpcell.00389.2021] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Mitochondria are primarily involved in energy production through the process of oxidative phosphorylation (OXPHOS). Increasing evidence has shown that mitochondrial function impacts a plethora of different cellular activities, including metabolism, epigenetics, and innate immunity. Like the nucleus, mitochondria own their genetic material, but this organellar genome is circular, present in multiple copies, and maternally inherited. The mitochondrial DNA (mtDNA) encodes 37 genes that are solely involved in OXPHOS. Maintenance of mtDNA, through replication and repair, requires the import of nuclear DNA-encoded proteins. Thus, mitochondria completely rely on the nucleus to prevent mitochondrial genetic alterations. As most cells contain hundreds to thousands of mitochondria, it follows that the shear number of organelles allows for the buffering of dysfunction-at least to some extent-before tissue homeostasis becomes impaired. Only red blood cells lack mitochondria entirely. Impaired mitochondrial function is a hallmark of aging and is involved in a number of different disorders, including neurodegenerative diseases, diabetes, cancer, and autoimmunity. Although alterations in mitochondrial processes unrelated to OXPHOS, such as fusion and fission, contribute to aging and disease, maintenance of mtDNA integrity is critical for proper organellar function. Here, we focus on how mtDNA damage contributes to cellular dysfunction and health outcomes.
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Affiliation(s)
- Cristina A. Nadalutti
- 1Mechanistic Toxicology Branch, Division of the National Toxicology
Program (DNTP), National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Research Triangle Park, North Carolina
| | - Sylvette Ayala-Peña
- 2Department of Pharmacology and Toxicology, University of Puerto Rico Medical Sciences Campus, San Juan, Puerto Rico
| | - Janine H. Santos
- 1Mechanistic Toxicology Branch, Division of the National Toxicology
Program (DNTP), National Institute of Environmental Health Sciences (NIEHS), National Institutes of Health (NIH), Research Triangle Park, North Carolina
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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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Musson R, Gąsior Ł, Bisogno S, Ptak GE. DNA damage in preimplantation embryos and gametes: specification, clinical relevance and repair strategies. Hum Reprod Update 2022; 28:376-399. [PMID: 35021196 PMCID: PMC9071077 DOI: 10.1093/humupd/dmab046] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/13/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND DNA damage is a hazard that affects all cells of the body. DNA-damage repair (DDR) mechanisms are in place to repair damage and restore cellular function, as are other damage-induced processes such as apoptosis, autophagy and senescence. The resilience of germ cells and embryos in response to DNA damage is less well studied compared with other cell types. Given that recent studies have described links between embryonic handling techniques and an increased likelihood of disease in post-natal life, an update is needed to summarize the sources of DNA damage in embryos and their capacity to repair it. In addition, numerous recent publications have detailed novel techniques for detecting and repairing DNA damage in embryos. This information is of interest to medical or scientific personnel who wish to obtain undamaged embryos for use in offspring generation by ART. OBJECTIVE AND RATIONALE This review aims to thoroughly discuss sources of DNA damage in male and female gametes and preimplantation embryos. Special consideration is given to current knowledge and limits in DNA damage detection and screening strategies. Finally, obstacles and future perspectives in clinical diagnosis and treatment (repair) of DNA damaged embryos are discussed. SEARCH METHODS Using PubMed and Google Scholar until May 2021, a comprehensive search for peer-reviewed original English-language articles was carried out using keywords relevant to the topic with no limits placed on time. Keywords included ‘DNA damage repair’, ‘gametes’, ‘sperm’, ‘oocyte’, ‘zygote’, ‘blastocyst’ and ‘embryo’. References from retrieved articles were also used to obtain additional articles. Literature on the sources and consequences of DNA damage on germ cells and embryos was also searched. Additional papers cited by primary references were included. Results from our own studies were included where relevant. OUTCOMES DNA damage in gametes and embryos can differ greatly based on the source and severity. This damage affects the development of the embryo and can lead to long-term health effects on offspring. DDR mechanisms can repair damage to a certain extent, but the factors that play a role in this process are numerous and altogether not well characterized. In this review, we describe the multifactorial origin of DNA damage in male and female gametes and in the embryo, and suggest screening strategies for the selection of healthy gametes and embryos. Furthermore, possible therapeutic solutions to decrease the frequency of DNA damaged gametes and embryos and eventually to repair DNA and increase mitochondrial quality in embryos before their implantation is discussed. WIDER IMPLICATIONS Understanding DNA damage in gametes and embryos is essential for the improvement of techniques that could enhance embryo implantation and pregnancy success. While our knowledge about DNA damage factors and regulatory mechanisms in cells has advanced greatly, the number of feasible practical techniques to avoid or repair damaged embryos remains scarce. Our intention is therefore to focus on strategies to obtain embryos with as little DNA damage as possible, which will impact reproductive biology research with particular significance for reproductive clinicians and embryologists.
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Affiliation(s)
- Richard Musson
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Łukasz Gąsior
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Simona Bisogno
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Grażyna Ewa Ptak
- Malopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
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Leuthner TC, Meyer JN. Mitochondrial DNA Mutagenesis: Feature of and Biomarker for Environmental Exposures and Aging. Curr Environ Health Rep 2021; 8:294-308. [PMID: 34761353 PMCID: PMC8826492 DOI: 10.1007/s40572-021-00329-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/24/2021] [Indexed: 01/12/2023]
Abstract
PURPOSE OF REVIEW Mitochondrial dysfunction is a hallmark of aging. Mitochondrial genome (mtDNA) instability contributes to mitochondrial dysfunction, and mtDNA mutagenesis may contribute to aging. However, the origin of mtDNA mutations remains somewhat controversial. The goals of this review are to introduce and review recent literature on mtDNA mutagenesis and aging, address recent animal and epidemiological evidence for the effects of chemicals on mtDNA damage and mutagenesis, propose hypotheses regarding the contribution of environmental toxicant exposure to mtDNA mutagenesis in the context of aging, and suggest future directions and approaches for environmental health researchers. RECENT FINDINGS Stressors such as pollutants, pharmaceuticals, and ultraviolet radiation can damage the mitochondrial genome or disrupt mtDNA replication, repair, and organelle homeostatic processes, potentially influencing the rate of accumulation of mtDNA mutations. Accelerated mtDNA mutagenesis could contribute to aging, diseases of aging, and sensitize individuals with pathogenic mtDNA variants to stressors. We propose three potential mechanisms of toxicant-induced effects on mtDNA mutagenesis over lifespan: (1) increased de novo mtDNA mutations, (2) altered frequencies of mtDNA mutations, or (3) both. There are remarkably few studies that have investigated the impact of environmental chemical exposures on mtDNA instability and mutagenesis, and even fewer in the context of aging. More studies are warranted because people are exposed to tens of thousands of chemicals, and are living longer. Finally, we suggest that toxicant-induced mtDNA damage and mutational signatures may be a sensitive biomarker for some exposures.
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Affiliation(s)
- Tess C Leuthner
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA
| | - Joel N Meyer
- Nicholas School of the Environment, 9 Circuit Dr, Box 90328, Duke University, NC, 27708, USA.
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Abdullaev SA, Glukhov SI, Gaziev AI. Radioprotective and Radiomitigative Effects of Melatonin in Tissues with Different Proliferative Activity. Antioxidants (Basel) 2021; 10:1885. [PMID: 34942988 PMCID: PMC8698738 DOI: 10.3390/antiox10121885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 11/18/2021] [Accepted: 11/24/2021] [Indexed: 12/13/2022] Open
Abstract
We used various markers to analyze damage to mouse tissues (spleen and cerebral cortex) which have different proliferative activity and sensitivity to ionizing radiation (IR). We also assessed the degree of modulation of damages that occurs when melatonin is administered to mice prior to and after their X-ray irradiation. The data from this study showed that lesions in nuclear DNA (nDNA) were repaired more actively in the spleen than in the cerebral cortex of mice irradiated and treated with melatonin (N-acetyl-5-methoxytryptamine). Mitochondrial biogenesis involving mitochondrial DNA (mtDNA) synthesis was activated in both tissues of irradiated mice. A significant proportion of the newly synthesized mtDNA molecules were mutant copies that increase oxidative stress. Melatonin reduced the number of mutant mtDNA copies and the level of H2O2 in both tissues of the irradiated mice. Melatonin promoted the restoration of ATP levels in the tissues of irradiated mice. In the mouse tissues after exposure to X-ray, the level of malondialdehyde (MDA) increased and melatonin was able to reduce it. The MDA concentration was higher in the cerebral cortex tissue than that in the spleen tissue of the mouse. In mouse tissues following irradiation, the glutathione (GSH) level was low. The spleen GSH content was more than twice as low as that in the cerebral cortex. Melatonin helped restore the GSH levels in the mouse tissues. Although the spleen and cerebral cortex tissues of mice differ in the baseline values of the analyzed markers, the radioprotective and radiomitigative potential of melatonin was observed in both tissues.
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Affiliation(s)
- Serazhutdin A. Abdullaev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, 142290 Moscow Region, Russia; (S.I.G.); (A.I.G.)
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Allkanjari K, Baldock RA. Beyond base excision repair: an evolving picture of mitochondrial DNA repair. Biosci Rep 2021; 41:BSR20211320. [PMID: 34608928 PMCID: PMC8527207 DOI: 10.1042/bsr20211320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 09/29/2021] [Accepted: 10/04/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondria are highly specialised organelles required for key cellular processes including ATP production through cellular respiration and controlling cell death via apoptosis. Unlike other organelles, mitochondria contain their own DNA genome which encodes both protein and RNA required for cellular respiration. Each cell may contain hundreds to thousands of copies of the mitochondrial genome, which is essential for normal cellular function - deviation of mitochondrial DNA (mtDNA) copy number is associated with cellular ageing and disease. Furthermore, mtDNA lesions can arise from both endogenous or exogenous sources and must either be tolerated or corrected to preserve mitochondrial function. Importantly, replication of damaged mtDNA can lead to stalling and introduction of mutations or genetic loss, mitochondria have adapted mechanisms to repair damaged DNA. These mechanisms rely on nuclear-encoded DNA repair proteins that are translocated into the mitochondria. Despite the presence of many known nuclear DNA repair proteins being found in the mitochondrial proteome, it remains to be established which DNA repair mechanisms are functional in mammalian mitochondria. Here, we summarise the existing and emerging research, alongside examining proteomic evidence, demonstrating that mtDNA damage can be repaired using Base Excision Repair (BER), Homologous Recombination (HR) and Microhomology-mediated End Joining (MMEJ). Critically, these repair mechanisms do not operate in isolation and evidence for interplay between pathways and repair associated with replication is discussed. Importantly, characterising non-canonical functions of key proteins and understanding the bespoke pathways used to tolerate, repair or bypass DNA damage will be fundamental in fully understanding the causes of mitochondrial genome mutations and mitochondrial dysfunction.
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Affiliation(s)
- Kathrin Allkanjari
- Formerly: Solent University Southampton, East Park Terrace, Southampton, SO14 0YN, UK
| | - Robert A. Baldock
- School of Natural and Social Sciences, University of Gloucestershire, Francis Close Hall, Swindon Road, Cheltenham GL50 4AZ, UK
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Tang JX, Pyle A, Taylor RW, Oláhová M. Interrogating Mitochondrial Biology and Disease Using CRISPR/Cas9 Gene Editing. Genes (Basel) 2021; 12:genes12101604. [PMID: 34680998 PMCID: PMC8536160 DOI: 10.3390/genes12101604] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/07/2021] [Accepted: 10/09/2021] [Indexed: 12/21/2022] Open
Abstract
Mitochondrial disease originates from genetic changes that impact human bodily functions by disrupting the mitochondrial oxidative phosphorylation system. MitoCarta is a curated and published inventory that sheds light on the mitochondrial proteome, but the function of some mitochondrially-localised proteins remains poorly characterised. Consequently, various gene editing systems have been employed to uncover the involvement of these proteins in mitochondrial biology and disease. CRISPR/Cas9 is an efficient, versatile, and highly accurate genome editing tool that was first introduced over a decade ago and has since become an indispensable tool for targeted genetic manipulation in biological research. The broad spectrum of CRISPR/Cas9 applications serves as an attractive and tractable system to study genes and pathways that are essential for the regulation and maintenance of mitochondrial health. It has opened possibilities of generating reliable cell and animal models of human disease, and with further exploitation of the technology, large-scale genomic screenings have uncovered a wealth of fundamental mechanistic insights. In this review, we describe the applications of CRISPR/Cas9 system as a genome editing tool to uncover new insights into pathomechanisms of mitochondrial diseases and/or biological processes involved in mitochondrial function.
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Affiliation(s)
- Jia-Xin Tang
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (J.-X.T.); (A.P.); (R.W.T.)
| | - Angela Pyle
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (J.-X.T.); (A.P.); (R.W.T.)
| | - Robert W. Taylor
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (J.-X.T.); (A.P.); (R.W.T.)
- NHS Highly Specialised Service for Rare Mitochondrial Disorders, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne NE2 4HH, UK
| | - Monika Oláhová
- Wellcome Centre for Mitochondrial Research, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, UK; (J.-X.T.); (A.P.); (R.W.T.)
- Correspondence:
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Nadalutti CA, Prasad R, Wilson SH. Perspectives on formaldehyde dysregulation: Mitochondrial DNA damage and repair in mammalian cells. DNA Repair (Amst) 2021; 105:103134. [PMID: 34116475 PMCID: PMC9014805 DOI: 10.1016/j.dnarep.2021.103134] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Revised: 04/21/2021] [Accepted: 05/09/2021] [Indexed: 12/15/2022]
Abstract
Maintaining genome stability involves coordination between different subcellular compartments providing cells with DNA repair systems that safeguard against environmental and endogenous stresses. Organisms produce the chemically reactive molecule formaldehyde as a component of one-carbon metabolism, and cells maintain systems to regulate endogenous levels of formaldehyde under physiological conditions, preventing genotoxicity, among other adverse effects. Dysregulation of formaldehyde is associated with several diseases, including cancer and neurodegenerative disorders. In the present review, we discuss the complex topic of endogenous formaldehyde metabolism and summarize advances in research on fo dysregulation, along with future research perspectives.
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Affiliation(s)
- Cristina A Nadalutti
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Rajendra Prasad
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA
| | - Samuel H Wilson
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, Research Triangle Park, NC 27709, USA.
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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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Mosquera A, Guillén R, Otero F, Rego-Pérez I, Blanco FJ, Fernández JL. Design of a digital-PCR assay to quantify fragmented human mitochondrial DNA. ENVIRONMENTAL AND MOLECULAR MUTAGENESIS 2021; 62:364-373. [PMID: 34115400 DOI: 10.1002/em.22449] [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: 04/21/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 06/12/2023]
Abstract
Digital PCR (dPCR) has been adapted to quantify the proportion of mitochondrial DNA (mtDNA) molecules without and with double-strand DNA breaks (DSBs). This is based on a break-apart approach of two differentially labeled target sequences distantly located in the circular DNA molecule. When the two targets amplify in separated reaction partitions, the original mtDNA molecule should be fragmented by two DSBs at least, each in a different segment between targets. When both targets amplify in the same partition, it must correspond to a circular or linear mtDNA molecule. These two possibilities may be distinguished through a restriction endonuclease (RE) induced unique DSB within a DNA segment between the targets. After RE-digestion, separation of both target signals in different partitions must indicate the presence of a previous linear mtDNA molecule. Otherwise, joint amplification in the same partition would correspond to an initial circular mtDNA that has been linearized by the endonuclease. The procedure was validated by assaying different proportions of mtDNA fragmented by in vitro digestion with REs, evidencing a perfect accordance between the expected theoretical values and dPCR quantification. Samples from peripheral blood cells, cellular and extracellular DNA from the U2OS cell line, as well as cells incubated with ethidium bromide to induce mtDNA depletion, were evaluated. The technique may be of interest to complement the studies of mtDNA in relation to aging and human disease, as well as to assess possible adverse effects of certain drugs that could be related to affectation of mtDNA.
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Affiliation(s)
- Alejandro Mosquera
- Genetics Unit, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Rebeca Guillén
- Genetics Unit, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
- Centro Oncológico de Galicia, Laboratory of Genetics and Radiobiology, A Coruña, Spain
| | - Fátima Otero
- Genetics Unit, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
- Centro Oncológico de Galicia, Laboratory of Genetics and Radiobiology, A Coruña, Spain
| | - Ignacio Rego-Pérez
- Rheumatology Division, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - Francisco J Blanco
- Rheumatology Division, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
| | - José Luis Fernández
- Genetics Unit, INIBIC-Complexo Hospitalario Universitario A Coruña (CHUAC), A Coruña, Spain
- Centro Oncológico de Galicia, Laboratory of Genetics and Radiobiology, A Coruña, Spain
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46
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Liang H, Liu J, Su S, Zhao Q. Mitochondrial noncoding RNAs: new wine in an old bottle. RNA Biol 2021; 18:2168-2182. [PMID: 34110970 DOI: 10.1080/15476286.2021.1935572] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Mitochondrial noncoding RNAs (mt-ncRNAs) include noncoding RNAs inside the mitochondria that are transcribed from the mitochondrial genome or nuclear genome, and noncoding RNAs transcribed from the mitochondrial genome that are transported to the cytosol or nucleus. Recent findings have revealed that mt-ncRNAs play important roles in not only mitochondrial functions, but also other cellular activities. This review proposes a classification of mt-ncRNAs and outlines the emerging understanding of mitochondrial circular RNAs (mt-circRNAs), mitochondrial microRNAs (mitomiRs), and mitochondrial long noncoding RNAs (mt-lncRNAs), with an emphasis on their identification and functions.
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Affiliation(s)
- Huixin Liang
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China
| | - Jiayu Liu
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Shicheng Su
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Breast Tumor Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Department of Immunology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
| | - Qiyi Zhao
- Department of Infectious Diseases, the Third Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Liver Disease Research, the Third Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong Province, China.,Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, Guangdong Province, China
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47
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Tang C, Cai J, Yin XM, Weinberg JM, Venkatachalam MA, Dong Z. Mitochondrial quality control in kidney injury and repair. Nat Rev Nephrol 2021; 17:299-318. [PMID: 33235391 PMCID: PMC8958893 DOI: 10.1038/s41581-020-00369-0] [Citation(s) in RCA: 220] [Impact Index Per Article: 73.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/19/2020] [Indexed: 01/30/2023]
Abstract
Mitochondria are essential for the activity, function and viability of eukaryotic cells and mitochondrial dysfunction is involved in the pathogenesis of acute kidney injury (AKI) and chronic kidney disease, as well as in abnormal kidney repair after AKI. Multiple quality control mechanisms, including antioxidant defence, protein quality control, mitochondrial DNA repair, mitochondrial dynamics, mitophagy and mitochondrial biogenesis, have evolved to preserve mitochondrial homeostasis under physiological and pathological conditions. Loss of these mechanisms may induce mitochondrial damage and dysfunction, leading to cell death, tissue injury and, potentially, organ failure. Accumulating evidence suggests a role of disturbances in mitochondrial quality control in the pathogenesis of AKI, incomplete or maladaptive kidney repair and chronic kidney disease. Moreover, specific interventions that target mitochondrial quality control mechanisms to preserve and restore mitochondrial function have emerged as promising therapeutic strategies to prevent and treat kidney injury and accelerate kidney repair. However, clinical translation of these findings is challenging owing to potential adverse effects, unclear mechanisms of action and a lack of knowledge of the specific roles and regulation of mitochondrial quality control mechanisms in kidney resident and circulating cell types during injury and repair of the kidney.
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Affiliation(s)
- Chengyuan Tang
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Juan Cai
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China
| | - Xiao-Ming Yin
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Joel M. Weinberg
- Department of Medicine, University of Michigan Medical Center, Ann Arbor, MI, USA
| | - Manjeri A. Venkatachalam
- Department of Pathology, University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Zheng Dong
- Department of Nephrology, Hunan Key Laboratory of Kidney Disease and Blood Purification, The Second Xiangya Hospital at Central South University, Changsha, China.,Department of Cellular Biology and Anatomy, Medical College of Georgia at Augusta University and Charlie Norwood VA Medical Center, Augusta, GA, USA.,
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48
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Oshima Y, Cartier E, Boyman L, Verhoeven N, Polster BM, Huang W, Kane M, Lederer WJ, Karbowski M. Parkin-independent mitophagy via Drp1-mediated outer membrane severing and inner membrane ubiquitination. J Cell Biol 2021; 220:211984. [PMID: 33851959 PMCID: PMC8050842 DOI: 10.1083/jcb.202006043] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 02/02/2021] [Accepted: 03/15/2021] [Indexed: 02/07/2023] Open
Abstract
Here, we report that acute reduction in mitochondrial translation fidelity (MTF) causes ubiquitination of the inner mitochondrial membrane (IMM) proteins, including TRAP1 and CPOX, which occurs selectively in mitochondria with a severed outer mitochondrial membrane (OMM). Ubiquitinated IMM recruits the autophagy machinery. Inhibiting autophagy leads to increased accumulation of mitochondria with severed OMM and ubiquitinated IMM. This process occurs downstream of the accumulation of cytochrome c/CPOX in a subset of mitochondria heterogeneously distributed throughout the cell (“mosaic distribution”). Formation of mosaic mitochondria, OMM severing, and IMM ubiquitination require active mitochondrial translation and mitochondrial fission, but not the proapoptotic proteins Bax and Bak. In contrast, in Parkin-overexpressing cells, MTF reduction does not lead to the severing of the OMM or IMM ubiquitination, but it does induce Drp1-independent ubiquitination of the OMM. Furthermore, high–cytochrome c/CPOX mitochondria are preferentially targeted by Parkin, indicating that in the context of reduced MTF, they are mitophagy intermediates regardless of Parkin expression. In sum, Parkin-deficient cells adapt to mitochondrial proteotoxicity through a Drp1-mediated mechanism that involves the severing of the OMM and autophagy targeting ubiquitinated IMM proteins.
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Affiliation(s)
- Yumiko Oshima
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD
| | - Etienne Cartier
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD
| | - Liron Boyman
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD
| | - Nicolas Verhoeven
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD
| | - Brian M Polster
- Department of Anesthesiology and Center for Shock, Trauma, and Anesthesiology Research, University of Maryland School of Medicine, Baltimore, MD
| | - Weiliang Huang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - Maureen Kane
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD
| | - W Jonathan Lederer
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD.,Department of Physiology, University of Maryland School of Medicine, Baltimore, MD
| | - Mariusz Karbowski
- Center for Biomedical Engineering and Technology, University of Maryland School of Medicine, Baltimore, MD.,Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD
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49
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Hussain SRA, Yalvac ME, Khoo B, Eckardt S, McLaughlin KJ. Adapting CRISPR/Cas9 System for Targeting Mitochondrial Genome. Front Genet 2021; 12:627050. [PMID: 33889176 PMCID: PMC8055930 DOI: 10.3389/fgene.2021.627050] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Gene editing of the mitochondrial genome using the CRISPR-Cas9 system is highly challenging mainly due to sub-efficient delivery of guide RNA and Cas9 enzyme complexes into the mitochondria. In this study, we were able to perform gene editing in the mitochondrial DNA by appending an NADH-ubiquinone oxidoreductase chain 4 (ND4) targeting guide RNA to an RNA transport-derived stem loop element (RP-loop) and expressing the Cas9 enzyme with a preceding mitochondrial localization sequence. We observe mitochondrial colocalization of RP-loop gRNA and a marked reduction of ND4 expression in the cells carrying a 11205G variant in their ND4 sequence coincidently decreasing the mtDNA levels. This proof-of-concept study suggests that a stem-loop element added sgRNA can be transported to the mitochondria and functionally interact with Cas9 to mediate sequence-specific mtDNA cleavage. Using this novel approach to target the mtDNA, our results provide further evidence that CRISPR-Cas9-mediated gene editing might potentially be used to treat mitochondrial-related diseases.
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Affiliation(s)
- Syed-Rehan A Hussain
- Center for Molecular and Human Genetics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States.,Center for Clinical and Translational Research, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States
| | - Mehmet E Yalvac
- Department of Neurology, The Ohio State University Wexner Medical Center, Columbus, OH, United States
| | - Benedict Khoo
- Center for Molecular and Human Genetics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States
| | - Sigrid Eckardt
- Center for Molecular and Human Genetics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States
| | - K John McLaughlin
- Center for Molecular and Human Genetics, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, United States
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50
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Elesela S, Lukacs NW. Role of Mitochondria in Viral Infections. Life (Basel) 2021; 11:life11030232. [PMID: 33799853 PMCID: PMC7998235 DOI: 10.3390/life11030232] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 12/15/2022] Open
Abstract
Viral diseases account for an increasing proportion of deaths worldwide. Viruses maneuver host cell machinery in an attempt to subvert the intracellular environment favorable for their replication. The mitochondrial network is highly susceptible to physiological and environmental insults, including viral infections. Viruses affect mitochondrial functions and impact mitochondrial metabolism, and innate immune signaling. Resurgence of host-virus interactions in recent literature emphasizes the key role of mitochondria and host metabolism on viral life processes. Mitochondrial dysfunction leads to damage of mitochondria that generate toxic compounds, importantly mitochondrial DNA, inducing systemic toxicity, leading to damage of multiple organs in the body. Mitochondrial dynamics and mitophagy are essential for the maintenance of mitochondrial quality control and homeostasis. Therefore, metabolic antagonists may be essential to gain a better understanding of viral diseases and develop effective antiviral therapeutics. This review briefly discusses how viruses exploit mitochondrial dynamics for virus proliferation and induce associated diseases.
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Affiliation(s)
- Srikanth Elesela
- Department of Pathology, Michigan Medicine, Ann Arbor, MI 48109, USA
- Correspondence:
| | - Nicholas W. Lukacs
- Mary H. Weiser Food Allergy Center, Michigan Medicine, Ann Arbor, MI 48109, USA;
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