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Yardeni T, Olali AZ, Chen HW, Wang L, Halton JA, Zenab A, Morrow R, Butic A, Murdock DG, Waymire KG, MacGregor GR, Boursi B, Beier UH, Hancock WW, Wallace DC. Mitochondrial DNA lineages determine tumor progression through T cell reactive oxygen signaling. Proc Natl Acad Sci U S A 2025; 122:e2417252121. [PMID: 39752523 PMCID: PMC11725793 DOI: 10.1073/pnas.2417252121] [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: 08/24/2024] [Accepted: 11/25/2024] [Indexed: 01/15/2025] Open
Abstract
Mitochondrial DNA (mtDNA) is highly polymorphic, and host mtDNA variation has been associated with altered cancer severity. To determine the basis of this mtDNA-cancer association, we analyzed conplastic mice with the C57BL/6J (B6) nucleus but two naturally occurring mtDNA lineages, mtDNAB6 and mtDNANZB, where mtDNANZB mitochondria generate more oxidative phosphorylation (OXPHOS)-derived reactive oxygen species (mROS). In a cardiac transplant model, mtDNAB6 Foxp3+ T regulatory (Treg) cells supported long-term allograft survival, whereas mtDNANZB Treg cells failed to suppress host T effector (Teff) cells, leading to acute rejection. When challenged with melanoma or colon cancer cells, the mtDNANZB mice exhibited strikingly impaired tumor growth while mtDNAB6 mice showed Treg-dependent inhibition of Teff cells and allowed rapid tumor growth. Transcriptional analysis showed that activation of mtDNANZB Teff cells increased mitochondrial gene expression while activation of mtDNANZB Treg cells impaired mitochondrial gene expression and resulted in mtDNANZB Treg cell exhaustion. Induction of the mitochondrially targeted catalytic antioxidant, mCAT, in hematopoietic cells normalized mtDNANZB Treg function in both transplant and tumor models, indicating a key role for mROS in promoting Treg dysfunction. Anti-PD-L1 therapy did not modulate these effects, indicating that modulation of host mitochondrial function provides an independent approach for enhancing tumor cell destruction.
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Affiliation(s)
- Tal Yardeni
- Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Bert Strassburger Metabolic Center for Preventive Medicine, Sheba Medical Center, Tel Hashomer5262000, Israel
| | - Arnold Z. Olali
- Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Hsiao-Wen Chen
- Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Liqing Wang
- Division of Transplant Immunology, Children’s Hospital of Philadelphia and Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Jeffrey A. Halton
- Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Angi Zenab
- Bert Strassburger Metabolic Center for Preventive Medicine, Sheba Medical Center, Tel Hashomer5262000, Israel
| | - Ryan Morrow
- Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Arrienne Butic
- Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
| | - Deborah G. Murdock
- Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Division of Human Genetics, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Katrina G. Waymire
- Department of Developmental and Cell Biology, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA92697-2300
| | - Grant R. MacGregor
- Department of Developmental and Cell Biology, Charlie Dunlop School of Biological Sciences, University of California, Irvine, CA92697-2300
| | - Ben Boursi
- Division of Oncology, Sheba Medical Center, Tel-Hashomer, Tel-Aviv University, Tel Aviv5262000, Israel
- Center for Clinical Epidemiology and Biostatistics, Department of Biostatistics and Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Ulf H. Beier
- Immunology, Johnson & Johnson Innovative Medicine, Spring House, PA19477
| | - Wayne W. Hancock
- Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Division of Transplant Immunology, Children’s Hospital of Philadelphia and Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA19104
| | - Douglas C. Wallace
- Center for Mitochondrial and Epigenomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA19104
- Division of Human Genetics, Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA19104
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Chen S, Lu H, Yin G, Zhang X, Meng D, Yu W, Wang L, Liu H, Zhang F. Hesperitin prevents non-alcoholic steatohepatitis by modulating mitochondrial dynamics and mitophagy via the AMPKα-Drp1/PINK1-Parkin signaling pathway. Biochim Biophys Acta Mol Cell Biol Lipids 2025; 1870:159570. [PMID: 39454819 DOI: 10.1016/j.bbalip.2024.159570] [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: 11/20/2023] [Revised: 10/02/2024] [Accepted: 10/07/2024] [Indexed: 10/28/2024]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is becoming a global public health burden, yet effective therapeutic strategies are notably lacking. NAFLD development may be mediated by mitochondrial dysfunction, according to new research. Producing mitochondrial regulators from plant-based substances to treat mitochondrial dysfunction is an appealing approach to treating NAFLD. Hesperetin (HES) is a flavonoid that is found naturally and is a member of the flavanone family. This study aims to clarify the mechanism of HES in preventing NAFLD which is caused by a high-fat diet (HFD). Serum and liver biochemical parameters, liver histology, lipid profiles, and mitochondrial function were evaluated in HFD-induced NAFLD Sprague-Dawley (SD) rats. HES treatment significantly reduced body weight gain, liver weight, and the liver index, while also improving hepatic steatosis, lipid metabolism disorders, and mitochondrial dysfunction in rats with NAFLD. The mechanism was investigated and confirmed using western blot and real-time quantitative polymerase chain reaction (RT-qPCR). We showed that in the liver of NAFLD rats, HES decreased the expression of dynamic-related protein 1 (Drp1), phosphorylated Drp1 at serine-616 (Drp1-pS616) and induced phosphorylated Drp1 at serine-637 (Drp1-pS637), PTEN-induced kinase 1 (PINK1), and E3 Ubiquitin-Protein Ligase Parkin (Parkin) via an AMP-activated protein kinase alpha (AMPKα)-dependent mechanism. Moreover, HES increased the expression of the mitochondrial fusion proteins mitofusin-2 (Mfn2) and optic atrophy 1 (Opa1) while suppressing the expression of fission protein 1 (Fis1). In this work, we identify a unique mechanism by which HES prevents NAFLD from developing. HES may be an attractive potential therapeutic agent to cure NAFLD.
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Affiliation(s)
- Suwen Chen
- Shandong University of Traditional Chinese Medicine, Jinan 250013, China; Department of Cardiology, Guang'anmen Hospital, China Academy of Chinese Medical Sciences, Beijing 100032, China
| | - Haifei Lu
- Huanggang Hospital of Chinese Medicine, Affiliated to Hubei University of Chinese Medicine, Huanggang 438000, China
| | - Guoliang Yin
- Shandong University of Traditional Chinese Medicine, Jinan 250013, China
| | - Xin Zhang
- Shandong University of Traditional Chinese Medicine, Jinan 250013, China
| | - Decheng Meng
- Shandong University of Traditional Chinese Medicine, Jinan 250013, China
| | - Wenfei Yu
- Shandong University of Traditional Chinese Medicine, Jinan 250013, China
| | - Linya Wang
- Shandong University of Traditional Chinese Medicine, Jinan 250013, China
| | - Hongshuai Liu
- Shandong University of Traditional Chinese Medicine, Jinan 250013, China
| | - Fengxia Zhang
- Department of Neurology, Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250013, China.
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3
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Liang R, Zhu L, Huang Y, Chen J, Tang Q. Mitochondria: fundamental characteristics, challenges, and impact on aging. Biogerontology 2024; 25:923-941. [PMID: 39196438 DOI: 10.1007/s10522-024-10132-8] [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: 07/09/2024] [Accepted: 08/20/2024] [Indexed: 08/29/2024]
Abstract
As one of the most vital organelles within biological cells, mitochondria hold an irreplaceable status and play crucial roles in various diseases. Research and therapies targeting mitochondria have achieved significant progress in numerous conditions. Throughout an organism's lifespan, mitochondrial dynamics persist continuously, and due to their inherent characteristics and various external factors, mitochondria are highly susceptible to damage. This susceptibility is particularly evident during aging, where the decline in biological function is closely intertwined with mitochondrial dysfunction. Despite being an ancient and enigmatic organelle, much remains unknown about mitochondria. Here, we will explore the past and present knowledge of mitochondria, providing a comprehensive review of their intrinsic properties and interactions with nuclear DNA, as well as the challenges and impacts they face during the aging process.
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Affiliation(s)
- Runyu Liang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Luwen Zhu
- Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China
| | - Yongyin Huang
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Jia Chen
- Heilongjiang University of Chinese Medicine, Harbin, China
| | - Qiang Tang
- Second Affiliated Hospital of Heilongjiang University of Chinese Medicine, Harbin, China.
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Veeraragavan S, Johansen M, Johnston IG. Evolution and maintenance of mtDNA gene content across eukaryotes. Biochem J 2024; 481:1015-1042. [PMID: 39101615 PMCID: PMC11346449 DOI: 10.1042/bcj20230415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Revised: 06/26/2024] [Accepted: 07/18/2024] [Indexed: 08/06/2024]
Abstract
Across eukaryotes, most genes required for mitochondrial function have been transferred to, or otherwise acquired by, the nucleus. Encoding genes in the nucleus has many advantages. So why do mitochondria retain any genes at all? Why does the set of mtDNA genes vary so much across different species? And how do species maintain functionality in the mtDNA genes they do retain? In this review, we will discuss some possible answers to these questions, attempting a broad perspective across eukaryotes. We hope to cover some interesting features which may be less familiar from the perspective of particular species, including the ubiquity of recombination outside bilaterian animals, encrypted chainmail-like mtDNA, single genes split over multiple mtDNA chromosomes, triparental inheritance, gene transfer by grafting, gain of mtDNA recombination factors, social networks of mitochondria, and the role of mtDNA dysfunction in feeding the world. We will discuss a unifying picture where organismal ecology and gene-specific features together influence whether organism X retains mtDNA gene Y, and where ecology and development together determine which strategies, importantly including recombination, are used to maintain the mtDNA genes that are retained.
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Affiliation(s)
| | - Maria Johansen
- Department of Mathematics, University of Bergen, Bergen, Norway
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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Burr SP, Chinnery PF. Origins of tissue and cell-type specificity in mitochondrial DNA (mtDNA) disease. Hum Mol Genet 2024; 33:R3-R11. [PMID: 38779777 PMCID: PMC11112380 DOI: 10.1093/hmg/ddae059] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 12/21/2023] [Accepted: 02/05/2024] [Indexed: 05/25/2024] Open
Abstract
Mutations of mitochondrial (mt)DNA are a major cause of morbidity and mortality in humans, accounting for approximately two thirds of diagnosed mitochondrial disease. However, despite significant advances in technology since the discovery of the first disease-causing mtDNA mutations in 1988, the comprehensive diagnosis and treatment of mtDNA disease remains challenging. This is partly due to the highly variable clinical presentation linked to tissue-specific vulnerability that determines which organs are affected. Organ involvement can vary between different mtDNA mutations, and also between patients carrying the same disease-causing variant. The clinical features frequently overlap with other non-mitochondrial diseases, both rare and common, adding to the diagnostic challenge. Building on previous findings, recent technological advances have cast further light on the mechanisms which underpin the organ vulnerability in mtDNA diseases, but our understanding is far from complete. In this review we explore the origins, current knowledge, and future directions of research in this area.
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Affiliation(s)
- Stephen P Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0QQ, United Kingdom
| | - Patrick F Chinnery
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
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Durán-Sotuela A, Oreiro N, Fernández-Moreno M, Vázquez-García J, Relaño-Fernández S, Balboa-Barreiro V, Blanco FJ, Rego-Pérez I. Mitonuclear epistasis involving TP63 and haplogroup Uk: Risk of rapid progression of knee OA in patients from the OAI. Osteoarthritis Cartilage 2024; 32:526-534. [PMID: 38190960 DOI: 10.1016/j.joca.2023.12.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 12/22/2023] [Accepted: 12/30/2023] [Indexed: 01/10/2024]
Abstract
OBJECTIVE To investigate genetic interactions between mitochondrial deoxyribonucleic acid (mtDNA) haplogroups and nuclear single nucleotide polymorphisms (nSNPs) to analyze their impact on the development of the rapid progression of knee osteoarthritis (OA). DESIGN A total of 1095 subjects from the Osteoarthritis Initiative, with a follow-up time of at least 48-months, were included. Appropriate statistical approaches were performed, including generalized estimating equations adjusting for age, gender, body mass index, contralateral knee OA, Western Ontario and McMaster Universities Osteoarthritis Index pain, previous injury in target knee and the presence of the mtDNA variant m.16519C. Additional genomic data consisted in the genotyping of Caucasian mtDNA haplogroups and eight nSNPs previously associated with the risk of knee OA in robust genome-wide association studies. RESULTS The simultaneous presence of the G allele of rs12107036 at TP63 and the haplogroup Uk significantly increases the risk of a rapid progression of knee OA (odds ratio = 1.670; 95% confidence interval [CI]: 1.031-2.706; adjusted p-value = 0.027). The assessment of the population attributable fraction showed that the highest proportion of rapid progressors was under the simultaneous presence of the G allele of rs12107036 and the haplogroup Uk (23.4%) (95%CI: 7.89-38.9; p-value < 0.05). The area under the curve of the cross-validation model (0.730) was very similar to the obtained for the predictive model (0.735). A nomogram was constructed to help clinicians to perform clinical trials or epidemiologic studies. CONCLUSIONS This study demonstrates the existence of a mitonuclear epistasis in OA, providing new mechanisms by which nuclear and mitochondrial variation influence the susceptibility to develop different OA phenotypes.
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Affiliation(s)
- Alejandro Durán-Sotuela
- Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), C/ As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Natividad Oreiro
- Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), C/ As Xubias de Arriba 84, 15006 A Coruña, Spain; Centro de Investigación Biomédica en Red de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Mercedes Fernández-Moreno
- Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), C/ As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Jorge Vázquez-García
- Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), C/ As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Sara Relaño-Fernández
- Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), C/ As Xubias de Arriba 84, 15006 A Coruña, Spain
| | - Vanesa Balboa-Barreiro
- Unidad de Apoyo a la Investigación, Grupo de Investigación en Enfermería y Cuidados en Salud, Grupo de Investigación en Reumatología y Salud (GIR-S), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), As Xubias, 15006 A Coruña, Spain
| | - Francisco J Blanco
- Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), C/ As Xubias de Arriba 84, 15006 A Coruña, Spain; Universidade da Coruña (UDC), Centro de Investigación de Ciencias Avanzadas (CICA), Grupo de Investigación en Reumatología y Salud (GIR-S), Departamento de Fisioterapia, Medicina y Ciencias Biomédicas, Facultad de Fisioterapia, Campus de Oza, 15008 A Coruña, Spain
| | - Ignacio Rego-Pérez
- Grupo de Investigación en Reumatología (GIR), Instituto de Investigación Biomédica de A Coruña (INIBIC), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), C/ As Xubias de Arriba 84, 15006 A Coruña, Spain.
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van Heyningen V. Stochasticity in genetics and gene regulation. Philos Trans R Soc Lond B Biol Sci 2024; 379:20230476. [PMID: 38432316 PMCID: PMC10909507 DOI: 10.1098/rstb.2023.0476] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/20/2023] [Indexed: 03/05/2024] Open
Abstract
Development from fertilized egg to functioning multi-cellular organism requires precision. There is no precision, and often no survival, without plasticity. Plasticity is conferred partly by stochastic variation, present inherently in all biological systems. Gene expression levels fluctuate ubiquitously through transcription, alternative splicing, translation and turnover. Small differences in gene expression are exploited to trigger early differentiation, conferring distinct function on selected individual cells and setting in motion regulatory interactions. Non-selected cells then acquire new functions along the spatio-temporal developmental trajectory. The differentiation process has many stochastic components. Meiotic segregation, mitochondrial partitioning, X-inactivation and the dynamic DNA binding of transcription factor assemblies-all exhibit randomness. Non-random X-inactivation generally signals deleterious X-linked mutations. Correct neural wiring, such as retina to brain, arises through repeated confirmatory activity of connections made randomly. In immune system development, both B-cell antibody generation and the emergence of balanced T-cell categories begin through stochastic trial and error followed by functional selection. Aberrant selection processes lead to immune dysfunction. DNA sequence variants also arise through stochastic events: some involving environmental fluctuation (radiation or presence of pollutants), or genetic repair system malfunction. The phenotypic outcome of mutations is also fluid. Mutations may be advantageous in some circumstances, deleterious in others. This article is part of a discussion meeting issue 'Causes and consequences of stochastic processes in development and disease'.
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Affiliation(s)
- Veronica van Heyningen
- UCL Institute of Ophthalmology, University College London, London, EC1V 9EL, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh EH4 2XU, UK
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Spinazzola A, Perez-Rodriguez D, Ježek J, Holt IJ. Mitochondrial DNA competition: starving out the mutant genome. Trends Pharmacol Sci 2024; 45:225-242. [PMID: 38402076 DOI: 10.1016/j.tips.2024.01.011] [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: 09/24/2023] [Revised: 01/11/2024] [Accepted: 01/22/2024] [Indexed: 02/26/2024]
Abstract
High levels of pathogenic mitochondrial DNA (mtDNA) variants lead to severe genetic diseases, and the accumulation of such mutants may also contribute to common disorders. Thus, selecting against these mutants is a major goal in mitochondrial medicine. Although mutant mtDNA can drift randomly, mounting evidence indicates that active forces play a role in the selection for and against mtDNA variants. The underlying mechanisms are beginning to be clarified, and recent studies suggest that metabolic cues, including fuel availability, contribute to shaping mtDNA heteroplasmy. In the context of pathological mtDNAs, remodeling of nutrient metabolism supports mitochondria with deleterious mtDNAs and enables them to outcompete functional variants owing to a replicative advantage. The elevated nutrient requirement represents a mutant Achilles' heel because small molecules that restrict nutrient consumption or interfere with nutrient sensing can purge cells of deleterious mtDNAs and restore mitochondrial respiration. These advances herald the dawn of a new era of small-molecule therapies to counteract pathological mtDNAs.
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Affiliation(s)
- Antonella Spinazzola
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK.
| | - Diego Perez-Rodriguez
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Jan Ježek
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK
| | - Ian J Holt
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, Royal Free Campus, London NW3 2PF, UK; Biodonostia Health Research Institute, 20014 San Sebastián, Spain; IKERBASQUE (Basque Foundation for Science), 48013 Bilbao, Spain; CIBERNED (Center for Networked Biomedical Research on Neurodegenerative Diseases, Ministry of Economy and Competitiveness, Institute Carlos III), 28031 Madrid, Spain; Universidad de País Vasco, Barrio Sarriena s/n, 48940 Leioa, Bilbao, Spain.
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Glynos A, Bozhilova LV, Frison M, Burr S, Stewart JB, Chinnery PF. High-throughput single-cell analysis reveals progressive mitochondrial DNA mosaicism throughout life. SCIENCE ADVANCES 2023; 9:eadi4038. [PMID: 37878704 PMCID: PMC10599618 DOI: 10.1126/sciadv.adi4038] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/21/2023] [Indexed: 10/27/2023]
Abstract
Heteroplasmic mitochondrial DNA (mtDNA) mutations are a major cause of inherited disease and contribute to common late-onset human disorders. The late onset and clinical progression of mtDNA-associated disease is thought to be due to changing heteroplasmy levels, but it is not known how and when this occurs. Performing high-throughput single-cell genotyping in two mouse models of human mtDNA disease, we saw unanticipated cell-to-cell differences in mtDNA heteroplasmy levels that emerged prenatally and progressively increased throughout life. Proliferating spleen cells and nondividing brain cells had a similar single-cell heteroplasmy variance, implicating mtDNA or organelle turnover as the major force determining cell heteroplasmy levels. The two different mtDNA mutations segregated at different rates with no evidence of selection, consistent with different rates of random genetic drift in vivo, leading to the accumulation of cells with a very high mutation burden at different rates. This provides an explanation for differences in severity seen in human diseases caused by similar mtDNA mutations.
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Affiliation(s)
- Angelos Glynos
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Lyuba V. Bozhilova
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Michele Frison
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - Stephen Burr
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
| | - James B. Stewart
- Biosciences Institute, Faculty of Medical Sciences, Wellcome Centre for Mitochondrial Research, Newcastle University, Newcastle upon Tyne, UK
| | - Patrick F. Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK
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10
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Behnam B, Taghizadeh-Hesary F. Mitochondrial Metabolism: A New Dimension of Personalized Oncology. Cancers (Basel) 2023; 15:4058. [PMID: 37627086 PMCID: PMC10452105 DOI: 10.3390/cancers15164058] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Energy is needed by cancer cells to stay alive and communicate with their surroundings. The primary organelles for cellular metabolism and energy synthesis are mitochondria. Researchers recently proved that cancer cells can steal immune cells' mitochondria using nanoscale tubes. This finding demonstrates the dependence of cancer cells on normal cells for their living and function. It also denotes the importance of mitochondria in cancer cells' biology. Emerging evidence has demonstrated how mitochondria are essential for cancer cells to survive in the harsh tumor microenvironments, evade the immune system, obtain more aggressive features, and resist treatments. For instance, functional mitochondria can improve cancer resistance against radiotherapy by scavenging the released reactive oxygen species. Therefore, targeting mitochondria can potentially enhance oncological outcomes, according to this notion. The tumors' responses to anticancer treatments vary, ranging from a complete response to even cancer progression during treatment. Therefore, personalized cancer treatment is of crucial importance. So far, personalized cancer treatment has been based on genomic analysis. Evidence shows that tumors with high mitochondrial content are more resistant to treatment. This paper illustrates how mitochondrial metabolism can participate in cancer resistance to chemotherapy, immunotherapy, and radiotherapy. Pretreatment evaluation of mitochondrial metabolism can provide additional information to genomic analysis and can help to improve personalized oncological treatments. This article outlines the importance of mitochondrial metabolism in cancer biology and personalized treatments.
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Affiliation(s)
- Babak Behnam
- Department of Regulatory Affairs, Amarex Clinical Research, NSF International, Germantown, MD 20874, USA
| | - Farzad Taghizadeh-Hesary
- ENT and Head and Neck Research Center and Department, The Five Senses Health Institute, School of Medicine, Iran University of Medical Sciences, Tehran 1445613131, Iran
- Department of Radiation Oncology, Iran University of Medical Sciences, Tehran 1445613131, Iran
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11
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Rosenberg AM, Saggar M, Monzel AS, Devine J, Rogu P, Limoges A, Junker A, Sandi C, Mosharov EV, Dumitriu D, Anacker C, Picard M. Brain mitochondrial diversity and network organization predict anxiety-like behavior in male mice. Nat Commun 2023; 14:4726. [PMID: 37563104 PMCID: PMC10415311 DOI: 10.1038/s41467-023-39941-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 07/04/2023] [Indexed: 08/12/2023] Open
Abstract
The brain and behavior are under energetic constraints, limited by mitochondrial energy transformation capacity. However, the mitochondria-behavior relationship has not been systematically studied at a brain-wide scale. Here we examined the association between multiple features of mitochondrial respiratory chain capacity and stress-related behaviors in male mice with diverse behavioral phenotypes. Miniaturized assays of mitochondrial respiratory chain enzyme activities and mitochondrial DNA (mtDNA) content were deployed on 571 samples across 17 brain areas, defining specific patterns of mito-behavior associations. By applying multi-slice network analysis to our brain-wide mitochondrial dataset, we identified three large-scale networks of brain areas with shared mitochondrial signatures. A major network composed of cortico-striatal areas exhibited the strongest mitochondria-behavior correlations, accounting for up to 50% of animal-to-animal behavioral differences, suggesting that this mito-based network is functionally significant. The mito-based brain networks also overlapped with regional gene expression and structural connectivity, and exhibited distinct molecular mitochondrial phenotype signatures. This work provides convergent multimodal evidence anchored in enzyme activities, gene expression, and animal behavior that distinct, behaviorally-relevant mitochondrial phenotypes exist across the male mouse brain.
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Affiliation(s)
- Ayelet M Rosenberg
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Manish Saggar
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Anna S Monzel
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Jack Devine
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Peter Rogu
- Columbia University Institute for Developmental Sciences, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Aaron Limoges
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Division of Systems Neuroscience, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Alex Junker
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Carmen Sandi
- Brain Mind Institute, Ecole Polytechnique Federal de Lausanne (EPFL), Lausanne, Switzerland
| | - Eugene V Mosharov
- Division of Molecular Therapeutics, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
| | - Dani Dumitriu
- Columbia University Institute for Developmental Sciences, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, NY, USA
- Division of Developmental Neuroscience, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
| | - Christoph Anacker
- Columbia University Institute for Developmental Sciences, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- Division of Systems Neuroscience, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA
- New York State Psychiatric Institute, New York, NY, USA
| | - Martin Picard
- Division of Behavioral Medicine, Department of Psychiatry, Columbia University Irving Medical Center, New York, NY, USA.
- New York State Psychiatric Institute, New York, NY, USA.
- Department of Neurology, H. Houston Merritt Center, Columbia Translational Neuroscience Initiative, Columbia University Irving Medical Center, New York, NY, USA.
- Robert N Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, NY, USA.
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12
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Tsyba N, Feng G, Grub LK, Held JP, Strozak AM, Burkewitz K, Patel MR. Tissue-specific heteroplasmy segregation is accompanied by a sharp mtDNA decline in Caenorhabditis elegans soma. iScience 2023; 26:106349. [PMID: 36968071 PMCID: PMC10031119 DOI: 10.1016/j.isci.2023.106349] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/08/2022] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Mutations in the mitochondrial genome (mtDNA) can be pathogenic. Owing to the multi-copy nature of mtDNA, wild-type copies can compensate for the effects of mutant mtDNA. Wild-type copies available for compensation vary depending on the mutant load and the total copy number. Here, we examine both mutant load and copy number in the tissues of Caenorhabditis elegans. We found that neurons, but not muscles, have modestly higher mutant load than rest of the soma. We also uncovered different effect of aak-2 knockout on the mutant load in the two tissues. The most surprising result was a sharp decline in somatic mtDNA content over time. The scale of the copy number decline surpasses the modest shifts in mutant load, suggesting that it may exert a substantial effect on mitochondrial function. In summary, measuring both the copy number and the mutant load provides a more comprehensive view of the mutant mtDNA dynamics.
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Affiliation(s)
- Nikita Tsyba
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Gaomin Feng
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232, USA
| | - Lantana K. Grub
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - James P. Held
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Adrianna M. Strozak
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Kristopher Burkewitz
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232, USA
| | - Maulik R. Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN37232, USA
- Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN37232, USA
- Evolutionary Studies, Vanderbilt University, Nashville, TN37235, USA
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13
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Durán-Sotuela A, Fernandez-Moreno M, Suárez-Ulloa V, Vázquez-García J, Relaño S, Hermida-Gómez T, Balboa-Barreiro V, Lourido-Salas L, Calamia V, Fernandez-Puente P, Ruiz-Romero C, Fernández-Tajes J, Vaamonde-García C, de Andrés MC, Oreiro N, Blanco FJ, Rego-Perez I. A meta-analysis and a functional study support the influence of mtDNA variant m.16519C on the risk of rapid progression of knee osteoarthritis. Ann Rheum Dis 2023:ard-2022-223570. [PMID: 37024296 DOI: 10.1136/ard-2022-223570] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 03/17/2023] [Indexed: 04/08/2023]
Abstract
OBJECTIVES To identify mitochondrial DNA (mtDNA) genetic variants associated with the risk of rapid progression of knee osteoarthritis (OA) and to characterise their functional significance using a cellular model of transmitochondrial cybrids. METHODS Three prospective cohorts contributed participants. The osteoarthritis initiative (OAI) included 1095 subjects, the Cohort Hip and Cohort Knee included 373 and 326 came from the PROspective Cohort of Osteoarthritis from A Coruña. mtDNA variants were screened in an initial subset of 450 subjects from the OAI by in-depth sequencing of mtDNA. A meta-analysis of the three cohorts was performed. A model of cybrids was constructed to study the functional consequences of harbouring the risk mtDNA variant by assessing: mtDNA copy number, mitochondrial biosynthesis, mitochondrial fission and fusion, mitochondrial reactive oxygen species (ROS), oxidative stress, autophagy and a whole transcriptome analysis by RNA-sequencing. RESULTS mtDNA variant m.16519C is over-represented in rapid progressors (combined OR 1.546; 95% CI 1.163 to 2.054; p=0.0027). Cybrids with this variant show increased mtDNA copy number and decreased mitochondrial biosynthesis; they produce higher amounts of mitochondrial ROS, are less resistant to oxidative stress, show a lower expression of the mitochondrial fission-related gene fission mitochondrial 1 and an impairment of autophagic flux. In addition, its presence modulates the transcriptome of cybrids, especially in terms of inflammation, where interleukin 6 emerges as one of the most differentially expressed genes. CONCLUSIONS The presence of the mtDNA variant m.16519C increases the risk of rapid progression of knee OA. Among the most modulated biological processes associated with this variant, inflammation and negative regulation of cellular process stand out. The design of therapies based on the maintenance of mitochondrial function is recommended.
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Affiliation(s)
- Alejandro Durán-Sotuela
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Mercedes Fernandez-Moreno
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Victoria Suárez-Ulloa
- Grupo de Avances en Telemedicina e Informática Sanitaria (ATIS), Plataforma de Bioinformática, Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Jorge Vázquez-García
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Sara Relaño
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Tamara Hermida-Gómez
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
- Grupo GBTTC-CHUAC, Centro de Investigación Biomédica en Red Bioingeniería Biomateriales y Nanomedicina, Madrid, Spain
| | - Vanesa Balboa-Barreiro
- Unidad de apoyo a la investigación, Grupo de Investigación en Enfermería y Cuidados en Salud, Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Lucia Lourido-Salas
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Valentina Calamia
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Patricia Fernandez-Puente
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Cristina Ruiz-Romero
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
- Grupo GBTTC-CHUAC, Centro de Investigación Biomédica en Red Bioingeniería Biomateriales y Nanomedicina, Madrid, Spain
| | - Juan Fernández-Tajes
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Carlos Vaamonde-García
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - María C de Andrés
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
| | - Natividad Oreiro
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
- Grupo GBTTC-CHUAC, Centro de Investigación Biomédica en Red Bioingeniería Biomateriales y Nanomedicina, Madrid, Spain
| | - Francisco J Blanco
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
- Grupo de Investigación en Reumatología y Salud (GIR-S), Departamento de Fisioterapia, Medicina y Ciencias Biomédicas, Facultad de Fisioterapia, Campus de Oza, Universidade da Coruña, A Coruna, Galicia, Spain
| | - Ignacio Rego-Perez
- Grupo de Investigación en Reumatología (GIR), Complexo Hospitalario Universitario de A Coruña (CHUAC), Sergas, Universidade da Coruña (UDC), Instituto de Investigación Biomédica de A Coruña, A Coruna, Galicia, Spain
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14
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Stacpoole PW, McCall CE. The pyruvate dehydrogenase complex: Life's essential, vulnerable and druggable energy homeostat. Mitochondrion 2023; 70:59-102. [PMID: 36863425 DOI: 10.1016/j.mito.2023.02.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 01/30/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023]
Abstract
Found in all organisms, pyruvate dehydrogenase complexes (PDC) are the keystones of prokaryotic and eukaryotic energy metabolism. In eukaryotic organisms these multi-component megacomplexes provide a crucial mechanistic link between cytoplasmic glycolysis and the mitochondrial tricarboxylic acid (TCA) cycle. As a consequence, PDCs also influence the metabolism of branched chain amino acids, lipids and, ultimately, oxidative phosphorylation (OXPHOS). PDC activity is an essential determinant of the metabolic and bioenergetic flexibility of metazoan organisms in adapting to changes in development, nutrient availability and various stresses that challenge maintenance of homeostasis. This canonical role of the PDC has been extensively probed over the past decades by multidisciplinary investigations into its causal association with diverse physiological and pathological conditions, the latter making the PDC an increasingly viable therapeutic target. Here we review the biology of the remarkable PDC and its emerging importance in the pathobiology and treatment of diverse congenital and acquired disorders of metabolic integration.
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Affiliation(s)
- Peter W Stacpoole
- Department of Medicine (Division of Endocrinology, Metabolism and Diabetes), and Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, FL, United States.
| | - Charles E McCall
- Department of Internal Medicine and Translational Sciences, and Department of Microbiology and Immunology, Wake Forest University School of Medicine, Winston-Salem, NC, United States
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15
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Burgstaller JP, Chiaratti MR. Mitochondrial Inheritance Following Nuclear Transfer: From Cloned Animals to Patients with Mitochondrial Disease. Methods Mol Biol 2023; 2647:83-104. [PMID: 37041330 DOI: 10.1007/978-1-0716-3064-8_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Mitochondria are indispensable power plants of eukaryotic cells that also act as a major biochemical hub. As such, mitochondrial dysfunction, which can originate from mutations in the mitochondrial genome (mtDNA), may impair organism fitness and lead to severe diseases in humans. MtDNA is a multi-copy, highly polymorphic genome that is uniparentally transmitted through the maternal line. Several mechanisms act in the germline to counteract heteroplasmy (i.e., coexistence of two or more mtDNA variants) and prevent expansion of mtDNA mutations. However, reproductive biotechnologies such as cloning by nuclear transfer can disrupt mtDNA inheritance, resulting in new genetic combinations that may be unstable and have physiological consequences. Here, we review the current understanding of mitochondrial inheritance, with emphasis on its pattern in animals and human embryos generated by nuclear transfer.
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Affiliation(s)
- Jörg P Burgstaller
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine, Vienna, Austria
| | - Marcos R Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil.
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16
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Combination of common mtDNA variants results in mitochondrial dysfunction and a connective tissue dysregulation. Proc Natl Acad Sci U S A 2022; 119:e2212417119. [PMID: 36322731 PMCID: PMC9659340 DOI: 10.1073/pnas.2212417119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Mitochondrial dysfunction can be associated with a range of clinical manifestations. Here, we report a family with a complex phenotype including combinations of connective tissue, neurological, and metabolic symptoms that were passed on to all surviving children. Analysis of the maternally inherited mtDNA revealed a novel genotype encompassing the haplogroup J - defining mitochondrial DNA (mtDNA) ND5 m.13708G>A (A458T) variant arising on the mtDNA haplogroup H7A background, an extremely rare combination. Analysis of transmitochondrial cybrids with the 13708A-H7 mtDNA revealed a lower mitochondrial respiration, increased reactive oxygen species production (mROS), and dysregulation of connective tissue gene expression. The mitochondrial dysfunction was exacerbated by histamine, explaining why all eight surviving children inherited the dysfunctional histidine decarboxylase allele (W327X) from the father. Thus, certain combinations of common mtDNA variants can cause mitochondrial dysfunction, mitochondrial dysfunction can affect extracellular matrix gene expression, and histamine-activated mROS production can augment the severity of mitochondrial dysfunction. Most important, we have identified a previously unreported genetic cause of mitochondrial disorder arising from the incompatibility of common, nonpathogenic mtDNA variants.
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17
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Chiaratti MR, Chinnery PF. Modulating mitochondrial DNA mutations: factors shaping heteroplasmy in the germ line and somatic cells. Pharmacol Res 2022; 185:106466. [PMID: 36174964 DOI: 10.1016/j.phrs.2022.106466] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/21/2022] [Accepted: 09/23/2022] [Indexed: 11/30/2022]
Abstract
Until recently it was thought that most humans only harbor one type of mitochondrial DNA (mtDNA), however, deep sequencing and single-cell analysis has shown the converse - that mixed populations of mtDNA (heteroplasmy) are the norm. This is important because heteroplasmy levels can change dramatically during transmission in the female germ line, leading to high levels causing severe mitochondrial diseases. There is also emerging evidence that low level mtDNA mutations contribute to common late onset diseases such as neurodegenerative disorders and cardiometabolic diseases because the inherited mutation levels can change within developing organs and non-dividing cells over time. Initial predictions suggested that the segregation of mtDNA heteroplasmy was largely stochastic, with an equal tendency for levels to increase or decrease. However, transgenic animal work and single-cell analysis have shown this not to be the case during germ-line transmission and in somatic tissues during life. Mutation levels in specific mtDNA regions can increase or decrease in different contexts and the underlying molecular mechanisms are starting to be unraveled. In this review we provide a synthesis of recent literature on the mechanisms of selection for and against mtDNA variants. We identify the most pertinent gaps in our understanding and suggest ways these could be addressed using state of the art techniques.
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Affiliation(s)
- Marcos R Chiaratti
- Departamento de Genética e Evolução, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos, São Carlos, Brazil.
| | - Patrick F Chinnery
- Department of Clinical Neurosciences, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK; Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UK.
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18
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Radzvilavicius AL, Johnston IG. Organelle bottlenecks facilitate evolvability by traversing heteroplasmic fitness valleys. Front Genet 2022; 13:974472. [PMID: 36386853 PMCID: PMC9650085 DOI: 10.3389/fgene.2022.974472] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 10/11/2022] [Indexed: 07/09/2024] Open
Abstract
Bioenergetic organelles-mitochondria and plastids-retain their own genomes (mtDNA and ptDNA), and these organelle DNA (oDNA) molecules are vital for eukaryotic life. Like all genomes, oDNA must be able to evolve to suit new environmental challenges. However, mixed oDNA populations in cells can challenge cellular bioenergetics, providing a penalty to the appearance and adaptation of new mutations. Here we show that organelle "bottlenecks," mechanisms increasing cell-to-cell oDNA variability during development, can overcome this mixture penalty and facilitate the adaptation of beneficial mutations. We show that oDNA heteroplasmy and bottlenecks naturally emerge in evolutionary simulations subjected to fluctuating environments, demonstrating that this evolvability is itself evolvable. Usually thought of as a mechanism to clear damaging mutations, organelle bottlenecks therefore also resolve the tension between intracellular selection for pure cellular oDNA populations and the "bet-hedging" need for evolvability and adaptation to new environments. This general theory suggests a reason for the maintenance of organelle heteroplasmy in cells, and may explain some of the observed diversity in organelle maintenance and inheritance across taxa.
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Affiliation(s)
- Arunas L. Radzvilavicius
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
| | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Bergen, Norway
- Computational Biology Unit, University of Bergen, Bergen, Norway
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19
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Tostes K, dos Santos AC, Alves LO, Bechara LRG, Marascalchi R, Macabelli CH, Grejo MP, Festuccia WT, Gottlieb RA, Ferreira JCB, Chiaratti MR. Autophagy deficiency abolishes liver mitochondrial DNA segregation. Autophagy 2022; 18:2397-2408. [PMID: 35220898 PMCID: PMC9542960 DOI: 10.1080/15548627.2022.2038501] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Mutations in the mitochondrial genome (mtDNA) are ubiquitous in humans and can lead to a broad spectrum of disorders. However, due to the presence of multiple mtDNA molecules in the cell, co-existence of mutant and wild-type mtDNAs (termed heteroplasmy) can mask disease phenotype unless a threshold of mutant molecules is reached. Importantly, the mutant mtDNA level can change across lifespan as mtDNA segregates in an allele- and cell-specific fashion, potentially leading to disease. Segregation of mtDNA is mainly evident in hepatic cells, resulting in an age-dependent increase of mtDNA variants, including non-synonymous potentially deleterious mutations. Here we modeled mtDNA segregation using a well-established heteroplasmic mouse line with mtDNA of NZB/BINJ and C57BL/6N origin on a C57BL/6N nuclear background. This mouse line showed a pronounced age-dependent NZB mtDNA accumulation in the liver, thus leading to enhanced respiration capacity per mtDNA molecule. Remarkably, liver-specific atg7 (autophagy related 7) knockout abolished NZB mtDNA accumulat ion, resulting in close-to-neutral mtDNA segregation through development into adulthood. prkn (parkin RBR E3 ubiquitin protein ligase) knockout also partially prevented NZB mtDNA accumulation in the liver, but to a lesser extent. Hence, we propose that age-related liver mtDNA segregation is a consequence of macroautophagic clearance of the less-fit mtDNA. Considering that NZB/BINJ and C57BL/6N mtDNAs have a level of divergence comparable to that between human Eurasian and African mtDNAs, these findings have potential implications for humans, including the safe use of mitochondrial replacement therapy.Abbreviations: Apob: apolipoprotein B; Atg1: autophagy-related 1; Atg7: autophagy related 7; Atp5a1: ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit 1; BL6: C57BL/6N mouse strain; BNIP3: BCL2/adenovirus E1B interacting protein 3; FCCP: carbonyl cyanide 4-(trifluoromethoxy)phenylhydrazone; GAPDH: glyceraldehyde-3-phosphate dehydrogenase; MAP1LC3A: microtubule-associated protein 1 light chain 3 alpha; MAP1LC3B: microtubule-associated protein 1 light chain 3 beta; mt-Atp8: mitochondrially encoded ATP synthase 8; MT-CO1: mitochondrially encoded cytochrome c oxidase I; MT-CO2: mitochondrially encoded cytochrome c oxidase II; mt-Co3: mitochondrially encoded cytochrome c oxidase III; mt-Cytb: mitochondrially encoded cytochrome b; mtDNA: mitochondrial DNA; MUL1: mitochondrial ubiquitin ligase activator of NFKB 1; nDNA: nuclear DNA; Ndufa9: NADH:ubiquinone oxireductase subunit A9; NDUFB8: NADH:ubiquinone oxireductase subunit B8; Nnt: nicotinamide nucleotide transhydrogenase; NZB: NZB/BINJ mouse strain; OXPHOS: oxidative phosphorylation; PINK1: PTEN induced putative kinase 1; Polg2: polymerase (DNA directed), gamma 2, accessory subunit; Ppara: peroxisome proliferator activated receptor alpha; Ppia: peptidylprolyl isomerase A; Prkn: parkin RBR E3 ubiquitin protein ligase; P10: post-natal day 10; P21: post-natal day 21; P100: post-natal day 100; qPCR: quantitative polymerase chain reaction; Rpl19: ribosomal protein L19; Rps18: ribosomal protein S18; SD: standard deviation; SEM: standard error of the mean; SDHB: succinate dehydrogenase complex, subunit B, iron sulfur (Ip); SQSTM1: sequestosome 1; Ssbp1: single-stranded DNA binding protein 1; TFAM: transcription factor A, mitochondrial; Tfb1m: transcription factor B1, mitochondrial; Tfb2m: transcription factor B2, mitochondrial; TOMM20: translocase of outer mitochondrial membrane 20; UQCRC2: ubiquinol cytochrome c reductase core protein 2; WT: wild-type.
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Affiliation(s)
- Katiane Tostes
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Angélica C. dos Santos
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Lindomar O. Alves
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Luiz R. G. Bechara
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Rachel Marascalchi
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Carolina H. Macabelli
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - Mateus P. Grejo
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil
| | - William T. Festuccia
- Department of Physiology and Biophysics, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil
| | - Roberta A. Gottlieb
- Department of Cardiology, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Julio C. B. Ferreira
- Department of Anatomy, Institute of Biomedical Sciences, University of Sao Paulo, São Paulo, Brazil,Department of Chemical and Systems Biology, Stanford University School of Medicine, CA, USA
| | - Marcos R. Chiaratti
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, Brazil,CONTACT Marcos R. Chiaratti Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos13565-905, Brazil
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Holt AG, Davies AM. A comparison of mtDNA deletion mutant proliferation mechanisms. J Theor Biol 2022; 551-552:111244. [PMID: 35973607 DOI: 10.1016/j.jtbi.2022.111244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 07/17/2022] [Accepted: 08/08/2022] [Indexed: 11/18/2022]
Abstract
In this paper we use simulation methods to investigate the proliferation of deletion mutations of mitochondrial DNA in neurons. We simulate three mtDNA proliferation mechanisms, namely, random drift, replicative advantage and vicious cycle. For each mechanism, we investigated the effect mutation rates have on neuron loss within a human host. We also compare heteroplasmy of each mechanism at mutation rates that yield the levels neuron loss that would be associated with dementia. Both random drift and vicious cycle predicted high levels of heteroplasmy, while replicative advantage showed a small number of dominant clones with a low background of heteroplasmy.
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21
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Lechuga-Vieco AV, Latorre-Pellicer A, Calvo E, Torroja C, Pellico J, Acín-Pérez R, García-Gil ML, Santos A, Bagwan N, Bonzon-Kulichenko E, Magni R, Benito M, Justo-Méndez R, Simon AK, Sánchez-Cabo F, Vázquez J, Ruíz-Cabello J, Enríquez JA. Heteroplasmy of Wild Type Mitochondrial DNA Variants in Mice Causes Metabolic Heart Disease With Pulmonary Hypertension and Frailty. Circulation 2022; 145:1084-1101. [PMID: 35236094 PMCID: PMC8969846 DOI: 10.1161/circulationaha.121.056286] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Background: In most eukaryotic cells, the mitochondrial DNA (mtDNA) is uniparentally transmitted and present in multiple copies derived from the clonal expansion of maternally inherited mtDNA. All copies are therefore near-identical, or homoplasmic. The presence of more than one mtDNA variant in the same cytoplasm can arise naturally or result from new medical technologies aimed at preventing mitochondrial genetic diseases and improving fertility. The latter is called divergent non-pathological mtDNAs heteroplasmy (DNPH). We hypothesized that DNPH is maladaptive and usually prevented by the cell. Methods: We engineered and characterized DNPH mice throughout their lifespan using transcriptomic, metabolomic, biochemical, physiological and phenotyping techniques. We focused on in vivo imaging techniques for non-invasive assessment of cardiac and pulmonary energy metabolism. Results: We show that DNPH impairs mitochondrial function, with profound consequences in critical tissues that cannot resolve heteroplasmy, particularly cardiac and skeletal muscle. Progressive metabolic stress in these tissues leads to severe pathology in adulthood, including pulmonary hypertension and heart failure, skeletal muscle wasting, frailty, and premature death. Symptom severity is strongly modulated by the nuclear context. Conclusions: Medical interventions that may generate DNPH should address potential incompatibilities between donor and recipient mtDNA.
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Affiliation(s)
- Ana Victoria Lechuga-Vieco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain; The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom; Ciber de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ana Latorre-Pellicer
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain; Unit of Clinical Genetics and Functional Genomics, Department of Pharmacology-Physiology, School of Medicine, University of Zaragoza, ISS-Aragon, Zaragoza, Spain
| | - Enrique Calvo
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain
| | - Carlos Torroja
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain
| | - Juan Pellico
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain; Ciber de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Rebeca Acín-Pérez
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain
| | - María Luisa García-Gil
- Centro Nacional de Microscopia Electrónica (ICTS-CNME), Universidad Complutense de Madrid, Madrid, Spain
| | - Arnoldo Santos
- Ciber de Enfermedades Respiratorias (CIBERES), Madrid, Spain; ITC, Ingeniería y Técnicas Clínicas, Madrid, Spain
| | - Navratan Bagwan
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain
| | - Elena Bonzon-Kulichenko
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain; Ciber de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ricardo Magni
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | | | - Raquel Justo-Méndez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
| | - Anna Katharina Simon
- The Kennedy Institute of Rheumatology, NDORMS, University of Oxford, Oxford, United Kingdom
| | | | - Jesús Vázquez
- Ciber de Fragilidad y Envejecimiento Saludable (CIBERFES) Madrid, Spain; Ciber de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Jesús Ruíz-Cabello
- CIC biomaGUNE, 2014, Donostia-San Sebastián, Spain; IKERBASQUE, Basque Foundation for Science, Spain; Universidad Complutense de Madrid, Madrid, Spain
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22
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Dabravolski SA, Nikiforov NG, Zhuravlev AD, Orekhov NA, Grechko AV, Orekhov AN. Role of the mtDNA Mutations and Mitophagy in Inflammaging. Int J Mol Sci 2022; 23:ijms23031323. [PMID: 35163247 PMCID: PMC8836173 DOI: 10.3390/ijms23031323] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/12/2022] [Accepted: 01/17/2022] [Indexed: 12/14/2022] Open
Abstract
Ageing is an unavoidable multi-factorial process, characterised by a gradual decrease in physiological functionality and increasing vulnerability of the organism to environmental factors and pathogens, ending, eventually, in death. One of the most elaborated ageing theories implies a direct connection between ROS-mediated mtDNA damage and mutations. In this review, we focus on the role of mitochondrial metabolism, mitochondria generated ROS, mitochondrial dynamics and mitophagy in normal ageing and pathological conditions, such as inflammation. Also, a chronic form of inflammation, which could change the long-term status of the immune system in an age-dependent way, is discussed. Finally, the role of inflammaging in the most common neurodegenerative diseases, such as Alzheimer’s and Parkinson’s, is also discussed.
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Affiliation(s)
- Siarhei A. Dabravolski
- Department of Clinical Diagnostics, Vitebsk State Academy of Veterinary Medicine [UO VGAVM], 7/11 Dovatora Str., 210026 Vitebsk, Belarus
- Correspondence:
| | - Nikita G. Nikiforov
- AP Avtsyn Research Institute of Human Morphology, 3 Tsyurupa Street, 117418 Moscow, Russia; (N.G.N.); (A.D.Z.)
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 34/5 Vavilova Street, 119334 Moscow, Russia
- Laboratory of Angiopathology, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315 Moscow, Russia
| | - Alexander D. Zhuravlev
- AP Avtsyn Research Institute of Human Morphology, 3 Tsyurupa Street, 117418 Moscow, Russia; (N.G.N.); (A.D.Z.)
| | - Nikolay A. Orekhov
- Institute for Atherosclerosis Research, Osennyaya Street 4-1-207, 121609 Moscow, Russia; (N.A.O.); (A.N.O.)
| | - Andrey V. Grechko
- Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, 14-3 Solyanka Street, 109240 Moscow, Russia;
| | - Alexander N. Orekhov
- Institute for Atherosclerosis Research, Osennyaya Street 4-1-207, 121609 Moscow, Russia; (N.A.O.); (A.N.O.)
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23
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Moreira JD, Gopal DM, Kotton DN, Fetterman JL. Gaining Insight into Mitochondrial Genetic Variation and Downstream Pathophysiology: What Can i(PSCs) Do? Genes (Basel) 2021; 12:1668. [PMID: 34828274 PMCID: PMC8624338 DOI: 10.3390/genes12111668] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are specialized organelles involved in energy production that have retained their own genome throughout evolutionary history. The mitochondrial genome (mtDNA) is maternally inherited and requires coordinated regulation with nuclear genes to produce functional enzyme complexes that drive energy production. Each mitochondrion contains 5-10 copies of mtDNA and consequently, each cell has several hundreds to thousands of mtDNAs. Due to the presence of multiple copies of mtDNA in a mitochondrion, mtDNAs with different variants may co-exist, a condition called heteroplasmy. Heteroplasmic variants can be clonally expanded, even in post-mitotic cells, as replication of mtDNA is not tied to the cell-division cycle. Heteroplasmic variants can also segregate during germ cell formation, underlying the inheritance of some mitochondrial mutations. Moreover, the uneven segregation of heteroplasmic variants is thought to underlie the heterogeneity of mitochondrial variation across adult tissues and resultant differences in the clinical presentation of mitochondrial disease. Until recently, however, the mechanisms mediating the relation between mitochondrial genetic variation and disease remained a mystery, largely due to difficulties in modeling human mitochondrial genetic variation and diseases. The advent of induced pluripotent stem cells (iPSCs) and targeted gene editing of the nuclear, and more recently mitochondrial, genomes now provides the ability to dissect how genetic variation in mitochondrial genes alter cellular function across a variety of human tissue types. This review will examine the origins of mitochondrial heteroplasmic variation and propagation, and the tools used to model mitochondrial genetic diseases. Additionally, we discuss how iPSC technologies represent an opportunity to advance our understanding of human mitochondrial genetics in disease.
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Affiliation(s)
- Jesse D. Moreira
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
| | - Deepa M. Gopal
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
- Cardiovascular Medicine Section, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Darrell N. Kotton
- Boston Medical Center, Center for Regenerative Medicine of Boston University, Boston, MA 02118, USA;
- The Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - Jessica L. Fetterman
- Evans Department of Medicine and the Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA; (J.D.M.); (D.M.G.)
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24
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Wei W, Gaffney DJ, Chinnery PF. Cell reprogramming shapes the mitochondrial DNA landscape. Nat Commun 2021; 12:5241. [PMID: 34475388 PMCID: PMC8413449 DOI: 10.1038/s41467-021-25482-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 08/14/2021] [Indexed: 12/25/2022] Open
Abstract
Individual induced pluripotent stem cells (iPSCs) show considerable phenotypic heterogeneity, but the reasons for this are not fully understood. Comprehensively analysing the mitochondrial genome (mtDNA) in 146 iPSC and fibroblast lines from 151 donors, we show that most age-related fibroblast mtDNA mutations are lost during reprogramming. However, iPSC-specific mutations are seen in 76.6% (108/141) of iPSC lines at a mutation rate of 8.62 × 10-5/base pair. The mutations observed in iPSC lines affect a higher proportion of mtDNA molecules, favouring non-synonymous protein-coding and tRNA variants, including known disease-causing mutations. Analysing 11,538 single cells shows stable heteroplasmy in sub-clones derived from the original donor during differentiation, with mtDNA variants influencing the expression of key genes involved in mitochondrial metabolism and epidermal cell differentiation. Thus, the dynamic mtDNA landscape contributes to the heterogeneity of human iPSCs and should be considered when using reprogrammed cells experimentally or as a therapy.
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Affiliation(s)
- Wei Wei
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK
- Medical Research Council Mitochondrial Biology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Daniel J Gaffney
- Human Induced Pluripotent Stem Cell Initiative, Wellcome Genome Campus, Hinxton, UK
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - Patrick F Chinnery
- Department of Clinical Neuroscience, University of Cambridge, Cambridge, UK.
- Medical Research Council Mitochondrial Biology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
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25
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Pérez-Amado CJ, Bazan-Cordoba A, Hidalgo-Miranda A, Jiménez-Morales S. Mitochondrial Heteroplasmy Shifting as a Potential Biomarker of Cancer Progression. Int J Mol Sci 2021; 22:7369. [PMID: 34298989 PMCID: PMC8304746 DOI: 10.3390/ijms22147369] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [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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Affiliation(s)
- Carlos Jhovani Pérez-Amado
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (C.J.P.-A.); (A.B.-C.); (A.H.-M.)
- Programa de Maestría y Doctorado, Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Amellalli Bazan-Cordoba
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (C.J.P.-A.); (A.B.-C.); (A.H.-M.)
- Programa de Maestría y Doctorado, Posgrado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (C.J.P.-A.); (A.B.-C.); (A.H.-M.)
| | - Silvia Jiménez-Morales
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica, Mexico City 14610, Mexico; (C.J.P.-A.); (A.B.-C.); (A.H.-M.)
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26
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mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences. Life (Basel) 2021; 11:life11070633. [PMID: 34209862 PMCID: PMC8307225 DOI: 10.3390/life11070633] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 06/24/2021] [Indexed: 12/11/2022] Open
Abstract
Mitochondrial DNA (mtDNA) is predominately uniparentally transmitted. This results in organisms with a single type of mtDNA (homoplasmy), but two or more mtDNA haplotypes have been observed in low frequency in several species (heteroplasmy). In this review, we aim to highlight several aspects of heteroplasmy regarding its origin and its significance on mtDNA function and evolution, which has been progressively recognized in the last several years. Heteroplasmic organisms commonly occur through somatic mutations during an individual’s lifetime. They also occur due to leakage of paternal mtDNA, which rarely happens during fertilization. Alternatively, heteroplasmy can be potentially inherited maternally if an egg is already heteroplasmic. Recent advances in sequencing techniques have increased the ability to detect and quantify heteroplasmy and have revealed that mitochondrial DNA copies in the nucleus (NUMTs) can imitate true heteroplasmy. Heteroplasmy can have significant evolutionary consequences on the survival of mtDNA from the accumulation of deleterious mutations and for its coevolution with the nuclear genome. Particularly in humans, heteroplasmy plays an important role in the emergence of mitochondrial diseases and determines the success of the mitochondrial replacement therapy, a recent method that has been developed to cure mitochondrial diseases.
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27
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Pereira CV, Gitschlag BL, Patel MR. Cellular mechanisms of mtDNA heteroplasmy dynamics. Crit Rev Biochem Mol Biol 2021; 56:510-525. [PMID: 34120542 DOI: 10.1080/10409238.2021.1934812] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heteroplasmy refers to the coexistence of more than one variant of the mitochondrial genome (mtDNA). Mutated or partially deleted mtDNAs can induce chronic metabolic impairment and cause mitochondrial diseases when their heteroplasmy levels exceed a critical threshold. These mutant mtDNAs can be maternally inherited or can arise de novo. Compelling evidence has emerged showing that mutant mtDNA levels can vary and change in a nonrandom fashion across generations and amongst tissues of an individual. However, our lack of understanding of the basic cellular and molecular mechanisms of mtDNA heteroplasmy dynamics has made it difficult to predict who will inherit or develop mtDNA-associated diseases. More recently, with the advances in technology and the establishment of tractable model systems, insights into the mechanisms underlying the selection forces that modulate heteroplasmy dynamics are beginning to emerge. In this review, we summarize evidence from different organisms, showing that mutant mtDNA can experience both positive and negative selection. We also review the recently identified mechanisms that modulate heteroplasmy dynamics. Taken together, this is an opportune time to survey the literature and to identify key cellular pathways that can be targeted to develop therapies for diseases caused by heteroplasmic mtDNA mutations.
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Affiliation(s)
- Claudia V Pereira
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.,Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.,Diabetes Research and Training Center, Vanderbilt University School of Medicine, Nashville, TN, USA
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28
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Mitochondrial DNA Heteroplasmy as an Informational Reservoir Dynamically Linked to Metabolic and Immunological Processes Associated with COVID-19 Neurological Disorders. Cell Mol Neurobiol 2021; 42:99-107. [PMID: 34117968 PMCID: PMC8196276 DOI: 10.1007/s10571-021-01117-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/07/2021] [Indexed: 12/21/2022]
Abstract
Mitochondrial DNA (mtDNA) heteroplasmy is the dynamically determined co-expression of wild type (WT) inherited polymorphisms and collective time-dependent somatic mutations within individual mtDNA genomes. The temporal expression and distribution of cell-specific and tissue-specific mtDNA heteroplasmy in healthy individuals may be functionally associated with intracellular mitochondrial signaling pathways and nuclear DNA gene expression. The maintenance of endogenously regulated tissue-specific copy numbers of heteroplasmic mtDNA may represent a sensitive biomarker of homeostasis of mitochondrial dynamics, metabolic integrity, and immune competence. Myeloid cells, monocytes, macrophages, and antigen-presenting dendritic cells undergo programmed changes in mitochondrial metabolism according to innate and adaptive immunological processes. In the central nervous system (CNS), the polarization of activated microglial cells is dependent on strategically programmed changes in mitochondrial function. Therefore, variations in heteroplasmic mtDNA copy numbers may have functional consequences in metabolically competent mitochondria in innate and adaptive immune processes involving the CNS. Recently, altered mitochondrial function has been demonstrated in the progression of coronavirus disease 2019 (COVID-19) due to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Accordingly, our review is organized to present convergent lines of empirical evidence that potentially link expression of mtDNA heteroplasmy by functionally interactive CNS cell types to the extent and severity of acute and chronic post-COVID-19 neurological disorders.
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29
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Generation of Reactive Oxygen Species by Mitochondria. Antioxidants (Basel) 2021; 10:antiox10030415. [PMID: 33803273 PMCID: PMC8001687 DOI: 10.3390/antiox10030415] [Citation(s) in RCA: 198] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 02/28/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022] Open
Abstract
Reactive oxygen species (ROS) are series of chemical products originated from one or several electron reductions of oxygen. ROS are involved in physiology and disease and can also be both cause and consequence of many biological scenarios. Mitochondria are the main source of ROS in the cell and, particularly, the enzymes in the electron transport chain are the major contributors to this phenomenon. Here, we comprehensively review the modes by which ROS are produced by mitochondria at a molecular level of detail, discuss recent advances in the field involving signalling and disease, and the involvement of supercomplexes in these mechanisms. Given the importance of mitochondrial ROS, we also provide a schematic guide aimed to help in deciphering the mechanisms involved in their production in a variety of physiological and pathological settings.
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30
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Zakirova EG, Muzyka VV, Mazunin IO, Orishchenko KE. Natural and Artificial Mechanisms of Mitochondrial Genome Elimination. Life (Basel) 2021; 11:life11020076. [PMID: 33498399 PMCID: PMC7909434 DOI: 10.3390/life11020076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/18/2021] [Accepted: 01/19/2021] [Indexed: 01/11/2023] Open
Abstract
The generally accepted theory of the genetic drift of mitochondrial alleles during mammalian ontogenesis is based on the presence of a selective bottleneck in the female germline. However, there is a variety of different theories on the pathways of genetic regulation of mitochondrial DNA (mtDNA) dynamics in oogenesis and adult somatic cells. The current review summarizes present knowledge on the natural mechanisms of mitochondrial genome elimination during mammalian development. We also discuss the variety of existing and developing methodologies for artificial manipulation of the mtDNA heteroplasmy level. Understanding of the basics of mtDNA dynamics will shed the light on the pathogenesis and potential therapies of human diseases associated with mitochondrial dysfunction.
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Affiliation(s)
- Elvira G. Zakirova
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
| | - Vladimir V. Muzyka
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Ilya O. Mazunin
- Skolkovo Institute of Science and Technology, 143026 Skolkovo, Russia;
| | - Konstantin E. Orishchenko
- Federal Research Center Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia; (E.G.Z.); (V.V.M.)
- Department of Genetic Technologies, Novosibirsk State University, 630090 Novosibirsk, Russia
- Correspondence:
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31
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Lechuga-Vieco AV, Justo-Méndez R, Enríquez JA. Not all mitochondrial DNAs are made equal and the nucleus knows it. IUBMB Life 2020; 73:511-529. [PMID: 33369015 PMCID: PMC7985871 DOI: 10.1002/iub.2434] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022]
Abstract
The oxidative phosphorylation (OXPHOS) system is the only structure in animal cells with components encoded by two genomes, maternally transmitted mitochondrial DNA (mtDNA), and biparentally transmitted nuclear DNA (nDNA). MtDNA‐encoded genes have to physically assemble with their counterparts encoded in the nucleus to build together the functional respiratory complexes. Therefore, structural and functional matching requirements between the protein subunits of these molecular complexes are rigorous. The crosstalk between nDNA and mtDNA needs to overcome some challenges, as the nuclear‐encoded factors have to be imported into the mitochondria in a correct quantity and match the high number of organelles and genomes per mitochondria that encode and synthesize their own components locally. The cell is able to sense the mito‐nuclear match through changes in the activity of the OXPHOS system, modulation of the mitochondrial biogenesis, or reactive oxygen species production. This implies that a complex signaling cascade should optimize OXPHOS performance to the cellular‐specific requirements, which will depend on cell type, environmental conditions, and life stage. Therefore, the mitochondria would function as a cellular metabolic information hub integrating critical information that would feedback the nucleus for it to respond accordingly. Here, we review the current understanding of the complex interaction between mtDNA and nDNA.
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Affiliation(s)
- Ana Victoria Lechuga-Vieco
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain.,MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Raquel Justo-Méndez
- Centro Nacional de Investigaciones Cardiovasculares Carlos III, Madrid, Spain
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