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Gitschlag BL, Pereira CV, Held JP, McCandlish DM, Patel MR. Multiple distinct evolutionary mechanisms govern the dynamics of selfish mitochondrial genomes in Caenorhabditis elegans. Nat Commun 2024; 15:8237. [PMID: 39300074 DOI: 10.1038/s41467-024-52596-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 09/13/2024] [Indexed: 09/22/2024] Open
Abstract
Cells possess multiple mitochondrial DNA (mtDNA) copies, which undergo semi-autonomous replication and stochastic inheritance. This enables mutant mtDNA variants to arise and selfishly compete with cooperative (wildtype) mtDNA. Selfish mitochondrial genomes are subject to selection at different levels: they compete against wildtype mtDNA directly within hosts and indirectly through organism-level selection. However, determining the relative contributions of selection at different levels has proven challenging. We overcome this challenge by combining mathematical modeling with experiments designed to isolate the levels of selection. Applying this approach to many selfish mitochondrial genotypes in Caenorhabditis elegans reveals an unexpected diversity of evolutionary mechanisms. Some mutant genomes persist at high frequency for many generations, despite a host fitness cost, by aggressively outcompeting cooperative genomes within hosts. Conversely, some mutant genomes persist by evading inter-organismal selection. Strikingly, the mutant genomes vary dramatically in their susceptibility to genetic drift. Although different mechanisms can cause high frequency of selfish mtDNA, we show how they give rise to characteristically different distributions of mutant frequency among individuals. Given that heteroplasmic frequency represents a key determinant of phenotypic severity, this work outlines an evolutionary theoretic framework for predicting the distribution of phenotypic consequences among individuals carrying a selfish mitochondrial genome.
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Affiliation(s)
- Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA.
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, USA.
| | - Claudia V Pereira
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - James P Held
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, USA
| | - David M McCandlish
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, 11724, 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.
- Evolutionary Studies, Vanderbilt University, VU Box #34-1634, Nashville, TN, USA.
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2
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Cha JH, Lee SH, Yun Y, Choi WH, Koo H, Jung SH, Chae HB, Lee DH, Lee SJ, Jo DH, Kim JH, Song JJ, Chae JH, Lee JH, Park J, Kang JY, Bae S, Lee SY. Discovery of novel disease-causing mutation in SSBP1 and its correction using adenine base editor to improve mitochondrial function. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102257. [PMID: 39104869 PMCID: PMC11299580 DOI: 10.1016/j.omtn.2024.102257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 06/14/2024] [Indexed: 08/07/2024]
Abstract
Mutations in nuclear genes regulating mitochondrial DNA (mtDNA) replication are associated with mtDNA depletion syndromes. Using whole-genome sequencing, we identified a heterozygous mutation (c.272G>A:p.Arg91Gln) in single-stranded DNA-binding protein 1 (SSBP1), a crucial protein involved in mtDNA replisome. The proband manifested symptoms including sensorineural deafness, congenital cataract, optic atrophy, macular dystrophy, and myopathy. This mutation impeded multimer formation and DNA-binding affinity, leading to reduced efficiency of mtDNA replication, altered mitochondria dynamics, and compromised mitochondrial function. To correct this mutation, we tested two adenine base editor (ABE) variants on patient-derived fibroblasts. One variant, NG-Cas9-based ABE8e (NG-ABE8e), showed higher editing efficacy (≤30%) and enhanced mitochondrial replication and function, despite off-target editing frequencies; however, risks from bystander editing were limited due to silent mutations and off-target sites in non-translated regions. The other variant, NG-Cas9-based ABE8eWQ (NG-ABE8eWQ), had a safer therapeutic profile with very few off-target effects, but this came at the cost of lower editing efficacy (≤10% editing). Despite this, NG-ABE8eWQ-edited cells still restored replication and improved mtDNA copy number, which in turn recovery of compromised mitochondrial function. Taken together, base editing-based gene therapies may be a promising treatment for mitochondrial diseases, including those associated with SSBP1 mutations.
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Affiliation(s)
- Ju Hyuen Cha
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Seok-Hoon Lee
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yejin Yun
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Won Hoon Choi
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Hansol Koo
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Ho Jung
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ho Byung Chae
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | | | - Seok Jae Lee
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Dong Hyun Jo
- Department of Anatomy and Cell Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong Hun Kim
- Fight Against Angiogenesis-Related Blindness (FARB) Laboratory, Clinical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Ophthalmology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jae-Jin Song
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Bundang Hospital, Seongnam, Republic of Korea
| | - Jong-Hee Chae
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jun Ho Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
| | - Jiho Park
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Sangsu Bae
- Department of Biomedical Sciences, Seoul National University College of Medicine, Seoul, Republic of Korea
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
- Medical Research Center of Genomic Medicine Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sang-Yeon Lee
- Department of Otorhinolaryngology, Seoul National University College of Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Department of Genomic Medicine, Seoul National University Hospital, Seoul, Republic of Korea
- Sensory Organ Research Institute, Seoul National University Medical Research Center, Seoul, Republic of Korea
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3
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Dubie JJ, Katju V, Bergthorsson U. Dissecting the sequential evolution of a selfish mitochondrial genome in Caenorhabditis elegans. Heredity (Edinb) 2024; 133:186-197. [PMID: 38969772 PMCID: PMC11349875 DOI: 10.1038/s41437-024-00704-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/07/2024] Open
Abstract
Mitochondrial genomes exist in a nested hierarchy of populations where mitochondrial variants are subject to genetic drift and selection at each level of organization, sometimes engendering conflict between different levels of selection, and between the nuclear and mitochondrial genomes. Deletion mutants in the Caenorhabditis elegans mitochondrial genome can reach high intracellular frequencies despite strongly detrimental effects on fitness. During a mutation accumulation (MA) experiment in C. elegans, a 499 bp deletion in ctb-1 rose to 90% frequency within cells while significantly reducing fitness. During the experiment, the deletion-bearing mtDNA acquired three additional mutations in nd5, namely two single insertion frameshift mutations in a homopolymeric run, and a base substitution. Despite an additional fitness cost of these secondary mutations, all deletion-bearing molecules contained the nd5 mutations at the termination of the MA experiment. The presence of mutant mtDNA was associated with increased mtDNA copy-number. Variation in mtDNA copy-number was greater in the MA lines than in a wildtype nuclear background, including a severe reduction in copy-number at one generational timepoint. Evolutionary replay experiments using different generations of the MA experiment as starting points suggests that two of the secondary mutations contribute to the proliferation of the original ctb-1 deletion by unknown mechanisms.
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Affiliation(s)
- Joseph J Dubie
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA
- Department of Integrative Biology, University of Texas, Austin, TX, USA
| | - Vaishali Katju
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
| | - Ulfar Bergthorsson
- Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA.
- Evolutionary Biology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 752 36, Uppsala, Sweden.
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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] [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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von der Dunk SHA, Hogeweg P, Snel B. Intracellular signaling in proto-eukaryotes evolves to alleviate regulatory conflicts of endosymbiosis. PLoS Comput Biol 2024; 20:e1011860. [PMID: 38335232 PMCID: PMC10883579 DOI: 10.1371/journal.pcbi.1011860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2023] [Revised: 02/22/2024] [Accepted: 01/24/2024] [Indexed: 02/12/2024] Open
Abstract
The complex eukaryotic cell resulted from a merger between simpler prokaryotic cells, yet the role of the mitochondrial endosymbiosis with respect to other eukaryotic innovations has remained under dispute. To investigate how the regulatory challenges associated with the endosymbiotic state impacted genome and network evolution during eukaryogenesis, we study a constructive computational model where two simple cells are forced into an obligate endosymbiosis. Across multiple in silico evolutionary replicates, we observe the emergence of different mechanisms for the coordination of host and symbiont cell cycles, stabilizing the endosymbiotic relationship. In most cases, coordination is implicit, without signaling between host and symbiont. Signaling only evolves when there is leakage of regulatory products between host and symbiont. In the fittest evolutionary replicate, the host has taken full control of the symbiont cell cycle through signaling, mimicking the regulatory dominance of the nucleus over the mitochondrion that evolved during eukaryogenesis.
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Affiliation(s)
| | - Paulien Hogeweg
- Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Berend Snel
- Department of Biology, Utrecht University, Utrecht, The Netherlands
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Volpe KE, Samuels DC, Elson JL, Steyn JS, Gebretsadik T, Ellis RJ, Heaton RK, Kallianpur AR, Letendre S, Hulgan T. Mitochondrial DNA mutation pathogenicity score and neurocognitive performance in persons with HIV. Mitochondrion 2024; 74:101820. [PMID: 37989461 PMCID: PMC10872545 DOI: 10.1016/j.mito.2023.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 10/06/2023] [Accepted: 11/03/2023] [Indexed: 11/23/2023]
Abstract
BACKGROUND Mitochondrial DNA (mtDNA) genetic variation is associated with neurocognitive (NC) impairment (NCI) in people with HIV (PWH). Other approaches use sequence conservation and protein structure to predict the impact of mtDNA variants on protein function. We examined predicted mtDNA variant pathogenicity in the CHARTER study using MutPred scores, hypothesizing that persons with higher scores (greater predicted pathogenicity) have more NCI. METHODS CHARTER included NC testing in PWH from 2003 to 2007. MutPred scores were assigned to CHARTER participants with mtDNA sequence; any score > 0.5 was considered potentially deleterious. Outcomes at cohort entry were NCI, defined by global and seven NC domain deficit scores, and by mean global and domain NC performance T-scores. Univariate and multivariable regression analyses assessed associations between having a deleterious variant and NCI. Additional models included estimated peripheral blood cell mtDNA copy number. RESULTS Data were available for 744 PWH (357 African ancestry; 317 European; 70 Hispanic). In the overall cohort, PWH having any potentially deleterious variant were less likely to have motor impairment (16 vs. 25 %, p = 0.001). In multivariable analysis, having a deleterious variant remained associated with lower likelihood of motor impairment (adjusted odds ratio 0.59 [95 % CI 0.41-0.88]; p = 0.009), and better motor performance by T-score (β 1.71 [0.31-3.10], p = 0.02). Associations persisted after adjustment for estimated mtDNA quantity. CONCLUSIONS In these PWH, having a potentially deleterious mtDNA variant was associated with less motor impairment. These unexpected findings suggest that potentially deleterious mtDNA variations may confer protection against impaired motor function by as yet unknown mechanisms.
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Affiliation(s)
- Karen E Volpe
- Vanderbilt University Medical Center, Nashville, TN, USA
| | - David C Samuels
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Joanna L Elson
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Jannetta S Steyn
- Biosciences Institute, Newcastle University, Newcastle Upon Tyne, UK
| | | | | | | | | | | | - Todd Hulgan
- Vanderbilt University Medical Center, Nashville, TN, USA.
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Guerbette T, Boudry G, Lan A. Mitochondrial function in intestinal epithelium homeostasis and modulation in diet-induced obesity. Mol Metab 2022; 63:101546. [PMID: 35817394 PMCID: PMC9305624 DOI: 10.1016/j.molmet.2022.101546] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 11/30/2022] Open
Abstract
Background Systemic low-grade inflammation observed in diet-induced obesity has been associated with dysbiosis and disturbance of intestinal homeostasis. This latter relies on an efficient epithelial barrier and coordinated intestinal epithelial cell (IEC) renewal that are supported by their mitochondrial function. However, IEC mitochondrial function might be impaired by high fat diet (HFD) consumption, notably through gut-derived metabolite production and fatty acids, that may act as metabolic perturbators of IEC. Scope of review This review presents the current general knowledge on mitochondria, before focusing on IEC mitochondrial function and its role in the control of intestinal homeostasis, and featuring the known effects of nutrients and metabolites, originating from the diet or gut bacterial metabolism, on IEC mitochondrial function. It then summarizes the impact of HFD on mitochondrial function in IEC of both small intestine and colon and discusses the possible link between mitochondrial dysfunction and altered intestinal homeostasis in diet-induced obesity. Major conclusions HFD consumption provokes a metabolic shift toward fatty acid β-oxidation in the small intestine epithelial cells and impairs colonocyte mitochondrial function, possibly through downstream consequences of excessive fatty acid β-oxidation and/or the presence of deleterious metabolites produced by the gut microbiota. Decreased levels of ATP and concomitant O2 leaks into the intestinal lumen could explain the alterations of intestinal epithelium dynamics, barrier disruption and dysbiosis that contribute to the loss of epithelial homeostasis in diet-induced obesity. However, the effect of HFD on IEC mitochondrial function in the small intestine remains unknown and the precise mechanisms by which HFD induces mitochondrial dysfunction in the colon have not been elucidated so far.
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Affiliation(s)
| | - Gaëlle Boudry
- Institut Numecan, INSERM, INRAE, Univ Rennes, Rennes, France.
| | - Annaïg Lan
- Institut Numecan, INSERM, INRAE, Univ Rennes, Rennes, France; Université Paris-Saclay, AgroParisTech, INRAE, UMR PNCA, Paris, France
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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: 22] [Impact Index Per Article: 7.3] [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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9
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Edwards DM, Røyrvik EC, Chustecki JM, Giannakis K, Glastad RC, Radzvilavicius AL, Johnston IG. Avoiding organelle mutational meltdown across eukaryotes with or without a germline bottleneck. PLoS Biol 2021; 19:e3001153. [PMID: 33891583 PMCID: PMC8064548 DOI: 10.1371/journal.pbio.3001153] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 02/23/2021] [Indexed: 11/25/2022] Open
Abstract
Mitochondrial DNA (mtDNA) and plastid DNA (ptDNA) encode vital bioenergetic apparatus, and mutations in these organelle DNA (oDNA) molecules can be devastating. In the germline of several animals, a genetic “bottleneck” increases cell-to-cell variance in mtDNA heteroplasmy, allowing purifying selection to act to maintain low proportions of mutant mtDNA. However, most eukaryotes do not sequester a germline early in development, and even the animal bottleneck remains poorly understood. How then do eukaryotic organelles avoid Muller’s ratchet—the gradual buildup of deleterious oDNA mutations? Here, we construct a comprehensive and predictive genetic model, quantitatively describing how different mechanisms segregate and decrease oDNA damage across eukaryotes. We apply this comprehensive theory to characterise the animal bottleneck with recent single-cell observations in diverse mouse models. Further, we show that gene conversion is a particularly powerful mechanism to increase beneficial cell-to-cell variance without depleting oDNA copy number, explaining the benefit of observed oDNA recombination in diverse organisms which do not sequester animal-like germlines (for example, sponges, corals, fungi, and plants). Genomic, transcriptomic, and structural datasets across eukaryotes support this mechanism for generating beneficial variance without a germline bottleneck. This framework explains puzzling oDNA differences across taxa, suggesting how Muller’s ratchet is avoided in different eukaryotes. A comprehensive model for mitochondrial and plasmid DNA segregation, supported by with genomic, transcriptomic, and single-cell data, shows how the attritional effects of Muller’s ratchet can be avoided in the organelles of diverse eukaryotes.
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Affiliation(s)
| | | | | | | | | | | | - Iain G. Johnston
- Department of Mathematics, University of Bergen, Norway
- Computational Biology Unit, University of Bergen, Norway
- * E-mail:
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10
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Kirby CS, Patel MR. Elevated mitochondrial DNA copy number found in ubiquinone-deficient clk-1 mutants is not rescued by ubiquinone precursor 2-4-dihydroxybenzoate. Mitochondrion 2021; 58:38-48. [PMID: 33581333 DOI: 10.1016/j.mito.2021.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 01/13/2021] [Accepted: 02/01/2021] [Indexed: 01/28/2023]
Abstract
Inside mitochondria reside semi-autonomous genomes, called mtDNA. mtDNA is multi-copy per cell and mtDNA copy number can vary from hundreds to thousands of copies per cell. The variability of mtDNA copy number between tissues, combined with the lack of variability of copy number within a tissue, suggest a homeostatic copy number regulation mechanism. Mutations in the gene encoding the Caenorhabditis elegans hydroxylase, CLK-1, result in elevated mtDNA. CLK-1's canonical role in ubiquinone biosynthesis results in clk-1 mutants lacking ubiquinone. Importantly, clk-1 mutants also exhibit slowed biological timing phenotypes (pharyngeal pumping, defecation, development) and an activated stress response (UPRmt). These biological timing and stress phenotypes have been attributed to ubiquinone deficiency; however, it is unknown whether the mtDNA phenotype is also due to ubiquinone deficiency. To test this, in animals carrying the uncharacterized clk-1 (ok1247) mutant allele, we supplemented with an exogenous ubiquinone precursor 2-4-dihydroxybenzoate (DHB), which has previously been shown to restore ubiquinone biosynthesis. We measured phenotypes as a function of DHB across a log-scale range. Unlike the biological timing and stress phenotypes, the elevated mtDNA phenotype was not rescued. Since CLK-1's canonical role is in ubiquinone biosynthesis and DHB does not rescue mtDNA copy number, we infer CLK-1 has an additional function in homeostatic mtDNA copy number regulation.
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Affiliation(s)
- Cait S Kirby
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA; Diabetes Research and Training Center, Vanderbilt University, Nashville, TN 37232, USA.
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11
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Du J, Pan B, Cao X, Li J, Yang J, Nie J. Urinary polycyclic aromatic hydrocarbon metabolites, peripheral blood mitochondrial DNA copy number, and neurobehavioral function in coke oven workers. CHEMOSPHERE 2020; 261:127628. [PMID: 32731016 DOI: 10.1016/j.chemosphere.2020.127628] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 04/14/2020] [Accepted: 07/06/2020] [Indexed: 05/18/2023]
Abstract
BACKGROUND Polycyclic aromatic hydrocarbons (PAHs) are the risk factors for workers' neurological performance, which were widely exist in the occupational environment. OBJECTIVE We aimed to investigate the dose-response relationship between various PAH metabolites and workers' neurobehavioral changes and to explore whether mitochondrial DNA copy number (mtDNAcn) can be used as a potential biomarker to reflect changes in neurobehavioral behavior. METHOD A total of 697 workers were recruited from a coke oven plant. The concentrations of eleven PAHs metabolites were determined by HPLC-MS/MS. Peripheral blood mtDNAcn was measured using QPCR. Neurobehavioral function was measured by NCTB questionnaire. The dose-response relationships were evaluated using restricted cubic spline models. Mediation analysis was also carried out. RESULTS We found dose-response relationships between urinary 2-hydroxynaphthalene (2-OH Nap), sum of PAH metabolites (Ʃ -OH PAHs) and total digit span (DSP), backward digit span (DSPB), forward digit span (DSPF) and mtDNAcn. Each one-unit increase in ln-transformed of 2-OH Nap or Ʃ -OH PAHs was associated with a 2.64 or 3.22 decrease in DSP, a 1.20 or 1.58 decrease in DSPF, a 1.44 or 1.62 decrease in DSPB and a 0.13 or 0.12 decrease in mtDNAcn. However, we did not find a significant mediation effect of mtDNAcn between PAHs metabolites and DSP, DSPF, or DSPB. CONCLUSION Our data indicated that workers urinary 2-hydroxynaphthalene and sum of PAH metabolites levels were inversely associated with mtDNAcn and neurobehavior, especially their auditory memory. However, there was no significant mediation effect of mtDNAcn between urinary PAHs metabolites and neurobehavior.
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Affiliation(s)
- Juanjuan Du
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Baolong Pan
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China; General Hospital of Taiyuan Iron & Steel (Group) Co., Ltd., China
| | - Xiaomin Cao
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Jinyu Li
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Jin Yang
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China
| | - Jisheng Nie
- Department of Occupational Health, School of Public Health, Shanxi Medical University, Taiyuan, Shanxi, 030001, China.
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12
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Klucnika A, Ma H. A battle for transmission: the cooperative and selfish animal mitochondrial genomes. Open Biol 2020; 9:180267. [PMID: 30890027 PMCID: PMC6451365 DOI: 10.1098/rsob.180267] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mitochondrial genome is an evolutionarily persistent and cooperative component of metazoan cells that contributes to energy production and many other cellular processes. Despite sharing the same host as the nuclear genome, the multi-copy mitochondrial DNA (mtDNA) follows very different rules of replication and transmission, which translate into differences in the patterns of selection. On one hand, mtDNA is dependent on the host for its transmission, so selections would favour genomes that boost organismal fitness. On the other hand, genetic heterogeneity within an individual allows different mitochondrial genomes to compete for transmission. This intra-organismal competition could select for the best replicator, which does not necessarily give the fittest organisms, resulting in mito-nuclear conflict. In this review, we discuss the recent advances in our understanding of the mechanisms and opposing forces governing mtDNA transmission and selection in bilaterians, and what the implications of these are for mtDNA evolution and mitochondrial replacement therapy.
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Affiliation(s)
- Anna Klucnika
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
| | - Hansong Ma
- 1 Wellcome Trust/Cancer Research UK Gurdon Institute , Tennis Court Road, Cambridge CB2 1QN , UK.,2 Department of Genetics, University of Cambridge , Downing Street, Cambridge CB2 3EH , UK
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13
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Evolving mtDNA populations within cells. Biochem Soc Trans 2020; 47:1367-1382. [PMID: 31484687 PMCID: PMC6824680 DOI: 10.1042/bst20190238] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/06/2019] [Accepted: 08/08/2019] [Indexed: 12/14/2022]
Abstract
Mitochondrial DNA (mtDNA) encodes vital respiratory machinery. Populations of mtDNA molecules exist in most eukaryotic cells, subject to replication, degradation, mutation, and other population processes. These processes affect the genetic makeup of cellular mtDNA populations, changing cell-to-cell distributions, means, and variances of mutant mtDNA load over time. As mtDNA mutant load has nonlinear effects on cell functionality, and cell functionality has nonlinear effects on tissue performance, these statistics of cellular mtDNA populations play vital roles in health, disease, and inheritance. This mini review will describe some of the better-known ways in which these populations change over time in different organisms, highlighting the importance of quantitatively understanding both mutant load mean and variance. Due to length constraints, we cannot attempt to be comprehensive but hope to provide useful links to some of the many excellent studies on these topics.
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14
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Mitry MA, Laurent D, Keith BL, Sira E, Eisenberg CA, Eisenberg LM, Joshi S, Gupte S, Edwards JG. Accelerated cardiomyocyte senescence contributes to late-onset doxorubicin-induced cardiotoxicity. Am J Physiol Cell Physiol 2020; 318:C380-C391. [PMID: 31913702 DOI: 10.1152/ajpcell.00073.2019] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Children surviving cancer and chemotherapy are at risk for adverse health events including heart failure that may be delayed by years. Although the early effects of doxorubicin-induced cardiotoxicity may be attributed to a direct effect on the cardiomyocytes, the mechanisms underlying the delayed or late effects (8-20 yr) are unknown. The goal of this project was to develop a model of late-onset doxorubicin-induced cardiotoxicity to better delineate the underlying pathophysiology responsible. The underlying hypothesis was that doxorubicin-induced "late-onset cardiotoxicity" was the result of mitochondrial dysfunction leading to cell failure and death. Wistar rats, 3-4 wk of age, were randomly assigned to vehicle or doxorubicin injection groups (1-45 mg/kg). Cardiovascular function was unaltered at the lower dosages (1-15 kg/mg), but beginning at 6 mo after injection significant cardiac degradation was observed in the 45 mg/kg group. Doxorubicin significantly increased myocardial mitochondrial DNA (mtDNA) damage. In contrast, in isolated c-kit left ventricular (LV) cells, doxorubicin treatment did not increase mtDNA damage. Biomarkers of senescence within the LV were significantly increased, suggesting accelerated aging of the LV. Doxorubicin also significantly increased LV histamine content suggestive of mast cell activation. With the use of flow cytometry, a significant expansion of the c-kit and stage-specific embryonic antigen 1 cell populations within the LV were concomitant with significant decreases in the circulating peripheral blood population of these cells. These results are consistent with the concept that doxorubicin induced significant damage to the cardiomyocyte population and that although the heart attempted to compensate it eventually succumbed to an inability for self-repair.
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Affiliation(s)
- Maria A Mitry
- Department of Physiology, New York Medical College, Valhalla, New York
| | - Dimitri Laurent
- Department of Physiology, New York Medical College, Valhalla, New York
| | - Britny L Keith
- Department of Physiology, New York Medical College, Valhalla, New York
| | - Elizabeth Sira
- Department of Physiology, New York Medical College, Valhalla, New York
| | - Carol A Eisenberg
- Department of Physiology, New York Medical College, Valhalla, New York
| | | | - Sachindra Joshi
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - Sachin Gupte
- Department of Pharmacology, New York Medical College, Valhalla, New York
| | - John G Edwards
- Department of Physiology, New York Medical College, Valhalla, New York
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15
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Johnston IG. Varied Mechanisms and Models for the Varying Mitochondrial Bottleneck. Front Cell Dev Biol 2019; 7:294. [PMID: 31824946 PMCID: PMC6879659 DOI: 10.3389/fcell.2019.00294] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 11/06/2019] [Indexed: 12/22/2022] Open
Abstract
Mitochondrial DNA (mtDNA) molecules exist in populations within cells, and may carry mutations. Different cells within an organism, and organisms within a family, may have different proportions of mutant mtDNA in these cellular populations. This diversity is often thought of as arising from a “genetic bottleneck.” This article surveys approaches to characterize and model the generation of this genetic diversity, aiming to provide an introduction to the range of concepts involved, and to highlight some recent advances in understanding. In particular, differences between the statistical “genetic bottleneck” (mutant proportion spread) and the physical mtDNA bottleneck and other cellular processes are highlighted. Particular attention is paid to the quantitative analysis of the “genetic bottleneck,” estimation of its magnitude from observed data, and inference of its underlying mechanisms. Evidence that the “genetic bottleneck” (mutant proportion spread) varies with age, between individuals and species, and across mtDNA sequences, is described. The interpretation issues that arise from sampling errors, selection, and different quantitative definitions are also discussed.
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Affiliation(s)
- Iain G Johnston
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
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16
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Kim E, Kim JY, Lee JY. Mathematical Modeling of p53 Pathways. Int J Mol Sci 2019; 20:ijms20205179. [PMID: 31635420 PMCID: PMC6834204 DOI: 10.3390/ijms20205179] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 10/15/2019] [Accepted: 10/15/2019] [Indexed: 12/30/2022] Open
Abstract
Cells have evolved balanced systems that ensure an appropriate response to stress. The systems elicit repair responses in temporary or moderate stress but eliminate irreparable cells via apoptosis in detrimental conditions of prolonged or severe stress. The tumor suppressor p53 is a central player in these stress response systems. When activated under DNA damage stress, p53 regulates hundreds of genes that are involved in DNA repair, cell cycle, and apoptosis. Recently, increasing studies have demonstrated additional regulatory roles of p53 in metabolism and mitochondrial physiology. Due to the inherent complexity of feedback loops between p53 and its target genes, the application of mathematical modeling has emerged as a novel approach to better understand the multifaceted functions and dynamics of p53. In this review, we discuss several mathematical modeling approaches in exploring the p53 pathways.
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Affiliation(s)
- Eunjung Kim
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon 34134, Korea.
| | - Jae-Young Kim
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon 34134, Korea.
- Korea Basic Science Institute, Daejeon 34133, Korea.
| | - Joo-Yong Lee
- Graduate School of Analytical Science and Technology (GRAST), Chungnam National University, Daejeon 34134, Korea.
- Korea Basic Science Institute, Daejeon 34133, Korea.
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17
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Aryaman J, Bowles C, Jones NS, Johnston IG. Mitochondrial Network State Scales mtDNA Genetic Dynamics. Genetics 2019; 212:1429-1443. [PMID: 31253641 PMCID: PMC6707450 DOI: 10.1534/genetics.119.302423] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 06/28/2019] [Indexed: 11/18/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations cause severe congenital diseases but may also be associated with healthy aging. mtDNA is stochastically replicated and degraded, and exists within organelles which undergo dynamic fusion and fission. The role of the resulting mitochondrial networks in the time evolution of the cellular proportion of mutated mtDNA molecules (heteroplasmy), and cell-to-cell variability in heteroplasmy (heteroplasmy variance), remains incompletely understood. Heteroplasmy variance is particularly important since it modulates the number of pathological cells in a tissue. Here, we provide the first wide-reaching theoretical framework which bridges mitochondrial network and genetic states. We show that, under a range of conditions, the (genetic) rate of increase in heteroplasmy variance and de novo mutation are proportionally modulated by the (physical) fraction of unfused mitochondria, independently of the absolute fission-fusion rate. In the context of selective fusion, we show that intermediate fusion:fission ratios are optimal for the clearance of mtDNA mutants. Our findings imply that modulating network state, mitophagy rate, and copy number to slow down heteroplasmy dynamics when mean heteroplasmy is low could have therapeutic advantages for mitochondrial disease and healthy aging.
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Affiliation(s)
- Juvid Aryaman
- Department of Mathematics, Imperial College London, SW7 2AZ, United Kingdom
- Department of Clinical Neurosciences, University of Cambridge, CB2 0QQ, United Kingdom
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, CB2 0XY, United Kingdom
| | - Charlotte Bowles
- School of Biosciences, University of Birmingham, B15 2TT, United Kingdom
| | - Nick S Jones
- Department of Mathematics, Imperial College London, SW7 2AZ, United Kingdom
- Engineering and Physical Sciences Research Council Centre for the Mathematics of Precision Healthcare, Imperial College London, SW7 2AZ, United Kingdom
| | - Iain G Johnston
- Faculty of Mathematics and Natural Sciences, University of Bergen, 5007, Norway
- Alan Turing Institute, London NW1 2DB, United Kingdom
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18
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Johnston IG. Tension and Resolution: Dynamic, Evolving Populations of Organelle Genomes within Plant Cells. MOLECULAR PLANT 2019; 12:764-783. [PMID: 30445187 DOI: 10.1016/j.molp.2018.11.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 10/25/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Mitochondria and plastids form dynamic, evolving populations physically embedded in the fluctuating environment of the plant cell. Their evolutionary heritage has shaped how the cell controls the genetic structure and the physical behavior of its organelle populations. While the specific genes involved in these processes are gradually being revealed, the governing principles underlying this controlled behavior remain poorly understood. As the genetic and physical dynamics of these organelles are central to bioenergetic performance and plant physiology, this challenges both fundamental biology and strategies to engineer better-performing plants. This article reviews current knowledge of the physical and genetic behavior of mitochondria and chloroplasts in plant cells. An overarching hypothesis is proposed whereby organelles face a tension between genetic robustness and individual control and responsiveness, and different species resolve this tension in different ways. As plants are immobile and thus subject to fluctuating environments, their organelles are proposed to favor individual responsiveness, sacrificing genetic robustness. Several notable features of plant organelles, including large genomes, mtDNA recombination, fragmented organelles, and plastid/mitochondrial differences may potentially be explained by this hypothesis. Finally, the ways that quantitative and systems biology can help shed light on the plethora of open questions in this field are highlighted.
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Affiliation(s)
- Iain G Johnston
- School of Biosciences, University of Birmingham, Birmingham, UK; Birmingham Institute for Forest Research, University of Birmingham, Birmingham, UK.
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19
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Abstract
Mitochondria, a nearly ubiquitous feature of eukaryotes, are derived from an ancient symbiosis. Despite billions of years of cooperative coevolution - in what is arguably the most important mutualism in the history of life - the persistence of mitochondrial genomes also creates conditions for genetic conflict with the nucleus. Because mitochondrial genomes are present in numerous copies per cell, they are subject to both within- and among-organism levels of selection. Accordingly, 'selfish' genotypes that increase their own proliferation can rise to high frequencies even if they decrease organismal fitness. It has been argued that uniparental (often maternal) inheritance of cytoplasmic genomes evolved to curtail such selfish replication by minimizing within-individual variation and, hence, within-individual selection. However, uniparental inheritance creates conditions for cytonuclear conflict over sex determination and sex ratio, as well as conditions for sexual antagonism when mitochondrial variants increase transmission by enhancing maternal fitness but have the side-effect of being harmful to males (i.e., 'mother's curse'). Here, we review recent advances in understanding selfish replication and sexual antagonism in the evolution of mitochondrial genomes and the mechanisms that suppress selfish interactions, drawing parallels and contrasts with other organelles (plastids) and bacterial endosymbionts that arose more recently. Although cytonuclear conflict is widespread across eukaryotes, it can be cryptic due to nuclear suppression, highly variable, and lineage-specific, reflecting the diverse biology of eukaryotes and the varying architectures of their cytoplasmic genomes.
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Affiliation(s)
- Justin C Havird
- Department of Integrative Biology, The University of Texas, Austin, TX 78712, USA.
| | - Evan S Forsythe
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Alissa M Williams
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - John H Werren
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria 3800, Australia
| | - Daniel B Sloan
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
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20
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Hoitzing H, Gammage PA, Haute LV, Minczuk M, Johnston IG, Jones NS. Energetic costs of cellular and therapeutic control of stochastic mitochondrial DNA populations. PLoS Comput Biol 2019; 15:e1007023. [PMID: 31242175 PMCID: PMC6615642 DOI: 10.1371/journal.pcbi.1007023] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2018] [Revised: 07/09/2019] [Accepted: 04/11/2019] [Indexed: 12/28/2022] Open
Abstract
The dynamics of the cellular proportion of mutant mtDNA molecules is crucial for mitochondrial diseases. Cellular populations of mitochondria are under homeostatic control, but the details of the control mechanisms involved remain elusive. Here, we use stochastic modelling to derive general results for the impact of cellular control on mtDNA populations, the cost to the cell of different mtDNA states, and the optimisation of therapeutic control of mtDNA populations. This formalism yields a wealth of biological results, including that an increasing mtDNA variance can increase the energetic cost of maintaining a tissue, that intermediate levels of heteroplasmy can be more detrimental than homoplasmy even for a dysfunctional mutant, that heteroplasmy distribution (not mean alone) is crucial for the success of gene therapies, and that long-term rather than short intense gene therapies are more likely to beneficially impact mtDNA populations.
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Affiliation(s)
- Hanne Hoitzing
- Department of Mathematics, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Payam A. Gammage
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
- CRUK Beatson Institute for Cancer Research, Glasgow, United Kingdom
| | - Lindsey Van Haute
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Michal Minczuk
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, CB2 0XY, United Kingdom
| | - Iain G. Johnston
- Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
- Alan Turing Institute, London, United Kingdom
| | - Nick S. Jones
- Department of Mathematics, Imperial College London, London, SW7 2AZ, United Kingdom
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21
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Abstract
Cell-to-cell heterogeneity drives a range of (patho)physiologically important phenomena, such as cell fate and chemotherapeutic resistance. The role of metabolism, and particularly of mitochondria, is increasingly being recognized as an important explanatory factor in cell-to-cell heterogeneity. Most eukaryotic cells possess a population of mitochondria, in the sense that mitochondrial DNA (mtDNA) is held in multiple copies per cell, where the sequence of each molecule can vary. Hence, intra-cellular mitochondrial heterogeneity is possible, which can induce inter-cellular mitochondrial heterogeneity, and may drive aspects of cellular noise. In this review, we discuss sources of mitochondrial heterogeneity (variations between mitochondria in the same cell, and mitochondrial variations between supposedly identical cells) from both genetic and non-genetic perspectives, and mitochondrial genotype-phenotype links. We discuss the apparent homeostasis of mtDNA copy number, the observation of pervasive intra-cellular mtDNA mutation (which is termed "microheteroplasmy"), and developments in the understanding of inter-cellular mtDNA mutation ("macroheteroplasmy"). We point to the relationship between mitochondrial supercomplexes, cristal structure, pH, and cardiolipin as a potential amplifier of the mitochondrial genotype-phenotype link. We also discuss mitochondrial membrane potential and networks as sources of mitochondrial heterogeneity, and their influence upon the mitochondrial genome. Finally, we revisit the idea of mitochondrial complementation as a means of dampening mitochondrial genotype-phenotype links in light of recent experimental developments. The diverse sources of mitochondrial heterogeneity, as well as their increasingly recognized role in contributing to cellular heterogeneity, highlights the need for future single-cell mitochondrial measurements in the context of cellular noise studies.
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Affiliation(s)
- Juvid Aryaman
- Department of Mathematics, Imperial College London, London, United Kingdom
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, United Kingdom
- MRC Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Iain G. Johnston
- School of Biosciences, University of Birmingham, Birmingham, United Kingdom
- EPSRC Centre for the Mathematics of Precision Healthcare, Imperial College London, London, United Kingdom
| | - Nick S. Jones
- Department of Mathematics, Imperial College London, London, United Kingdom
- EPSRC Centre for the Mathematics of Precision Healthcare, Imperial College London, London, United Kingdom
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22
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Nuclear genes involved in mitochondrial diseases caused by instability of mitochondrial DNA. J Appl Genet 2018; 59:43-57. [PMID: 29344903 PMCID: PMC5799321 DOI: 10.1007/s13353-017-0424-3] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Accepted: 12/20/2017] [Indexed: 02/07/2023]
Abstract
Mitochondrial diseases are defined by a respiratory chain dysfunction and in most of the cases manifest as multisystem disorders with predominant expression in muscles and nerves and may be caused by mutations in mitochondrial (mtDNA) or nuclear (nDNA) genomes. Most of the proteins involved in respiratory chain function are nuclear encoded, although 13 subunits of respiratory chain complexes (together with 2 rRNAs and 22 tRNAs necessary for their translation) encoded by mtDNA are essential for cell function. nDNA encodes not only respiratory chain subunits but also all the proteins responsible for mtDNA maintenance, especially those involved in replication, as well as other proteins necessary for the transcription and copy number control of this multicopy genome. Mutations in these genes can cause secondary instability of the mitochondrial genome in the form of depletion (decreased number of mtDNA molecules in the cell), vast multiple deletions or accumulation of point mutations which in turn leads to mitochondrial diseases inherited in a Mendelian fashion. The list of genes involved in mitochondrial DNA maintenance is long, and still incomplete.
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23
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Wong JYY, Hu W, Downward GS, Seow WJ, Bassig BA, Ji BT, Wei F, Wu G, Li J, He J, Liu CS, Cheng WL, Huang Y, Yang K, Chen Y, Rothman N, Vermeulen RC, Lan Q. Personal exposure to fine particulate matter and benzo[a]pyrene from indoor air pollution and leukocyte mitochondrial DNA copy number in rural China. Carcinogenesis 2017; 38:893-899. [PMID: 28911003 DOI: 10.1093/carcin/bgx068] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 06/22/2017] [Indexed: 12/31/2022] Open
Abstract
Households in Xuanwei and Fuyuan, China, possess hazardous levels of fine particulate matter with an aerodynamic diameter <2.5 microns (PM2.5) and polycyclic aromatic hydrocarbons (PAHs) from coal combustion. Previous studies found that increased exposure to PM2.5 and benzo[a]pyrene (BaP; a PAH) were associated with decreased mitochondrial DNA copy number (mtDNAcn), a marker of oxidative stress. We further evaluated these associations in a cross-sectional study of 148 healthy non-smoking women from Xuanwei and Fuyuan. Personal exposure to PM2.5 and BaP was measured using portable devices. MtDNAcn was measured using qPCR amplification of leukocyte DNA that was collected after air measurements. Linear regression models were used to estimate the associations between personal exposure to PM2.5 and BaP, and mtDNAcn adjusted for age, body mass index (BMI) and fuel type. We found inverse associations between exposure to PM2.5 and BaP, and mtDNAcn. Each incremental log-μg/m3 increase in PM2.5 was associated with a significant decrease in mtDNAcn of -10.3 copies per cell [95% confidence interval (95% CI): -18.6, -2.0; P = 0.02]. Additionally, each log-ng/m3 increase in BaP was associated with a significant decrease in mtDNAcn of -5.4 copies per cell (95% CI: -9.9, -0.8, P = 0.02). Age, BMI, fuel type and coal mine type were not significantly associated with mtDNAcn. Exposure to PM2.5 and BaP may alter mitochondrial dynamics in non-smoking Chinese women. MtDNAcn may be a potential mediator of indoor air pollution on chronic disease development.
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Affiliation(s)
- Jason Y Y Wong
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Rockville, MD, 20850, USA
| | - Wei Hu
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Rockville, MD, 20850, USA
| | - George S Downward
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, 3508 TD, the Netherlands
| | - Wei Jie Seow
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Rockville, MD, 20850, USA.,Saw Swee Hock School of Public Health, National University of Singapore and National University Health System.,Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore and National University Health System, 117549, Singapore
| | - Bryan A Bassig
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Rockville, MD, 20850, USA
| | - Bu-Tian Ji
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Rockville, MD, 20850, USA
| | - Fusheng Wei
- China National Environmental Monitoring Center, Beijing 100012, People's Republic of China
| | - Guoping Wu
- China National Environmental Monitoring Center, Beijing 100012, People's Republic of China
| | - Jihua Li
- Qujing Center for Diseases Control and Prevention, Sanjiangdadao, Qujing, Yunnan 655099, People's Republic of China
| | - Jun He
- Qujing Center for Diseases Control and Prevention, Sanjiangdadao, Qujing, Yunnan 655099, People's Republic of China
| | - Chin-San Liu
- Department of Neurology and Vascular and Genomic Center, Changhua Christian Hospital, Changhua, Taiwan, Graduate Institute of Integrated Medicine, College of Chinese Medicine, China Medical University, Taichung 500, Taiwan
| | - Wen-Ling Cheng
- Laboratory of Mitochondrial Medicine, Chunghua Christian Hospital, Taipei 500, Taiwan
| | - Yunchao Huang
- Department of Cardiothoracic Surgery, Third Affiliated Hospital of Kunming Medical University (Yunnan Tumor Hospital), Kunming 650118, People's Republic of China
| | - Kaiyun Yang
- Department of Cardiothoracic Surgery, Third Affiliated Hospital of Kunming Medical University (Yunnan Tumor Hospital), Kunming 650118, People's Republic of China
| | - Ying Chen
- Department of Cardiothoracic Surgery, Third Affiliated Hospital of Kunming Medical University (Yunnan Tumor Hospital), Kunming 650118, People's Republic of China
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Rockville, MD, 20850, USA
| | - Roel C Vermeulen
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, 3508 TD, the Netherlands
| | - Qing Lan
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Rockville, MD, 20850, USA
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24
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Tan J, Song M, Zhou M, Hu Y. Antibiotic tigecycline enhances cisplatin activity against human hepatocellular carcinoma through inducing mitochondrial dysfunction and oxidative damage. Biochem Biophys Res Commun 2017; 483:17-23. [PMID: 28069382 DOI: 10.1016/j.bbrc.2017.01.021] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Accepted: 01/05/2017] [Indexed: 01/08/2023]
Abstract
Targeting mitochondrial metabolism has been recently demonstrated to be a promising therapeutic strategy for the treatment of various cancer. In this work, we demonstrate that antibiotic tigecycline is selectively against hepatocellular carcinoma (HCC) through inducing mitochondrial dysfunction and oxidative damage. Tigecycline is more effective in inhibiting proliferation and inducing apoptosis of HCC than normal liver cells. Importantly, tigecycline significantly enhances the inhibitory effects of chemotherapeutic drug cisplatin in HCC in vitro and in vivo. Mechanistically, tigecycline specifically inhibits mitochondrial translation as shown by the decreased protein levels of Cox-1 and -2 but not Cox-4 or Grp78, and increased mRNA levels of Cox-1 and -2 but not Cox-4 in HCC cells exposed to tigecycline. In addition, tigecycline significantly induces mitochondrial dysfunction in HCC cells via decreasing mitochondrial membrane potential, complex I and IV activities, mitochondrial respiration and ATP levels. Tigecycline also increases levels of mitochondrial superoxide, hydrogen peroxide and ROS levels. Consistent with oxidative stress, oxidative damage on DNA, protein and lipid are also observed in tigecycline-treated cells. Importantly, antioxidant N-acetyl-l-cysteine (NAC) reverses the effects of tigecycline, suggesting that oxidative stress is required for the action of tigecycline in HCC cells. We further show that HCC cells have higher level of mitochondrial biogenesis than normal liver cells which might explain the different sensitivity to tigecycline between HCC and normal liver cells. Our work is the first to demonstrate that tigecycline is a promising candidate for HCC treatment and highlight the therapeutic value of targeting mitochondrial metabolism in HCC.
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Affiliation(s)
- Jun Tan
- Department of Hepatology, Ningbo No. 2 Hospital, Ningbo, 315010, China
| | - Meijun Song
- Department of Respiratory Medicine, Ningbo Medical Treatment Center Li Huili Hospital, Ningbo, 315041, China
| | - Mi Zhou
- School of Medicine, Ningbo University, Ningbo, 315211, China.
| | - Yaoren Hu
- Department of Hepatology, Ningbo No. 2 Hospital, Ningbo, 315010, China.
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25
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Evolution of Cell-to-Cell Variability in Stochastic, Controlled, Heteroplasmic mtDNA Populations. Am J Hum Genet 2016; 99:1150-1162. [PMID: 27843124 DOI: 10.1016/j.ajhg.2016.09.016] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 09/22/2016] [Indexed: 11/20/2022] Open
Abstract
Populations of physiologically vital mitochondrial DNA (mtDNA) molecules evolve in cells under control from the nucleus. The evolution of populations of mixed mtDNA types is complicated and poorly understood, and variability of these controlled admixtures plays a central role in the inheritance and onset of genetic disease. Here, we develop a mathematical theory describing the evolution of, and variability in, these stochastic populations for any type of cellular control, showing that cell-to-cell variability in mtDNA and mutant load inevitably increases with time, according to rates that we derive and which are notably independent of the mechanistic details of feedback signaling. We show with a set of experimental case studies that this theory explains disparate quantitative results from classical and modern experimental and computational research on heteroplasmy variance in different species. We demonstrate that our general model provides a host of specific insights, including a modification of the often-used but hard-to-interpret Wright formula to correspond directly to biological observables, the ability to quantify selective and mutational pressure in mtDNA populations, and characterization of the pronounced variability inevitably arising from the action of possible mtDNA quality-control mechanisms. Our general theoretical framework, supported by existing experimental results, thus helps us to understand and predict the evolution of stochastic mtDNA populations in cell biology.
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26
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Gitschlag BL, Kirby CS, Samuels DC, Gangula RD, Mallal SA, Patel MR. Homeostatic Responses Regulate Selfish Mitochondrial Genome Dynamics in C. elegans. Cell Metab 2016; 24:91-103. [PMID: 27411011 PMCID: PMC5287496 DOI: 10.1016/j.cmet.2016.06.008] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 05/27/2016] [Accepted: 06/13/2016] [Indexed: 02/08/2023]
Abstract
Mutant mitochondrial genomes (mtDNA) can be viewed as selfish genetic elements that persist in a state of heteroplasmy despite having potentially deleterious metabolic consequences. We sought to study regulation of selfish mtDNA dynamics. We establish that the large 3.1-kb deletion-bearing mtDNA variant uaDf5 is a selfish genome in Caenorhabditis elegans. Next, we show that uaDf5 mutant mtDNA replicates in addition to, not at the expense of, wild-type mtDNA. These data suggest the existence of a homeostatic copy-number control that is exploited by uaDf5 to "hitchhike" to high frequency. We also observe activation of the mitochondrial unfolded protein response (UPR(mt)) in uaDf5 animals. Loss of UPR(mt) causes a decrease in uaDf5 frequency, whereas its constitutive activation increases uaDf5 levels. UPR(mt) activation protects uaDf5 from mitophagy. Taken together, we propose that mtDNA copy-number control and UPR(mt) represent two homeostatic response mechanisms that play important roles in regulating selfish mitochondrial genome dynamics.
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Affiliation(s)
- Bryan L Gitschlag
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Interdisciplinary Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - Cait S Kirby
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Biological Sciences Graduate Program, Vanderbilt University, Nashville, TN 37232, USA
| | - David C Samuels
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN 37232, USA; Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37232, USA
| | - Rama D Gangula
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
| | - Simon A Mallal
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Department of Pathology, Microbiology and Immunology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA; Institute for Immunology and Infectious Diseases, Murdoch University, Murdoch, WA 6150, Australia
| | - Maulik R Patel
- Department of Biological Sciences, Vanderbilt University, Nashville, TN 37232, USA; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37232, USA.
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Yu M, Li R, Zhang J. Repositioning of antibiotic levofloxacin as a mitochondrial biogenesis inhibitor to target breast cancer. Biochem Biophys Res Commun 2016; 471:639-45. [PMID: 26902121 DOI: 10.1016/j.bbrc.2016.02.072] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 02/17/2016] [Indexed: 01/07/2023]
Abstract
Targeting mitochondrial biogenesis has become a potential therapeutic strategy in cancer due to their unique metabolic dependencies. In this study, we show that levofloxacin, a FDA-approved antibiotic, is an attractive candidate for breast cancer treatment. This is achieved by the inhibition of proliferation and induction of apoptosis in a panel of breast cancer cell lines while sparing normal breast cells. It also acts synergistically with conventional chemo drug in two independent in vivo breast xenograft mouse models. Importantly, levofloxacin inhibits mitochondrial biogenesis as shown by the decreased level of mitochondrial respiration, membrane potential and ATP. In addition, the anti-proliferative and pro-apoptotic effects of levofloxacin are reversed by acetyl-L-Carnitine (ALCAR, a mitochondrial fuel), confirming that levofloxacin's action in breast cancer cells is through inhibition of mitochondrial biogenesis. A consequence of mitochondrial biogenesis inhibition by levofloxacin in breast cancer cells is the deactivation of PI3K/Akt/mTOR and MAPK/ERK pathways. We further demonstrate that breast cancer cells have increased mitochondrial biogenesis than normal breast cells, and this explains their different sensitivity to levofloxacin. Our work suggest that levofloxacin is a useful addition to breast cancer treatment. Our work also establish the essential role of mitochondrial biogenesis on the activation of PI3K/Akt/mTOR and MAPK/ERK pathways in breast cancer cells.
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Affiliation(s)
- Min Yu
- Galactophore Department, JingZhou Central Hospital, JingZhou, People's Republic of China
| | - Ruishu Li
- Forensic Surgery Department, JingZhou Traditional Chinese Medicine Hospital, JingZhou, People's Republic of China.
| | - Juan Zhang
- Endocrinology Department, JingZhou Central Hospital, JingZhou, People's Republic of China
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28
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van Osch FHM, Voets AM, Schouten LJ, Gottschalk RWH, Simons CCJM, van Engeland M, Lentjes MHFM, van den Brandt PA, Smeets HJM, Weijenberg MP. Mitochondrial DNA copy number in colorectal cancer: between tissue comparisons, clinicopathological characteristics and survival. Carcinogenesis 2015; 36:1502-10. [PMID: 26476438 DOI: 10.1093/carcin/bgv151] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 10/07/2015] [Indexed: 12/29/2022] Open
Abstract
Low mitochondrial DNA (mtDNA) copy number in tumors has been associated with worse prognosis in colorectal cancer (CRC). This study further deciphers the role of mtDNA copy number in CRC by comparing mtDNA copy number between healthy, adenoma and carcinoma tissue, by investigating its association according to several clinicopathological characteristics in CRC, and by relating it to CRC-specific survival in CRC patients. A hospital-based series of samples including cancer, adenoma and adjacent histologically normal tissue from primary CRC patients (n = 56) and recurrent CRC (n = 16) was studied as well as colon mucosa samples from healthy subjects (n = 76). Furthermore, mtDNA copy number was assessed in carcinomas of 693 CRC cases identified from the population-based Netherlands Cohort Study (NLCS). MtDNA copy number was significantly lower in carcinoma tissue (P = 0.011) and adjacent tissue (P < 0.001) compared to earlier resected adenoma tissue and in primary CRC tissue compared to recurrent CRC tissue (P = 0.011). Within both study populations, mtDNA copy number was significantly lower in mutated BRAF (P = 0.027 and P = 0.006) and in microsatellite unstable (MSI) tumors (P = 0.033 and P < 0.001) and higher in KRAS mutated tumors (P = 0.004). Furthermore, the association between mtDNA and survival seemed to follow an inverse U-shape with the highest HR observed in the second quintile of mtDNA copy number (HR = 1.70, 95% CI = 1.18, 2.44) compared to the first quintile. These results might reflect an association of mtDNA copy number with various malignant processes in cancer cells and warrants further research on tumor energy metabolism in CRC prognosis.
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Affiliation(s)
| | | | | | | | | | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht 6200MD, The Netherlands
| | - Marjolein H F M Lentjes
- Department of Pathology, GROW - School for Oncology and Developmental Biology, Maastricht University, Maastricht 6200MD, The Netherlands
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29
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Johnston IG, Jones NS. Closed-form stochastic solutions for non-equilibrium dynamics and inheritance of cellular components over many cell divisions. Proc Math Phys Eng Sci 2015; 471:20150050. [PMID: 26339194 PMCID: PMC4550007 DOI: 10.1098/rspa.2015.0050] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2015] [Accepted: 06/05/2015] [Indexed: 12/23/2022] Open
Abstract
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for treating several important examples of these stochastic processes, most notably gene expression and random partitioning at single-cell divisions or after a steady state has been reached. Comparatively little work exists exploring different and specific ways that repeated cell divisions can lead to stochastic inheritance of unequilibrated cellular populations. Here we introduce a mathematical formalism to describe cellular agents that are subject to random creation, replication and/or degradation, and are inherited according to a range of random dynamics at cell divisions. We obtain closed-form generating functions describing systems at any time after any number of cell divisions for binomial partitioning and divisions provoking a deterministic or random, subtractive or additive change in copy number, and show that these solutions agree exactly with stochastic simulation. We apply this general formalism to several example problems involving the dynamics of mitochondrial DNA during development and organismal lifetimes.
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Affiliation(s)
- Iain G Johnston
- Department of Mathematics , Imperial College London , South Kensington Campus, London SW7 2AZ, UK
| | - Nick S Jones
- Department of Mathematics , Imperial College London , South Kensington Campus, London SW7 2AZ, UK
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Johnston IG, Burgstaller JP, Havlicek V, Kolbe T, Rülicke T, Brem G, Poulton J, Jones NS. Stochastic modelling, Bayesian inference, and new in vivo measurements elucidate the debated mtDNA bottleneck mechanism. eLife 2015; 4:e07464. [PMID: 26035426 PMCID: PMC4486817 DOI: 10.7554/elife.07464] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Accepted: 05/29/2015] [Indexed: 12/14/2022] Open
Abstract
Dangerous damage to mitochondrial DNA (mtDNA) can be ameliorated during mammalian development through a highly debated mechanism called the mtDNA bottleneck. Uncertainty surrounding this process limits our ability to address inherited mtDNA diseases. We produce a new, physically motivated, generalisable theoretical model for mtDNA populations during development, allowing the first statistical comparison of proposed bottleneck mechanisms. Using approximate Bayesian computation and mouse data, we find most statistical support for a combination of binomial partitioning of mtDNAs at cell divisions and random mtDNA turnover, meaning that the debated exact magnitude of mtDNA copy number depletion is flexible. New experimental measurements from a wild-derived mtDNA pairing in mice confirm the theoretical predictions of this model. We analytically solve a mathematical description of this mechanism, computing probabilities of mtDNA disease onset, efficacy of clinical sampling strategies, and effects of potential dynamic interventions, thus developing a quantitative and experimentally-supported stochastic theory of the bottleneck. DOI:http://dx.doi.org/10.7554/eLife.07464.001 Mitochondria are structures that provide vital sources of energy in our cells. DNA contained within mitochondria encodes important mitochondrial machinery, and most human cells contain hundreds or thousands of mitochondrial DNA molecules in addition to the DNA that is stored in the nucleus. Mitochondrial DNA is inherited from mothers via the egg, and the details of this inheritance are poorly understood. This question is important because inherited mistakes in mitochondrial DNA can have detrimental consequences on health, with links to fatal diseases and many other conditions. An unfertilised egg cell contains many copies of mitochondrial DNA molecules; some may have mutations and some may not. After fertilisation, the egg divides, the number of cells in the developing embryo increases, and the number of mitochondrial DNA molecules per cell changes. If the original egg cell contained defective mitochondrial DNA, some of these new cells end up containing more defective copies than others, leading to cell-to-cell differences in the developing embryo. This potentially allows cells with the greatest number of defective mitochondria to be eliminated. The increase in this cell-to-cell variability is called ‘bottlenecking’, and its mechanism remains highly debated. Johnston et al. have now used tools from maths, statistics and new experiments to address this debate, in the light of several studies that measured the mitochondrial DNA content in developing mice. This approach allowed a new theoretical model of mitochondrial DNA during the growth of an organism to be produced, which encompasses a wide range of existing theories and allows them to be compared. This model starts from the viewpoint that the hundreds or thousands of mitochondrial DNA molecules in a cell can be thought of as a population undergoing random ‘birth’ and ‘death’, and it allows the first statistical comparison of the many proposed bottleneck mechanisms. Johnston et al. find support for two ways that cells segregate mitochondria as they multiply, and show that the decrease in the number of mitochondrial DNA molecules during bottlenecking is flexible. This reconciles a debate amongst previous studies. These findings are confirmed using new experimental data from mice, which are genetically distinct from existing studies, illustrating the generality of the model's findings. Furthermore, an analytic mathematical description that describes in detail how bottlenecking might work is produced. Finally, Johnston et al. provide examples using this new theoretical model to suggest therapeutic strategies for diseases caused by mitochondrial DNA mutations. Future work will need to test these suggestions, and link mathematical understanding of mitochondria with healthcare data. DOI:http://dx.doi.org/10.7554/eLife.07464.002
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Affiliation(s)
- Iain G Johnston
- Department of Mathematics, Imperial College London, London, United Kingdom
| | - Joerg P Burgstaller
- Biotechnology in Animal Production, Department for Agrobiotechnology, IFA Tulln, IFA Tulln, Tulln, Austria
| | - Vitezslav Havlicek
- Reproduction Centre Wieselburg, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
| | - Thomas Kolbe
- Biomodels Austria, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Thomas Rülicke
- Institute of Laboratory Animal Science, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna, Austria
| | - Jo Poulton
- Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, United Kingdom
| | - Nick S Jones
- Department of Mathematics, Imperial College London, London, United Kingdom
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31
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Chen Y, Zhang J, Huang X, Zhang J, Zhou X, Hu J, Li G, He S, Xing J. High leukocyte mitochondrial DNA content contributes to poor prognosis in glioma patients through its immunosuppressive effect. Br J Cancer 2015; 113:99-106. [PMID: 26022928 PMCID: PMC4647544 DOI: 10.1038/bjc.2015.184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2014] [Revised: 04/13/2015] [Accepted: 04/27/2015] [Indexed: 02/07/2023] Open
Abstract
Background: Epidemiological studies have indicated significant associations of leukocyte mitochondrial DNA (mtDNA) copy number with risk of several malignancies, including glioma. However, whether mtDNA content can predict the clinical outcome of glioma patients has not been investigated. Methods: The mtDNA content of peripheral blood leukocytes from 336 glioma patients was examined using a real-time PCR-based method. Kaplan–Meier curves and Cox proportional hazards regression model were used to examine the association of mtDNA content with overall survival (OS) and progression-free survival (PFS) of patients. To explore the potential mechanism, the immune phenotypes of peripheral blood mononuclear cells (PBMCs) and plasma concentrations of several cytokines from another 20 glioma patients were detected by flow cytometry and enzyme-linked immunosorbent assay (ELISA), respectively. Results: Patients with high mtDNA content showed both poorer OS and PFS than those with low mtDNA content. Multivariate Cox regression analysis demonstrated that mtDNA content was an independent prognostic factor for both OS and PFS. Stratified analyses showed that high mtDNA content was significantly associated with poor prognosis of patients with younger age, high-grade glioma or adjuvant radiochemotherapy. Immunological analysis indicated that patients with high mtDNA content had significantly lower frequency of natural killer cells in PBMCs and higher plasma concentrations of interleukin-2 and tumour necrosis factor-α, suggesting an immunosuppression-related mechanism involved in mtDNA-mediated prognosis. Conclusions: Our study for the first time demonstrated that leukocyte mtDNA content could serve as an independent prognostic marker and an indicator of immune functions in glioma patients.
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Affiliation(s)
- Y Chen
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, China
| | - J Zhang
- Department of Oncology, The First affiliated Hospital of Chengdu Medical College, Chengdu, Sichuan 610500, China
| | - X Huang
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, China
| | - J Zhang
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, China
| | - X Zhou
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, China
| | - J Hu
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, China
| | - G Li
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, 1 Xinsi Road, Xi'an, Shaanxi 710038, China
| | - S He
- Department of Neurosurgery, Tangdu Hospital, Fourth Military Medical University, 1 Xinsi Road, Xi'an, Shaanxi 710038, China
| | - J Xing
- State Key Laboratory of Cancer Biology and Experimental Teaching Center of Basic Medicine, Fourth Military Medical University, 169 Changle West Road, Xi'an, Shaanxi 710032, China
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32
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Context-Dependent Role of Mitochondrial Fusion-Fission in Clonal Expansion of mtDNA Mutations. PLoS Comput Biol 2015; 11:e1004183. [PMID: 25996936 PMCID: PMC4440705 DOI: 10.1371/journal.pcbi.1004183] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/09/2015] [Indexed: 12/14/2022] Open
Abstract
The accumulation of mutant mitochondrial DNA (mtDNA) molecules in aged cells has been associated with mitochondrial dysfunction, age-related diseases and the ageing process itself. This accumulation has been shown to often occur clonally, where mutant mtDNA grow in number and overpopulate the wild-type mtDNA. However, the cell possesses quality control (QC) mechanisms that maintain mitochondrial function, in which dysfunctional mitochondria are isolated and removed by selective fusion and mitochondrial autophagy (mitophagy), respectively. The aim of this study is to elucidate the circumstances related to mitochondrial QC that allow the expansion of mutant mtDNA molecules. For the purpose of the study, we have developed a mathematical model of mitochondrial QC process by extending our previous validated model of mitochondrial turnover and fusion-fission. A global sensitivity analysis of the model suggested that the selectivity of mitophagy and fusion is the most critical QC parameter for clearing de novo mutant mtDNA molecules. We further simulated several scenarios involving perturbations of key QC parameters to gain a better understanding of their dynamic and synergistic interactions. Our model simulations showed that a higher frequency of mitochondrial fusion-fission can provide a faster clearance of mutant mtDNA, but only when mutant–rich mitochondria that are transiently created are efficiently prevented from re-fusing with other mitochondria and selectively removed. Otherwise, faster fusion-fission quickens the accumulation of mutant mtDNA. Finally, we used the insights gained from model simulations and analysis to propose a possible circumstance involving deterioration of mitochondrial QC that permits mutant mtDNA to expand with age. Mitochondria are responsible for most energy generation in human and animal cells. Loss or pathological alteration of mitochondrial function is a hallmark of many age-related diseases. Mitochondrial dysfunction may be a central and conserved feature of the ageing process. As part of quality control (QC), mitochondria are continually replicated and degraded. Furthermore, two mitochondria can fuse to form a single mitochondrion, and a mitochondrion can divide (fission) into two separate organelles. Despite this QC, mutant mitochondrial DNA (mtDNA) molecules have been observed to accumulate in cells with age which may lead to mitochondrial dysfunction. In this study, we created a detailed mathematical model of mitochondrial QC and performed model simulations to investigate circumstances allowing or preventing the accumulation of mutant mtDNA. We found that more frequent fusion-fission could quicken mutant mtDNA clearance, but only when mitochondria harboring a high fraction of mutant molecules were strongly prevented from fusing with other mitochondria and selectively degraded. Otherwise, faster fusion-fission would actually enhance the accumulation of mutant mtDNA. Our results suggested that the expansion of mutant mtDNA likely involves a decline in the selectivity of mitochondrial degradation and fusion. This insight might open new avenues for experiment and possible development of future therapies.
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33
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Williams SB, Ye Y, Huang M, Chang DW, Kamat AM, Pu X, Dinney CP, Wu X. Mitochondrial DNA Content as Risk Factor for Bladder Cancer and Its Association with Mitochondrial DNA Polymorphisms. Cancer Prev Res (Phila) 2015; 8:607-13. [PMID: 25896234 DOI: 10.1158/1940-6207.capr-14-0414] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/01/2015] [Indexed: 01/05/2023]
Abstract
Mitochondrial DNA (mtDNA) content has been shown to be associated with cancer susceptibility. We identified 926 bladder cancer patients and compared these with 926 healthy controls frequency matched on age, gender, and ethnicity. Patients diagnosed with bladder cancer had significantly decreased mtDNA content when compared with control subjects (median, 0.98 vs. 1.04, P < 0.001). Low mtDNA content (i.e., less than the median in control subjects) was associated with a statistically significant increased risk of bladder cancer, when compared with high mtDNA content [Odds ratio (OR), 1.37; 95% confidence interval (CI), 1.13-1.66; P < 0.001). In a trend analysis, a statistically significant dose-response relationship was detected between lower mtDNA content and increasing risk of bladder cancer (Ptrend <0.001). When stratified by host characteristics, advanced age (>65 years), male sex and positive smoking history were significantly associated with low mtDNA content and increased risk of bladder cancer. We identified two unique mtDNA polymorphisms significantly associated with risk of bladder cancer: mitot10464c (OR, 1.39; 95% CI, 1.00-1.93; P = 0.048) and mitoa4918g (OR, 1.40; 95% CI, 1.00-1.95; P = 0.049). Analysis of the joint effect of low mtDNA content and unfavorable mtDNA polymorphisms revealed a 2.5-fold increased risk of bladder cancer (OR, 2.50; 95% CI, 1.60-3.94; P < 0.001). Significant interaction was observed between mitoa4918g and mtDNA content (Pinteraction = 0.028). Low mtDNA content was associated with increased risk of bladder cancer and we identified new susceptibility mtDNA alleles associated with increased risk that require further investigation into the biologic underpinnings of bladder carcinogenesis.
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Affiliation(s)
- Stephen B Williams
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yuanqing Ye
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Maosheng Huang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David W Chang
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Ashish M Kamat
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xia Pu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Colin P Dinney
- Department of Urology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xifeng Wu
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Sitarz KS, Yu-Wai-Man P, Pyle A, Stewart JD, Rautenstrauss B, Seeman P, Reilly MM, Horvath R, Chinnery PF. MFN2 mutations cause compensatory mitochondrial DNA proliferation. ACTA ACUST UNITED AC 2012; 135:e219, 1-3; author reply e220, 1-3. [PMID: 22492563 PMCID: PMC3407419 DOI: 10.1093/brain/aws049] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kamil S. Sitarz
- 1 Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Patrick Yu-Wai-Man
- 1 Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- 2 Department of Ophthalmology, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | - Angela Pyle
- 1 Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
| | - Joanna D. Stewart
- 1 Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- 3 IfADo – Leibniz Research Centre for Working Environment and Human Factors, Dortmund, Germany
| | | | - Pavel Seeman
- 5 Department of Child Neurology, DNA Laboratory, Charles University, 2nd School of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Mary M. Reilly
- 6 MRC Centre for Neuromuscular Diseases, UCL Institute of Neurology, Queen Square, London, WC1N 3BG, UK
| | - Rita Horvath
- 1 Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- 7 Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
| | - Patrick F. Chinnery
- 1 Wellcome Trust Centre for Mitochondrial Research, Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, NE1 3BZ, UK
- 7 Department of Neurology, Royal Victoria Infirmary, Newcastle upon Tyne, NE1 4LP, UK
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35
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Škrtić M, Sriskanthadevan S, Jhas B, Gebbia M, Wang X, Wang Z, Hurren R, Jitkova Y, Gronda M, Maclean N, Lai CK, Eberhard Y, Bartoszko J, Spagnuolo P, Rutledge AC, Datti A, Ketela T, Moffat J, Robinson BH, Cameron JH, Wrana J, Eaves CJ, Minden MD, Wang JC, Dick JE, Humphries K, Nislow C, Giaever G, Schimmer AD. Inhibition of mitochondrial translation as a therapeutic strategy for human acute myeloid leukemia. Cancer Cell 2011; 20:674-88. [PMID: 22094260 PMCID: PMC3221282 DOI: 10.1016/j.ccr.2011.10.015] [Citation(s) in RCA: 483] [Impact Index Per Article: 37.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2011] [Revised: 09/05/2011] [Accepted: 10/14/2011] [Indexed: 12/17/2022]
Abstract
To identify FDA-approved agents targeting leukemic cells, we performed a chemical screen on two human leukemic cell lines and identified the antimicrobial tigecycline. A genome-wide screen in yeast identified mitochondrial translation inhibition as the mechanism of tigecycline-mediated lethality. Tigecycline selectively killed leukemia stem and progenitor cells compared to their normal counterparts and also showed antileukemic activity in mouse models of human leukemia. ShRNA-mediated knockdown of EF-Tu mitochondrial translation factor in leukemic cells reproduced the antileukemia activity of tigecycline. These effects were derivative of mitochondrial biogenesis that, together with an increased basal oxygen consumption, proved to be enhanced in AML versus normal hematopoietic cells and were also important for their difference in tigecycline sensitivity.
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Affiliation(s)
- Marko Škrtić
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Shrivani Sriskanthadevan
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Bozhena Jhas
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Marinella Gebbia
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Xiaoming Wang
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Zezhou Wang
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Rose Hurren
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Yulia Jitkova
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Marcela Gronda
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Neil Maclean
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Courteney K. Lai
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3 Canada
| | - Yanina Eberhard
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Justyna Bartoszko
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Paul Spagnuolo
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Angela C. Rutledge
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Alessandro Datti
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5 Canada
| | - Troy Ketela
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Jason Moffat
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Brian H. Robinson
- Genetics and Genome Biology, The Research Institute, The Hospital for Sick Children, Toronto, ON, M5G 1X8 Canada
| | - Jessie H. Cameron
- Genetics and Genome Biology, The Research Institute, The Hospital for Sick Children, Toronto, ON, M5G 1X8 Canada
| | - Jeffery Wrana
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, M5G 1X5 Canada
| | - Connie J. Eaves
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3 Canada
| | - Mark D. Minden
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
| | - Jean C.Y. Wang
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
- Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research/Ontario Cancer Institute, Toronto, Ontario M5G 1L7, Canada
| | - John E. Dick
- Division of Stem Cell and Developmental Biology, Campbell Family Institute for Cancer Research/Ontario Cancer Institute, Toronto, Ontario M5G 1L7, Canada
| | - Keith Humphries
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, V5Z 1L3 Canada
| | - Corey Nislow
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Guri Giaever
- Department of Molecular Genetics, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, Ontario, M5S 3E1 Canada
| | - Aaron D. Schimmer
- The Campbell Family Cancer Research Institute, The Princess Margaret Hospital, The Ontario Cancer Institute, Toronto, ON, M5G 2M9 Canada
- To whom correspondence should be addressed: Aaron D. Schimmer, Princess Margaret Hospital, Rm 9-516, 610 University Ave, Toronto, ON, Canada M5G 2M9, Tel: 416-946-2838, Fax: 416-946-6546,
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Crain MJ, Chernoff MC, Oleske JM, Brogly SB, Malee KM, Borum PR, Meyer WA, Mitchell WG, Moye JH, Ford-Chatterton HM, Van Dyke RB, Seage Iii GR. Possible mitochondrial dysfunction and its association with antiretroviral therapy use in children perinatally infected with HIV. J Infect Dis 2010; 202:291-301. [PMID: 20533872 DOI: 10.1086/653497] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND Mitochondrial dysfunction has been associated with both human immunodeficiency virus (HIV) infection and exposure to antiretroviral therapy. Mitochondrial dysfunction has not been widely studied in HIV-infected children. We estimated the incidence of clinically defined mitochondrial dysfunction among children with perinatal HIV infection. METHODS Children with perinatal HIV infection enrolled in a prospective cohort study (Pediatric AIDS Clinical Trials Group protocols 219 and 219C) from 1993 through 2004 were included. Two clinical case definitions of mitochondrial dysfunction, the Enquête Périnatale Française criteria and the Mitochondrial Disease Classification criteria, were used to classify signs and symptoms that were consistent with possible mitochondrial dysfunction. Adjusted odds ratios of the associations between single and dual nucleoside reverse-transcriptase inhibitor use and possible mitochondrial dysfunction were estimated using logistic regression. RESULTS Overall, 982 (33.5%) of 2931 children met 1 or both case definitions of possible mitochondrial dysfunction. Mortality was highest among the 96 children who met both case definitions (20%). After adjusting for confounders, there was a higher risk of possible mitochondrial dysfunction among children who received stavudine regardless of exposure to other medications (odds ratio, 3.44 [95% confidence interval, 1.91-6.20]) or who received stavudine-didanosine combination therapy (odds ratio, 2.23 [95% confidence interval, 1.19-4.21]). Exposure to lamivudine and to lamivudine-stavudine were also associated with an increased risk of mitochondrial dysfunction. CONCLUSIONS Receipt of nucleoside reverse-transcriptase inhibitors, especially stavudine and lamivudine, was associated with possible mitochondrial dysfunction in children with perinatal HIV infection. Further studies are warranted to elucidate potential mechanisms of nucleoside reverse-transcriptase inhibitor toxicities.
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Affiliation(s)
- Marilyn J Crain
- University of Alabama School of Medicine, Birmingham, AL 35233, USA.
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Yu-Wai-Man P, Sitarz KS, Samuels DC, Griffiths PG, Reeve AK, Bindoff LA, Horvath R, Chinnery PF. OPA1 mutations cause cytochrome c oxidase deficiency due to loss of wild-type mtDNA molecules. Hum Mol Genet 2010; 19:3043-52. [PMID: 20484224 PMCID: PMC2901142 DOI: 10.1093/hmg/ddq209] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Pathogenic OPA1 mutations cause autosomal dominant optic atrophy (DOA), a condition characterized by the preferential loss of retinal ganglion cells and progressive optic nerve degeneration. Approximately 20% of affected patients will also develop more severe neuromuscular complications, an important disease subgroup known as DOA+. Cytochrome c oxidase (COX)-negative fibres and multiple mitochondrial DNA (mtDNA) deletions have been identified in skeletal muscle biopsies from patients manifesting both the pure and syndromal variants, raising the possibility that the accumulation of somatic mtDNA defects contribute to the disease process. In this study, we investigated the mtDNA changes induced by OPA1 mutations in skeletal muscle biopsies from 15 patients with both pure DOA and DOA+ phenotypes. We observed a 2- to 4-fold increase in mtDNA copy number at the single-fibre level, and patients with DOA+ features had significantly greater mtDNA proliferation in their COX-negative skeletal muscle fibres compared with patients with isolated optic neuropathy. Low levels of wild-type mtDNA molecules were present in COX-deficient muscle fibres from both pure DOA and DOA+ patients, implicating haplo-insufficiency as the mechanism responsible for the biochemical defect. Our findings are consistent with the ‘maintenance of wild-type’ hypothesis, the secondary mtDNA deletions induced by OPA1 mutations triggering a compensatory mitochondrial proliferative response in order to maintain an optimal level of wild-type mtDNA genomes. However, when deletion levels reach a critical level, further mitochondrial proliferation leads to replication of the mutant species at the expense of wild-type mtDNA, resulting in the loss of respiratory chain COX activity.
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Affiliation(s)
- Patrick Yu-Wai-Man
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Ophthalmology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Kamil S. Sitarz
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - David C. Samuels
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Philip G. Griffiths
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Department of Ophthalmology, Royal Victoria Infirmary, Newcastle upon Tyne, UK
| | - Amy K. Reeve
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Laurence A. Bindoff
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
- Department of Neurology, Haukeland University Hospital, Bergen, Norway and
| | - Rita Horvath
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Patrick F. Chinnery
- Mitochondrial Research Group, Institute for Ageing and Health, The Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
- Institute of Human Genetics, Newcastle University, Newcastle upon Tyne, UK
- To whom correspondence should be addressed. Tel: +44 1912824375; Fax: +44 1912824373;
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38
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Xing J, Chen M, Wood CG, Lin J, Spitz MR, Ma J, Amos CI, Shields PG, Benowitz NL, Gu J, de Andrade M, Swan GE, Wu X. Mitochondrial DNA content: its genetic heritability and association with renal cell carcinoma. J Natl Cancer Inst 2008; 100:1104-12. [PMID: 18664653 DOI: 10.1093/jnci/djn213] [Citation(s) in RCA: 211] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND The extent to which mitochondrial DNA (mtDNA) content (also termed mtDNA copy number) in normal human cells is influenced by genetic factors has yet to be established. In addition, whether inherited variation of mtDNA content in normal cells contributes to cancer susceptibility remains unclear. Renal cell carcinoma accounts for 85% of all renal cancers. No studies have investigated the association between mtDNA content and the risk of renal cell carcinoma. METHODS We first used a classic twin study design to estimate the genetic contribution to the determination of mtDNA content. mtDNA content was measured by quantitative real-time polymerase chain reaction in peripheral blood lymphocytes from 250 monozygotic twins, 92 dizygotic twins, and 33 siblings (ie, individual siblings of a pair of twins). We used biometric genetic modeling to estimate heritability of mtDNA content. We then used a case-control study with 260 case patients with renal cell carcinoma and 281 matched control subjects and multivariable logistic regression analysis to examine the association between mtDNA content in peripheral blood lymphocytes and the risk of renal cell carcinoma. All statistical tests were two-sided. RESULTS The heritability (ie, proportion of phenotypic variation in a population that is attributable to genetic variation among individuals) of mtDNA content was 65% (95% confidence interval [CI] = 50% to 72%; P < .001). Case patients with renal cell carcinoma had a statistically significantly lower mtDNA content (1.18 copies) than control subjects (1.29 copies) (difference = 0.11, 95% CI = 0.03 to 0.17; P = .006). Low mtDNA content (ie, less than the median in control subjects) was associated with a statistically significantly increased risk of renal cell carcinoma, compared with high content (odds ratio = 1.53, 95% CI = 1.07 to 2.19). In a trend analysis, a statistically significant dose-response relationship was detected between lower mtDNA content and increasing risk of renal cell carcinoma (P for trend <.001). CONCLUSIONS mtDNA content appears to have high heritability. Low mtDNA content appears to be associated with increased risk of renal cell carcinoma.
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Affiliation(s)
- Jinliang Xing
- Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Rajasimha HK, Chinnery PF, Samuels DC. Selection against pathogenic mtDNA mutations in a stem cell population leads to the loss of the 3243A-->G mutation in blood. Am J Hum Genet 2008; 82:333-43. [PMID: 18252214 PMCID: PMC2427290 DOI: 10.1016/j.ajhg.2007.10.007] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2007] [Revised: 09/18/2007] [Accepted: 10/03/2007] [Indexed: 12/30/2022] Open
Abstract
The mutation 3243A-->G is the most common heteroplasmic pathogenic mitochondrial DNA (mtDNA) mutation in humans, but it is not understood why the proportion of this mutation decreases in blood during life. Changing levels of mtDNA heteroplasmy are fundamentally related to the pathophysiology of the mitochondrial disease and correlate with clinical progression. To understand this process, we simulated the segregation of mtDNA in hematopoietic stem cells and leukocyte precursors. Our observations show that the percentage of mutant mtDNA in blood decreases exponentially over time. This is consistent with the existence of a selective process acting at the stem cell level and explains why the level of mutant mtDNA in blood is almost invariably lower than in nondividing (postmitotic) tissues such as skeletal muscle. By using this approach, we derived a formula from human data to correct for the change in heteroplasmy over time. A comparison of age-corrected blood heteroplasmy levels with skeletal muscle, an embryologically distinct postmitotic tissue, provides independent confirmation of the model. These findings indicate that selection against pathogenic mtDNA mutations occurs in a stem cell population.
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Affiliation(s)
- Harsha Karur Rajasimha
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
| | - Patrick F. Chinnery
- Mitochondrial Research Group and Institute of Human Genetics, Newcastle University, The Medical School, Newcastle-upon-Tyne NE2 4HH, UK
| | - David C. Samuels
- Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061 USA
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Durham SE, Samuels DC, Cree LM, Chinnery PF. Normal levels of wild-type mitochondrial DNA maintain cytochrome c oxidase activity for two pathogenic mitochondrial DNA mutations but not for m.3243A-->G. Am J Hum Genet 2007; 81:189-95. [PMID: 17564976 PMCID: PMC1950909 DOI: 10.1086/518901] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 04/17/2007] [Indexed: 12/29/2022] Open
Abstract
Mitochondrial DNA (mtDNA) mutations are a common cause of human disease and accumulate as part of normal ageing and in common neurodegenerative disorders. Cells express a biochemical defect only when the proportion of mutated mtDNA exceeds a critical threshold, but it is not clear whether the actual cause of this defect is a loss of wild-type mtDNA, an excess of mutated mtDNA, or a combination of the two. Here, we show that segments of human skeletal muscle fibers harboring two pathogenic mtDNA mutations retain normal cytochrome c oxidase (COX) activity by maintaining a minimum amount of wild-type mtDNA. For these mutations, direct measurements of mutated and wild-type mtDNA molecules within the same skeletal muscle fiber are consistent with the "maintenance of wild type" hypothesis, which predicts that there is nonselective proliferation of mutated and wild-type mtDNA in response to the molecular defect. However, for the m.3243A-->G mutation, a superabundance of wild-type mtDNA was found in many muscle-fiber sections with negligible COX activity, indicating that the pathogenic mechanism for this particular mutation involves interference with the function of the wild-type mtDNA or wild-type gene products.
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Affiliation(s)
- Steve E Durham
- Mitochondrial Research Group, Newcastle University, Newcastle, UK
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