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Ruparelia AA, Montandon M, Merriner J, Huang C, Wong SFL, Sonntag C, Hardee JP, Lynch GS, Miles LB, Siegel A, Hall TE, Schittenhelm RB, Currie PD. Atrogin-1 promotes muscle homeostasis by regulating levels of endoplasmic reticulum chaperone BiP. JCI Insight 2024; 9:e167578. [PMID: 38530354 DOI: 10.1172/jci.insight.167578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/14/2024] [Indexed: 03/27/2024] Open
Abstract
Skeletal muscle wasting results from numerous pathological conditions affecting both the musculoskeletal and nervous systems. A unifying feature of these pathologies is the upregulation of members of the E3 ubiquitin ligase family, resulting in increased proteolytic degradation of target proteins. Despite the critical role of E3 ubiquitin ligases in regulating muscle mass, the specific proteins they target for degradation and the mechanisms by which they regulate skeletal muscle homeostasis remain ill-defined. Here, using zebrafish loss-of-function models combined with in vivo cell biology and proteomic approaches, we reveal a role of atrogin-1 in regulating the levels of the endoplasmic reticulum chaperone BiP. Loss of atrogin-1 resulted in an accumulation of BiP, leading to impaired mitochondrial dynamics and a subsequent loss in muscle fiber integrity. We further implicated a disruption in atrogin-1-mediated BiP regulation in the pathogenesis of Duchenne muscular dystrophy. We revealed that BiP was not only upregulated in Duchenne muscular dystrophy, but its inhibition using pharmacological strategies, or by upregulating atrogin-1, significantly ameliorated pathology in a zebrafish model of Duchenne muscular dystrophy. Collectively, our data implicate atrogin-1 and BiP in the pathogenesis of Duchenne muscular dystrophy and highlight atrogin-1's essential role in maintaining muscle homeostasis.
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Affiliation(s)
- Avnika A Ruparelia
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- Department of Anatomy and Physiology, School of Biomedical Sciences, Faculty of Medicine Dentistry and Health Sciences, and
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Margo Montandon
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Jo Merriner
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Cheng Huang
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Siew Fen Lisa Wong
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Carmen Sonntag
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Justin P Hardee
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Gordon S Lynch
- Centre for Muscle Research, Department of Anatomy and Physiology, University of Melbourne, Melbourne, Victoria, Australia
| | - Lee B Miles
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Ashley Siegel
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
| | - Thomas E Hall
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Ralf B Schittenhelm
- Monash Proteomics and Metabolomics Facility, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria, Australia
| | - Peter D Currie
- Australian Regenerative Medicine Institute, Monash University, Clayton, Victoria, Australia
- EMBL Australia, Victorian Node, Monash University, Clayton, Victoria, Australia
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2
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Rollwitz E, Jastroch M. Plate-Based Respirometry to Assess Thermal Sensitivity of Zebrafish Embryo Bioenergetics in situ. Front Physiol 2021; 12:746367. [PMID: 34621190 PMCID: PMC8491625 DOI: 10.3389/fphys.2021.746367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 08/24/2021] [Indexed: 11/19/2022] Open
Abstract
Oxygen consumption allows measuring the metabolic activity of organisms. Here, we adopted the multi-well plate-based respirometry of the extracellular flux analyzer (Seahorse XF96) to investigate the effect of temperature on the bioenergetics of zebrafish embryos (Danio rerio) in situ. We show that the removal of the embryonic chorion is beneficial for oxygen consumption rates (OCR) and penetration of various mitochondrial inhibitors, and confirm that sedation reduces the variability of OCR. At 48h post-fertilization, embryos (maintained at a routine temperature of 28°C) were exposed to different medium temperatures ranging from 18°C to 37°C for 20h prior OCR measurement. Measurement temperatures from 18°C to 45°C in the XF96 were achieved by lowering the room temperature and active in-built heating. At 18°C assay temperature, basal OCR was low due to decreased ATP-linked respiration, which was not limited by mitochondrial power, as seen in substantial spare respiratory capacity. Basal OCR of the embryos increased with assay temperature and were stable up to 37°C assay temperature, with pre-exposure of 37°C resulting in more thermo-resistant basal OCR measured at 41°C. Adverse effects of the mitochondrial inhibitor oligomycin were seen at 37°C and chemical uncouplers disrupted substrate oxidation gradually with increasing assay temperature. Proton leak respiration increased at assay temperatures above 28°C and compromised the efficiency of ATP production, calculated as coupling efficiency. Thus, temperature impacts mitochondrial respiration by reduced cellular ATP turnover at lower temperatures and by increased proton leak at higher temperatures. This conclusion is coherent with the assessment of heart rate, an independent indicator of systemic metabolic rate, which increased with exposure temperature, peaking at 28°C, and decreased at higher temperatures. Collectively, plate-based respirometry allows assessing distinct parts of mitochondrial energy transduction in zebrafish embryos and investigating the effect of temperature and temperature acclimation on mitochondrial bioenergetics in situ.
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Affiliation(s)
- Erik Rollwitz
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Martin Jastroch
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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3
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β-Glucans as Dietary Supplement to Improve Locomotion and Mitochondrial Respiration in a Model of Duchenne Muscular Dystrophy. Nutrients 2021; 13:nu13051619. [PMID: 34065946 PMCID: PMC8151547 DOI: 10.3390/nu13051619] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 05/03/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022] Open
Abstract
Duchenne muscular dystrophy (DMD) is a severe X-linked neuromuscular childhood disorder that causes progressive muscle weakness and degeneration. A lack of dystrophin in DMD leads to inflammatory response, autophagic dysregulation, and oxidative stress in skeletal muscle fibers that play a key role in the progression of the pathology. β-glucans can modulate immune function by modifying the phagocytic activity of immunocompetent cells, notably macrophages. Mitochondrial function is also involved in an important mechanism of the innate and adaptive immune responses, owing to high need for energy of immune cells. In the present study, the effects of 1,3-1,6 β-glucans on five-day-old non-dystrophic and dystrophic (sapje) zebrafish larvae were investigated. The effects of the sonication of β-glucans and the dechorionation of embryos were also evaluated. The results showed that the incidence of dystrophic phenotypes was reduced when dystrophic embryos were exposed to 2 and 4 mg L-1 of 1,3-1,6 β-glucans. Moreover, when the dystrophic larvae underwent 8 mg L-1 treatment, an improvement of the locomotor performances and mitochondrial respiration were observed. In conclusion, the observed results demonstrated that 1,3-1,6 β-glucans improve locomotor performances and mitochondrial function in dystrophic zebrafish. Therefore, for ameliorating their life quality, 1,3-1,6 β-glucans look like a promising diet supplement for DMD patients, even though further investigations are required.
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Jaroszynska N, Harding P, Moosajee M. Metabolism in the Zebrafish Retina. J Dev Biol 2021; 9:10. [PMID: 33804189 PMCID: PMC8006245 DOI: 10.3390/jdb9010010] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 03/08/2021] [Accepted: 03/11/2021] [Indexed: 12/12/2022] Open
Abstract
Retinal photoreceptors are amongst the most metabolically active cells in the body, consuming more glucose as a metabolic substrate than even the brain. This ensures that there is sufficient energy to establish and maintain photoreceptor functions during and after their differentiation. Such high dependence on glucose metabolism is conserved across vertebrates, including zebrafish from early larval through to adult retinal stages. As the zebrafish retina develops rapidly, reaching an adult-like structure by 72 hours post fertilisation, zebrafish larvae can be used to study metabolism not only during retinogenesis, but also in functionally mature retinae. The interplay between rod and cone photoreceptors and the neighbouring retinal pigment epithelium (RPE) cells establishes a metabolic ecosystem that provides essential control of their individual functions, overall maintaining healthy vision. The RPE facilitates efficient supply of glucose from the choroidal vasculature to the photoreceptors, which produce metabolic products that in turn fuel RPE metabolism. Many inherited retinal diseases (IRDs) result in photoreceptor degeneration, either directly arising from photoreceptor-specific mutations or secondary to RPE loss, leading to sight loss. Evidence from a number of vertebrate studies suggests that the imbalance of the metabolic ecosystem in the outer retina contributes to metabolic failure and disease pathogenesis. The use of larval zebrafish mutants with disease-specific mutations that mirror those seen in human patients allows us to uncover mechanisms of such dysregulation and disease pathology with progression from embryonic to adult stages, as well as providing a means of testing novel therapeutic approaches.
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Affiliation(s)
| | - Philippa Harding
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
| | - Mariya Moosajee
- Institute of Ophthalmology, University College London, London EC1V 9EL, UK;
- Moorfields Eye Hospital NHS Foundation Trust, London EC1V 2PD, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, London WC1N 3JH, UK
- The Francis Crick Institute, London NW1 1AT, UK
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5
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Banerji R, Huynh C, Figueroa F, Dinday MT, Baraban SC, Patel M. Enhancing glucose metabolism via gluconeogenesis is therapeutic in a zebrafish model of Dravet syndrome. Brain Commun 2021; 3:fcab004. [PMID: 33842883 PMCID: PMC8023476 DOI: 10.1093/braincomms/fcab004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/14/2020] [Accepted: 12/16/2020] [Indexed: 01/18/2023] Open
Abstract
Energy-producing pathways are novel therapeutic targets for the treatment of neurodevelopmental disorders. Here, we focussed on correcting metabolic defects in a catastrophic paediatric epilepsy, Dravet syndrome which is caused by mutations in sodium channel NaV1.1 gene, SCN1A. We utilized a translatable zebrafish model of Dravet syndrome (scn1lab) which exhibits key characteristics of patients with Dravet syndrome and shows metabolic deficits accompanied by down-regulation of gluconeogenesis genes, pck1 and pck2. Using a metabolism-based small library screen, we identified compounds that increased gluconeogenesis via up-regulation of pck1 gene expression in scn1lab larvae. Treatment with PK11195, a pck1 activator and a translocator protein ligand, normalized dys-regulated glucose levels, metabolic deficits, translocator protein expression and significantly decreased electrographic seizures in mutant larvae. Inhibition of pck1 in wild-type larvae mimicked metabolic and behaviour defects observed in scn1lab mutants. Together, this suggests that correcting dys-regulated metabolic pathways can be therapeutic in neurodevelopmental disorders such as Dravet syndrome arising from ion channel dysfunction.
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Affiliation(s)
- Rajeswari Banerji
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, CA 80045, USA
| | - Christopher Huynh
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, CA 80045, USA
| | - Francisco Figueroa
- Department of Neurological Surgery, Epilepsy Research Laboratory, University of California, San Francisco, CA 94143, USA
| | - Matthew T Dinday
- Department of Neurological Surgery, Epilepsy Research Laboratory, University of California, San Francisco, CA 94143, USA
| | - Scott C Baraban
- Department of Neurological Surgery, Epilepsy Research Laboratory, University of California, San Francisco, CA 94143, USA
| | - Manisha Patel
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Anschutz Medical Campus, Aurora, Colorado, CA 80045, USA
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6
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García‐Poyatos C, Cogliati S, Calvo E, Hernansanz‐Agustín P, Lagarrigue S, Magni R, Botos M, Langa X, Amati F, Vázquez J, Mercader N, Enríquez JA. Scaf1 promotes respiratory supercomplexes and metabolic efficiency in zebrafish. EMBO Rep 2020; 21:e50287. [PMID: 32496654 PMCID: PMC7332985 DOI: 10.15252/embr.202050287] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/13/2020] [Accepted: 04/28/2020] [Indexed: 01/01/2023] Open
Abstract
The oxidative phosphorylation (OXPHOS) system is a dynamic system in which the respiratory complexes coexist with super-assembled quaternary structures called supercomplexes (SCs). The physiological role of SCs is still disputed. Here, we used zebrafish to study the relevance of respiratory SCs. We combined immunodetection analysis and deep data-independent proteomics to characterize these structures and found similar SCs to those described in mice, as well as novel SCs including III2 + IV2 , I + IV, and I + III2 + IV2 . To study the physiological role of SCs, we generated two null allele zebrafish lines for supercomplex assembly factor 1 (scaf1). scaf1-/- fish displayed altered OXPHOS activity due to the disrupted interaction of complexes III and IV. scaf1-/- fish were smaller in size and showed abnormal fat deposition and decreased female fertility. These physiological phenotypes were rescued by doubling the food supply, which correlated with improved bioenergetics and alterations in the metabolic gene expression program. These results reveal that SC assembly by Scaf1 modulates OXPHOS efficiency and allows the optimization of metabolic resources.
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Affiliation(s)
- Carolina García‐Poyatos
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
- Institute of AnatomyUniversity of BernBernSwitzerland
| | - Sara Cogliati
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
- Instituto de Nutrición y Tecnología de los Alimentos (INYTA)Universidad de GranadaGranadaSpain
| | - Enrique Calvo
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
| | | | - Sylviane Lagarrigue
- Aging and Muscle Metabolism LaboratoryDepartment of Biomedical SciencesUniversity of LausanneLausanneSwitzerland
| | - Ricardo Magni
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
| | - Marius Botos
- Institute of AnatomyUniversity of BernBernSwitzerland
| | - Xavier Langa
- Institute of AnatomyUniversity of BernBernSwitzerland
| | - Francesca Amati
- Aging and Muscle Metabolism LaboratoryDepartment of Biomedical SciencesUniversity of LausanneLausanneSwitzerland
| | - Jesús Vázquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
- CIBERCVMadridSpain
| | - Nadia Mercader
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
| | - José Antonio Enríquez
- Centro Nacional de Investigaciones Cardiovasculares Carlos IIIMadridSpain
- CIBERFESMadridSpain
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7
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Beirowski B. Measuring Bioenergetic Signatures of Peripheral Nerve Segments by Extracellular Flux Analysis. Methods Mol Biol 2020; 2143:191-203. [PMID: 32524482 DOI: 10.1007/978-1-0716-0585-1_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Changes of energy metabolism in axons and their adjacent glia as well as alterations in metabolic axon-glia cross talk are emerging as central mechanistic components underlying axon degeneration. The analysis of extracellular flux with commercial metabolic analyzers greatly facilitates the measurement of key parameters of glycolytic and mitochondrial energy metabolism in cells and tissues. In this chapter, I describe a straightforward method to capture bioenergetic profiles of acutely isolated peripheral nerve segments using the Agilent Seahorse XFe24 platform.
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Affiliation(s)
- Bogdan Beirowski
- Hunter James Kelly Research Institute, New York State Center of Excellence in Bioinformatics & Life Sciences (CBLS) RM B4-314, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA. .,Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
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8
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van Steijn L, Verbeek FJ, Spaink HP, Merks RM. Predicting Metabolism from Gene Expression in an Improved Whole-Genome Metabolic Network Model of Danio rerio. Zebrafish 2019; 16:348-362. [PMID: 31216234 PMCID: PMC6822484 DOI: 10.1089/zeb.2018.1712] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Zebrafish is a useful modeling organism for the study of vertebrate development, immune response, and metabolism. Metabolic studies can be aided by mathematical reconstructions of the metabolic network of zebrafish. These list the substrates and products of all biochemical reactions that occur in the zebrafish. Mathematical techniques such as flux-balance analysis then make it possible to predict the possible metabolic flux distributions that optimize, for example, the turnover of food into biomass. The only available genome-scale reconstruction of zebrafish metabolism is ZebraGEM. In this study, we present ZebraGEM 2.0, an updated and validated version of ZebraGEM. ZebraGEM 2.0 is extended with gene-protein-reaction associations (GPRs) that are required to integrate genetic data with the metabolic model. To demonstrate the use of these GPRs, we performed an in silico genetic screening for knockouts of metabolic genes and validated the results against published in vivo genetic knockout and knockdown screenings. Among the single knockout simulations, we identified 74 essential genes, whose knockout stopped growth completely. Among these, 11 genes are known have an abnormal knockout or knockdown phenotype in vivo (partial), and 41 have human homologs associated with metabolic diseases. We also added the oxidative phosphorylation pathway, which was unavailable in the published version of ZebraGEM. The updated model performs better than the original model on a predetermined list of metabolic functions. We also determined a minimal feed composition. The oxidative phosphorylation pathways were validated by comparing with published experiments in which key components of the oxidative phosphorylation pathway were pharmacologically inhibited. To test the utility of ZebraGEM2.0 for obtaining new results, we integrated gene expression data from control and Mycobacterium marinum-infected zebrafish larvae. The resulting model predicts impeded growth and altered histidine metabolism in the infected larvae.
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Affiliation(s)
| | - Fons J. Verbeek
- Leiden Institute of Advanced Computer Science, Leiden University, Leiden, Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Herman P. Spaink
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
| | - Roeland M.H. Merks
- Mathematical Institute, Leiden University, Leiden, Netherlands
- Institute of Biology Leiden, Leiden University, Leiden, Netherlands
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9
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Pyrazinib (P3), [(E)-2-(2-Pyrazin-2-yl-vinyl)-phenol], a small molecule pyrazine compound enhances radiosensitivity in oesophageal adenocarcinoma. Cancer Lett 2019; 447:115-129. [DOI: 10.1016/j.canlet.2019.01.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/13/2018] [Accepted: 01/07/2019] [Indexed: 02/06/2023]
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10
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Ibhazehiebo K, Gavrilovici C, de la Hoz CL, Ma SC, Rehak R, Kaushik G, Meza Santoscoy PL, Scott L, Nath N, Kim DY, Rho JM, Kurrasch DM. A novel metabolism-based phenotypic drug discovery platform in zebrafish uncovers HDACs 1 and 3 as a potential combined anti-seizure drug target. Brain 2018; 141:744-761. [PMID: 29373639 PMCID: PMC5837409 DOI: 10.1093/brain/awx364] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 10/29/2017] [Accepted: 11/05/2017] [Indexed: 01/01/2023] Open
Abstract
Despite the development of newer anti-seizure medications over the past 50 years, 30-40% of patients with epilepsy remain refractory to treatment. One explanation for this lack of progress is that the current screening process is largely biased towards transmembrane channels and receptors, and ignores intracellular proteins and enzymes that might serve as efficacious molecular targets. Here, we report the development of a novel drug screening platform that harnesses the power of zebrafish genetics and combines it with in vivo bioenergetics screening assays to uncover therapeutic agents that improve mitochondrial health in diseased animals. By screening commercially available chemical libraries of approved drugs, for which the molecular targets and pathways are well characterized, we were able to reverse-identify the proteins targeted by efficacious compounds and confirm the physiological roles that they play by utilizing other pharmacological ligands. Indeed, using an 870-compound screen in kcna1-morpholino epileptic zebrafish larvae, we uncovered vorinostat (Zolinza™; suberanilohydroxamic acid, SAHA) as a potent anti-seizure agent. We further demonstrated that vorinostat decreased average daily seizures by ∼60% in epileptic Kcna1-null mice using video-EEG recordings. Given that vorinostat is a broad histone deacetylase (HDAC) inhibitor, we then delineated a specific subset of HDACs, namely HDACs 1 and 3, as potential drug targets for future screening. In summary, we have developed a novel phenotypic, metabolism-based experimental therapeutics platform that can be used to identify new molecular targets for future drug discovery in epilepsy.
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Affiliation(s)
- Kingsley Ibhazehiebo
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Cezar Gavrilovici
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
- Departments of Pediatrics, Clinical Neurosciences, Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Cristiane L de la Hoz
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Shun-Chieh Ma
- Departments of Neurology and Neurobiology, Barrow Neurological Institute, St Joseph’s Hospital and Medical Center, Phoenix, Arizona, USA
| | - Renata Rehak
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Gaurav Kaushik
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Paola L Meza Santoscoy
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Lucas Scott
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
- Departments of Pediatrics, Clinical Neurosciences, Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Nandan Nath
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
| | - Do-Young Kim
- Departments of Neurology and Neurobiology, Barrow Neurological Institute, St Joseph’s Hospital and Medical Center, Phoenix, Arizona, USA
| | - Jong M Rho
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
- Departments of Pediatrics, Clinical Neurosciences, Physiology and Pharmacology, Cumming School of Medicine, University of Calgary, Calgary, Canada
| | - Deborah M Kurrasch
- Department of Medical Genetics, Cumming School of Medicine, University of Calgary, Calgary, Canada
- Alberta Children’s Hospital Research Institute, University of Calgary, Canada
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11
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Bond ST, McEwen KA, Yoganantharajah P, Gibert Y. Live Metabolic Profile Analysis of Zebrafish Embryos Using a Seahorse XF 24 Extracellular Flux Analyzer. Methods Mol Biol 2018; 1797:393-401. [PMID: 29896705 DOI: 10.1007/978-1-4939-7883-0_21] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Agilent Seahorse Extracellular Flux Analyzer can be used to measure the oxygen consumption rate (OCR) and extra cellular acidification rate (ECAR), from which mitochondrial bioenergetics measurements can be determined including basal respiration, respiration due to ATP turnover, uncoupled respiration/proton leak, and maximum respiration. This novel method demonstrates how to use a Seahorse XF 24 Extracellular Flux Analyzer to measure the bioenergetic flux of zebrafish embryos in vivo during development. This provides a tool that enables characterization of metabolic parameters in a living organism, utilizing Agilent Islet Capture Microplates where respiration parameters can be compared between controls and genetically altered/pharmacologically treated embryos in real time. This method can be used to analyze and identify novel pharmaceuticals and genes that influence respiration, mitochondrial function, and metabolism.
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Affiliation(s)
- Simon T Bond
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Kevin A McEwen
- Metabolic Genetic Diseases Laboratory, Metabolic Research Unit, Deakin University School of Medicine, Geelong, VIC, Australia
| | - Prusothman Yoganantharajah
- Metabolic Genetic Diseases Laboratory, Metabolic Research Unit, Deakin University School of Medicine, Geelong, VIC, Australia
| | - Yann Gibert
- Metabolic Genetic Diseases Laboratory, Metabolic Research Unit, Deakin University School of Medicine, Geelong, VIC, Australia.
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12
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Neville KE, Bosse TL, Klekos M, Mills JF, Weicksel SE, Waters JS, Tipping M. A novel ex vivo method for measuring whole brain metabolism in model systems. J Neurosci Methods 2017; 296:32-43. [PMID: 29287743 DOI: 10.1016/j.jneumeth.2017.12.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/21/2017] [Accepted: 12/24/2017] [Indexed: 01/31/2023]
Abstract
BACKGROUND Many neuronal and glial diseases have been associated with changes in metabolism. Therefore, metabolic reprogramming has become an important area of research to better understand disease at the cellular level, as well as to identify targets for treatment. Model systems are ideal for interrogating metabolic questions in a tissue dependent context. However, while new tools have been developed to study metabolism in cultured cells there has been less progress towards studies in vivo and ex vivo. NEW METHOD We have developed a method using newly designed tissue restraints to adapt the Agilent XFe96 metabolic analyzer for whole brain analysis. These restraints create a chamber for Drosophila brains and other small model system tissues to reside undisrupted, while still remaining in the zone for measurements by sensor probes. RESULTS This method generates reproducible oxygen consumption and extracellular acidification rate data for Drosophila larval and adult brains. Single brains are effectively treated with inhibitors and expected metabolic readings are observed. Measuring metabolic changes, such as glycolytic rate, in transgenic larval brains demonstrates the potential for studying how genotype affects metabolism. COMPARISON WITH EXISTING METHODS AND CONCLUSIONS Current methodology either utilizes whole animal chambers to measure respiration, not allowing for targeted tissue analysis, or uses technically challenging MRI technology for in vivo analysis that is not suitable for smaller model systems. This new method allows for novel metabolic investigation of intact brains and other tissues ex vivo in a quick, and simplistic way with the potential for large-scale studies.
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Affiliation(s)
- Kathryn E Neville
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI 02918, United States.
| | - Timothy L Bosse
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI 02918, United States.
| | - Mia Klekos
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI 02918, United States.
| | - John F Mills
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI 02918, United States.
| | - Steven E Weicksel
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI 02918, United States.
| | - James S Waters
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI 02918, United States.
| | - Marla Tipping
- Department of Biology, Providence College, 1 Cunningham Square, Providence, RI 02918, United States.
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13
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Noel P, Muñoz R, Rogers GW, Neilson A, Von Hoff DD, Han H. Preparation and Metabolic Assay of 3-dimensional Spheroid Co-cultures of Pancreatic Cancer Cells and Fibroblasts. J Vis Exp 2017. [PMID: 28872142 PMCID: PMC5614363 DOI: 10.3791/56081] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Many cancer types, including pancreatic cancer, have a dense fibrotic stroma that plays an important role in tumor progression and invasion. Activated cancer associated fibroblasts are a key component of the tumor stroma that interact with cancer cells and support their growth and survival. Models that recapitulate the interaction of cancer cells and activated fibroblasts are important tools for studying the stromal biology and for development of antitumor agents. Here, a method is described for the rapid generation of robust 3-dimensional (3D) spheroid co-culture of pancreatic cancer cells and activated pancreatic fibroblasts that can be used for subsequent biological studies. Additionally, described is the use of 3D spheroids in carrying out functional metabolic assays to probe cellular bioenergetics pathways using an extracellular flux analyzer paired with a spheroid microplate. Pancreatic cancer cells (Patu8902) and activated pancreatic fibroblast cells (PS1) were co-cultured and magnetized using a biocompatible nanoparticle assembly. Magnetized cells were rapidly bioprinted using magnetic drives in a 96 well format, in growth media to generate spheroids with a diameter ranging between 400-600 µm within 5-7 days of culture. Functional metabolic assays using Patu8902-PS1 spheroids were then carried out using the extracellular flux technology to probe cellular energetic pathways. The method herein is simple, allows consistent generation of cancer cell-fibroblast spheroid co-cultures and can be potentially adapted to other cancer cell types upon optimization of the current described methodology.
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Affiliation(s)
- Pawan Noel
- Molecular Medicine Division, Translational Genomics Research Institute
| | - Ruben Muñoz
- Molecular Medicine Division, Translational Genomics Research Institute
| | | | | | - Daniel D Von Hoff
- Molecular Medicine Division, Translational Genomics Research Institute
| | - Haiyong Han
- Molecular Medicine Division, Translational Genomics Research Institute;
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14
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Raftery TD, Jayasundara N, Di Giulio RT. A bioenergetics assay for studying the effects of environmental stressors on mitochondrial function in vivo in zebrafish larvae. Comp Biochem Physiol C Toxicol Pharmacol 2017; 192:23-32. [PMID: 27939721 PMCID: PMC5218841 DOI: 10.1016/j.cbpc.2016.12.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 12/01/2016] [Accepted: 12/02/2016] [Indexed: 01/29/2023]
Abstract
Mitochondria, an integral component of cellular energy metabolism and other key functions, are extremely vulnerable to damage by environmental stressors. Although methods to measure mitochondrial function in vitro exist, sensitive, medium- to high-throughput assays that assess respiration within physiologically-relevant whole organisms are needed to identify drugs and/or chemicals that disrupt mitochondrial function, particularly at sensitive early developmental stages. Consequently, we have developed and optimized an assay to measure mitochondrial bioenergetics in zebrafish larvae using the XFe24 Extracellular Flux Analyzer. To prevent larval movement from confounding oxygen consumption measurements, we relied on MS-222-based anesthetization. We obtained stable measurement values in the absence of effects on average oxygen consumption rate and subsequently optimized the use of pharmacological agents for metabolic partitioning. To confirm assay reproducibility we demonstrated that triclosan, a positive control, significantly decreased spare respiratory capacity. We then exposed zebrafish from 5 hours post-fertilization (hpf) to 6days post-fertilization (dpf) to three polycyclic aromatic hydrocarbons (PAHs) - benzo(a)pyrene (BaP), phenanthrene (Phe), and fluoranthene (FL) - and measured various fundamental parameters of mitochondrial respiratory chain function, including maximal respiration, spare respiratory capacity, mitochondrial and non-mitochondrial respiration. Exposure to all three PAHs decreased spare respiratory capacity and maximal respiration. Additionally, Phe exposure increased non-mitochondrial respiration and FL exposure decreased mitochondrial respiration and increased non-mitochondrial respiration. Overall, this whole organism-based assay provides a platform for examining mitochondrial dysfunction in vivo at critical developmental stages. It has important implications in biomedical sciences, toxicology and ecophysiology, particularly to examine the effects of environmental chemicals and/or drugs on mitochondrial bioenergetics.
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Affiliation(s)
- Tara D Raftery
- Nicholas School of the Environment, Duke University, Durham, NC 27708, United States.
| | - Nishad Jayasundara
- Nicholas School of the Environment, Duke University, Durham, NC 27708, United States
| | - Richard T Di Giulio
- Nicholas School of the Environment, Duke University, Durham, NC 27708, United States
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15
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Koopman M, Michels H, Dancy BM, Kamble R, Mouchiroud L, Auwerx J, Nollen EA, Houtkooper RH. A screening-based platform for the assessment of cellular respiration in Caenorhabditis elegans. Nat Protoc 2016; 11:1798-816. [PMID: 27583642 PMCID: PMC5040492 DOI: 10.1038/nprot.2016.106] [Citation(s) in RCA: 92] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mitochondrial dysfunction is at the core of many diseases ranging from inherited metabolic diseases to common conditions that are associated with aging. Although associations between aging and mitochondrial function have been identified using mammalian models, much of the mechanistic insight has emerged from Caenorhabditis elegans. Mitochondrial respiration is recognized as an indicator of mitochondrial health. The Seahorse XF96 respirometer represents the state-of-the-art platform for assessing respiration in cells, and we adapted the technique for applications involving C. elegans. Here we provide a detailed protocol to optimize and measure respiration in C. elegans with the XF96 respirometer, including the interpretation of parameters and results. The protocol takes ∼2 d to complete, excluding the time spent culturing C. elegans, and it includes (i) the preparation of C. elegans samples, (ii) selection and loading of compounds to be injected, (iii) preparation and execution of a run with the XF96 respirometer and (iv) postexperimental data analysis, including normalization. In addition, we compare our XF96 application with other existing techniques, including the eight-well Seahorse XFp. The main benefits of the XF96 include the limited number of worms required and the high throughput capacity due to the 96-well format.
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Affiliation(s)
- Mandy Koopman
- University of Groningen, University Medical Center Groningen, European Research Institute for the Biology of Ageing, Laboratory of Molecular Neurobiology of Ageing, Groningen, The Netherlands
| | - Helen Michels
- University of Groningen, University Medical Center Groningen, European Research Institute for the Biology of Ageing, Laboratory of Molecular Neurobiology of Ageing, Groningen, The Netherlands
| | - Beverley M. Dancy
- Laboratory of Cardiac Energetics, National Heart, Lung and Blood Institute, Bethesda, United States
| | - Rashmi Kamble
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, The Netherlands
| | - Laurent Mouchiroud
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, Ecole Polytechnique Federale de Lausanne, Lausanne, Switzerland
| | - Ellen A.A. Nollen
- University of Groningen, University Medical Center Groningen, European Research Institute for the Biology of Ageing, Laboratory of Molecular Neurobiology of Ageing, Groningen, The Netherlands
| | - Riekelt H. Houtkooper
- Laboratory Genetic Metabolic Diseases, Academic Medical Center, Amsterdam, The Netherlands
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16
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Shim J, Weatherly LM, Luc RH, Dorman MT, Neilson A, Ng R, Kim CH, Millard PJ, Gosse JA. Triclosan is a mitochondrial uncoupler in live zebrafish. J Appl Toxicol 2016; 36:1662-1667. [PMID: 27111768 DOI: 10.1002/jat.3311] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 01/20/2016] [Accepted: 01/20/2016] [Indexed: 11/09/2022]
Abstract
Triclosan (TCS) is a synthetic antimicrobial agent used in many consumer goods at millimolar concentrations. As a result of exposure, TCS has been detected widely in humans. We have recently discovered that TCS is a proton ionophore mitochondrial uncoupler in multiple types of living cells. Here, we present novel data indicating that TCS is also a mitochondrial uncoupler in a living organism: 24-hour post-fertilization (hpf) zebrafish embryos. These experiments were conducted using a Seahorse Bioscience XFe 96 Extracellular Flux Analyzer modified for bidirectional temperature control, using the XF96 spheroid plate to position and measure one zebrafish embryo per well. Using this method, after acute exposure to TCS, the basal oxygen consumption rate (OCR) increases, without a decrease in survival or heartbeat rate. TCS also decreases ATP-linked respiration and spare respiratory capacity and increases proton leak: all indicators of mitochondrial uncoupling. Our data indicate, that TCS is a mitochondrial uncoupler in vivo, which should be taken into consideration when assessing the toxicity and/or pharmaceutical uses of TCS. This is the first example of usage of a Seahorse Extracellular Flux Analyzer to measure bioenergetic flux of a single zebrafish embryo per well in a 96-well assay format. The method developed in this study provides a high-throughput tool to identify previously unknown mitochondrial uncouplers in a living organism. Copyright © 2016 John Wiley & Sons, Ltd.
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Affiliation(s)
- Juyoung Shim
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Lisa M Weatherly
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, 04469, USA.,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, 04469, USA
| | - Richard H Luc
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Maxwell T Dorman
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, 04469, USA
| | - Andy Neilson
- Seahorse Bioscience, Inc., North Billerica, Massachusetts, 01862, USA
| | - Ryan Ng
- Seahorse Bioscience, Inc., North Billerica, Massachusetts, 01862, USA
| | - Carol H Kim
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, 04469, USA.,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, 04469, USA
| | - Paul J Millard
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, 04469, USA.,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, 04469, USA.,Department of Chemical and Biological Engineering and the Laboratory for Surface Science & Technology, University of Maine, Orono, Maine, 04469, USA
| | - Julie A Gosse
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, 04469, USA. .,Graduate School of Biomedical Science and Engineering, University of Maine, Orono, Maine, 04469, USA.
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17
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Schlegel A, Gut P. Metabolic insights from zebrafish genetics, physiology, and chemical biology. Cell Mol Life Sci 2015; 72:2249-60. [PMID: 25556679 PMCID: PMC4439526 DOI: 10.1007/s00018-014-1816-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 12/15/2014] [Accepted: 12/19/2014] [Indexed: 01/01/2023]
Abstract
Metabolic diseases—atherosclerotic cardiovascular disease, type 2 diabetes mellitus, obesity, and non-alcoholic fatty liver disease––have reached pandemic proportions. Across gene, cell, organ, organism, and social-environmental scales, fundamental discoveries of the derangements that occur in these diseases are required to develop effective new treatments. Here we will review genetic, physiological, pathological and chemical biological discoveries in the emerging zebrafish model for studying metabolism and metabolic diseases. We present a synthesis of recent studies using forward and reverse genetic tools to make new contributions to our understanding of lipid trafficking, diabetes pathogenesis and complications, and to β-cell biology. The technical and physiological advantages and the pharmacological potential of this organism for discovery and validation of metabolic disease targets are stressed by our summary of recent findings. We conclude by arguing that metabolic research using zebrafish will benefit from adoption of conventional blood and tissue metabolite measurements, employment of modern imaging techniques, and development of more rigorous metabolic flux methods.
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Affiliation(s)
- Amnon Schlegel
- University of Utah Molecular Medicine Program, School of Medicine, University of Utah, 15 North 2030 East, Room 3240B, Salt Lake City, UT, 84112, USA,
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