51
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Lim EW, Parker SJ, Metallo CM. Deuterium Tracing to Interrogate Compartment-Specific NAD(P)H Metabolism in Cultured Mammalian Cells. Methods Mol Biol 2020; 2088:51-71. [PMID: 31893370 DOI: 10.1007/978-1-0716-0159-4_4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Oxidation-reduction (redox) reactions are ubiquitous in biology and typically occur in specific subcellular compartments. In cells, the electron transfer between molecules and organelles is commonly facilitated by pyridine nucleotides such as nicotinamide adenine dinucleotide phosphate (NADPH) and nicotinamide adenine dinucleotide (NADH). While often taken for granted, these metabolic reactions are critically important for maintaining redox homeostasis and biochemical potentials across membranes. While 13C tracing and metabolic flux analysis (MFA) have emerged as powerful tools to study intracellular metabolism, this approach is limited when applied to pathways catalyzed in multiple cellular compartments. To address this issue, we and others have applied 2H (deuterium) tracers to observe transfer of labeled hydride anions, which accompanies electron transfer. Furthermore, we have developed a reporter system for indirectly quantifying NADPH enrichment in specific subcellular compartments. Here, we provide a detailed description of 2H tracing applications and the interrogation of mitochondrial versus cytosolic NAD(P)H metabolism in cultured mammalian cells. Specifically, we describe the generation of reporter cell lines that express epitope-tagged R132H-IDH1 or R172K-IDH2 and produce (D)2-hydroxyglutarate in a doxycycline-dependent manner. These tools and methods allow for quantitation of reducing equivalent turnover rates, the directionality of pathways present in multiple compartments, and the estimation of pathway contributions to NADPH pools.
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Affiliation(s)
- Esther W Lim
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Seth J Parker
- Department of Radiation Oncology, Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
- Moores Cancer Center, University of California San Diego, La Jolla, CA, USA.
- Diabetes and Endocrinology Research Center, University of California San Diego, La Jolla, CA, USA.
- Institute of Engineering in Medicine, University of California San Diego, La Jolla, CA, USA.
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52
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Maniam S, Maniam S. Cancer Cell Metabolites: Updates on Current Tracing Methods. Chembiochem 2020; 21:3476-3488. [PMID: 32639076 DOI: 10.1002/cbic.202000290] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/07/2020] [Indexed: 12/15/2022]
Abstract
Cancer is the second leading cause of death-1 in 6 deaths globally is due to cancer. Cancer metabolism is a complex and one of the most actively researched area in cancer biology. Metabolic reprogramming in cancer cells entails activities that involve several enzymes and metabolites to convert nutrient into building blocks that alter energy metabolism to fuel rapid cell division. Metabolic dependencies in cancer generate signature metabolites that have key regulatory roles in tumorigenesis. In this minireview, we highlight recent advances in the popular methods ingrained in biochemistry research such as stable and flux isotope analysis, as well as radioisotope labeling, which are valuable in elucidating cancer metabolites. These methods together with analytical tools such as chromatography, nuclear magnetic resonance spectroscopy and mass spectrometry have helped to bring about exploratory work in understanding the role of important as well as obscure metabolites in cancer cells. Information obtained from these analyses significantly contribute in the diagnosis and prognosis of tumors leading to potential therapeutic targets for cancer therapy.
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Affiliation(s)
- Subashani Maniam
- School of Applied Science, RMIT University, 240 La Trobe Street, Melbourne, VIC 3001, Australia
| | - Sandra Maniam
- Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor Darul Ehsan, Malaysia
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53
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Suthers PF, Foster CJ, Sarkar D, Wang L, Maranas CD. Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms. Metab Eng 2020; 63:13-33. [PMID: 33310118 DOI: 10.1016/j.ymben.2020.11.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/13/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022]
Abstract
Understanding the governing principles behind organisms' metabolism and growth underpins their effective deployment as bioproduction chassis. A central objective of metabolic modeling is predicting how metabolism and growth are affected by both external environmental factors and internal genotypic perturbations. The fundamental concepts of reaction stoichiometry, thermodynamics, and mass action kinetics have emerged as the foundational principles of many modeling frameworks designed to describe how and why organisms allocate resources towards both growth and bioproduction. This review focuses on the latest algorithmic advancements that have integrated these foundational principles into increasingly sophisticated quantitative frameworks.
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Affiliation(s)
- Patrick F Suthers
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, USA
| | - Charles J Foster
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Debolina Sarkar
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Lin Wang
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
| | - Costas D Maranas
- Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, The Pennsylvania State University, University Park, PA, USA.
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54
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Veliova M, Ferreira CM, Benador IY, Jones AE, Mahdaviani K, Brownstein AJ, Desousa BR, Acín-Pérez R, Petcherski A, Assali EA, Stiles L, Divakaruni AS, Prentki M, Corkey BE, Liesa M, Oliveira MF, Shirihai OS. Blocking mitochondrial pyruvate import in brown adipocytes induces energy wasting via lipid cycling. EMBO Rep 2020; 21:e49634. [PMID: 33275313 PMCID: PMC7726774 DOI: 10.15252/embr.201949634] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 09/15/2020] [Accepted: 10/07/2020] [Indexed: 12/20/2022] Open
Abstract
Combined fatty acid esterification and lipolysis, termed lipid cycling, is an ATP‐consuming process that contributes to energy expenditure. Therefore, interventions that stimulate energy expenditure through lipid cycling are of great interest. Here we find that pharmacological and genetic inhibition of the mitochondrial pyruvate carrier (MPC) in brown adipocytes activates lipid cycling and energy expenditure, even in the absence of adrenergic stimulation. We show that the resulting increase in ATP demand elevates mitochondrial respiration coupled to ATP synthesis and fueled by lipid oxidation. We identify that glutamine consumption and the Malate‐Aspartate Shuttle are required for the increase in Energy Expenditure induced by MPC inhibition in Brown Adipocytes (MAShEEBA). We thus demonstrate that energy expenditure through enhanced lipid cycling can be activated in brown adipocytes by decreasing mitochondrial pyruvate availability. We present a new mechanism to increase energy expenditure and fat oxidation in brown adipocytes, which does not require adrenergic stimulation of mitochondrial uncoupling.
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Affiliation(s)
- Michaela Veliova
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Caroline M Ferreira
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Ilan Y Benador
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| | - Anthony E Jones
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Kiana Mahdaviani
- Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| | - Alexandra J Brownstein
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Molecular Cellular Integrative Physiology, University of California, Los Angeles, CA, USA
| | - Brandon R Desousa
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Rebeca Acín-Pérez
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Anton Petcherski
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Essam A Assali
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Department of Clinical Biochemistry, School of Medicine, Ben Gurion University of The Negev, Beer-Sheva, Israel
| | - Linsey Stiles
- Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Ajit S Divakaruni
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marc Prentki
- Department of Nutrition, , Université de Montréal, Montreal Diabetes Research Center and CRCHUM, Montréal, QC, Canada
| | - Barbara E Corkey
- Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
| | - Marc Liesa
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
| | - Marcus F Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Orian S Shirihai
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Division of Endocrinology, Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA.,Nutrition and Metabolism, Graduate Medical Sciences, Boston University School of Medicine, Boston, MA, USA
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55
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Metabolic flux analysis reaching genome wide coverage: lessons learned and future perspectives. Curr Opin Chem Eng 2020. [DOI: 10.1016/j.coche.2020.05.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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56
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Wang Y, Wondisford FE, Song C, Zhang T, Su X. Metabolic Flux Analysis-Linking Isotope Labeling and Metabolic Fluxes. Metabolites 2020; 10:metabo10110447. [PMID: 33172051 PMCID: PMC7694648 DOI: 10.3390/metabo10110447] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 01/02/2023] Open
Abstract
Metabolic flux analysis (MFA) is an increasingly important tool to study metabolism quantitatively. Unlike the concentrations of metabolites, the fluxes, which are the rates at which intracellular metabolites interconvert, are not directly measurable. MFA uses stable isotope labeled tracers to reveal information related to the fluxes. The conceptual idea of MFA is that in tracer experiments the isotope labeling patterns of intracellular metabolites are determined by the fluxes, therefore by measuring the labeling patterns we can infer the fluxes in the network. In this review, we will discuss the basic concept of MFA using a simplified upper glycolysis network as an example. We will show how the fluxes are reflected in the isotope labeling patterns. The central idea we wish to deliver is that under metabolic and isotopic steady-state the labeling pattern of a metabolite is the flux-weighted average of the substrates’ labeling patterns. As a result, MFA can tell the relative contributions of converging metabolic pathways only when these pathways make substrates in different labeling patterns for the shared product. This is the fundamental principle guiding the design of isotope labeling experiment for MFA including tracer selection. In addition, we will also discuss the basic biochemical assumptions of MFA, and we will show the flux-solving procedure and result evaluation. Finally, we will highlight the link between isotopically stationary and nonstationary flux analysis.
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Affiliation(s)
- Yujue Wang
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Fredric E. Wondisford
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
| | - Chi Song
- Division of Biostatistics, College of Public Health, The Ohio State University, Columbus, OH 43210, USA;
| | - Teng Zhang
- Department of Mathematics, University of Central Florida, Orlando, FL 32816, USA;
| | - Xiaoyang Su
- Department of Medicine, Rutgers-Robert Wood Johnson Medical School, New Brunswick, NJ 08901, USA; (Y.W.); (F.E.W.)
- Metabolomics Shared Resource, Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
- Correspondence: ; Tel.: +1-732-235-5447
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57
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Antoniewicz MR. A guide to metabolic flux analysis in metabolic engineering: Methods, tools and applications. Metab Eng 2020; 63:2-12. [PMID: 33157225 DOI: 10.1016/j.ymben.2020.11.002] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Revised: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 12/22/2022]
Abstract
The field of metabolic engineering is primarily concerned with improving the biological production of value-added chemicals, fuels and pharmaceuticals through the design, construction and optimization of metabolic pathways, redirection of intracellular fluxes, and refinement of cellular properties relevant for industrial bioprocess implementation. Metabolic network models and metabolic fluxes are central concepts in metabolic engineering, as was emphasized in the first paper published in this journal, "Metabolic fluxes and metabolic engineering" (Metabolic Engineering, 1: 1-11, 1999). In the past two decades, a wide range of computational, analytical and experimental approaches have been developed to interrogate the capabilities of biological systems through analysis of metabolic network models using techniques such as flux balance analysis (FBA), and quantify metabolic fluxes using constrained-based modeling approaches such as metabolic flux analysis (MFA) and more advanced experimental techniques based on the use of stable-isotope tracers, i.e. 13C-metabolic flux analysis (13C-MFA). In this review, we describe the basic principles of metabolic flux analysis, discuss current best practices in flux quantification, highlight potential pitfalls and alternative approaches in the application of these tools, and give a broad overview of pragmatic applications of flux analysis in metabolic engineering practice.
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Affiliation(s)
- Maciek R Antoniewicz
- Department of Chemical Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Michigan, Ann Arbor, MI, 48109, USA.
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58
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Rezinciuc S, Bezavada L, Bahadoran A, Duan S, Wang R, Lopez-Ferrer D, Finkelstein D, McGargill MA, Green DR, Pasa-Tolic L, Smallwood HS. Dynamic metabolic reprogramming in dendritic cells: An early response to influenza infection that is essential for effector function. PLoS Pathog 2020; 16:e1008957. [PMID: 33104753 PMCID: PMC7707590 DOI: 10.1371/journal.ppat.1008957] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 12/01/2020] [Accepted: 09/03/2020] [Indexed: 01/19/2023] Open
Abstract
Infection with the influenza virus triggers an innate immune response that initiates the adaptive response to halt viral replication and spread. However, the metabolic response fueling the molecular mechanisms underlying changes in innate immune cell homeostasis remain undefined. Although influenza increases parasitized cell metabolism, it does not productively replicate in dendritic cells. To dissect these mechanisms, we compared the metabolism of dendritic cells to that of those infected with active and inactive influenza A virus and those treated with toll-like receptor agonists. Using quantitative mass spectrometry, pulse chase substrate utilization assays and metabolic flux measurements, we found global metabolic changes in dendritic cells 17 hours post infection, including significant changes in carbon commitment via glycolysis and glutaminolysis, as well as mitochondrial respiration. Influenza infection of dendritic cells led to a metabolic phenotype distinct from that induced by TLR agonists, with significant resilience in terms of metabolic plasticity. We identified c-Myc as one transcription factor modulating this response. Restriction of c-Myc activity or mitochondrial substrates significantly changed the immune functions of dendritic cells, such as reducing motility and T cell activation. Transcriptome analysis of inflammatory dendritic cells isolated following influenza infection showed similar metabolic reprogramming occurs in vivo. Thus, early in the infection process, dendritic cells respond with global metabolic restructuring, that is present in inflammatory lung dendritic cells after infection, and this is important for effector function. These findings suggest metabolic switching in dendritic cells plays a vital role in initiating the immune response to influenza infection. Dendritic cells are critical in mounting an effective immune response to influenza infection by initiating the immune response to influenza and activating the adaptive response to mediate viral clearance and manifest immune memory for protection against subsequent infections. We found dendritic cells undergo a profound metabolic shift after infection. They alter the concentration and location of hundreds of proteins, including c-Myc, facilitating a shift to a highly glycolytic phenotype that is also flexible in terms of fueling respiration. Nonetheless, we found limiting access to specific metabolic pathways or substrates diminished key immune functions. We previously described an immediate, fixed hypermetabolic state in infected respiratory epithelial cells. Here we present data indicating the metabolic response of dendritic cells is increased yet flexible, distinct from what we previously showed for epithelial cells. Additionally, we demonstrate dendritic cells tailor their metabolic response to the pathogen or TLR stimulus. This metabolic reprogramming occurs rapidly in vitro and is sustained in inflammatory dendritic cells in vivo for at least 9 days following influenza infection. These studies introduce the possibility of modulating the immune response to viral infection using customized metabolic therapy to enhance or diminish the function of specific cells.
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Affiliation(s)
- Svetlana Rezinciuc
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Lavanya Bezavada
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Azadeh Bahadoran
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
| | - Susu Duan
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, The Research Institute at Nationwide Children's Hospital, The Ohio State University School of Medicine, Columbus, Ohio, United States of America
| | - Daniel Lopez-Ferrer
- Chromatography and Mass Spectrometry Division, Thermo Fisher Scientific, CA, United States of America
| | - David Finkelstein
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Maureen A. McGargill
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Douglas R. Green
- Department of Immunology, St. Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Ljiljana Pasa-Tolic
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, United States of America
| | - Heather S. Smallwood
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, Tennessee, United States of America
- * E-mail:
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59
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Tang S, Xie J, Wu W, Yi B, Liu L, Zhang H. High ammonia exposure regulates lipid metabolism in the pig skeletal muscle via mTOR pathway. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 740:139917. [PMID: 32563870 DOI: 10.1016/j.scitotenv.2020.139917] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 03/23/2020] [Accepted: 06/01/2020] [Indexed: 06/11/2023]
Abstract
Ambient ammonia exposure has been known to perturb lipid metabolism in farm animals, but the underlying mechanism is unclear. The current study was conducted to investigate how ambient ammonia exposure influences lipid metabolism in the pig model. Twelve pigs were randomly divided into two groups, either exposed to 0 or 35 mg/m3 atmospheric ammonia for 25 days. Serum ammonia remained unchanged (p > 0.05), but increased serum urea concentration was found (p < 0.05) after ammonia exposure. Ammonia exposure also caused an increased C18:0, C18:2n6c, C18:3n6, C18:3n3, C20:0, C20:2, C20:3n6, C20:3n3, C22:0 concentrations and fat content in the longissimus dorsi muscle (p < 0.05), and also serum total triglyceride (p = 0.0294) and ApoB (p = 0.0061) contents. Analysis of serum free amino acids profile revealed that concentrations of ornithine, tyrosine, asparagine, histidine, phenylalanine, leucine, isoleucine, glutamine and valine were significantly increased in the pigs exposed to 35 mg/m3 ammonia (p < 0.05). RNA-Seq analysis showed that genes encoding enzymes involved in lipid synthesis (FASN, SCD and FADS1) and uptake (LDLR) were up-regulated, whereas genes related to lipolysis (PNPLA4, ANGPTL4 and CEL), transport (CPT1A, CPT1B and CPT2) and β-oxidation (ACADL, ACADVL, UCP2 and UCP3) were down-regulated. Furthermore, exposure to 35 mg/m3 atmospheric ammonia increased expression of mTOR (p = 0.0377) and its downstream P70S6K (p = 0.0139) and p-P70S6K (p = 0.0431), but decreased AMPK (p < 0.0001) and p-AMPK (p = 0.0071) in the longissimus dorsi muscle. In conclusion, high concentration of atmospheric ammonia exposure greatly interferes with amino acid metabolism, resulting in increased BCAAs and aromatic amino acids. The increased BCAAs production can up-regulate lipid synthesis and down-regulate β-oxidation by activating mTOR signaling and inhibiting AMPK signaling.
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Affiliation(s)
- Shanlong Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Jingjing Xie
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
| | - Weida Wu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Bao Yi
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Lei Liu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, PR China.
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60
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Ozone Activates the Nrf2 Pathway and Improves Preservation of Explanted Adipose Tissue In Vitro. Antioxidants (Basel) 2020; 9:antiox9100989. [PMID: 33066365 PMCID: PMC7602229 DOI: 10.3390/antiox9100989] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 10/12/2020] [Indexed: 12/20/2022] Open
Abstract
In clinical practice, administration of low ozone (O3) dosages is a complementary therapy for many diseases, due to the capability of O3 to elicit an antioxidant response through the Nuclear Factor Erythroid 2-Related Factor 2 (Nrf2)-dependent pathway. Nrf2 is also involved in the adipogenic differentiation of mesenchymal stem cells, and low O3 concentrations have been shown to stimulate lipid accumulation in human adipose-derived adult stem cells in vitro. Thus, O3 treatment is a promising procedure to improve the survival of explanted adipose tissue, whose reabsorption after fat grafting is a major problem in regenerative medicine. In this context, we carried out a pilot study to explore the potential of mild O3 treatment in preserving explanted murine adipose tissue in vitro. Scanning and transmission electron microscopy, Western blot, real-time polymerase chain reaction and nuclear magnetic resonance spectroscopy were used. Exposure to low O3 concentrations down in the degradation of the explanted adipose tissue and induced a concomitant increase in the protein abundance of Nrf2 and in the expression of its target gene Hmox1. These findings provide a promising background for further studies aimed at the clinical application of O3 as an adjuvant treatment to improve fat engraftment.
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61
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Tanosaki S, Tohyama S, Fujita J, Someya S, Hishiki T, Matsuura T, Nakanishi H, Ohto-Nakanishi T, Akiyama T, Morita Y, Kishino Y, Okada M, Tani H, Soma Y, Nakajima K, Kanazawa H, Sugimoto M, Ko MSH, Suematsu M, Fukuda K. Fatty Acid Synthesis Is Indispensable for Survival of Human Pluripotent Stem Cells. iScience 2020; 23:101535. [PMID: 33083764 PMCID: PMC7509212 DOI: 10.1016/j.isci.2020.101535] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 07/26/2020] [Accepted: 09/02/2020] [Indexed: 12/12/2022] Open
Abstract
The role of lipid metabolism in human pluripotent stem cells (hPSCs) is poorly understood. We have used large-scale targeted proteomics to demonstrate that undifferentiated hPSCs express different fatty acid (FA) biosynthesis-related enzymes, including ATP citrate lyase and FA synthase (FASN), than those expressed in hPSC-derived cardiomyocytes (hPSC-CMs). Detailed lipid profiling revealed that inhibition of FASN resulted in significant reduction of sphingolipids and phosphatidylcholine (PC); moreover, we found that PC was the key metabolite for cell survival in hPSCs. Inhibition of FASN induced cell death in undifferentiated hPSCs via mitochondria-mediated apoptosis; however, it did not affect cell survival in hPSC-CMs, neurons, or hepatocytes as there was no significant reduction of PC. Furthermore, we did not observe tumor formation following transplantation of FASN inhibitor-treated cells. Our findings demonstrate the importance of de novo FA synthesis in the survival of undifferentiated hPSCs and suggest applications for FASN inhibition in regenerative medicine. Undifferentiated hPSCs upregulate de novo FA synthesis-related enzymes Inhibition of de novo FA synthesis induces cell death in undifferentiated hPSCs Phosphatidylcholine is the key metabolite required for hPSC survival FASN inhibition eliminates undifferentiated hPSCs from hPSC derivatives
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Affiliation(s)
- Sho Tanosaki
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.,Department of Emergency and Critical Care Medicine, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Shugo Tohyama
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.,Department of Organ Fabrication, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Jun Fujita
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.,Endowed Course for Severe Heart Failure Treatment II, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Shota Someya
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.,Department of Emergency and Critical Care Medicine, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Takako Hishiki
- Department of Biochemistry, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan.,Clinical and Translational Research Center, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Tomomi Matsuura
- Clinical and Translational Research Center, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | | | | | - Tomohiko Akiyama
- Department of Systems Medicine, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Yuika Morita
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Yoshikazu Kishino
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Marina Okada
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Hidenori Tani
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Yusuke Soma
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Kazuaki Nakajima
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Hideaki Kanazawa
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Masahiro Sugimoto
- Research and Development Center for Minimally Invasive Therapies Health Promotion and Preemptive Medicine, Tokyo Medical University, Shinjuku, Tokyo 160-8402, Japan.,Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997-0052, Japan
| | - Minoru S H Ko
- Department of Systems Medicine, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Makoto Suematsu
- Department of Biochemistry, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
| | - Keiichi Fukuda
- Department of Cardiology, Keio University School of Medicine, Shinjuku, Tokyo 160-8582, Japan
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62
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Smolková K, Špačková J, Gotvaldová K, Dvořák A, Křenková A, Hubálek M, Holendová B, Vítek L, Ježek P. SIRT3 and GCN5L regulation of NADP+- and NADPH-driven reactions of mitochondrial isocitrate dehydrogenase IDH2. Sci Rep 2020; 10:8677. [PMID: 32457458 PMCID: PMC7250847 DOI: 10.1038/s41598-020-65351-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 04/29/2020] [Indexed: 12/22/2022] Open
Abstract
Wild type mitochondrial isocitrate dehydrogenase (IDH2) was previously reported to produce oncometabolite 2-hydroxyglutarate (2HG). Besides, mitochondrial deacetylase SIRT3 has been shown to regulate the oxidative function of IDH2. However, regulation of 2HG formation by SIRT3-mediated deacetylation was not investigated yet. We aimed to study mitochondrial IDH2 function in response to acetylation and deacetylation, and focus specifically on 2HG production by IDH2. We used acetylation surrogate mutant of IDH2 K413Q and assayed enzyme kinetics of oxidative decarboxylation of isocitrate, 2HG production by the enzyme, and 2HG production in cells. The purified IDH2 K413Q exhibited lower oxidative reaction rates than IDH2 WT. 2HG production by IDH2 K413Q was largely diminished at the enzymatic and cellular level, and knockdown of SIRT3 also inhibited 2HG production by IDH2. Contrary, the expression of putative mitochondrial acetylase GCN5L likely does not target IDH2. Using mass spectroscopy, we further identified lysine residues within IDH2, which are the substrates of SIRT3. In summary, we demonstrate that 2HG levels arise from non-mutant IDH2 reductive function and decrease with increasing acetylation level. The newly identified lysine residues might apply in regulation of IDH2 function in response to metabolic perturbations occurring in cancer cells, such as glucose-free conditions.
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Affiliation(s)
- Katarína Smolková
- Laboratory of Mitochondrial Physiology, No.75, Institute of Physiology of the Czech Academy of Sciences (IPHYS CAS), Vídeňská 1083, 14220, Prague, Czech Republic.
| | - Jitka Špačková
- Laboratory of Mitochondrial Physiology, No.75, Institute of Physiology of the Czech Academy of Sciences (IPHYS CAS), Vídeňská 1083, 14220, Prague, Czech Republic
| | - Klára Gotvaldová
- Laboratory of Mitochondrial Physiology, No.75, Institute of Physiology of the Czech Academy of Sciences (IPHYS CAS), Vídeňská 1083, 14220, Prague, Czech Republic
| | - Aleš Dvořák
- Laboratory of Mitochondrial Physiology, No.75, Institute of Physiology of the Czech Academy of Sciences (IPHYS CAS), Vídeňská 1083, 14220, Prague, Czech Republic
- Institute of Medical Biochemistry and Laboratory Diagnostics, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Alena Křenková
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB CAS), Prague, Czech Republic
| | - Martin Hubálek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences (IOCB CAS), Prague, Czech Republic
| | - Blanka Holendová
- Laboratory of Mitochondrial Physiology, No.75, Institute of Physiology of the Czech Academy of Sciences (IPHYS CAS), Vídeňská 1083, 14220, Prague, Czech Republic
| | - Libor Vítek
- Institute of Medical Biochemistry and Laboratory Diagnostics, 1st Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Petr Ježek
- Laboratory of Mitochondrial Physiology, No.75, Institute of Physiology of the Czech Academy of Sciences (IPHYS CAS), Vídeňská 1083, 14220, Prague, Czech Republic
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63
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Chen PS, Chiu WT, Hsu PL, Lin SC, Peng IC, Wang CY, Tsai SJ. Pathophysiological implications of hypoxia in human diseases. J Biomed Sci 2020; 27:63. [PMID: 32389123 PMCID: PMC7212687 DOI: 10.1186/s12929-020-00658-7] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 05/06/2020] [Indexed: 12/11/2022] Open
Abstract
Oxygen is essentially required by most eukaryotic organisms as a scavenger to remove harmful electron and hydrogen ions or as a critical substrate to ensure the proper execution of enzymatic reactions. All nucleated cells can sense oxygen concentration and respond to reduced oxygen availability (hypoxia). When oxygen delivery is disrupted or reduced, the organisms will develop numerous adaptive mechanisms to facilitate cells survived in the hypoxic condition. Normally, such hypoxic response will cease when oxygen level is restored. However, the situation becomes complicated if hypoxic stress persists (chronic hypoxia) or cyclic normoxia-hypoxia phenomenon occurs (intermittent hypoxia). A series of chain reaction-like gene expression cascade, termed hypoxia-mediated gene regulatory network, will be initiated under such prolonged or intermittent hypoxic conditions and subsequently leads to alteration of cellular function and/or behaviors. As a result, irreversible processes occur that may cause physiological disorder or even pathological consequences. A growing body of evidence implicates that hypoxia plays critical roles in the pathogenesis of major causes of mortality including cancer, myocardial ischemia, metabolic diseases, and chronic heart and kidney diseases, and in reproductive diseases such as preeclampsia and endometriosis. This review article will summarize current understandings regarding the molecular mechanism of hypoxia in these common and important diseases.
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Affiliation(s)
- Pai-Sheng Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China.,Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China
| | - Wen-Tai Chiu
- Department of Biomedical Engineering, College of Engineering, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China
| | - Pei-Ling Hsu
- Department of Physiology, College of Medicine, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China
| | - Shih-Chieh Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China
| | - I-Chen Peng
- Department of Life Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China
| | - Chia-Yih Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China.,Department of Cell Biology and Anatomy, College of Medicine, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China
| | - Shaw-Jenq Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China. .,Department of Physiology, College of Medicine, National Cheng Kung University, 1 University Road, Tainan, 70101, Taiwan, Republic of China.
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64
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Im D, Hong J, Gu B, Sung C, Oh M. 13
C Metabolic Flux Analysis of
Escherichia coli
Engineered for Gamma‐Aminobutyrate Production. Biotechnol J 2020; 15:e1900346. [DOI: 10.1002/biot.201900346] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/12/2020] [Indexed: 12/28/2022]
Affiliation(s)
- Dae‐Kyun Im
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
| | - Jaeseung Hong
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
| | - Boncheol Gu
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
| | - Changmin Sung
- Doping Control CenterKorea Institute of Science and Technology 5 Hwarang‐ro 14‐gil, Seongbuk‐gu Seoul 02792 Korea
| | - Min‐Kyu Oh
- Department of Chemical and Biological EngineeringKorea University 145 Anam‐ro, Seongbuk‐gu Seoul 02841 Korea
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65
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Ye S, Xu P, Huang M, Chen X, Zeng S, Wang Q, Chen J, Li K, Gao W, Liu R, Liu J, Shao Y, Zhang H, Xu Y, Zhang Q, Zhong Z, Wei Z, Wang J, Hao B, Huang W, Liu Q. The heterocyclic compound Tempol inhibits the growth of cancer cells by interfering with glutamine metabolism. Cell Death Dis 2020; 11:312. [PMID: 32366855 PMCID: PMC7198543 DOI: 10.1038/s41419-020-2499-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 04/05/2020] [Accepted: 04/06/2020] [Indexed: 12/17/2022]
Abstract
Tempol (4-hydroxy-2,2,6,6-Tetramethylpiperidine-1-oxyl, TPL), a nitroxide compound, inhibits proliferation and increases the vulnerability of cancer cells to apoptosis induced by cytotoxic agents. However, the molecular mechanism of TPL inhibiting cancer cell proliferation has not been fully understood. In this study, we evaluated the metabolic effect of TPL on cancer cells and explored its cancer therapeutic potential. Extracellular flow assays showed that TPL inhibited cellular basal and maximal oxygen consumption rates of mitochondrial. 13C metabolic flux analysis showed that TPL treatment had minimal effect on glycolysis. However, we found that TPL inhibits glutamine metabolism by interfering with the oxidative tricarboxylic acid cycle (TCA) process and reductive glutamine process. We found that the inhibitory effect of TPL on metabolism occurs mainly on the step from citrate to α-ketoglutarate or vice versa. We also found that activity of isocitrate dehydrogenase IDH1 and IDH2, the key enzymes in TCA, were inhibited by TPL treatment. In xenograft mouse model, TPL treatment reduced tumor growth by inhibiting cellular proliferation of xenograft tumors. Thus, we provided a mechanism of TPL inhibiting cancer cell proliferation by interfering with glutamine utilization that is important for survival and proliferation of cancer cells. The study may help the development of a therapeutic strategy of TPL combined with other anticancer medicines.
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Affiliation(s)
- Shuangyan Ye
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Pengfei Xu
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Mengqiu Huang
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Xi Chen
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Sisi Zeng
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qianli Wang
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Jianping Chen
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Keyi Li
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Wenwen Gao
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Ruiyuan Liu
- School of Biomedical Engineering, Southern Medical University, Guangzhou, China
| | - Jingxian Liu
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Yihao Shao
- The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Hui Zhang
- Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Yang Xu
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Qianbing Zhang
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
| | - Zhuo Zhong
- Guangzhou Hospital of integrated Traditional and West Medicine, Guangzhou, China
| | - Zibo Wei
- Center for medical transformation, Shunde Hospital, Southern Medical University, Foshan, China
| | - Jiale Wang
- Center for medical transformation, Shunde Hospital, Southern Medical University, Foshan, China
| | - Bingtao Hao
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
| | - Wenhua Huang
- National Key Discipline of Human Anatomy, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. .,Department of Human Anatomy, School of Basic Medical Sciences, Guangdong Medical University, Guangzhou, China.
| | - Qiuzhen Liu
- Cancer Research Institute, Guangdong Provincial Key Laboratory of Cancer Immunotherapy, Guangzhou Key Laboratory of Tumor Immunology Research, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China. .,Center for medical transformation, Shunde Hospital, Southern Medical University, Foshan, China.
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66
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Dai W, Xu L, Yu X, Zhang G, Guo H, Liu H, Song G, Weng S, Dong L, Zhu J, Liu T, Guo C, Shen X. OGDHL silencing promotes hepatocellular carcinoma by reprogramming glutamine metabolism. J Hepatol 2020; 72:909-923. [PMID: 31899205 DOI: 10.1016/j.jhep.2019.12.015] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 11/20/2019] [Accepted: 12/04/2019] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Mitochondrial dysfunction and subsequent metabolic deregulation are commonly observed in cancers, including hepatocellular carcinoma (HCC). When mitochondrial function is impaired, reductive glutamine metabolism is a major cellular carbon source for de novo lipogenesis to support cancer cell growth. The underlying regulators of reductively metabolized glutamine in mitochondrial dysfunction are not completely understood in tumorigenesis. METHODS We systematically investigated the role of oxoglutarate dehydrogenase-like (OGDHL), one of the rate-limiting components of the key mitochondrial multi-enzyme OGDH complex (OGDHC), in the regulation of lipid metabolism in hepatoma cells and mouse xenograft models. RESULTS Lower expression of OGDHL was associated with advanced tumor stage, significantly worse survival and more frequent tumor recurrence in 3 independent cohorts totaling 681 postoperative HCC patients. Promoter hypermethylation and DNA copy deletion of OGDHL were independently correlated with reduced OGDHL expression in HCC specimens. Additionally, OGDHL overexpression significantly inhibited the growth of hepatoma cells in mouse xenografts, while knockdown of OGDHL promoted proliferation of hepatoma cells. Mechanistically, OGDHL downregulation upregulated the α-ketoglutarate (αKG):citrate ratio by reducing OGDHC activity, which subsequently drove reductive carboxylation of glutamine-derived αKG via retrograde tricarboxylic acid cycling in hepatoma cells. Notably, silencing of OGDHL activated the mTORC1 signaling pathway in an αKG-dependent manner, inducing transcription of enzymes with key roles in de novo lipogenesis. Meanwhile, metabolic reprogramming in OGDHL-negative hepatoma cells provided an abundant supply of NADPH and glutathione to support the cellular antioxidant system. The reduction of reductive glutamine metabolism through OGDHL overexpression or glutaminase inhibitors sensitized tumor cells to sorafenib, a molecular-targeted therapy for HCC. CONCLUSION Our findings established that silencing of OGDHL contributed to HCC development and survival by regulating glutamine metabolic pathways. OGDHL is a promising prognostic biomarker and therapeutic target for HCC. LAY SUMMARY Hepatocellular carcinoma (HCC) is one of the most prevalent tumors worldwide and is correlated with a high mortality rate. In patients with HCC, lower expression of the enzyme OGDHL is significantly associated with worse survival. Herein, we show that silencing of OGDHL induces lipogenesis and influences the chemosensitization effect of sorafenib in liver cancer cells by reprogramming glutamine metabolism. OGDHL is a promising prognostic biomarker and potential therapeutic target in OGDHL-negative liver cancer.
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Affiliation(s)
- Weiqi Dai
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Ling Xu
- Department of Gastroenterology, Shanghai Tongren Hospital, Jiaotong University of Medicine, Shanghai, P.R. China
| | - Xiangnan Yu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Guangcong Zhang
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Hongying Guo
- Department of Severe Hepatitis, Shanghai Public Health Clinical Center, Fudan University, Shanghai, P.R. China
| | - Hailin Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Guangqi Song
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Shuqiang Weng
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Ling Dong
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Jimin Zhu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Taotao Liu
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China
| | - Chuanyong Guo
- Department of Gastroenterology, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai, P.R. China.
| | - Xizhong Shen
- Department of Gastroenterology and Hepatology, Zhongshan Hospital, Fudan University, Shanghai, P.R. China; Shanghai Institute of Liver Diseases, Shanghai, P.R. China; Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, Shanghai, P.R. China.
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67
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Yang L, Garcia Canaveras JC, Chen Z, Wang L, Liang L, Jang C, Mayr JA, Zhang Z, Ghergurovich JM, Zhan L, Joshi S, Hu Z, McReynolds MR, Su X, White E, Morscher RJ, Rabinowitz JD. Serine Catabolism Feeds NADH when Respiration Is Impaired. Cell Metab 2020; 31:809-821.e6. [PMID: 32187526 PMCID: PMC7397714 DOI: 10.1016/j.cmet.2020.02.017] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 12/09/2019] [Accepted: 02/26/2020] [Indexed: 01/18/2023]
Abstract
NADH provides electrons for aerobic ATP production. In cells deprived of oxygen or with impaired electron transport chain activity, NADH accumulation can be toxic. To minimize such toxicity, elevated NADH inhibits the classical NADH-producing pathways: glucose, glutamine, and fat oxidation. Here, through deuterium-tracing studies in cultured cells and mice, we show that folate-dependent serine catabolism also produces substantial NADH. Strikingly, when respiration is impaired, serine catabolism through methylene tetrahydrofolate dehydrogenase (MTHFD2) becomes a major NADH source. In cells whose respiration is slowed by hypoxia, metformin, or genetic lesions, mitochondrial serine catabolism inhibition partially normalizes NADH levels and facilitates cell growth. In mice with engineered mitochondrial complex I deficiency (NDUSF4-/-), serine's contribution to NADH is elevated, and progression of spasticity is modestly slowed by pharmacological blockade of serine degradation. Thus, when respiration is impaired, serine catabolism contributes to toxic NADH accumulation.
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Affiliation(s)
- Lifeng Yang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Juan Carlos Garcia Canaveras
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Zihong Chen
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Lin Wang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Lingfan Liang
- School of Pharmaceutical Sciences, Tsinghua University, Beijing 100084, China
| | - Cholsoon Jang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Johannes A Mayr
- Department of Pediatrics, Salzburger Landeskliniken and Paracelsus Medical University, Salzburg 5020, Austria
| | - Zhaoyue Zhang
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Jonathan M Ghergurovich
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA
| | - Le Zhan
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Shilpy Joshi
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Zhixian Hu
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA
| | - Melanie R McReynolds
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Xiaoyang Su
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Department of Medicine, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ 08901, USA
| | - Eileen White
- Rutgers Cancer Institute of New Jersey, New Brunswick, NJ 08903, USA; Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08854, USA
| | | | - Joshua D Rabinowitz
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA; Department of Chemistry, Princeton University, Princeton, NJ 08544, USA; Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA.
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68
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Capitanio D, Moriggi M, Torretta E, Barbacini P, De Palma S, Viganò A, Lochmüller H, Muntoni F, Ferlini A, Mora M, Gelfi C. Comparative proteomic analyses of Duchenne muscular dystrophy and Becker muscular dystrophy muscles: changes contributing to preserve muscle function in Becker muscular dystrophy patients. J Cachexia Sarcopenia Muscle 2020; 11:547-563. [PMID: 31991054 PMCID: PMC7113522 DOI: 10.1002/jcsm.12527] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 11/08/2019] [Accepted: 11/24/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Duchenne muscular dystrophy (DMD) and Becker muscular dystrophy (BMD) are characterized by muscle wasting leading to loss of ambulation in the first or third decade, respectively. In DMD, the lack of dystrophin hampers connections between intracellular cytoskeleton and cell membrane leading to repeated cycles of necrosis and regeneration associated with inflammation and loss of muscle ordered structure. BMD has a similar muscle phenotype but milder. Here, we address the question whether proteins at variance in BMD compared with DMD contribute to the milder phenotype in BMD, thus identifying a specific signature to be targeted for DMD treatment. METHODS Proteins extracted from skeletal muscle from DMD/BMD patients and young healthy subjects were either reduced and solubilized prior two-dimensional difference in gel electrophoresis/mass spectrometry differential analysis or tryptic digested prior label-free liquid chromatography with tandem mass spectrometry. Statistical analyses of proteins and peptides were performed by DeCyder and Perseus software and protein validation and verification by immunoblotting. RESULTS Proteomic results indicate minor changes in the extracellular matrix (ECM) protein composition in BMD muscles with retention of mechanotransduction signalling, reduced changes in cytoskeletal and contractile proteins. Conversely, in DMD patients, increased levels of several ECM cytoskeletal and contractile proteins were observed whereas some proteins of fast fibres and of Z-disc decreased. Detyrosinated alpha-tubulin was unchanged in BMD and increased in DMD although neuronal nitric oxide synthase was unchanged in BMD and greatly reduced in DMD. Metabolically, the tissue is characterized by a decrement of anaerobic metabolism both in DMD and BMD compared with controls, with increased levels of the glycogen metabolic pathway in BMD. Oxidative metabolism is severely compromised in DMD with impairment of malate shuttle; conversely, it is active in BMD supporting the tricarboxylic acid cycle and respiratory chain. Adipogenesis characterizes DMD, whereas proteins involved in fatty acids beta-oxidation are increased in BMD. Proteins involved in protein/amino acid metabolism, cell development, calcium handling, endoplasmic reticulum/sarcoplasmic reticulum stress response, and inflammation/immune response were increased in DMD. Both disorders are characterized by the impairment of N-linked protein glycosylation in the endoplasmic reticulum. Authophagy was decreased in DMD whereas it was retained in BMD. CONCLUSIONS The mechanosensing and metabolic disruption are central nodes of DMD/BMD phenotypes. The ECM proteome composition and the metabolic rewiring in BMD lead to preservation of energy levels supporting autophagy and cell renewal, thus promoting the retention of muscle function. Conversely, DMD patients are characterized by extracellular and cytoskeletal protein dysregulation and by metabolic restriction at the level of α-ketoglutarate leading to shortage of glutamate-derived molecules that over time triggers lipogenesis and lipotoxicity.
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Affiliation(s)
- Daniele Capitanio
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
| | - Manuela Moriggi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Enrica Torretta
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Pietro Barbacini
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Sara De Palma
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Agnese Viganò
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy
| | - Hanns Lochmüller
- Department of Neuropediatrics and Muscle Disorders, Faculty of Medicine, Medical Center-University of Freiburg, Freiburg, Germany.,Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Catalonia, Spain.,Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Canada.,Division of Neurology, Department of Medicine, The Ottawa Hospital, Ottawa, Canada
| | - Francesco Muntoni
- Dubowitz Neuromuscular Centre, University College London, Institute of Child Health, London, UK.,NIHR Great Ormond Street Hospital Biomedical Research Centre, Great Ormond Street Institute of Child Health, University College London, & Great Ormond Street Hospital Trust, London, UK
| | - Alessandra Ferlini
- Dubowitz Neuromuscular Centre, University College London, Institute of Child Health, London, UK.,Unit of Medical Genetics, Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Marina Mora
- Neuromuscular Diseases and Neuroimmunology Unit, Fondazione IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
| | - Cecilia Gelfi
- Department of Biomedical Sciences for Health, University of Milan, Milan, Italy.,IRCCS Istituto Ortopedico Galeazzi, Milan, Italy
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Bennett RK, Dillon M, Gerald Har JR, Agee A, von Hagel B, Rohlhill J, Antoniewicz MR, Papoutsakis ET. Engineering Escherichia coli for methanol-dependent growth on glucose for metabolite production. Metab Eng 2020; 60:45-55. [PMID: 32179162 DOI: 10.1016/j.ymben.2020.03.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/25/2020] [Accepted: 03/08/2020] [Indexed: 02/05/2023]
Abstract
Synthetic methylotrophy aims to engineer methane and methanol utilization pathways in platform hosts like Escherichia coli for industrial bioprocessing of natural gas and biogas. While recent attempts to engineer synthetic methanol auxotrophs have proved successful, these studies focused on scarce and expensive co-substrates. Here, we engineered E. coli for methanol-dependent growth on glucose, an abundant and inexpensive co-substrate, via deletion of glucose 6-phosphate isomerase (pgi), phosphogluconate dehydratase (edd), and ribose 5-phosphate isomerases (rpiAB). Since the parental strain did not exhibit methanol-dependent growth on glucose in minimal medium, we first achieved methanol-dependent growth via amino acid supplementation and used this medium to evolve the strain for methanol-dependent growth in glucose minimal medium. The evolved strain exhibited a maximum growth rate of 0.15 h-1 in glucose minimal medium with methanol, which is comparable to that of other synthetic methanol auxotrophs. Whole genome sequencing and 13C-metabolic flux analysis revealed the causative mutations in the evolved strain. A mutation in the phosphotransferase system enzyme I gene (ptsI) resulted in a reduced glucose uptake rate to maintain a one-to-one molar ratio of substrate utilization. Deletion of the e14 prophage DNA region resulted in two non-synonymous mutations in the isocitrate dehydrogenase (icd) gene, which reduced TCA cycle carbon flux to maintain the internal redox state. In high cell density glucose fed-batch fermentation, methanol-dependent acetone production resulted in 22% average carbon labeling of acetone from 13C-methanol, which far surpasses that of the previous best (2.4%) found with methylotrophic E. coli Δpgi. This study addresses the need to identify appropriate co-substrates for engineering synthetic methanol auxotrophs and provides a basis for the next steps toward industrial one-carbon bioprocessing.
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Affiliation(s)
- R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Michael Dillon
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Jie Ren Gerald Har
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
| | - Alec Agee
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Bryan von Hagel
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Julia Rohlhill
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA; The Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA.
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Paluchova V, Oseeva M, Brezinova M, Cajka T, Bardova K, Adamcova K, Zacek P, Brejchova K, Balas L, Chodounska H, Kudova E, Schreiber R, Zechner R, Durand T, Rossmeisl M, Abumrad NA, Kopecky J, Kuda O. Lipokine 5-PAHSA Is Regulated by Adipose Triglyceride Lipase and Primes Adipocytes for De Novo Lipogenesis in Mice. Diabetes 2020; 69:300-312. [PMID: 31806624 PMCID: PMC7118252 DOI: 10.2337/db19-0494] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 11/30/2019] [Indexed: 12/18/2022]
Abstract
Branched esters of palmitic acid and hydroxystearic acid (PAHSA) are anti-inflammatory and antidiabetic lipokines that connect glucose and lipid metabolism. We aimed to characterize involvement of the 5-PAHSA regioisomer in the adaptive metabolic response of white adipose tissue (WAT) to cold exposure (CE) in mice, exploring the cross talk between glucose utilization and lipid metabolism. CE promoted local production of 5- and 9-PAHSAs in WAT. Metabolic labeling of de novo lipogenesis (DNL) using 2H2O revealed that 5-PAHSA potentiated the effects of CE and stimulated triacylglycerol (TAG)/fatty acid (FA) cycling in WAT through impacting lipogenesis and lipolysis. Adipocyte lipolytic products were altered by 5-PAHSA through selective FA re-esterification. The impaired lipolysis in global adipose triglyceride lipase (ATGL) knockout mice reduced free PAHSA levels and uncovered a metabolite reservoir of TAG-bound PAHSAs (TAG estolides) in WAT. Utilization of 13C isotope tracers and dynamic metabolomics documented that 5-PAHSA primes adipocytes for glucose metabolism in a different way from insulin, promoting DNL and impeding TAG synthesis. In summary, our data reveal new cellular and physiological mechanisms underlying the beneficial effects of 5-PAHSA and its relation to insulin action in adipocytes and independently confirm a PAHSA metabolite reservoir linked to ATGL-mediated lipolysis.
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Affiliation(s)
- Veronika Paluchova
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Marina Oseeva
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Marie Brezinova
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tomas Cajka
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Kristina Bardova
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Katerina Adamcova
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Petr Zacek
- Proteomics Core Facility, Faculty of Science, Charles University, Division BIOCEV, Vestec, Czech Republic
| | - Kristyna Brejchova
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Laurence Balas
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Université Montpellier, and Faculté de Pharmacie, ENSCM, Montpellier, France
| | - Hana Chodounska
- Neurosteroids, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Eva Kudova
- Neurosteroids, Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague, Czech Republic
| | - Renate Schreiber
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Rudolf Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Thierry Durand
- Institut des Biomolécules Max Mousseron, UMR 5247, CNRS, Université Montpellier, and Faculté de Pharmacie, ENSCM, Montpellier, France
| | - Martin Rossmeisl
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Nada A Abumrad
- Department of Medicine, Washington University School of Medicine, St. Louis, MO
| | - Jan Kopecky
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Ondrej Kuda
- Institute of Physiology of the Czech Academy of Sciences, Prague, Czech Republic
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71
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Allen DK, Young JD. Tracing metabolic flux through time and space with isotope labeling experiments. Curr Opin Biotechnol 2019; 64:92-100. [PMID: 31864070 PMCID: PMC7302994 DOI: 10.1016/j.copbio.2019.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
Metabolism is dynamic and must function in context-specific ways to adjust to changes in the surrounding cellular and ecological environment. When isotopic tracers are used, metabolite flow (i.e. metabolic flux) can be quantified through biochemical networks to assess metabolic pathway operation. The cellular activities considered across multiple tissues and organs result in the observed phenotype and can be analyzed to discover emergent, whole-system properties of biology and elucidate misconceptions about network operation. However, temporal and spatial challenges remain significant hurdles and require novel approaches and creative solutions. We survey current investigations in higher plant and animal systems focused on dynamic isotope labeling experiments, spatially resolved measurement strategies, and observations from re-analysis of our own studies that suggest prospects for future work. Related discoveries will be necessary to push the frontier of our understanding of metabolism to suggest novel solutions to cure disease and feed a growing future world population.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Jamey D Young
- Department of Chemical & Biomolecular Engineering, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States; Department of Molecular Physiology & Biophysics, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States.
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72
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Tang S, Xie J, Zhang S, Wu W, Yi B, Zhang H. Atmospheric Ammonia Affects Myofiber Development and Lipid Metabolism in Growing Pig Muscle. Animals (Basel) 2019; 10:ani10010002. [PMID: 31861338 PMCID: PMC7022806 DOI: 10.3390/ani10010002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 12/10/2019] [Accepted: 12/14/2019] [Indexed: 12/27/2022] Open
Abstract
Ammonia, an aerial pollutant in animal facilities, affects animal health. Recent studies showed that aerial ammonia negatively impacts meat quality but the mechanism remains unknown. To understand how ammonia drives its adverse effects on pig meat quality, 18 crossbred gilts were exposed to 0, 10 or 25 mg/m3 ammonia for 25 days. Ammonia exposure increased fat content in the Longissimus dorsi muscle, and meat color got lighter after 25 mg/m3 ammonia exposure. Analysis of MyHC isoforms showed an increased MyHC IIx but decreased MyHC I after ammonia exposure. Besides, muscular glutamine decreased significantly as aerial ammonia increased. Although hyperammonemia was reported to upregulate MSTN and inhibit downstream mTOR pathway, no changes have been found in the mRNA expression level of MSTN and protein expression level of mTOR signal pathway after ammonia exposure. RNA-Seq showed that 10 mg/m3 ammonia exposure altered genes related to myofiber development (MyoD1, MyoG), whereas 25 mg/m3 ammonia affected genes associated with fatty acid synthesis and β-oxidation (SCD, FADS1, FASN, ACADL). Collectively, our findings showed aerial ammonia exposure appears to regulate myofiber development and lipid metabolism in the skeletal muscle, which results in the negative impacts on meat quality in pigs.
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Affiliation(s)
- Shanlong Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 10093, China; (S.T.); (J.X.); (W.W.); (B.Y.)
| | - Jingjing Xie
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 10093, China; (S.T.); (J.X.); (W.W.); (B.Y.)
| | - Sheng Zhang
- Institute of Biotechnology, Cornell University, Ithaca, NY 14853, USA;
| | - Weida Wu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 10093, China; (S.T.); (J.X.); (W.W.); (B.Y.)
| | - Bao Yi
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 10093, China; (S.T.); (J.X.); (W.W.); (B.Y.)
| | - Hongfu Zhang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 10093, China; (S.T.); (J.X.); (W.W.); (B.Y.)
- Correspondence:
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73
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Glutamine/glutamate metabolism rewiring in reprogrammed human hepatocyte-like cells. Sci Rep 2019; 9:17978. [PMID: 31784643 PMCID: PMC6884617 DOI: 10.1038/s41598-019-54357-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 11/13/2019] [Indexed: 12/19/2022] Open
Abstract
Human dermal fibroblasts can be reprogrammed into hepatocyte-like (HEP-L) cells by the expression of a set of transcription factors. Yet, the metabolic rewiring suffered by reprogrammed fibroblasts remains largely unknown. Here we report, using stable isotope-resolved metabolic analysis in combination with metabolomic-lipidomic approaches that HEP-L cells mirrors glutamine/glutamate metabolism in primary cultured human hepatocytes that is very different from parental human fibroblasts. HEP-L cells diverge glutamine from multiple metabolic pathways into deamidation and glutamate secretion, just like periportal hepatocytes do. Exceptionally, glutamine contribution to lipogenic acetyl-CoA through reductive carboxylation is increased in HEP-L cells, recapitulating that of primary cultured human hepatocytes. These changes can be explained by transcriptomic rearrangements of genes involved in glutamine/glutamate metabolism. Although metabolic changes in HEP-L cells are in line with reprogramming towards the hepatocyte lineage, our conclusions are limited by the fact that HEP-L cells generated do not display a complete mature phenotype. Nevertheless, our findings are the first to characterize metabolic adaptation in HEP-L cells that could ultimately be targeted to improve fibroblasts direct reprogramming to HEP-L cells.
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74
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Argus JP, Wilks MQ, Zhou QD, Hsieh WY, Khialeeva E, Hoi XP, Bui V, Xu S, Yu AK, Wang ES, Herschman HR, Williams KJ, Bensinger SJ. Development and Application of FASA, a Model for Quantifying Fatty Acid Metabolism Using Stable Isotope Labeling. Cell Rep 2019; 25:2919-2934.e8. [PMID: 30517876 PMCID: PMC6432944 DOI: 10.1016/j.celrep.2018.11.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/23/2018] [Accepted: 11/09/2018] [Indexed: 12/20/2022] Open
Abstract
It is well understood that fatty acids can be synthesized, imported, and modified to meet requisite demands in cells. However, following the movement of fatty acids through the multiplicity of these metabolic steps has remained difficult. To better address this problem, we developed Fatty Acid Source Analysis (FASA), a model that defines the contribution of synthesis, import, and elongation pathways to fatty acid homeostasis in saturated, monounsaturated, and polyunsaturated fatty acid pools. Application of FASA demonstrated that elongation can be a major contributor to cellular fatty acid content and showed that distinct pro-inflammatory stimuli (e.g., Toll-like receptors 2, 3, or 4) specifically reprogram homeostasis of fatty acids by differential utilization of synthetic and elongation pathways in macrophages. In sum, this modeling approach significantly advances our ability to interrogate cellular fatty acid metabolism and provides insight into how cells dynamically reshape their lipidomes in response to metabolic or inflammatory signals. Argus et al. developed Fatty Acid Source Analysis (FASA), a model that quantifies cellular fatty acid synthesis, elongation, and import. FASA is used to demonstrate that elongation can be a major contributor to cellular fatty acid content and that different stimuli reprogram macrophage fatty acid elongation pathways in distinct ways.
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Affiliation(s)
- Joseph P Argus
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Moses Q Wilks
- Gordon Center for Medical Imaging, Massachusetts General Hospital, Harvard Medical School, 149, 13(th) Street, Charlestown, MA 02129, USA
| | - Quan D Zhou
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA; Department of Surgical Oncology, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310003, P.R. China
| | - Wei Yuan Hsieh
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Elvira Khialeeva
- Molecular Biology Institute, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Xen Ping Hoi
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Viet Bui
- Division of Rheumatology, David Geffen School of Medicine, University of California, Los Angeles, 1000 Veteran Avenue, Los Angeles, CA 90095, USA
| | - Shili Xu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Amy K Yu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Eric S Wang
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Harvey R Herschman
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA; Molecular Biology Institute, University of California, Los Angeles, 611 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Kevin J Williams
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA
| | - Steven J Bensinger
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, 615 Charles E. Young Drive East, Los Angeles, CA 90095, USA.
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75
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Balcells C, Foguet C, Tarragó-Celada J, de Atauri P, Marin S, Cascante M. Tracing metabolic fluxes using mass spectrometry: Stable isotope-resolved metabolomics in health and disease. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2018.12.025] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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76
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Chen PH, Cai L, Huffman K, Yang C, Kim J, Faubert B, Boroughs L, Ko B, Sudderth J, McMillan EA, Girard L, Chen D, Peyton M, Shields MD, Yao B, Shames DS, Kim HS, Timmons B, Sekine I, Britt R, Weber S, Byers LA, Heymach JV, Chen J, White MA, Minna JD, Xiao G, DeBerardinis RJ. Metabolic Diversity in Human Non-Small Cell Lung Cancer Cells. Mol Cell 2019; 76:838-851.e5. [PMID: 31564558 DOI: 10.1016/j.molcel.2019.08.028] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/17/2019] [Accepted: 08/27/2019] [Indexed: 12/18/2022]
Abstract
Intermediary metabolism in cancer cells is regulated by diverse cell-autonomous processes, including signal transduction and gene expression patterns, arising from specific oncogenotypes and cell lineages. Although it is well established that metabolic reprogramming is a hallmark of cancer, we lack a full view of the diversity of metabolic programs in cancer cells and an unbiased assessment of the associations between metabolic pathway preferences and other cell-autonomous processes. Here, we quantified metabolic features, mostly from the 13C enrichment of molecules from central carbon metabolism, in over 80 non-small cell lung cancer (NSCLC) cell lines cultured under identical conditions. Because these cell lines were extensively annotated for oncogenotype, gene expression, protein expression, and therapeutic sensitivity, the resulting database enables the user to uncover new relationships between metabolism and these orthogonal processes.
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Affiliation(s)
- Pei-Hsuan Chen
- Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Ling Cai
- Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA; Quantitative Biomedical Research Center, Department of Population and Data Sciences at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Kenneth Huffman
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Chendong Yang
- Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Jiyeon Kim
- Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Brandon Faubert
- Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Lindsey Boroughs
- Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Bookyung Ko
- Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Jessica Sudderth
- Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | | | - Luc Girard
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390 USA
| | - Dong Chen
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Michael Peyton
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Misty D Shields
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Bo Yao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - David S Shames
- Department of Oncology Biomarker Development, Genentech Inc., South San Francisco, CA 94080, USA
| | - Hyun Seok Kim
- Department of Cell Biology, UTSW Medical Center, Dallas, TX 75390, USA
| | - Brenda Timmons
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Ikuo Sekine
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Rebecca Britt
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Stephanie Weber
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Lauren A Byers
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - John V Heymach
- Department of Thoracic/Head and Neck Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jing Chen
- Winship Cancer Institute, Emory University, Atlanta, GA 30322, USA
| | - Michael A White
- Department of Cell Biology, UTSW Medical Center, Dallas, TX 75390, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA; Department of Pharmacology, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390 USA; Department of Internal Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA
| | - Ralph J DeBerardinis
- Children's Medical Center Research Institute at UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, TX 75390, USA.
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77
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Long CP, Antoniewicz MR. High-resolution 13C metabolic flux analysis. Nat Protoc 2019; 14:2856-2877. [PMID: 31471597 DOI: 10.1038/s41596-019-0204-0] [Citation(s) in RCA: 113] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 06/03/2019] [Indexed: 02/07/2023]
Abstract
Precise quantification of metabolic pathway fluxes in biological systems is of major importance in guiding efforts in metabolic engineering, biotechnology, microbiology, human health, and cell culture. 13C metabolic flux analysis (13C-MFA) is the predominant technique used for determining intracellular fluxes. Here, we present a protocol for 13C-MFA that incorporates recent advances in parallel labeling experiments, isotopic labeling measurements, and statistical analysis, as well as best practices developed through decades of experience. Experimental design to ensure that fluxes are estimated with the highest precision is an integral part of the protocol. The protocol is based on growing microbes in two (or more) parallel cultures with 13C-labeled glucose tracers, followed by gas chromatography-mass spectrometry (GC-MS) measurements of isotopic labeling of protein-bound amino acids, glycogen-bound glucose, and RNA-bound ribose. Fluxes are then estimated using software for 13C-MFA, such as Metran, followed by comprehensive statistical analysis to determine the goodness of fit and calculate confidence intervals of fluxes. The presented protocol can be completed in 4 d and quantifies metabolic fluxes with a standard deviation of ≤2%, a substantial improvement over previous implementations. The presented protocol is exemplified using an Escherichia coli ΔtpiA case study with full supporting data, providing a hands-on opportunity to step through a complex troubleshooting scenario. Although applications to prokaryotic microbial systems are emphasized, this protocol can be easily adjusted for application to eukaryotic organisms.
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Affiliation(s)
- Christopher P Long
- Metabolic Engineering and Systems Biology Laboratory, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.,Ginkgo Bioworks, Boston, MA, USA
| | - Maciek R Antoniewicz
- Metabolic Engineering and Systems Biology Laboratory, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
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78
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Alptekin A, Ye B, Yu Y, Poole CJ, van Riggelen J, Zha Y, Ding HF. Glycine decarboxylase is a transcriptional target of MYCN required for neuroblastoma cell proliferation and tumorigenicity. Oncogene 2019; 38:7504-7520. [PMID: 31444411 PMCID: PMC6908766 DOI: 10.1038/s41388-019-0967-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 08/05/2019] [Accepted: 08/09/2019] [Indexed: 12/12/2022]
Abstract
Genomic amplification of the oncogene MYCN is a major driver in the development of high-risk neuroblastoma, a pediatric cancer with poor prognosis. Given the challenge in targeting MYCN directly for therapy, we sought to identify MYCN-dependent metabolic vulnerabilities that can be targeted therapeutically. Here, we report that the gene encoding glycine decarboxylase (GLDC), which catalyzes the first and rate-limiting step in glycine breakdown with the production of the one-carbon unit 5,10-methylene-tetrahydrofolate, is a direct transcriptional target of MYCN. As a result, GLDC expression is markedly elevated in MYCN-amplified neuroblastoma tumors and cell lines. This transcriptional upregulation of GLDC expression is of functional significance, as GLDC depletion by RNA interference inhibits the proliferation and tumorigenicity of MYCN-amplified neuroblastoma cell lines by inducing G1 arrest. Metabolomic profiling reveals that GLDC knockdown disrupts purine and central carbon metabolism and reduces citrate production, leading to a decrease in the steady-state levels of cholesterol and fatty acids. Moreover, blocking purine or cholesterol synthesis recapitulates the growth inhibitory effect of GLDC knockdown. These findings reveal a critical role of GLDC in sustaining the proliferation of neuroblastoma cells with high-level GLDC expression and suggest that MYCN amplification is a biomarker for GLDC-based therapeutic strategies against high-risk neuroblastoma.
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Affiliation(s)
- Ahmet Alptekin
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Bingwei Ye
- Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Yajie Yu
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, 443000, Yichang, China
| | - Candace J Poole
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Jan van Riggelen
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Yunhong Zha
- Institute of Neural Regeneration and Repair and Department of Neurology, The First Hospital of Yichang, Three Gorges University College of Medicine, 443000, Yichang, China
| | - Han-Fei Ding
- Department of Biochemistry and Molecular Biology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA. .,Georgia Cancer Center, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA. .,Department of Pathology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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79
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Lagziel S, Lee WD, Shlomi T. Studying metabolic flux adaptations in cancer through integrated experimental-computational approaches. BMC Biol 2019; 17:51. [PMID: 31272436 PMCID: PMC6609376 DOI: 10.1186/s12915-019-0669-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
| | | | - Tomer Shlomi
- Faculty of Computer Science, Technion, Haifa, Israel. .,Faculty of Biology, Technion, Haifa, Israel. .,Lokey Center for Life Science and Engineering, Technion, Haifa, Israel.
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80
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Füssy Z, Faitová T, Oborník M. Subcellular Compartments Interplay for Carbon and Nitrogen Allocation in Chromera velia and Vitrella brassicaformis. Genome Biol Evol 2019; 11:1765-1779. [PMID: 31192348 PMCID: PMC6668581 DOI: 10.1093/gbe/evz123] [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] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Endosymbioses necessitate functional cooperation of cellular compartments to avoid pathway redundancy and streamline the control of biological processes. To gain insight into the metabolic compartmentation in chromerids, phototrophic relatives to apicomplexan parasites, we prepared a reference set of proteins probably localized to mitochondria, cytosol, and the plastid, taking advantage of available genomic and transcriptomic data. Training of prediction algorithms with the reference set now allows a genome-wide analysis of protein localization in Chromera velia and Vitrella brassicaformis. We confirm that the chromerid plastids house enzymatic pathways needed for their maintenance and photosynthetic activity, but for carbon and nitrogen allocation, metabolite exchange is necessary with the cytosol and mitochondria. This indeed suggests that the regulatory mechanisms operate in the cytosol to control carbon metabolism based on the availability of both light and nutrients. We discuss that this arrangement is largely shared with apicomplexans and dinoflagellates, possibly stemming from a common ancestral metabolic architecture, and supports the mixotrophy of the chromerid algae.
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Affiliation(s)
- Zoltán Füssy
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Tereza Faitová
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
- Faculty of Engineering and Natural Sciences, Department of Computer Science, Johannes Kepler University, Linz, Austria
| | - Miroslav Oborník
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
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81
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Jacobson TB, Adamczyk PA, Stevenson DM, Regner M, Ralph J, Reed JL, Amador-Noguez D. 2H and 13C metabolic flux analysis elucidates in vivo thermodynamics of the ED pathway in Zymomonas mobilis. Metab Eng 2019; 54:301-316. [DOI: 10.1016/j.ymben.2019.05.006] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 11/30/2022]
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82
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High extracellular lactate causes reductive carboxylation in breast tissue cell lines grown under normoxic conditions. PLoS One 2019; 14:e0213419. [PMID: 31181081 PMCID: PMC6557470 DOI: 10.1371/journal.pone.0213419] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Accepted: 05/27/2019] [Indexed: 11/19/2022] Open
Abstract
In cancer tumors, lactate accumulation was initially attributed to high glucose consumption associated with the Warburg Effect. Now it is evident that lactate can also serve as an energy source in cancer cell metabolism. Additionally, lactate has been shown to promote metastasis, generate gene expression patterns in cancer cells consistent with "cancer stem cell" phenotypes, and result in treatment resistant tumors. Therefore, the goal of this work was to quantify the impact of lactate on metabolism in three breast cell lines (one normal and two breast cancer cell lines-MCF 10A, MCF7, and MDA-MB-231), in order to better understand the role lactate may have in different disease cell types. Parallel labeling metabolic flux analysis (13C-MFA) was used to quantify the intracellular fluxes under normal and high extracellular lactate culture conditions. Additionally, high extracellular lactate cultures were labelled in parallel with [U-13C] lactate, which provided qualitative information regarding the lactate uptake and metabolism. The 13C-MFA model, which incorporated the measured extracellular fluxes and the parallel labeling mass isotopomer distributions (MIDs) for five glycolysis, four tricarboxylic acid cycle (TCA), and three intracellular amino acid metabolites, predicted lower glycolysis fluxes in the high lactate cultures. All three cell lines experienced reductive carboxylation of glutamine to citrate in the TCA cycle as a result of high extracellular lactate. Reductive carboxylation previously has been observed under hypoxia and other mitochondrial stresses, whereas these cultures were grown aerobically. In addition, this is the first study to investigate the intracellular metabolic responses of different stages of breast cancer progression to high lactate exposure. These results provide insight into the role lactate accumulation has on metabolic reaction distributions in the different disease cell types while the cells are still proliferating in lactate concentrations that do not significantly decrease exponential growth rates.
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83
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Kshattry S, Saha A, Gries P, Tiziani S, Stone E, Georgiou G, DiGiovanni J. Enzyme-mediated depletion of l-cyst(e)ine synergizes with thioredoxin reductase inhibition for suppression of pancreatic tumor growth. NPJ Precis Oncol 2019; 3:16. [PMID: 31231686 PMCID: PMC6546752 DOI: 10.1038/s41698-019-0088-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Accepted: 05/01/2019] [Indexed: 01/05/2023] Open
Abstract
Perturbing redox homeostasis potentially constitutes a selective cancer-killing strategy. An engineered human enzyme, cyst(e)inase that degrades extracellular cysteine (l-Cys) and cystine (CSSC) leading to depletion of intracellular l-Cys and glutathione (GSH) was evaluated for its effects on pancreatic cancer cell lines. Cyst(e)inase caused oxidative stress and apoptosis in only Panc1 cells, whereas MIA-PaCa2 and BxPC3 cells demonstrated survival under conditions of cyst(e)inase-mediated l-Cys depletion through maintenance of mitochondrial metabolism and lower levels of reactive oxygen species (ROS). A correlation was also observed between thioredoxin 1 protein levels and resistance to cyst(e)inase treatment. Notably, cyst(e)inase in combination with auranofin, a thioredoxin reductase inhibitor, caused a synergistic increase in mitochondrial ROS and apoptosis and inhibition of mitophagy in the more resistant cells. In addition, auranofin treatment sensitized the more resistant pancreatic cancer xenografts to cyst(e)inase without systemic toxicity. These data provide strong rationale to further investigate therapeutic strategies that target multiple antioxidant pathways for treatment of pancreatic ductal adenocarcinoma.
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Affiliation(s)
- Sabin Kshattry
- Division of Pharmacology and Toxicology, Dell Pediatric Research Institute, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723 USA
| | - Achinto Saha
- Division of Pharmacology and Toxicology, Dell Pediatric Research Institute, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723 USA
| | - Paul Gries
- Department of Nutritional Sciences, Dell Pediatric Research Institute, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723 USA
| | - Stefano Tiziani
- Department of Nutritional Sciences, Dell Pediatric Research Institute, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723 USA
| | - Everett Stone
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712 USA
| | - George Georgiou
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712 USA
- Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712 USA
| | - John DiGiovanni
- Division of Pharmacology and Toxicology, Dell Pediatric Research Institute, The University of Texas at Austin, 1400 Barbara Jordan Blvd, Austin, TX 78723 USA
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84
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Meal for Two: Human Cytomegalovirus-Induced Activation of Cellular Metabolism. Viruses 2019; 11:v11030273. [PMID: 30893762 PMCID: PMC6466105 DOI: 10.3390/v11030273] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 03/12/2019] [Accepted: 03/13/2019] [Indexed: 12/18/2022] Open
Abstract
Viruses are parasites that depend on the host cell’s metabolic resources to provide the energy and molecular building blocks necessary for the production of viral progeny. It has become increasingly clear that viruses extensively modulate the cellular metabolic network to support productive infection. Here, we review the numerous ways through which human cytomegalovirus (HCMV) modulates cellular metabolism, highlighting known mechanisms of HCMV-mediated metabolic manipulation and identifying key outstanding questions that remain to be addressed.
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85
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Ježek P, Jabůrek M, Porter RK. Uncoupling mechanism and redox regulation of mitochondrial uncoupling protein 1 (UCP1). BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2019; 1860:259-269. [DOI: 10.1016/j.bbabio.2018.11.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Revised: 10/15/2018] [Accepted: 11/07/2018] [Indexed: 01/11/2023]
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86
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Diaz CA, Bennett RK, Papoutsakis ET, Antoniewicz MR. Deletion of four genes in Escherichia coli enables preferential consumption of xylose and secretion of glucose. Metab Eng 2019; 52:168-177. [DOI: 10.1016/j.ymben.2018.12.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Revised: 11/28/2018] [Accepted: 12/06/2018] [Indexed: 12/13/2022]
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87
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Jang C, Chen L, Rabinowitz JD. Metabolomics and Isotope Tracing. Cell 2019; 173:822-837. [PMID: 29727671 DOI: 10.1016/j.cell.2018.03.055] [Citation(s) in RCA: 467] [Impact Index Per Article: 93.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 02/21/2018] [Accepted: 03/21/2018] [Indexed: 12/15/2022]
Abstract
Great strides have been made over the past decade toward comprehensive study of metabolism. Mass spectrometry (MS) has played a central role by enabling measurement of many metabolites simultaneously. Tracking metabolite labeling from stable isotope tracers can in addition reveal pathway activities. Here, we describe the basics of metabolite measurement by MS, including sample preparation, metabolomic analysis, and data interpretation. In addition, drawing on examples of successful experiments, we highlight the ways in which metabolomics and isotope tracing can illuminate biology.
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Affiliation(s)
- Cholsoon Jang
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544, USA
| | - Li Chen
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544, USA
| | - Joshua D Rabinowitz
- Lewis Sigler Institute for Integrative Genomics and Department of Chemistry, Princeton University, Washington Rd, Princeton, NJ 08544, USA.
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88
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Wang H, Lu J, Kulkarni S, Zhang W, Gorka JE, Mandel JA, Goetzman ES, Prochownik EV. Metabolic and oncogenic adaptations to pyruvate dehydrogenase inactivation in fibroblasts. J Biol Chem 2019; 294:5466-5486. [PMID: 30755479 DOI: 10.1074/jbc.ra118.005200] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 02/05/2019] [Indexed: 01/15/2023] Open
Abstract
Eukaryotic cell metabolism consists of processes that generate available energy, such as glycolysis, the tricarboxylic acid (TCA) cycle, and oxidative phosphorylation (Oxphos), and those that consume it, including macromolecular synthesis, the maintenance of ionic gradients, and cellular detoxification. By converting pyruvate to acetyl-CoA (AcCoA), the pyruvate dehydrogenase (PDH) complex (PDC) links glycolysis and the TCA cycle. Surprisingly, disrupting the connection between glycolysis and the TCA cycle by inactivation of PDC has only minor effects on cell replication. However, the molecular basis for this metabolic re-equilibration is unclear. We report here that CRISPR/Cas9-generated PDH-knockout (PDH-KO) rat fibroblasts reprogrammed their metabolism and their response to short-term c-Myc (Myc) oncoprotein overexpression. PDH-KO cells replicated normally but produced surprisingly little lactate. They also exhibited higher rates of glycolysis and Oxphos. In addition, PDH-KO cells showed altered cytoplasmic and mitochondrial pH, redox states, and mitochondrial membrane potential (ΔΨM). Conditionally activated Myc expression affected some of these parameters in a PDH-dependent manner. PDH-KO cells had increased oxygen consumption rates in response to glutamate, but not to malate, and were depleted in all TCA cycle substrates between α-ketoglutarate and malate despite high rates of glutaminolysis, as determined by flux studies with isotopically labeled glutamine. Malate and pyruvate were diverted to produce aspartate, thereby potentially explaining the failure to accumulate lactate. We conclude that PDH-KO cells maintain proliferative capacity by utilizing glutamine to supply high rates of AcCoA-independent flux through the bottom portion of the TCA cycle while accumulating pyruvate and aspartate that rescue their redox defects.
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Affiliation(s)
- Huabo Wang
- From the Section of Hematology/Oncology and
| | - Jie Lu
- From the Section of Hematology/Oncology and
| | | | | | | | | | - Eric S Goetzman
- Division of Medical Genetics, Children's Hospital of Pittsburgh of UPMC, Pittsburgh, Pennsylvania 15224
| | - Edward V Prochownik
- From the Section of Hematology/Oncology and .,the Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania 15219, and.,the The Hillman Cancer Center of UPMC, Pittsburgh, Pennsylvania 15232
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89
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Choi J, Antoniewicz MR. Tandem Mass Spectrometry for 13C Metabolic Flux Analysis: Methods and Algorithms Based on EMU Framework. Front Microbiol 2019; 10:31. [PMID: 30733712 PMCID: PMC6353858 DOI: 10.3389/fmicb.2019.00031] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 01/09/2019] [Indexed: 02/01/2023] Open
Abstract
In the past two decades, 13C metabolic flux analysis (13C-MFA) has matured into a powerful and widely used scientific tool in metabolic engineering and systems biology. Traditionally, metabolic fluxes have been determined from measurements of isotopic labeling by means of mass spectrometry (MS) or nuclear magnetic resonance (NMR). In recent years, tandem MS has emerged as a new analytical technique that can provide additional information for high-resolution quantification of metabolic fluxes in complex biological systems. In this paper, we present recent advances in methods and algorithms for incorporating tandem MS measurements into existing 13C-MFA approaches that are based on the elementary metabolite units (EMU) framework. Specifically, efficient EMU-based algorithms are presented for simulating tandem MS data, tracing isotopic labeling in biochemical network models and for correcting tandem MS data for natural isotope abundances.
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Affiliation(s)
- Jungik Choi
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, United States
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, United States
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90
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Hollinshead W, He L, Tang YJ. 13C-Fingerprinting and Metabolic Flux Analysis of Bacterial Metabolisms. Methods Mol Biol 2019; 1927:215-230. [PMID: 30788795 DOI: 10.1007/978-1-4939-9142-6_15] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
13C-assisted metabolism analysis provides rigorous calculations of the intracellular reaction rates (i.e., fluxes) within the central metabolism of microbial hosts. This mapping of the intracellular network within microbes has proven to be essential for understanding the cell physiology. The approach is also a key to identifying central metabolic nodes, probing the rigidity of a metabolic network, revealing cofactor balances, and delineating hidden pathways. Here we present the methodology of using stable isotopic carbon substrates for both qualitative (13C-fingerprinting of functional pathways) and quantitative (Metabolic Flux Analysis) metabolism studies on bacterial species. In this methodology, we include step-by-step instructions to use the open source WUflux software for the steady-state flux calculations based on labeling information of amino acids or free metabolites.
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Affiliation(s)
- Whitney Hollinshead
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA
| | - Lian He
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA
| | - Yinjie J Tang
- Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA.
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91
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Schwechheimer SK, Becker J, Wittmann C. Towards better understanding of industrial cell factories: novel approaches for 13C metabolic flux analysis in complex nutrient environments. Curr Opin Biotechnol 2018; 54:128-137. [DOI: 10.1016/j.copbio.2018.07.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/10/2018] [Accepted: 07/12/2018] [Indexed: 12/13/2022]
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92
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Ahn WS, Dong W, Zhang Z, Cantor JR, Sabatini DM, Iliopoulos O, Stephanopoulos G. Glyceraldehyde 3-phosphate dehydrogenase modulates nonoxidative pentose phosphate pathway to provide anabolic precursors in hypoxic tumor cells. AIChE J 2018. [DOI: 10.1002/aic.16423] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Woo S. Ahn
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
| | - Wentao Dong
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
| | - Zhe Zhang
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
| | - Jason R. Cantor
- Dept. of Biology; Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology; Cambridge MA 02142
- Dept. of Biology; Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge MA 02139
- Koch Institute for Integrative Cancer Research; Cambridge MA 02139
- Broad Institute of Harvard and Massachusetts Institute of Technology; Cambridge MA 02142
| | - David M. Sabatini
- Dept. of Biology; Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology; Cambridge MA 02142
- Dept. of Biology; Howard Hughes Medical Institute, Massachusetts Institute of Technology; Cambridge MA 02139
- Koch Institute for Integrative Cancer Research; Cambridge MA 02139
- Broad Institute of Harvard and Massachusetts Institute of Technology; Cambridge MA 02142
| | - Othon Iliopoulos
- Center for Cancer Research; Massachusetts General Hospital Cancer Center; Boston MA 02114
- Dept. of Medicine; Harvard Medical School; Boston MA 02115
- Division of Hematology-Oncology, Dept. of Medicine; Massachusetts General Hospital; Boston MA 02114
| | - Gregory Stephanopoulos
- Dept. of Chemical Engineering; Massachusetts Institute of Technology; Cambridge MA 02139
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93
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McBrayer SK, Mayers JR, DiNatale GJ, Shi DD, Khanal J, Chakraborty AA, Sarosiek KA, Briggs KJ, Robbins AK, Sewastianik T, Shareef SJ, Olenchock BA, Parker SJ, Tateishi K, Spinelli JB, Islam M, Haigis MC, Looper RE, Ligon KL, Bernstein BE, Carrasco RD, Cahill DP, Asara JM, Metallo CM, Yennawar NH, Vander Heiden MG, Kaelin WG. Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma. Cell 2018; 175:101-116.e25. [PMID: 30220459 DOI: 10.1016/j.cell.2018.08.038] [Citation(s) in RCA: 210] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 06/22/2018] [Accepted: 08/17/2018] [Indexed: 12/31/2022]
Abstract
IDH1 mutations are common in low-grade gliomas and secondary glioblastomas and cause overproduction of (R)-2HG. (R)-2HG modulates the activity of many enzymes, including some that are linked to transformation and some that are probably bystanders. Although prior work on (R)-2HG targets focused on 2OG-dependent dioxygenases, we found that (R)-2HG potently inhibits the 2OG-dependent transaminases BCAT1 and BCAT2, likely as a bystander effect, thereby decreasing glutamate levels and increasing dependence on glutaminase for the biosynthesis of glutamate and one of its products, glutathione. Inhibiting glutaminase specifically sensitized IDH mutant glioma cells to oxidative stress in vitro and to radiation in vitro and in vivo. These findings highlight the complementary roles for BCATs and glutaminase in glutamate biosynthesis, explain the sensitivity of IDH mutant cells to glutaminase inhibitors, and suggest a strategy for maximizing the effectiveness of such inhibitors against IDH mutant gliomas.
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Affiliation(s)
- Samuel K McBrayer
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Jared R Mayers
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Gabriel J DiNatale
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Diana D Shi
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Januka Khanal
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Abhishek A Chakraborty
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Kristopher A Sarosiek
- John B. Little Center for Radiation Sciences, Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Kimberly J Briggs
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Alissa K Robbins
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Tomasz Sewastianik
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Experimental Hematology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Sarah J Shareef
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Benjamin A Olenchock
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Seth J Parker
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Kensuke Tateishi
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Neurosurgery, Yokohama City University, Yokohama, Kanagawa 2360004, Japan
| | - Jessica B Spinelli
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Mirazul Islam
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Marcia C Haigis
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ryan E Looper
- Department of Chemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Keith L Ligon
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA; Department of Pathology, Harvard Medical School, Boston, MA 02115, USA; Department of Pathology, Children's Hospital Boston, Boston, MA 02115, USA
| | - Bradley E Bernstein
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ruben D Carrasco
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Daniel P Cahill
- Department of Neurosurgery, Translational Neuro-Oncology Laboratory, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - John M Asara
- Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Cancer Center, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Neela H Yennawar
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew G Vander Heiden
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - William G Kaelin
- Department of Medical Oncology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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94
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A guide to 13C metabolic flux analysis for the cancer biologist. Exp Mol Med 2018; 50:1-13. [PMID: 29657327 PMCID: PMC5938039 DOI: 10.1038/s12276-018-0060-y] [Citation(s) in RCA: 162] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 12/21/2017] [Indexed: 01/15/2023] Open
Abstract
Cancer metabolism is significantly altered from normal cellular metabolism allowing cancer cells to adapt to changing microenvironments and maintain high rates of proliferation. In the past decade, stable-isotope tracing and network analysis have become powerful tools for uncovering metabolic pathways that are differentially activated in cancer cells. In particular, 13C metabolic flux analysis (13C-MFA) has emerged as the primary technique for quantifying intracellular fluxes in cancer cells. In this review, we provide a practical guide for investigators interested in getting started with 13C-MFA. We describe best practices in 13C-MFA, highlight potential pitfalls and alternative approaches, and conclude with new developments that can further enhance our understanding of cancer metabolism. Tracing tagged molecules can help researchers understand the altered metabolism of cancer cells. The abilities of cancer cells to multiply rapidly and invade new tissues are supported by metabolic alterations, which can be investigated by feeding tagged molecules to cells and tracing how they are metabolized. These techniques, such as 13C metabolic flux analysis (13C-MFA), have been perceived as difficult to use, but recent advances are making them more accessible. Maciek Antoniewicz, University of Delaware, Newark, USA, has published a practical guide for researchers wanting to use 13C-MFA. The review includes best practices, pitfalls, alternative approaches, and new developments, especially new user-friendly software that allows researchers without extensive training in mathematics, statistics, or coding to perform 13C-MFA. Broadening access to tools for investigating altered metabolic pathways may spur development of new cancer therapies targeting these pathways.
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95
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Fujisawa K, Takami T, Okada S, Hara K, Matsumoto T, Yamamoto N, Yamasaki T, Sakaida I. Analysis of Metabolomic Changes in Mesenchymal Stem Cells on Treatment with Desferrioxamine as a Hypoxia Mimetic Compared with Hypoxic Conditions. Stem Cells 2018; 36:1226-1236. [PMID: 29577517 DOI: 10.1002/stem.2826] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Revised: 02/06/2018] [Accepted: 02/18/2018] [Indexed: 01/08/2023]
Abstract
Mesenchymal stem cells (MSCs) are commonly used in regenerative medicine, but their therapeutic effects vary depending on the culture environment. Hypoxic culturing can be used to maintain stem cells in an undifferentiated state, but is expensive and difficult to perform. The aim of this study was to determine the effectiveness of desferrioxamine (DFO), a hypoxia-mimetic reagent, as an alternative to hypoxic culturing by analyzing metabolic changes in MSCs under hypoxic conditions compared with changes induced by DFO. Low concentrations of DFO reduced mitochondrial activity and apoptosis. Therefore, low concentrations of DFO may be useful for MSC preconditioning. Metabolome analysis showed that both hypoxic treatment and DFO administration exhibited similar metabolite patterns except purine, pyrimidine, and tricarboxylic acid cycle (TCA) cycle related metabolites. Therefore, the use of DFO at low concentrations is a potential substitute for hypoxic culturing. These findings may form the foundation for the development of future regenerative therapies using MSCs. Stem Cells 2018;36:1226-1236.
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Affiliation(s)
- Koichi Fujisawa
- Center for Regenerative Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan.,Department of Gastroenterology and Hepatology, Ube, Yamaguchi, Japan
| | - Taro Takami
- Department of Gastroenterology and Hepatology, Ube, Yamaguchi, Japan
| | - Sae Okada
- Department of Gastroenterology and Hepatology, Ube, Yamaguchi, Japan
| | - Kazusa Hara
- Department of Gastroenterology and Hepatology, Ube, Yamaguchi, Japan.,Faculty of Health Science, Department of Laboratory Science, Ube, Yamaguchi, Japan
| | | | - Naoki Yamamoto
- Department of Gastroenterology and Hepatology, Ube, Yamaguchi, Japan
| | - Takahiro Yamasaki
- Department of Oncology and Laboratory Medicine, Yamaguchi University Graduate School of Medicine, Ube, Yamaguchi, Japan
| | - Isao Sakaida
- Center for Regenerative Medicine, Yamaguchi University School of Medicine, Ube, Yamaguchi, Japan.,Department of Gastroenterology and Hepatology, Ube, Yamaguchi, Japan
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96
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Rosato A, Tenori L, Cascante M, De Atauri Carulla PR, Martins Dos Santos VAP, Saccenti E. From correlation to causation: analysis of metabolomics data using systems biology approaches. Metabolomics 2018; 14:37. [PMID: 29503602 PMCID: PMC5829120 DOI: 10.1007/s11306-018-1335-y] [Citation(s) in RCA: 122] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 01/31/2018] [Indexed: 12/26/2022]
Abstract
INTRODUCTION Metabolomics is a well-established tool in systems biology, especially in the top-down approach. Metabolomics experiments often results in discovery studies that provide intriguing biological hypotheses but rarely offer mechanistic explanation of such findings. In this light, the interpretation of metabolomics data can be boosted by deploying systems biology approaches. OBJECTIVES This review aims to provide an overview of systems biology approaches that are relevant to metabolomics and to discuss some successful applications of these methods. METHODS We review the most recent applications of systems biology tools in the field of metabolomics, such as network inference and analysis, metabolic modelling and pathways analysis. RESULTS We offer an ample overview of systems biology tools that can be applied to address metabolomics problems. The characteristics and application results of these tools are discussed also in a comparative manner. CONCLUSIONS Systems biology-enhanced analysis of metabolomics data can provide insights into the molecular mechanisms originating the observed metabolic profiles and enhance the scientific impact of metabolomics studies.
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Affiliation(s)
- Antonio Rosato
- Magnetic Resonance Center and Department of Chemistry "Ugo Schiff", University of Florence, Florence, Italy.
| | - Leonardo Tenori
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
| | - Marta Cascante
- CIBER de Enfermedades hepáticas y digestivas (CIBERHD, Madrid) and Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Pedro Ramon De Atauri Carulla
- CIBER de Enfermedades hepáticas y digestivas (CIBERHD, Madrid) and Department of Biochemistry and Molecular Biomedicine, Universitat de Barcelona, Barcelona, Spain
| | - Vitor A P Martins Dos Santos
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands
- LifeGlimmer GmbH, Berlin, Germany
| | - Edoardo Saccenti
- Laboratory of Systems and Synthetic Biology, Wageningen University & Research, Wageningen, The Netherlands.
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97
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Hexokinase-2 depletion inhibits glycolysis and induces oxidative phosphorylation in hepatocellular carcinoma and sensitizes to metformin. Nat Commun 2018; 9:446. [PMID: 29386513 PMCID: PMC5792493 DOI: 10.1038/s41467-017-02733-4] [Citation(s) in RCA: 286] [Impact Index Per Article: 47.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/20/2017] [Indexed: 12/27/2022] Open
Abstract
Hepatocellular carcinoma (HCC) cells are metabolically distinct from normal hepatocytes by expressing the high-affinity hexokinase (HK2) and suppressing glucokinase (GCK). This is exploited to selectively target HCC. Hepatic HK2 deletion inhibits tumor incidence in a mouse model of hepatocarcinogenesis. Silencing HK2 in human HCC cells inhibits tumorigenesis and increases cell death, which cannot be restored by GCK or mitochondrial binding deficient HK2. Upon HK2 silencing, glucose flux to pyruvate and lactate is inhibited, but TCA fluxes are maintained. Serine uptake and glycine secretion are elevated suggesting increased requirement for one-carbon contribution. Consistently, vulnerability to serine depletion increases. The decrease in glycolysis is coupled to elevated oxidative phosphorylation, which is diminished by metformin, further increasing cell death and inhibiting tumor growth. Neither HK2 silencing nor metformin alone inhibits mTORC1, but their combination inhibits mTORC1 in an AMPK-independent and REDD1-dependent mechanism. Finally, HK2 silencing synergizes with sorafenib to inhibit tumor growth. Hexokinase 2 (HK2) is selectively upregulated in hepatocellular carcinoma (HCC). Here the authors show that HK2 ablation decreases glycolysis and triggers oxidative phosphorylation (OXPHO) rendering HCC more susceptible to the OXPHO inhibitor metformin and to the FDA-approved drug sorafenib.
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98
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Badur MG, Metallo CM. Reverse engineering the cancer metabolic network using flux analysis to understand drivers of human disease. Metab Eng 2018; 45:95-108. [PMID: 29199104 PMCID: PMC5927620 DOI: 10.1016/j.ymben.2017.11.013] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 10/11/2017] [Accepted: 11/29/2017] [Indexed: 12/16/2022]
Abstract
Metabolic dysfunction has reemerged as an essential hallmark of tumorigenesis, and metabolic phenotypes are increasingly being integrated into pre-clinical models of disease. The complexity of these metabolic networks requires systems-level interrogation, and metabolic flux analysis (MFA) with stable isotope tracing present a suitable conceptual framework for such systems. Here we review efforts to elucidate mechanisms through which metabolism influences tumor growth and survival, with an emphasis on applications using stable isotope tracing and MFA. Through these approaches researchers can now quantify pathway fluxes in various in vitro and in vivo contexts to provide mechanistic insights at molecular and physiological scales respectively. Knowledge and discoveries in cancer models are paving the way toward applications in other biological contexts and disease models. In turn, MFA approaches will increasingly help to uncover new therapeutic opportunities that enhance human health.
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Affiliation(s)
- Mehmet G Badur
- Department of Bioengineering, University of California, San Diego, La Jolla, USA
| | - Christian M Metallo
- Department of Bioengineering, University of California, San Diego, La Jolla, USA; Moores Cancer Center, University of California, San Diego, La Jolla, USA; Diabetes and Endocrinology Research Center, University of California, San Diego, La Jolla, USA; Institute of Engineering in Medicine, University of California, San Diego, La Jolla, USA.
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99
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Goetzman ES, Prochownik EV. The Role for Myc in Coordinating Glycolysis, Oxidative Phosphorylation, Glutaminolysis, and Fatty Acid Metabolism in Normal and Neoplastic Tissues. Front Endocrinol (Lausanne) 2018; 9:129. [PMID: 29706933 PMCID: PMC5907532 DOI: 10.3389/fendo.2018.00129] [Citation(s) in RCA: 124] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Accepted: 03/13/2018] [Indexed: 12/24/2022] Open
Abstract
That cancer cells show patterns of metabolism different from normal cells has been known for over 50 years. Yet, it is only in the past decade or so that an appreciation of the benefits of these changes has begun to emerge. Altered cancer cell metabolism was initially attributed to defective mitochondria. However, we now realize that most cancers do not have mitochondrial mutations and that normal cells can transiently adopt cancer-like metabolism during periods of rapid proliferation. Indeed, an encompassing, albeit somewhat simplified, conceptual framework to explain both normal and cancer cell metabolism rests on several simple premises. First, the metabolic pathways used by cancer cells and their normal counterparts are the same. Second, normal quiescent cells use their metabolic pathways and the energy they generate largely to maintain cellular health and organelle turnover and, in some cases, to provide secreted products necessary for the survival of the intact organism. By contrast, undifferentiated cancer cells minimize the latter functions and devote their energy to producing the anabolic substrates necessary to maintain high rates of unremitting cellular proliferation. Third, as a result of the uncontrolled proliferation of cancer cells, a larger fraction of the metabolic intermediates normally used by quiescent cells purely as a source of energy are instead channeled into competing proliferation-focused and energy-consuming anabolic pathways. Fourth, cancer cell clones with the most plastic and rapidly adaptable metabolism will eventually outcompete their less well-adapted brethren during tumor progression and evolution. This attribute becomes increasingly important as tumors grow and as their individual cells compete in a constantly changing and inimical environment marked by nutrient, oxygen, and growth factor deficits. Here, we review some of the metabolic pathways whose importance has gained center stage for tumor growth, particularly those under the control of the c-Myc (Myc) oncoprotein. We discuss how these pathways differ functionally between quiescent and proliferating normal cells, how they are kidnapped and corrupted during the course of transformation, and consider potential therapeutic strategies that take advantage of common features of neoplastic and metabolic disorders.
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Affiliation(s)
- Eric S. Goetzman
- Division of Medical Genetics, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, United States
| | - Edward V. Prochownik
- Division of Hematology/Oncology, Children’s Hospital of Pittsburgh of UPMC, Pittsburgh, PA, United States
- Department of Microbiology and Molecular Genetics, University of Pittsburgh Medical Center, Pittsburgh, PA, United States
- University of Pittsburgh Hillman Cancer Center, Pittsburgh, PA, United States
- *Correspondence: Edward V. Prochownik,
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100
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Bennett RK, Gonzalez JE, Whitaker WB, Antoniewicz MR, Papoutsakis ET. Expression of heterologous non-oxidative pentose phosphate pathway from Bacillus methanolicus and phosphoglucose isomerase deletion improves methanol assimilation and metabolite production by a synthetic Escherichia coli methylotroph. Metab Eng 2017; 45:75-85. [PMID: 29203223 DOI: 10.1016/j.ymben.2017.11.016] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/02/2017] [Accepted: 11/29/2017] [Indexed: 11/30/2022]
Abstract
Synthetic methylotrophy aims to develop non-native methylotrophic microorganisms to utilize methane or methanol to produce chemicals and biofuels. We report two complimentary strategies to further engineer a previously engineered methylotrophic E. coli strain for improved methanol utilization. First, we demonstrate improved methanol assimilation in the presence of small amounts of yeast extract by expressing the non-oxidative pentose phosphate pathway (PPP) from Bacillus methanolicus. Second, we demonstrate improved co-utilization of methanol and glucose by deleting the phosphoglucose isomerase gene (pgi), which rerouted glucose carbon flux through the oxidative PPP. Both strategies led to significant improvements in methanol assimilation as determined by 13C-labeling in intracellular metabolites. Introduction of an acetone-formation pathway in the pgi-deficient methylotrophic E. coli strain led to improved methanol utilization and acetone titers during glucose fed-batch fermentation.
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Affiliation(s)
- R Kyle Bennett
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA; The Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
| | - Jacqueline E Gonzalez
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA.
| | - W Brian Whitaker
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA; The Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA.
| | - Eleftherios T Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, 150 Academy St., Newark, DE 19716, USA; The Delaware Biotechnology Institute, Molecular Biotechnology Laboratory, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA.
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