1
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Kang S, Antoniewicz MR, Hay N. Metabolic and transcriptomic reprogramming during contact inhibition-induced quiescence is mediated by YAP-dependent and YAP-independent mechanisms. Nat Commun 2024; 15:6777. [PMID: 39117624 PMCID: PMC11310444 DOI: 10.1038/s41467-024-51117-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 07/25/2024] [Indexed: 08/10/2024] Open
Abstract
Metabolic rewiring during the proliferation-to-quiescence transition is poorly understood. Here, using a model of contact inhibition-induced quiescence, we conducted 13C-metabolic flux analysis in proliferating (P) and quiescent (Q) mouse embryonic fibroblasts (MEFs) to investigate this process. Q cells exhibit reduced glycolysis but increased TCA cycle flux and mitochondrial respiration. Reduced glycolytic flux in Q cells correlates with reduced glycolytic enzyme expression mediated by yes-associated protein (YAP) inhibition. The increased TCA cycle activity and respiration in Q cells is mediated by induced mitochondrial pyruvate carrier (MPC) expression, rendering them vulnerable to MPC inhibition. The malate-to-pyruvate flux, which generates NADPH, is markedly reduced by modulating malic enzyme 1 (ME1) dimerization in Q cells. Conversely, the malate dehydrogenase 1 (MDH1)-mediated oxaloacetate-to-malate flux is reversed and elevated in Q cells, driven by high mitochondrial-derived malate levels, reduced cytosolic oxaloacetate, elevated MDH1 levels, and a high cytoplasmic NAD+/NADH ratio. Transcriptomic analysis revealed large number of genes are induced in Q cells, many of which are associated with the extracellular matrix (ECM), while YAP-dependent and cell cycle-related genes are repressed. The results suggest that high TCA cycle flux and respiration in Q cells are required to generate ATP and amino acids to maintain de-novo ECM protein synthesis and secretion.
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Affiliation(s)
- Soeun Kang
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Nissim Hay
- Department of Biochemistry and Molecular Genetics, College of Medicine, University of Illinois at Chicago, Chicago, IL, USA.
- Research and Development Section, Jesse Brown VA Medical Center, Chicago, IL, USA.
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2
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Wu T, Norouzi M, Park K. Dialysis rolled scaffold bioreactor allows extended production of monoclonal antibody with reduced media use. Biotechnol J 2024; 19:e2400249. [PMID: 39212207 DOI: 10.1002/biot.202400249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 07/28/2024] [Accepted: 07/30/2024] [Indexed: 09/04/2024]
Abstract
Rapidly expanding biopharmaceutical market demands more cost-effective platforms to produce protein therapeutics. To this end, novel approaches, such as perfusion culture or concentrated fed-batch, have been explored for higher yields and lower manufacturing costs. Although these new approaches produced promising results, but their wide-spread use in the industry is still limited. In this study, a dialysis rolled scaffold bioreactor was presented for long-term production of monoclonal antibodies with reduced media consumption. Media dialysis can selectively remove cellular bio-wastes without losing cells or produced recombinant proteins. The dialysis process was streamlined to significantly improve its efficiency. Then, extended culture of recombinant CHO cells for 41 days was successfully demonstrated with consistent production rate and minimal media consumption. The unique configuration of the developed bioreactor allows efficient dialysis for media management, as well as rapid media exchange to harvest produced recombinant proteins before they degrade. Taken together, it was envisioned that the developed bioreactor will enable cost-effective and long-term large-scale culture of various cells for biopharmaceutical production.
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Affiliation(s)
- Tongyao Wu
- Division of Electrical Computer Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Mohsen Norouzi
- Division of Electrical Computer Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Kidong Park
- Division of Electrical Computer Engineering, Louisiana State University, Baton Rouge, Louisiana, USA
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3
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Wang K, Xie W, Harcum SW. Metabolic regulatory network kinetic modeling with multiple isotopic tracers for iPSCs. Biotechnol Bioeng 2024; 121:1336-1354. [PMID: 38037741 DOI: 10.1002/bit.28609] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/26/2023] [Accepted: 11/15/2023] [Indexed: 12/02/2023]
Abstract
The rapidly expanding market for regenerative medicines and cell therapies highlights the need to advance the understanding of cellular metabolisms and improve the prediction of cultivation production process for human induced pluripotent stem cells (iPSCs). In this paper, a metabolic kinetic model was developed to characterize the underlying mechanisms of iPSC culture process, which can predict cell response to environmental perturbation and support process control. This model focuses on the central carbon metabolic network, including glycolysis, pentose phosphate pathway, tricarboxylic acid cycle, and amino acid metabolism, which plays a crucial role to support iPSC proliferation. Heterogeneous measures of extracellular metabolites and multiple isotopic tracers collected under multiple conditions were used to learn metabolic regulatory mechanisms. Systematic cross-validation confirmed the model's performance in terms of providing reliable predictions on cellular metabolism and culture process dynamics under various culture conditions. Thus, the developed mechanistic kinetic model can support process control strategies to strategically select optimal cell culture conditions at different times, ensure cell product functionality, and facilitate large-scale manufacturing of regenerative medicines and cell therapies.
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Affiliation(s)
- Keqi Wang
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts, USA
| | - Wei Xie
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts, USA
| | - Sarah W Harcum
- Department of Bioengineering, Clemson University, Clemson, South Carolina, USA
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4
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Reddy JV, Raudenbush K, Papoutsakis ET, Ierapetritou M. Cell-culture process optimization via model-based predictions of metabolism and protein glycosylation. Biotechnol Adv 2023; 67:108179. [PMID: 37257729 DOI: 10.1016/j.biotechadv.2023.108179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/18/2023] [Accepted: 05/21/2023] [Indexed: 06/02/2023]
Abstract
In order to meet the rising demand for biologics and become competitive on the developing biosimilar market, there is a need for process intensification of biomanufacturing processes. Process development of biologics has historically relied on extensive experimentation to develop and optimize biopharmaceutical manufacturing. Experimentation to optimize media formulations, feeding schedules, bioreactor operations and bioreactor scale up is expensive, labor intensive and time consuming. Mathematical modeling frameworks have the potential to enable process intensification while reducing the experimental burden. This review focuses on mathematical modeling of cellular metabolism and N-linked glycosylation as applied to upstream manufacturing of biologics. We review developments in the field of modeling cellular metabolism of mammalian cells using kinetic and stoichiometric modeling frameworks along with their applications to simulate, optimize and improve mechanistic understanding of the process. Interest in modeling N-linked glycosylation has led to the creation of various types of parametric and non-parametric models. Most published studies on mammalian cell metabolism have performed experiments in shake flasks where the pH and dissolved oxygen cannot be controlled. Efforts to understand and model the effect of bioreactor-specific parameters such as pH, dissolved oxygen, temperature, and bioreactor heterogeneity are critically reviewed. Most modeling efforts have focused on the Chinese Hamster Ovary (CHO) cells, which are most commonly used to produce monoclonal antibodies (mAbs). However, these modeling approaches can be generalized and applied to any mammalian cell-based manufacturing platform. Current and potential future applications of these models for Vero cell-based vaccine manufacturing, CAR-T cell therapies, and viral vector manufacturing are also discussed. We offer specific recommendations for improving the applicability of these models to industrially relevant processes.
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Affiliation(s)
- Jayanth Venkatarama Reddy
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716-3196, USA
| | - Katherine Raudenbush
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716-3196, USA
| | - Eleftherios Terry Papoutsakis
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716-3196, USA; Delaware Biotechnology Institute, Department of Biological Sciences, University of Delaware, USA.
| | - Marianthi Ierapetritou
- Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE 19716-3196, USA.
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5
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Ladiwala P, Dhara VG, Jenkins J, Kuang B, Hoang D, Yoon S, Betenbaugh MJ. Addressing amino acid-derived inhibitory metabolites and enhancing CHO cell culture performance through DOE-guided media modifications. Biotechnol Bioeng 2023; 120:2542-2558. [PMID: 37096798 DOI: 10.1002/bit.28403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 04/26/2023]
Abstract
Previously, we identified six inhibitory metabolites (IMs) accumulating in Chinese hamster ovary (CHO) cultures using AMBIC 1.0 community reference medium that negatively impacted culture performance. The goal of the current study was to modify the medium to control IM accumulation through design of experiments (DOE). Initial over-supplementation of precursor amino acids (AAs) by 100% to 200% in the culture medium revealed positive correlations between initial AA concentrations and IM levels. A screening design identified 5 AA targets, Lys, Ile, Trp, Leu, Arg, as key contributors to IMs. Response surface design analysis was used to reduce initial AA levels between 13% and 33%, and these were then evaluated in batch and fed-batch cultures. Lowering AAs in basal and feed medium and reducing feed rate from 10% to 5% reduced inhibitory metabolites HICA and NAP by up to 50%, MSA by 30%, and CMP by 15%. These reductions were accompanied by a 13% to 40% improvement in peak viable cell densities and 7% to 50% enhancement in IgG production in batch and fed-batch processes, respectively. This study demonstrates the value of tuning specific AA levels in reference basal and feed media using statistical design methodologies to lower problematic IMs.
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Affiliation(s)
- Pranay Ladiwala
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Venkata Gayatri Dhara
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jackson Jenkins
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bingyu Kuang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Duc Hoang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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6
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Jiménez del Val I, Kyriakopoulos S, Albrecht S, Stockmann H, Rudd PM, Polizzi KM, Kontoravdi C. CHOmpact: A reduced metabolic model of Chinese hamster ovary cells with enhanced interpretability. Biotechnol Bioeng 2023; 120:2479-2493. [PMID: 37272445 PMCID: PMC10952303 DOI: 10.1002/bit.28459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 05/19/2023] [Accepted: 05/22/2023] [Indexed: 06/06/2023]
Abstract
Metabolic modeling has emerged as a key tool for the characterization of biopharmaceutical cell culture processes. Metabolic models have also been instrumental in identifying genetic engineering targets and developing feeding strategies that optimize the growth and productivity of Chinese hamster ovary (CHO) cells. Despite their success, metabolic models of CHO cells still present considerable challenges. Genome-scale metabolic models (GeMs) of CHO cells are very large (>6000 reactions) and are difficult to constrain to yield physiologically consistent flux distributions. The large scale of GeMs also makes the interpretation of their outputs difficult. To address these challenges, we have developed CHOmpact, a reduced metabolic network that encompasses 101 metabolites linked through 144 reactions. Our compact reaction network allows us to deploy robust, nonlinear optimization and ensure that the computed flux distributions are physiologically consistent. Furthermore, our CHOmpact model delivers enhanced interpretability of simulation results and has allowed us to identify the mechanisms governing shifts in the anaplerotic consumption of asparagine and glutamate as well as an important mechanism of ammonia detoxification within mitochondria. CHOmpact, thus, addresses key challenges of large-scale metabolic models and will serve as a platform to develop dynamic metabolic models for the control and optimization of biopharmaceutical cell culture processes.
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Affiliation(s)
| | - Sarantos Kyriakopoulos
- Manufacturing Science and TechnologyBioMarin PharmaceuticalCorkIrelandIreland
- Present address:
Drug Product DevelopmentJanssen PharmaceuticalsSchaffhausenSwitzerland
| | - Simone Albrecht
- GlycoScience GroupNational Institute for Bioprocessing Research and TrainingDublinIreland
| | - Henning Stockmann
- GlycoScience GroupNational Institute for Bioprocessing Research and TrainingDublinIreland
| | - Pauline M. Rudd
- GlycoScience GroupNational Institute for Bioprocessing Research and TrainingDublinIreland
- Present address:
Bioprocessing Technology InstituteAgency for Science, Technology and Research (A*STAR)SingaporeSingapore
| | - Karen M. Polizzi
- Department of Chemical EngineeringImperial College LondonLondonUK
| | - Cleo Kontoravdi
- Department of Chemical EngineeringImperial College LondonLondonUK
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7
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Lee G, Lee SM, Kim HU. A contribution of metabolic engineering to addressing medical problems: Metabolic flux analysis. Metab Eng 2023; 77:283-293. [PMID: 37075858 DOI: 10.1016/j.ymben.2023.04.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 03/20/2023] [Accepted: 04/12/2023] [Indexed: 04/21/2023]
Abstract
Metabolic engineering has served as a systematic discipline for industrial biotechnology as it has offered systematic tools and methods for strain development and bioprocess optimization. Because these metabolic engineering tools and methods are concerned with the biological network of a cell with emphasis on metabolic network, they have also been applied to a range of medical problems where better understanding of metabolism has also been perceived to be important. Metabolic flux analysis (MFA) is a unique systematic approach initially developed in the metabolic engineering community, and has proved its usefulness and potential when addressing a range of medical problems. In this regard, this review discusses the contribution of MFA to addressing medical problems. For this, we i) provide overview of the milestones of MFA, ii) define two main branches of MFA, namely constraint-based reconstruction and analysis (COBRA) and isotope-based MFA (iMFA), and iii) present successful examples of their medical applications, including characterizing the metabolism of diseased cells and pathogens, and identifying effective drug targets. Finally, synergistic interactions between metabolic engineering and biomedical sciences are discussed with respect to MFA.
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Affiliation(s)
- GaRyoung Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Sang Mi Lee
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Hyun Uk Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, Daejeon, 34141, Republic of Korea.
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8
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Oates EH, Antoniewicz MR. 13C-Metabolic flux analysis of 3T3-L1 adipocytes illuminates its core metabolism under hypoxia. Metab Eng 2023; 76:158-166. [PMID: 36758664 DOI: 10.1016/j.ymben.2023.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Revised: 01/20/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023]
Abstract
Hypoxia has been identified as a major factor in the pathogenesis of adipose tissue inflammation, which is a hallmark of obesity and obesity-linked type 2 diabetes mellitus. In this study, we have investigated the impact of hypoxia (1% oxygen) on the physiology and metabolism of 3T3-L1 adipocytes, a widely used cell culture model of adipose. Specifically, we applied parallel labeling experiments, isotopomer spectral analysis, and 13C-metabolic flux analysis to quantify the impact of hypoxia on adipogenesis, de novo lipogenesis and metabolic flux reprogramming in adipocytes. We found that 3T3-L1 cells can successfully differentiate into lipid-accumulating adipocytes under hypoxia, although the production of lipids was reduced by about 40%. Quantitative flux analysis demonstrated that short-term (1 day) and long-term (7 days) exposure to hypoxia resulted in similar reprogramming of cellular metabolism. Overall, we found that hypoxia: 1) reduced redox and energy generation by more than 2-fold and altered the patterns of metabolic pathway contributions to production and consumption of energy and redox cofactors; 2) redirected glucose metabolism from pentose phosphate pathway and citric acid cycle to lactate production; 3) rewired glutamine metabolism, from net glutamine production to net glutamine catabolism; 4) suppressed branched chain amino acid consumption; and 5) reduced biosynthesis of odd-chain fatty acids and mono-unsaturated fatty acids, while synthesis of saturated even-chain fatty acids was not affected. Together, these results highlight the profound impact of extracellular microenvironment on adipocyte metabolic activity and function.
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Affiliation(s)
- Eleanor H Oates
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE 19716, USA.
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9
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Giacomello G, Otto C, Priller J, Ruprecht K, Böttcher C, Parr MK. 1,2- 13C 2-Glucose Tracing Approach to Assess Metabolic Alterations of Human Monocytes under Neuroinflammatory Conditions. Curr Issues Mol Biol 2023; 45:765-781. [PMID: 36661537 PMCID: PMC9857935 DOI: 10.3390/cimb45010051] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/17/2023] Open
Abstract
Neuroinflammation is one of the common features in most neurological diseases including multiple sclerosis (MScl) and neurodegenerative diseases such as Alzheimer's disease (AD). It is associated with local brain inflammation, microglial activation, and infiltration of peripheral immune cells into cerebrospinal fluid (CSF) and the central nervous system (CNS). It has been shown that the diversity of phenotypic changes in monocytes in CSF relates to neuroinflammation. It remains to be investigated whether these phenotypic changes are associated with functional or metabolic alteration, which may give a hint to their function or changes in cell states, e.g., cell activation. In this article, we investigate whether major metabolic pathways of blood monocytes alter after exposure to CSF of healthy individuals or patients with AD or MScl. Our findings show a significant alteration of the metabolism of monocytes treated with CSF from patients and healthy donors, including higher production of citric acid and glutamine, suggesting a more active glycolysis and tricarboxylic acid (TCA) cycle and reduced production of glycine and serine. These alterations suggest metabolic reprogramming of monocytes, possibly related to the change of compartment (from blood to CSF) and/or disease-related. Moreover, the levels of serine differ between AD and MScl, suggesting different phenotypic alterations between diseases.
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Affiliation(s)
- Ginevra Giacomello
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2 + 4, 14195 Berlin, Germany
| | - Carolin Otto
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Josef Priller
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Department of Psychiatry and Psychotherapy, School of Medicine, Technical University Munich, 81675 Munich, Germany
- UK Dementia Research Institute (UK DRI), University of Edinburgh, Edinburgh EH16 4SB, UK
| | - Klemens Ruprecht
- Department of Neurology, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
| | - Chotima Böttcher
- Department of Neuropsychiatry and Laboratory of Molecular Psychiatry, Charité—Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, 10117 Berlin, Germany
- Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association and Charité—Universitätsmedizin Berlin, 13125 Berlin, Germany
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Maria Kristina Parr
- Institute of Pharmacy, Freie Universität Berlin, Königin-Luise-Str. 2 + 4, 14195 Berlin, Germany
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10
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Metabolic rewiring revealed by cell-specific rate analyses from nontargeted exometabolomics during simultaneous consumption of glucose and lactic acid in a CHO fed-batch process. J Biotechnol 2022; 359:161-175. [DOI: 10.1016/j.jbiotec.2022.10.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/09/2022] [Accepted: 10/04/2022] [Indexed: 11/20/2022]
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11
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Quek LE, van Geldermalsen M, Guan YF, Wahi K, Mayoh C, Balaban S, Pang A, Wang Q, Cowley MJ, Brown KK, Turner N, Hoy AJ, Holst J. Glutamine addiction promotes glucose oxidation in triple-negative breast cancer. Oncogene 2022; 41:4066-4078. [PMID: 35851845 PMCID: PMC9391225 DOI: 10.1038/s41388-022-02408-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 06/30/2022] [Accepted: 07/01/2022] [Indexed: 11/30/2022]
Abstract
Glutamine is a conditionally essential nutrient for many cancer cells, but it remains unclear how consuming glutamine in excess of growth requirements confers greater fitness to glutamine-addicted cancers. By contrasting two breast cancer subtypes with distinct glutamine dependencies, we show that glutamine-indispensable triple-negative breast cancer (TNBC) cells rely on a non-canonical glutamine-to-glutamate overflow, with glutamine carbon routed once through the TCA cycle. Importantly, this single-pass glutaminolysis increases TCA cycle fluxes and replenishes TCA cycle intermediates in TNBC cells, a process that achieves net oxidation of glucose but not glutamine. The coupling of glucose and glutamine catabolism appears hard-wired via a distinct TNBC gene expression profile biased to strip and then sequester glutamine nitrogen, but hampers the ability of TNBC cells to oxidise glucose when glutamine is limiting. Our results provide a new understanding of how metabolically rigid TNBC cells are sensitive to glutamine deprivation and a way to select vulnerable TNBC subtypes that may be responsive to metabolic-targeted therapies.
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Affiliation(s)
- Lake-Ee Quek
- School of Mathematics and Statistics, The University of Sydney, Camperdown, NSW, Australia.
| | - Michelle van Geldermalsen
- Origins of Cancer Program, Centenary Institute, The University of Sydney, Camperdown, NSW, Australia
- Sydney Medical School, The University of Sydney, Camperdown, NSW, Australia
| | - Yi Fang Guan
- School of Medical Sciences and School of Clinical Medicine, UNSW Sydney, Kensington, NSW, Australia
| | - Kanu Wahi
- School of Medical Sciences and School of Clinical Medicine, UNSW Sydney, Kensington, NSW, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Seher Balaban
- School of Medical Sciences, Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Angel Pang
- School of Medical Sciences and School of Clinical Medicine, UNSW Sydney, Kensington, NSW, Australia
| | - Qian Wang
- School of Medical Sciences and School of Clinical Medicine, UNSW Sydney, Kensington, NSW, Australia
| | - Mark J Cowley
- Children's Cancer Institute, Lowy Cancer Centre, UNSW Sydney, Kensington, NSW, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, Australia
| | - Kristin K Brown
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Biochemistry and Pharmacology, The University of Melbourne, Melbourne, VIC, Australia
| | - Nigel Turner
- Department of Pharmacology, School of Medical Sciences, UNSW Sydney, Kensington, NSW, Australia
| | - Andrew J Hoy
- School of Medical Sciences, Charles Perkins Centre, The University of Sydney, Camperdown, NSW, Australia
| | - Jeff Holst
- School of Medical Sciences and School of Clinical Medicine, UNSW Sydney, Kensington, NSW, Australia.
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12
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Noguchi S, Wakita K, Matsuda F, Shimizu H. 13C metabolic flux analysis clarifies distinct metabolic phenotypes of cancer cell spheroid mimicking tumor hypoxia. Metab Eng 2022; 73:192-200. [DOI: 10.1016/j.ymben.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/09/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
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13
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Coulet M, Kepp O, Kroemer G, Basmaciogullari S. Metabolic Profiling of CHO Cells during the Production of Biotherapeutics. Cells 2022; 11:cells11121929. [PMID: 35741058 PMCID: PMC9221972 DOI: 10.3390/cells11121929] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 01/08/2023] Open
Abstract
As indicated by an ever-increasing number of FDA approvals, biotherapeutics constitute powerful tools for the treatment of various diseases, with monoclonal antibodies (mAbs) accounting for more than 50% of newly approved drugs between 2014 and 2018 (Walsh, 2018). The pharmaceutical industry has made great progress in developing reliable and efficient bioproduction processes to meet the demand for recombinant mAbs. Mammalian cell lines are preferred for the production of functional, complex recombinant proteins including mAbs, with Chinese hamster ovary (CHO) cells being used in most instances. Despite significant advances in cell growth control for biologics manufacturing, cellular responses to environmental changes need to be understood in order to further improve productivity. Metabolomics offers a promising approach for developing suitable strategies to unlock the full potential of cellular production. This review summarizes key findings on catabolism and anabolism for each phase of cell growth (exponential growth, the stationary phase and decline) with a focus on the principal metabolic pathways (glycolysis, the pentose phosphate pathway and the tricarboxylic acid cycle) and the families of biomolecules that impact these circuities (nucleotides, amino acids, lipids and energy-rich metabolites).
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Affiliation(s)
- Mathilde Coulet
- Sanofi R&D, 94400 Vitry-sur-Seine, France;
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France;
| | - Oliver Kepp
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France;
- Institut Universitaire de France, Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, 75006 Paris, France
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France;
- Institut Universitaire de France, Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, 75006 Paris, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
- Correspondence: (G.K.); (S.B.)
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14
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Sacco SA, Tuckowski AM, Trenary I, Kraft L, Betenbaugh MJ, Young JD, Smith KD. Attenuation of glutamine synthetase selection marker improves product titer and reduces glutamine overflow in Chinese hamster ovary cells. Biotechnol Bioeng 2022; 119:1712-1727. [PMID: 35312045 DOI: 10.1002/bit.28084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 02/25/2022] [Accepted: 03/07/2022] [Indexed: 11/10/2022]
Abstract
The glutamine synthetase (GS) expression system is commonly used to ensure stable transgene integration and amplification in CHO host lines. Transfected cell populations are typically grown in the presence of the GS inhibitor, methionine sulfoximine (MSX), to further select for increased transgene copy number. However, high levels of GS activity produce excess glutamine. We hypothesized that attenuating the GS promoter while keeping the strong IgG promoter on the GS-IgG expression vector would result in a more efficient cellular metabolic phenotype. Herein, we characterized CHO cell lines expressing GS from either an attenuated promoter or an SV40 promoter and selected with/without MSX. CHO cells with the attenuated GS promoter had higher IgG specific productivity and lower glutamine production compared to cells with SV40-driven GS expression. Selection with MSX increased both specific productivity and glutamine production, regardless of GS promoter strength. 13 C metabolic flux analysis (MFA) was performed to further assess metabolic differences between these cell lines. Interestingly, central carbon metabolism was unaltered by the attenuated GS promoter while the fate of glutamate and glutamine varied depending on promoter strength and selection conditions. This study highlights the ability to optimize the GS expression system to improve IgG production and reduce wasteful glutamine overflow, without significantly altering central metabolism. Additionally, a detailed supplementary analysis of two "lactate runaway" reactors provides insight into the poorly understood phenomenon of excess lactate production by some CHO cell cultures. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Sarah A Sacco
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Angela M Tuckowski
- Biotherapeutics Development, Janssen Research and Development, Spring House, PA, USA.,Department of Cellular and Molecular Biology, University of Michigan, Ann Arbor, MI, USA
| | - Irina Trenary
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA
| | - Lauren Kraft
- Biotherapeutics Development, Janssen Research and Development, Spring House, PA, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jamey D Young
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, TN, USA.,Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN, USA
| | - Kevin D Smith
- Biotherapeutics Development, Janssen Research and Development, Spring House, PA, USA.,Asimov, 1325 Boylston St, Boston, MA, 02215
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15
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Sake CL, Metcalf AJ, Meagher M, Paola JD, Neeves KB, Boyle NR. Isotopically nonstationary 13C metabolic flux analysis in resting and activated human platelets. Metab Eng 2022; 69:313-322. [PMID: 34954086 PMCID: PMC8905147 DOI: 10.1016/j.ymben.2021.12.007] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 01/03/2023]
Abstract
Platelet metabolism is linked to platelet hyper- and hypoactivity in numerous human diseases. Developing a detailed understanding of the link between metabolic shifts and platelet activation state is integral to improving human health. Here, we show the first application of isotopically nonstationary 13C metabolic flux analysis to quantitatively measure carbon fluxes in both resting and thrombin activated platelets. Metabolic flux analysis results show that resting platelets primarily metabolize glucose to lactate via glycolysis, while acetate is oxidized to fuel the tricarboxylic acid cycle. Upon activation with thrombin, a potent platelet agonist, platelets increase their uptake of glucose 3-fold. This results in an absolute increase in flux throughout central metabolism, but when compared to resting platelets they redistribute carbon dramatically. Activated platelets decrease relative flux to the oxidative pentose phosphate pathway and TCA cycle from glucose and increase relative flux to lactate. These results provide the first report of reaction-level carbon fluxes in platelets and allow us to distinguish metabolic fluxes with much higher resolution than previous studies.
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Affiliation(s)
- Cara L. Sake
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401 USA
| | - Alexander J. Metcalf
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401 USA
| | - Michelle Meagher
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Jorge Di Paola
- Department of Pediatrics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Keith B. Neeves
- Department of Bioengineering, University of Colorado, Aurora, CO, 80045 USA,Hemophilia and Thrombosis Center, University of Colorado, Aurora, CO, 80045 USA,Department of Pediatrics, Section of Hematology, Oncology, and Bone Marrow Transplant University of Colorado, Aurora, CO, 80045 USA
| | - Nanette R. Boyle
- Department of Chemical and Biological Engineering, Colorado School of Mines, Golden, CO, 80401 USA,Correspondence: , 423 Alderson Hall; 1613 Illinois St.; Golden, CO 80401
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16
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Oates EH, Antoniewicz MR. Coordinated reprogramming of metabolism and cell function in adipocytes from proliferation to differentiation. Metab Eng 2021; 69:221-230. [PMID: 34929419 DOI: 10.1016/j.ymben.2021.12.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 09/25/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022]
Abstract
Adipose tissue plays a major role in regulating lipid and energy homeostasis by storing excess nutrients, releasing energetic substrates through lipolysis, and regulating metabolism of other tissues and organs through endocrine and paracrine signaling. Adipocytes within fat tissues store excess nutrients through increased cell number (hyperplasia), increased cell size (hypertrophy), or both. The differentiation of pre-adipocytes into mature lipid-accumulating adipocytes requires a complex interaction of metabolic pathways that is still incompletely understood. Here, we applied parallel labeling experiments and 13C-metabolic flux analysis to quantify precise metabolic fluxes in proliferating and differentiated 3T3-L1 cells, a widely used model to study adipogenesis. We found that morphological and biomass composition changes in adipocytes were accompanied by significant shifts in metabolic fluxes, encompassing all major metabolic pathways. In contrast to proliferating cells, differentiated adipocytes 1) increased glucose uptake and redirected glucose utilization from lactate production to lipogenesis and energy generation; 2) increased pathway fluxes through glycolysis, oxidative pentose phosphate pathway and citric acid cycle; 3) reduced lactate secretion, resulting in increased ATP generation via oxidative phosphorylation; 4) rewired glutamine metabolism, from glutaminolysis to de novo glutamine synthesis; 5) increased cytosolic NADPH production, driven mostly by increased cytosolic malic enzyme flux; 6) increased production of monounsaturated C16:1; and 7) activated a mitochondrial pyruvate cycle through simultaneous activity of pyruvate carboxylase, malate dehydrogenase and malic enzyme. Taken together, these results quantitatively highlight the complex interplay between pathway fluxes and cell function in adipocytes, and suggest a functional role for metabolic reprogramming in adipose differentiation and lipogenesis.
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Affiliation(s)
- Eleanor H Oates
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, 19716, USA
| | - Maciek R Antoniewicz
- Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, Newark, DE, 19716, USA.
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17
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Rish AJ, Drennen JK, Anderson CA. Metabolic trends of Chinese hamster ovary cells in biopharmaceutical production under batch and fed-batch conditions. Biotechnol Prog 2021; 38:e3220. [PMID: 34676699 DOI: 10.1002/btpr.3220] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 10/05/2021] [Accepted: 10/19/2021] [Indexed: 11/07/2022]
Abstract
Extensive knowledge of Chinese hamster ovary (CHO) cell metabolism is required to improve process productivity and culture performance in biopharmaceutical manufacturing. However, CHO cells show a dynamic metabolism during culturing in batch and fed-batch bioreactors. CHO cell metabolism is generally described as taking place in three stages: exponential growth phase, stationary phase, and death phase. This review aims to summarize the trends of central metabolism for CHO cells during each stage. Additional insights into how culture conditions are related to phase transitions and force metabolic rewiring are provided. Understanding of CHO cell metabolism lends itself to improving culture qualities by, for example, identifying sources of toxic byproducts and pathways for cellular engineering. In summary, this review describes the changes in CHO cell central metabolism over the course of the culture.
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Affiliation(s)
- Adam J Rish
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
| | - James K Drennen
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
| | - Carl A Anderson
- Duquesne University Graduate School for Pharmaceutical Sciences, Pittsburgh, Pennsylvania, USA
- Duquesne Center for Pharmaceutical Technology, Duquesne University, Pittsburgh, Pennsylvania, USA
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18
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Keibler MA, Dong W, Korthauer KD, Hosios AM, Moon SJ, Sullivan LB, Liu N, Abbott KL, Arevalo OD, Ho K, Lee J, Phanse AS, Kelleher JK, Iliopoulos O, Coloff JL, Vander Heiden MG, Stephanopoulos G. Differential substrate use in EGF- and oncogenic KRAS-stimulated human mammary epithelial cells. FEBS J 2021; 288:5629-5649. [PMID: 33811729 PMCID: PMC8487438 DOI: 10.1111/febs.15858] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 03/01/2021] [Accepted: 03/31/2021] [Indexed: 11/30/2022]
Abstract
Many metabolic phenotypes in cancer cells are also characteristic of proliferating nontransformed mammalian cells, and attempts to distinguish between phenotypes resulting from oncogenic perturbation from those associated with increased proliferation are limited. Here, we examined the extent to which metabolic changes corresponding to oncogenic KRAS expression differed from those corresponding to epidermal growth factor (EGF)-driven proliferation in human mammary epithelial cells (HMECs). Removal of EGF from culture medium reduced growth rates and glucose/glutamine consumption in control HMECs despite limited changes in respiration and fatty acid synthesis, while the relative contribution of branched-chain amino acids to the TCA cycle and lipogenesis increased in the near-quiescent conditions. Most metabolic phenotypes measured in HMECs expressing mutant KRAS were similar to those observed in EGF-stimulated control HMECs that were growing at comparable rates. However, glucose and glutamine consumption as well as lactate and glutamate production were lower in KRAS-expressing cells cultured in media without added EGF, and these changes correlated with reduced sensitivity to GLUT1 inhibitor and phenformin treatment. Our results demonstrate the strong dependence of metabolic behavior on growth rate and provide a model to distinguish the metabolic influences of oncogenic mutations and nononcogenic growth.
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Affiliation(s)
- Mark A Keibler
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Wentao Dong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Keegan D Korthauer
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Harvard T. H. Chan School of Public Health, Boston, MA, USA
| | - Aaron M Hosios
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Sun Jin Moon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lucas B Sullivan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Nian Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Keene L Abbott
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Orlando D Arevalo
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kailing Ho
- Department of Chemistry, Wellesley College, Wellesley, MA, USA
| | - Jennifer Lee
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Aasavari S Phanse
- Department of Electrical Engineering & Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Joanne K Kelleher
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Othon Iliopoulos
- Center for Cancer Research, Massachusetts General Hospital Cancer Center, Charlestown, MA, USA
- Division of Hematology/Oncology, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Jonathan L Coloff
- Department of Cell Biology, Harvard Medical School, Boston, MA, USA
- Department of Physiology and Biophysics, University of Illinois Cancer Center, University of Illinois at Chicago, IL, USA
| | - Matthew G Vander Heiden
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
- Dana-Farber Cancer Institute, Boston, MA, USA
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
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19
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Wijaya AW, Ulmer A, Hundsdorfer L, Verhagen N, Teleki A, Takors R. Compartment-specific metabolome labeling enables the identification of subcellular fluxes that may serve as promising metabolic engineering targets in CHO cells. Bioprocess Biosyst Eng 2021; 44:2567-2578. [PMID: 34590184 PMCID: PMC8536584 DOI: 10.1007/s00449-021-02628-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 08/27/2021] [Indexed: 11/30/2022]
Abstract
13C labeling data are used to calculate quantitative intracellular flux patterns reflecting in vivo conditions. Given that approaches for compartment-specific metabolomics exist, the benefits they offer compared to conventional non-compartmented 13C flux studies remain to be determined. Using compartment-specific labeling information of IgG1-producing Chinese hamster ovary cells, this study investigated differences of flux patterns exploiting and ignoring metabolic labeling data of cytosol and mitochondria. Although cellular analysis provided good estimates for the majority of intracellular fluxes, half of the mitochondrial transporters, and NADH and ATP balances, severe differences were found for some reactions. Accurate flux estimations of almost all iso-enzymes heavily depended on the sub-cellular labeling information. Furthermore, key discrepancies were found for the mitochondrial carriers vAGC1 (Aspartate/Glutamate antiporter), vDIC (Malate/H+ symporter), and vOGC (α-ketoglutarate/malate antiporter). Special emphasis is given to the flux of cytosolic malic enzyme (vME): it could not be estimated without the compartment-specific malate labeling information. Interesting enough, cytosolic malic enzyme is an important metabolic engineering target for improving cell-specific IgG1 productivity. Hence, compartment-specific 13C labeling analysis serves as prerequisite for related metabolic engineering studies.
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Affiliation(s)
- Andy Wiranata Wijaya
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Andreas Ulmer
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Lara Hundsdorfer
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Natascha Verhagen
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany.
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20
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Schulze M, Niemann J, Wijffels RH, Matuszczyk J, Martens DE. Rapid intensification of an established CHO cell fed-batch process. Biotechnol Prog 2021; 38:e3213. [PMID: 34542245 PMCID: PMC9286570 DOI: 10.1002/btpr.3213] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 09/02/2021] [Accepted: 09/16/2021] [Indexed: 11/17/2022]
Abstract
Currently, the mammalian biomanufacturing industry explores process intensification (PI) to meet upcoming demands of biotherapeutics while keeping production flexible but, more importantly, as economic as possible. However, intensified processes often require more development time compared with conventional fed‐batches (FBs) preventing their implementation. Hence, rapid and efficient, yet straightforward strategies for PI are needed. In this study we demonstrate such a strategy for the intensification of an N‐stage FB by implementing N‐1 perfusion cell culture and high inoculum cell densities resulting in a robust intensified FB (iFB). Furthermore, we show successful combination of such an iFB with the addition of productivity enhancers, which has not been reported so far. The conventional CHO cell FB process was step‐wise improved and intensified rapidly in multi‐parallel small‐scale bioreactors using N‐1 perfusion. The iFBs were performed in 15 and 250 ml bioreactors and allowed to evaluate the impact on key process indicators (KPI): the space–time yield (STY) was successfully doubled from 0.28 to 0.55 g/L d, while product quality was maintained. This gain was generated by initially increasing the inoculation density, thus shrinking process time, and second supplementation with butyric acid (BA), which reduced cell growth and enhanced cell‐specific productivity from ~25 to 37 pg/(cell d). Potential impacts of PI on cell metabolism were evaluated using flux balance analysis. Initial metabolic differences between the standard and intensified process were observed but disappeared quickly. This shows that PI can be achieved rapidly for new as well as existing processes without introducing sustained changes in cellular and metabolic behavior.
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Affiliation(s)
- Markus Schulze
- Corporate Research, Sartorius Stedim Biotech GmbH, Göttingen, Germany.,Bioprocess Engineering, Wageningen University, Wageningen, Netherlands
| | - Julia Niemann
- Corporate Research, Sartorius Stedim Biotech GmbH, Göttingen, Germany
| | - Rene H Wijffels
- Bioprocess Engineering, Wageningen University, Wageningen, Netherlands.,Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Jens Matuszczyk
- Product Development, Sartorius Stedim Biotech GmbH, Göttingen, Germany
| | - Dirk E Martens
- Bioprocess Engineering, Wageningen University, Wageningen, Netherlands
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21
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Loss of SNORA73 reprograms cellular metabolism and protects against steatohepatitis. Nat Commun 2021; 12:5214. [PMID: 34471131 PMCID: PMC8410784 DOI: 10.1038/s41467-021-25457-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 08/06/2021] [Indexed: 02/07/2023] Open
Abstract
Dyslipidemia and resulting lipotoxicity are pathologic signatures of metabolic syndrome and type 2 diabetes. Excess lipid causes cell dysfunction and induces cell death through pleiotropic mechanisms that link to oxidative stress. However, pathways that regulate the response to metabolic stress are not well understood. Herein, we show that disruption of the box H/ACA SNORA73 small nucleolar RNAs encoded within the small nucleolar RNA hosting gene 3 (Snhg3) causes resistance to lipid-induced cell death and general oxidative stress in cultured cells. This protection from metabolic stress is associated with broad reprogramming of oxidative metabolism that is dependent on the mammalian target of rapamycin signaling axis. Furthermore, we show that knockdown of SNORA73 in vivo protects against hepatic steatosis and lipid-induced oxidative stress and inflammation. Our findings demonstrate a role for SNORA73 in the regulation of metabolism and lipotoxicity.
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22
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Matsuda F, Maeda K, Taniguchi T, Kondo Y, Yatabe F, Okahashi N, Shimizu H. mfapy: An open-source Python package for 13C-based metabolic flux analysis. Metab Eng Commun 2021; 13:e00177. [PMID: 34354925 PMCID: PMC8322459 DOI: 10.1016/j.mec.2021.e00177] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/01/2021] [Accepted: 07/05/2021] [Indexed: 11/28/2022] Open
Abstract
13C-based metabolic flux analysis (13C-MFA) is an essential tool for estimating intracellular metabolic flux levels in metabolic engineering and biology. In 13C-MFA, a metabolic flux distribution that explains the observed isotope labeling data was computationally estimated using a non-linear optimization method. Herein, we report the development of mfapy, an open-source Python package developed for more flexibility and extensibility for 13C-MFA. mfapy compels users to write a customized Python code by describing each step in the data analysis procedures of the isotope labeling experiments. The flexibility and extensibility provided by mfapy can support trial-and-error performance in the routine estimation of metabolic flux distributions, experimental design by computer simulations of 13C-MFA experiments, and development of new data analysis techniques for stable isotope labeling experiments. mfapy is available to the public from the Github repository (https://github.com/fumiomatsuda/mfapy). An open-source Python package, mfapy, is developed for 13C-MFA. mfapy enables users to write Python codes for data analysis procedures of 13C-MFA. mfapy has a flexibility and extensibility to support various data analysis procedures. Computer simulations of 13C-MFA experiments is supported for experimental design.
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Affiliation(s)
- Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takeo Taniguchi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuya Kondo
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Futa Yatabe
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka, 565-0871, Japan
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23
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Vappiani J, Eyster T, Orzechowski K, Ritz D, Patel P, Sévin D, Aon J. Exometabolome profiling reveals activation of the carnitine buffering pathway in fed-batch cultures of CHO cells co-fed with glucose and lactic acid. Biotechnol Prog 2021; 37:e3198. [PMID: 34328709 DOI: 10.1002/btpr.3198] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 07/22/2021] [Accepted: 07/26/2021] [Indexed: 11/06/2022]
Abstract
Adjustments to CHO cell physiology were recently observed during implementation of a Raman spectroscopy-based glucose and lactate control strategy. To further understand how these cells, under monoclonal antibody (mAb) production conditions, utilized the extra lactic acid fed, we performed a comprehensive semi-quantitative and time-dependent analysis of the exometabolome. This study focused on the CHO cell's metabolic shift from the fifth day of culture. We compared relative levels of extracellular metabolites in the absence or presence of a 2 g/L lactic acid setpoint while glucose was kept at 4 g/L. Our hypothesis is that extra lactic acid would supply more pyruvate, favoring oxidative phosphorylation. We subsequentially uncovered several carnitine derivatives as biomarkers of the simultaneous activation of TCA anaplerotic pathways as well as a carbon-buffering pathway. CHO cells exhibited a balance between intermediates from (i) amino acid catabolism, (ii) fatty acid β-oxidation, and (iii) pyruvate from glycolysis and lactic acid; and the secretion of their intermediate carnitine derivatives. In addition, 3-hydroxy-methyl-glutaric acid (HMG) and mevalonate syntheses were found as biomarkers of alternative acyl group removal. Together, under a limited capacity to assimilate the surplus of acyl-CoA groups as well as an ability to maintain the acyl-CoA: free CoA ratio for proper and continuous functioning of the TCA cycle, CHO cells activate the carnitine-buffering system, HMG, and mevalonate pathways.
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Affiliation(s)
| | - Tom Eyster
- Microbial & Cell Culture Development, GlaxoSmithKline, King of Prussia, Pennsylvania, USA
| | - Keegan Orzechowski
- Microbial & Cell Culture Development, GlaxoSmithKline, King of Prussia, Pennsylvania, USA
| | - Diana Ritz
- Microbial & Cell Culture Development, GlaxoSmithKline, King of Prussia, Pennsylvania, USA
| | - Pramthesh Patel
- Microbial & Cell Culture Development, GlaxoSmithKline, King of Prussia, Pennsylvania, USA
| | - Daniel Sévin
- Cellzome GmbH, GlaxoSmithKline, Heidelberg, Germany
| | - Juan Aon
- Microbial & Cell Culture Development, GlaxoSmithKline, King of Prussia, Pennsylvania, USA
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24
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Sinharoy P, McFarland KS, Majewska NI, Betenbaugh MJ, Handlogten MW. Redox as a bioprocess parameter: analytical redox quantification in biological therapeutic production. Curr Opin Biotechnol 2021; 71:49-54. [PMID: 34243034 DOI: 10.1016/j.copbio.2021.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/10/2021] [Accepted: 06/21/2021] [Indexed: 11/24/2022]
Abstract
Engineered Chinese hamster ovary (CHO) cells are the most widely utilized cell line for protein-based therapeutics production at industrial scales. Process development strategies which improve production capacity and quality are often implemented without an understanding of underlying intracellular changes. Intracellular redox conditions drive reactions in pathways critical to biologics production, including bioenergetic and biosynthetic pathways, necessitating methods to quantify redox-related changes. Advances in methods for analytical redox quantification presented here, including bioreactor probes, redox-targeted proteomics, genetically encoded redox-sensitive fluorescent proteins, and biochemical assays, are creating new opportunities to characterize the effects of redox in biologics production. Implementing these methods will lead to enhanced media formulations, improved bioprocess strategies, and new cell line engineering targets and ultimately develop redox into an optimizable bioprocess parameter to improve the yield and quality of these lifesaving medicines.
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Affiliation(s)
- Pritam Sinharoy
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, USA
| | - Kevin S McFarland
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, USA
| | - Natalia I Majewska
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, USA; Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, USA
| | - Michael W Handlogten
- Cell Culture and Fermentation Sciences, BioPharmaceuticals Development, R&D, AstraZeneca, Gaithersburg, USA.
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25
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Jin ES, Lee MH, Malloy CR. 13 C NMR of glutamate for monitoring the pentose phosphate pathway in myocardium. NMR IN BIOMEDICINE 2021; 34:e4533. [PMID: 33900680 DOI: 10.1002/nbm.4533] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 04/05/2021] [Accepted: 04/13/2021] [Indexed: 06/12/2023]
Abstract
After administration of 13 C-labeled glucose, the activity of the pentose phosphate pathway (PPP) is often assessed by the distribution of 13 C in lactate. However, in some tissues, such as the well-oxygenated heart, the concentration of lactate may be too low for convenient analysis by NMR. Here, we examined 13 C-labeled glutamate as an alternative biomarker of the PPP in the heart. Isolated rat hearts were perfused with media containing [2,3-13 C2 ]glucose and the tissue extracts were analyzed. Metabolism of [2,3-13 C2 ]glucose yields [1,2-13 C2 ]pyruvate via glycolysis and [2,3-13 C2 ]pyruvate via the PPP. Pyruvate is in exchange with lactate or is further metabolized to glutamate through pyruvate dehydrogenase and the TCA cycle. A doublet from [4,5-13 C2 ]glutamate, indicating flux through the PPP, was readily detected in 13 C NMR of heart extracts even when the corresponding doublet from [2,3-13 C2 ]lactate was minimal. Benfotiamine, known to induce the PPP, caused an increase in production of [4,5-13 C2 ]glutamate. In rats receiving [2,3-13 C2 ]glucose, brain extracts showed well-resolved signals from both [2,3-13 C2 ]lactate and [4,5-13 C2 ]glutamate in 13 C NMR spectra. Assessment of the PPP in the brain based on glutamate had a strong linear correlation with lactate-based assessment. In summary, 13 C NMR analysis of glutamate enabled detection of the low PPP activity in isolated hearts. This analyte is an alternative to lactate for monitoring the PPP with the use of [2,3-13 C2 ]glucose.
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Affiliation(s)
- Eunsook S Jin
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Min H Lee
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Craig R Malloy
- Advanced Imaging Research Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Radiology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- VA North Texas Health Care System, Dallas, Texas, USA
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Xu Y, Fu X, Sharkey TD, Shachar-Hill Y, Walker ABJ. The metabolic origins of non-photorespiratory CO2 release during photosynthesis: a metabolic flux analysis. PLANT PHYSIOLOGY 2021; 186:297-314. [PMID: 33591309 PMCID: PMC8154043 DOI: 10.1093/plphys/kiab076] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 01/16/2021] [Indexed: 05/02/2023]
Abstract
Respiration in the light (RL) releases CO2 in photosynthesizing leaves and is a phenomenon that occurs independently from photorespiration. Since RL lowers net carbon fixation, understanding RL could help improve plant carbon-use efficiency and models of crop photosynthesis. Although RL was identified more than 75 years ago, its biochemical mechanisms remain unclear. To identify reactions contributing to RL, we mapped metabolic fluxes in photosynthesizing source leaves of the oilseed crop and model plant camelina (Camelina sativa). We performed a flux analysis using isotopic labeling patterns of central metabolites during 13CO2 labeling time course, gas exchange, and carbohydrate production rate experiments. To quantify the contributions of multiple potential CO2 sources with statistical and biological confidence, we increased the number of metabolites measured and reduced biological and technical heterogeneity by using single mature source leaves and quickly quenching metabolism by directly injecting liquid N2; we then compared the goodness-of-fit between these data and data from models with alternative metabolic network structures and constraints. Our analysis predicted that RL releases 5.2 μmol CO2 g-1 FW h-1 of CO2, which is relatively consistent with a value of 9.3 μmol CO2 g-1 FW h-1 measured by CO2 gas exchange. The results indicated that ≤10% of RL results from TCA cycle reactions, which are widely considered to dominate RL. Further analysis of the results indicated that oxidation of glucose-6-phosphate to pentose phosphate via 6-phosphogluconate (the G6P/OPP shunt) can account for >93% of CO2 released by RL.
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Affiliation(s)
- Yuan Xu
- Department of Plant Biology, Michigan State University, Michigan 48824, USA
| | - Xinyu Fu
- Department of Plant Biology, Michigan State University, Michigan 48824, USA
- Department of Energy-Plant Research Laboratory, Michigan State University, Michigan 48824, USA
| | - Thomas D Sharkey
- Department of Energy-Plant Research Laboratory, Michigan State University, Michigan 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State University, Michigan 48824, USA
| | - Yair Shachar-Hill
- Department of Plant Biology, Michigan State University, Michigan 48824, USA
| | - and Berkley J Walker
- Department of Plant Biology, Michigan State University, Michigan 48824, USA
- Department of Energy-Plant Research Laboratory, Michigan State University, Michigan 48824, USA
- Author for communication:
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27
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Karottki KJLC, Hefzi H, Li S, Pedersen LE, Spahn PN, Joshi C, Ruckerbauer D, Bort JAH, Thomas A, Lee JS, Borth N, Lee GM, Kildegaard HF, Lewis NE. A metabolic CRISPR-Cas9 screen in Chinese hamster ovary cells identifies glutamine-sensitive genes. Metab Eng 2021; 66:114-122. [PMID: 33813034 DOI: 10.1016/j.ymben.2021.03.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 03/25/2021] [Accepted: 03/28/2021] [Indexed: 12/20/2022]
Abstract
Media and feed optimization have fueled many-fold improvements in mammalian biopharmaceutical production, but genome editing offers an emerging avenue for further enhancing cell metabolism and bioproduction. However, the complexity of metabolism, involving thousands of genes, makes it unclear which engineering strategies will result in desired traits. Here we present a comprehensive pooled CRISPR screen for CHO cell metabolism, including ~16,000 gRNAs against ~2500 metabolic enzymes and regulators. Using this screen, we identified a glutamine response network in CHO cells. Glutamine is particularly important since it is often over-fed to drive increased TCA cycle flux, but toxic ammonia may accumulate. With the screen we found one orphan glutamine-responsive gene with no clear connection to our network. Knockout of this novel and poorly characterized lipase, Abhd11, substantially increased growth in glutamine-free media by altering the regulation of the TCA cycle. Thus, the screen provides an invaluable targeted platform to comprehensively study genes involved in any metabolic trait, and elucidate novel regulators of metabolism.
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Affiliation(s)
| | - Hooman Hefzi
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA; Department of Pediatrics, University of California, San Diego, USA; Department of Bioengineering, University of California, San Diego, USA
| | - Songyuan Li
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Denmark
| | - Philipp N Spahn
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA; Department of Pediatrics, University of California, San Diego, USA
| | - Chintan Joshi
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA; Department of Pediatrics, University of California, San Diego, USA
| | - David Ruckerbauer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; University of Natural Resources and Life Sciences, Vienna, Austria
| | | | - Alex Thomas
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA
| | - Jae Seong Lee
- Department of Molecular Science and Technology, Ajou University, Suwon, 16499, Republic of Korea
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology, Vienna, Austria; University of Natural Resources and Life Sciences, Vienna, Austria
| | - Gyun Min Lee
- Department of Biological Sciences, Kaist, 291 Daehak-Ro, Yuseong-Gu, Daejeon, 305-701, Republic of Korea
| | | | - Nathan E Lewis
- The Novo Nordisk Foundation Center for Biosustainability at the University of California, San Diego, USA; Department of Pediatrics, University of California, San Diego, USA; Department of Bioengineering, University of California, San Diego, USA; National Biologics Facility, Technical University of Denmark, Denmark.
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28
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Polat IH, Tarrado-Castellarnau M, Bharat R, Perarnau J, Benito A, Cortés R, Sabatier P, Cascante M. Oxidative Pentose Phosphate Pathway Enzyme 6-Phosphogluconate Dehydrogenase Plays a Key Role in Breast Cancer Metabolism. BIOLOGY 2021; 10:85. [PMID: 33498665 PMCID: PMC7911610 DOI: 10.3390/biology10020085] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/18/2021] [Accepted: 01/20/2021] [Indexed: 02/07/2023]
Abstract
The pentose phosphate pathway (PPP) plays an essential role in the metabolism of breast cancer cells for the management of oxidative stress and the synthesis of nucleotides. 6-phosphogluconate dehydrogenase (6PGD) is one of the key enzymes of the oxidative branch of PPP and is involved in nucleotide biosynthesis and redox maintenance status. Here, we aimed to analyze the functional importance of 6PGD in a breast cancer cell model. Inhibition of 6PGD in MCF7 reduced cell proliferation and showed a significant decrease in glucose consumption and an increase in glutamine consumption, resulting in an important alteration in the metabolism of these cells. No difference in reactive oxygen species (ROS) production levels was observed after 6PGD inhibition, indicating that 6PGD, in contrast to glucose 6-phosphate dehydrogenase, is not involved in redox balance. We found that 6PGD inhibition also altered the stem cell characteristics and mammosphere formation capabilities of MCF7 cells, opening new avenues to prevent cancer recurrance after surgery or chemotherapy. Moreover, inhibition of 6PGD via chemical inhibitor S3 resulted in an induction of senescence, which, together with the cell cycle arrest and apoptosis induction, might be orchestrated by p53 activation. Therefore, we postulate 6PGD as a novel therapeutic target to treat breast cancer.
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Affiliation(s)
- Ibrahim H. Polat
- Department of Biochemistry and Molecular Biomedicine and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (R.B.); (J.P.); (A.B.); (R.C.)
- Equipe Environnement et Prédiction de la Santé des Populations, Laboratoire TIMC (UMR 5525), CHU de Grenoble, Université Grenoble Alpes, 38700 CEDEX La Tronche, France;
- Department of Medicine, Hematology/Oncology, Goethe-University Frankfurt, 60590 Frankfurt, Germany
| | - Míriam Tarrado-Castellarnau
- Department of Biochemistry and Molecular Biomedicine and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (R.B.); (J.P.); (A.B.); (R.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), 28001 Madrid, Spain
| | - Rohit Bharat
- Department of Biochemistry and Molecular Biomedicine and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (R.B.); (J.P.); (A.B.); (R.C.)
| | - Jordi Perarnau
- Department of Biochemistry and Molecular Biomedicine and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (R.B.); (J.P.); (A.B.); (R.C.)
| | - Adrian Benito
- Department of Biochemistry and Molecular Biomedicine and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (R.B.); (J.P.); (A.B.); (R.C.)
- Division of Cancer, Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London W12 0NN, UK
| | - Roldán Cortés
- Department of Biochemistry and Molecular Biomedicine and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (R.B.); (J.P.); (A.B.); (R.C.)
| | - Philippe Sabatier
- Equipe Environnement et Prédiction de la Santé des Populations, Laboratoire TIMC (UMR 5525), CHU de Grenoble, Université Grenoble Alpes, 38700 CEDEX La Tronche, France;
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine and Institute of Biomedicine (IBUB), Faculty of Biology, Universitat de Barcelona, Av Diagonal 643, 08028 Barcelona, Spain; (I.H.P.); (M.T.-C.); (R.B.); (J.P.); (A.B.); (R.C.)
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), 28001 Madrid, Spain
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Zhang X, Zink F, Hezel F, Vogt J, Wachter U, Wepler M, Loconte M, Kranz C, Hellmann A, Mizaikoff B, Radermacher P, Hartmann C. Metabolic substrate utilization in stress-induced immune cells. Intensive Care Med Exp 2020; 8:28. [PMID: 33336295 PMCID: PMC7746792 DOI: 10.1186/s40635-020-00316-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Accepted: 06/11/2020] [Indexed: 12/21/2022] Open
Abstract
Immune cell activation leads to the acquisition of new functions, such as proliferation, chemotaxis, and cytokine production. These functional changes require continuous metabolic adaption in order to sustain ATP homeostasis for sufficient host defense. The bioenergetic demands are usually met by the interconnected metabolic pathways glycolysis, TCA cycle, and oxidative phosphorylation. Apart from glucose, other sources, such as fatty acids and glutamine, are able to fuel the TCA cycle.Rising evidence has shown that cellular metabolism has a direct effect on the regulation of immune cell functions. Thus, quiescent immune cells maintain a basal metabolic state, which shifts to an accelerated metabolic level upon immune cell activation in order to promote key effector functions.This review article summarizes distinct metabolic signatures of key immune cell subsets from quiescence to activation and demonstrates a methodical concept of how to assess cellular metabolic pathways. It further discusses why metabolic functions are of rising interest for translational research and how they can be affected by the underlying pathophysiological condition and/or therapeutic interventions.
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Affiliation(s)
- Xiaomin Zhang
- Institut für Anästhesiologische Pathophysiologie und Verfahrensentwicklung, Universitätsklinikum Ulm, Helmholzstraße 8/1, 89081 Ulm, Germany
| | - Fabian Zink
- Institut für Anästhesiologische Pathophysiologie und Verfahrensentwicklung, Universitätsklinikum Ulm, Helmholzstraße 8/1, 89081 Ulm, Germany
| | - Felix Hezel
- Institut für Anästhesiologische Pathophysiologie und Verfahrensentwicklung, Universitätsklinikum Ulm, Helmholzstraße 8/1, 89081 Ulm, Germany
| | - Josef Vogt
- Institut für Anästhesiologische Pathophysiologie und Verfahrensentwicklung, Universitätsklinikum Ulm, Helmholzstraße 8/1, 89081 Ulm, Germany
| | - Ulrich Wachter
- Institut für Anästhesiologische Pathophysiologie und Verfahrensentwicklung, Universitätsklinikum Ulm, Helmholzstraße 8/1, 89081 Ulm, Germany
| | - Martin Wepler
- Institut für Anästhesiologische Pathophysiologie und Verfahrensentwicklung, Universitätsklinikum Ulm, Helmholzstraße 8/1, 89081 Ulm, Germany
- Klinik für Anästhesiologie, Universitätsklinikum Ulm, Ulm, Germany
| | - Maurizio Loconte
- Anesthesia and Intensive Care, San Martino Policlinico Hospital, IRCCS for Oncolocy and Neuroscience, Genoa, Italy
| | - Christine Kranz
- Institut für Analytische und Bioanalytische Chemie, Universität Ulm, Ulm, Germany
| | - Andreas Hellmann
- Institut für Analytische und Bioanalytische Chemie, Universität Ulm, Ulm, Germany
| | - Boris Mizaikoff
- Institut für Analytische und Bioanalytische Chemie, Universität Ulm, Ulm, Germany
| | - Peter Radermacher
- Institut für Anästhesiologische Pathophysiologie und Verfahrensentwicklung, Universitätsklinikum Ulm, Helmholzstraße 8/1, 89081 Ulm, Germany
| | - Clair Hartmann
- Institut für Anästhesiologische Pathophysiologie und Verfahrensentwicklung, Universitätsklinikum Ulm, Helmholzstraße 8/1, 89081 Ulm, Germany
- Klinik für Anästhesiologie, Universitätsklinikum Ulm, Ulm, Germany
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30
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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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31
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Odenwelder DC, Lu X, Harcum SW. Induced pluripotent stem cells can utilize lactate as a metabolic substrate to support proliferation. Biotechnol Prog 2020; 37:e3090. [PMID: 33029909 DOI: 10.1002/btpr.3090] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 09/10/2020] [Accepted: 09/28/2020] [Indexed: 01/07/2023]
Abstract
Human-induced pluripotent stem cells (iPSCs) hold the promise to improve cell-based therapies. Yet, to meet rising demands and become clinically impactful, sufficient high-quality iPSCs in quantity must be generated, a task that exceeds current capabilities. In this study, K3 iPSCs cultures were examined using parallel-labeling metabolic flux analysis (13 C-MFA) to quantify intracellular fluxes at relevant bioprocessing stages: glucose concentrations representative of initial media concentrations and high lactate concentrations representative of fed-batch culture conditions, prior to and after bolus glucose feeds. The glucose and lactate concentrations are also representative of concentrations that might be encountered at different locations within 3D cell aggregates. Furthermore, a novel method was developed to allow the isotopic tracer [U-13 C3 ] lactate to be used in the 13 C-MFA model. The results indicated that high extracellular lactate concentrations decreased glucose consumption and lactate production, while glucose concentrations alone did not affect rates of aerobic glycolysis. Moreover, for the high lactate cultures, lactate was used as a metabolic substrate to support oxidative mitochondrial metabolism. These results demonstrate that iPSCs have metabolic flexibility and possess the capacity to metabolize lactate to support exponential growth, and that high lactate concentrations alone do not adversely impact iPSC proliferation.
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Affiliation(s)
- Daniel C Odenwelder
- Department of Bioengineering, Clemson University, Clemson, South Carolina, USA
| | - Xiaoming Lu
- Department of Bioengineering, Clemson University, Clemson, South Carolina, USA
- Department of Biomolecular and Chemical Engineering, Clemson University, Clemson, South Carolina, USA
| | - Sarah W Harcum
- Department of Bioengineering, Clemson University, Clemson, South Carolina, USA
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32
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O'Brien CM, Mulukutla BC, Mashek DG, Hu WS. Regulation of Metabolic Homeostasis in Cell Culture Bioprocesses. Trends Biotechnol 2020; 38:1113-1127. [PMID: 32941791 DOI: 10.1016/j.tibtech.2020.02.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/11/2020] [Accepted: 02/12/2020] [Indexed: 12/26/2022]
Abstract
Mammalian cells are the main tool for the production of therapeutic proteins, viruses for gene therapy, and cells for cell therapy. In production processes cell metabolism is the main driver that causes changes in the growth environment and affects productivity and product quality. Of all nutrients, glucose has the most prominent impact on bioprocesses. We summarize recent findings on the regulation of glucose and energy metabolism in cultured cells. Local allosteric regulations and post-translational modifications of enzymes in metabolic networks interplay with global signaling and transcriptional regulation. These regulatory networks sustain homeostasis across the cytosolic and mitochondrial compartments. Understanding the regulation of glucose metabolism and metabolic state is crucial for enhancing process productivity and product quality.
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Affiliation(s)
- Conor M O'Brien
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA
| | | | - Douglas G Mashek
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Wei-Shou Hu
- Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455, USA.
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33
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Shi X, Xi B, Jasbi P, Turner C, Jin Y, Gu H. Comprehensive Isotopic Targeted Mass Spectrometry: Reliable Metabolic Flux Analysis with Broad Coverage. Anal Chem 2020; 92:11728-11738. [PMID: 32697570 PMCID: PMC7546585 DOI: 10.1021/acs.analchem.0c01767] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Metabolic flux analysis (MFA) is highly relevant to understanding metabolic mechanisms of various biological processes. While the pace of methodology development in MFA has been rapid, a major challenge the field continues to witness is limited metabolite coverage, often restricted to a small to moderate number of well-known compounds. In addition, isotopic peaks from an enriched metabolite tend to have low abundances, which makes liquid chromatography tandem mass spectrometry (LC-MS/MS) highly useful in MFA due to its high sensitivity and specificity. Previously we have built large-scale LC-MS/MS approaches that can be routinely used for measurement of up to ∼1,900 metabolite/feature levels [Gu et al. Anal. Chem. 2015, 87, 12355-12362. Shi et al. Anal. Chem. 2019, 91, 13737-13745.]. In this study, we aim to expand our previous studies focused on metabolite level measurements to flux analysis and establish a novel comprehensive isotopic targeted mass spectrometry (CIT-MS) method for reliable MFA analysis with broad coverage. As a proof-of-principle, we have applied CIT-MS to compare the steady-state enrichment of metabolites between Myc(oncogene)-On and Myc-Off Tet21N human neuroblastoma cells cultured with U-13C6-glucose medium. CIT-MS is operationalized using multiple reaction monitoring (MRM) mode and is able to perform MFA of 310 identified metabolites (142 reliably detected, 46 kinetically profiled) selected from >35 metabolic pathways of strong biological significance. Further, we developed a novel concept of relative flux, which eliminates the requirement of absolute quantitation in traditional MFA and thus enables comparative MFA under the pseudosteady state. As a result, CIT-MS was shown to possess the advantages of broad coverage, easy implementation, fast throughput, and more importantly, high fidelity and accuracy in MFA. In principle, CIT-MS can be easily adapted to track the flux of other labeled tracers (such as 15N-tracers) in any metabolite detectable by LC-MS/MS and in various biological models (such as mice). Therefore, CIT-MS has great potential to bring new insights to both basic and clinical metabolism research.
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Affiliation(s)
- Xiaojian Shi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, 13208 East Shea Boulevard, Scottsdale, Arizona 85259, United States
| | - Bowei Xi
- Department of Statistics, Purdue University, West Lafayette, Indiana 47907, United States
| | - Paniz Jasbi
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, 13208 East Shea Boulevard, Scottsdale, Arizona 85259, United States
| | - Cassidy Turner
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, 13208 East Shea Boulevard, Scottsdale, Arizona 85259, United States
| | - Yan Jin
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, 13208 East Shea Boulevard, Scottsdale, Arizona 85259, United States
| | - Haiwei Gu
- Arizona Metabolomics Laboratory, College of Health Solutions, Arizona State University, 13208 East Shea Boulevard, Scottsdale, Arizona 85259, United States
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Direct and quantitative analysis of altered metabolic flux distributions and cellular ATP production pathway in fumarate hydratase-diminished cells. Sci Rep 2020; 10:13065. [PMID: 32747645 PMCID: PMC7400513 DOI: 10.1038/s41598-020-70000-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/20/2020] [Indexed: 01/22/2023] Open
Abstract
Fumarate hydratase (FH) is an enzyme in the tricarboxylic acid (TCA) cycle, biallelic loss-of-function mutations of which are associated with hereditary leiomyomatosis and renal cell cancer. However, how FH defect modulates intracellular metabolic fluxes in human cells has remained unclear. This study aimed to reveal metabolic flux alterations induced by reduced FH activity. We applied 13C metabolic flux analysis (13C-MFA) to an established cell line with diminished FH activity (FHdim) and parental HEK293 cells. FHdim cells showed reduced pyruvate import flux into mitochondria and subsequent TCA cycle fluxes. Interestingly, the diminished FH activity decreased FH flux only by about 20%, suggesting a very low need for FH to maintain the oxidative TCA cycle. Cellular ATP production from the TCA cycle was dominantly suppressed compared with that from glycolysis in FHdim cells. Consistently, FHdim cells exhibited higher glucose dependence for ATP production and higher resistance to an ATP synthase inhibitor. In summary, using FHdim cells we demonstrated that FH defect led to suppressed pyruvate import into mitochondria, followed by downregulated TCA cycle activity and altered ATP production pathway balance from the TCA cycle to glycolysis. We confirmed that 13C-MFA can provide direct and quantitative information on metabolic alterations induced by FH defect.
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35
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Huang Z, Xu J, Yongky A, Morris CS, Polanco AL, Reily M, Borys MC, Li ZJ, Yoon S. CHO cell productivity improvement by genome-scale modeling and pathway analysis: Application to feed supplements. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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36
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Yilmaz D, Parulekar SJ, Cinar A. A dynamic EFM-based model for antibody producing cell lines and model based evaluation of fed-batch processes. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Matsuda F, Maeda K, Okahashi N. Computational data mining method for isotopomer analysis in the quantitative assessment of metabolic reprogramming. Sci Rep 2020; 10:286. [PMID: 31937835 PMCID: PMC6959353 DOI: 10.1038/s41598-019-57146-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/18/2019] [Indexed: 12/12/2022] Open
Abstract
Measurement of metabolic flux levels using stable isotope labeling has been successfully used to investigate metabolic redirection and reprogramming in living cells or tissues. The metabolic flux ratio between two reactions can be estimated from the 13C-labeling patterns of a few metabolites combined with the knowledge of atom mapping in the complicated metabolic network. However, it remains unclear whether an observed change in the labeling pattern of the metabolites is sufficient evidence of a shift in flux ratio between two metabolic states. In this study, a data analysis method was developed for the quantitative assessment of metabolic reprogramming. The Metropolis-Hastings algorithm was used with an in silico metabolic model to generate a probability distribution of metabolic flux levels under a condition in which the 13C-labeling pattern was observed. Reanalysis of literature data demonstrated that the developed method enables analysis of metabolic redirection using whole 13C-labeling pattern data. Quantitative assessment by Cohen’s effect size (d) enables a more detailed read-out of metabolic reprogramming information. The developed method will enable future applications of the metabolic isotopomer analysis to various targets, including cultured cells, whole tissues, and organs.
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Affiliation(s)
- Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan.
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka, Japan
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38
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Selivanov VA, Marin S, Tarragó-Celada J, Lane AN, Higashi RM, Fan TWM, de Atauri P, Cascante M. Software Supporting a Workflow of Quantitative Dynamic Flux Maps Estimation in Central Metabolism from SIRM Experimental Data. Methods Mol Biol 2020; 2088:271-298. [PMID: 31893378 DOI: 10.1007/978-1-0716-0159-4_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Stable isotope-resolved metabolomics (SIRM), based on the analysis of biological samples from living cells incubated with artificial isotope enriched substrates, enables mapping the rates of biochemical reactions (metabolic fluxes). We developed software supporting a workflow of analysis of SIRM data obtained with mass spectrometry (MS). The evaluation of fluxes starting from raw MS recordings requires at least three steps of computer support: first, extraction of mass spectra of metabolites of interest, then correction of the spectra for natural isotope abundance, and finally, evaluation of fluxes by simulation of the corrected spectra using a corresponding mathematical model. A kinetic model based on ordinary differential equations (ODEs) for isotopomers of metabolites of the corresponding biochemical network supports the final part of the analysis, which provides a dynamic flux map.
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Affiliation(s)
- Vitaly A Selivanov
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain. .,INB-Bioinformatics Platform Metabolomics Node, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
| | - Silvia Marin
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Josep Tarragó-Celada
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain
| | - Andrew N Lane
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Richard M Higashi
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Teresa W-M Fan
- Markey Cancer Center, University of Kentucky, Lexington, KY, USA.,Center for Environment and Systems Biochemistry and the Resource Center for Stable Isotope Resolved Metabolomics, University of Kentucky, Lexington, KY, USA.,Department of Toxicology and Cancer Biology, University of Kentucky, Lexington, KY, USA
| | - Pedro de Atauri
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain.,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain.,INB-Bioinformatics Platform Metabolomics Node, Instituto de Salud Carlos III (ISCIII), Madrid, Spain
| | - Marta Cascante
- Department of Biochemistry and Molecular Biomedicine, Faculty of Biology, Universitat de Barcelona, Barcelona, Spain. .,Institute of Biomedicine of Universitat de Barcelona (IBUB), Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Instituto de Salud Carlos III (ISCIII), Madrid, Spain. .,INB-Bioinformatics Platform Metabolomics Node, Instituto de Salud Carlos III (ISCIII), Madrid, Spain.
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39
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BCAT1 and BCAT2 disruption in CHO cells has cell line-dependent effects. J Biotechnol 2019; 306:24-31. [PMID: 31465797 DOI: 10.1016/j.jbiotec.2019.08.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 08/18/2019] [Accepted: 08/25/2019] [Indexed: 11/20/2022]
Abstract
In recombinant protein expression using Chinese hamster ovary (CHO) cells, chemically defined media contain essential amino acids such as branched chain amino acids (BCAAs) leucine, isoleucine and valine. Availability of amino acids is critical as these are building blocks for protein synthesis. However, breakdown of amino acids can lead to build up of toxic intermediates and metabolites that decrease cell growth, productivity and product quality. BCAA catabolism also hampers the usage of BCAAs for protein synthesis. In this work we studied the effects of disrupting the genes responsible for the first step of BCAA catabolism: branched chain aminotransferase 1 (Bcat1) and branched chain aminotransferase 2 (Bcat2). We evaluated the effect of disrupting the genes individually and in combination, and examined the effects in producer and non-producer host cells. Our experiments show that Bcat1 disruption improves cell growth in producer cells, but not in non-producers. Conversely, Bcat2 has a minor negative effect on growth in producer cells, and none in non-producers. Combined Bcat1 and Bcat2 disruption improves growth in producer cells. By-product metabolism is cell line-, clone- and producer-dependent. Overall, our results show that the effects of targeting Bcat1 and/or Bcat2 are cell line-dependent, and seemingly linked to the burden of recombinant protein expression.
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40
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Metabolic flux ratio analysis by parallel 13C labeling of isoprenoid biosynthesis in Rhodobacter sphaeroides. Metab Eng 2019; 57:228-238. [PMID: 31843486 DOI: 10.1016/j.ymben.2019.12.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 12/02/2019] [Accepted: 12/12/2019] [Indexed: 11/21/2022]
Abstract
Metabolic engineering for increased isoprenoid production often benefits from the simultaneous expression of the two naturally available isoprenoid metabolic routes, namely the 2-methyl-D-erythritol 4-phosphate (MEP) pathway and the mevalonate (MVA) pathway. Quantification of the contribution of these pathways to the overall isoprenoid production can help to obtain a better understanding of the metabolism within a microbial cell factory. Such type of investigation can benefit from 13C metabolic flux ratio studies. Here, we designed a method based on parallel labeling experiments (PLEs), using [1-13C]- and [4-13C]glucose as tracers to quantify the metabolic flux ratios in the glycolytic and isoprenoid pathways. By just analyzing a reporter isoprenoid molecule and employing only four equations, we could describe the metabolism involved from substrate catabolism to product formation. These equations infer 13C atom incorporation into the universal isoprenoid building blocks, isopentenyl-pyrophosphate (IPP) and dimethylallyl-pyrophosphate (DMAPP). Therefore, this renders the method applicable to the study of any of isoprenoid of interest. As proof of principle, we applied it to study amorpha-4,11-diene biosynthesis in the bacterium Rhodobacter sphaeroides. We confirmed that in this species the Entner-Doudoroff pathway is the major pathway for glucose catabolism, while the Embden-Meyerhof-Parnas pathway contributes to a lesser extent. Additionally, we demonstrated that co-expression of the MEP and MVA pathways caused a mutual enhancement of their metabolic flux capacity. Surprisingly, we also observed that the isoprenoid flux ratio remains constant under exponential growth conditions, independently from the expression level of the MVA pathway. Apart from proposing and applying a tool for studying isoprenoid biosynthesis within a microbial cell factory, our work reveals important insights from the co-expression of MEP and MVA pathways, including the existence of a yet unclear interaction between them.
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41
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Hu L, Zeng Z, Xia Q, Liu Z, Feng X, Chen J, Huang M, Chen L, Fang Z, Liu Q, Zeng H, Zhou X, Liu J. Metformin attenuates hepatoma cell proliferation by decreasing glycolytic flux through the HIF-1α/PFKFB3/PFK1 pathway. Life Sci 2019; 239:116966. [PMID: 31626790 DOI: 10.1016/j.lfs.2019.116966] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 10/12/2019] [Accepted: 10/13/2019] [Indexed: 12/24/2022]
Abstract
AIMS Enhanced aerobic glycolysis is an essential hallmark of malignant cancer. Blocking the glycolytic pathway has been suggested as a therapeutic strategy to impair the proliferation of tumor cells. Metformin, a widely used anti-diabetes drug, exhibits anti-tumor properties. However, the underlying molecular mechanism of its action linking glucose metabolism with the suppression of proliferation has not been fully clarified. MAIN METHODS Stable isotope tracing technology and gas chromatography-mass spectrometry method were utilized to analyze the effect of metformin on glycolytic flux in HCC cells. Western blot and immunohistochemistry were utilized to analyze the expression of phosphofructokinase-1 (PFK1) and 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) in HCC cells or xenograft tumor tissues. Lactate measurement and glucose uptake assay were used to analyze the level of lactate and glucose in the presence of frucose-2,6-diphosphate (F2,6BP) in HCC cells treated with metformin. KEY FINDINGS We found that metformin significantly impaired hepatoma cell proliferation by inhibiting the glycolytic flux via PFK1 blockade. Interestingly, activation of PFK1 by F2,6BP reverses the inhibitory effect of metformin on hepatoma cell proliferation and glycolysis. Mechanistically, PFKFB3,a potent allosteric activator of PFK1, was markedly suppressed through inhibiting hypoxia-induced factor 1 (HIF-1α) accumulation mediated by metformin. SIGNIFICANCE Taken together these data indicate that HIF-1α/PFKFB3/PFK1 regulatory axis is a vital determinant of glucose metabolic reprogramming in hepatocellular carcinoma, which gives new insights into the action of metformin in combatting liver cancer.
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Affiliation(s)
- La Hu
- Cancer Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Zicheng Zeng
- Cancer Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Qing Xia
- Department of Oncology, State Key Laboratory for Oncogenes and Related Genes, Renji Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai Cancer Institute, Shanghai, 200127, China
| | - Zhaoyu Liu
- Cancer Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Xiao Feng
- Cancer Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Jitao Chen
- Cancer Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Mengqiu Huang
- Cancer Institute, Southern Medical University, Guangzhou, 510515, China
| | - Liangcai Chen
- Cancer Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Zhiyuan Fang
- Cancer Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Qiuzhen Liu
- Cancer Institute, Southern Medical University, Guangzhou, 510515, China
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Xinke Zhou
- Cancer Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
| | - Jifang Liu
- Cancer Center, The Fifth Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China.
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42
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Chen Y, McConnell BO, Gayatri Dhara V, Mukesh Naik H, Li CT, Antoniewicz MR, Betenbaugh MJ. An unconventional uptake rate objective function approach enhances applicability of genome-scale models for mammalian cells. NPJ Syst Biol Appl 2019; 5:25. [PMID: 31341637 PMCID: PMC6650483 DOI: 10.1038/s41540-019-0103-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 07/08/2019] [Indexed: 12/18/2022] Open
Abstract
Constraint-based modeling has been applied to analyze metabolism of numerous organisms via flux balance analysis and genome-scale metabolic models, including mammalian cells such as the Chinese hamster ovary (CHO) cells-the principal cell factory platform for therapeutic protein production. Unfortunately, the application of genome-scale model methodologies using the conventional biomass objective function is challenged by the presence of overly-restrictive constraints, including essential amino acid exchange fluxes that can lead to improper predictions of growth rates and intracellular flux distributions. In this study, these constraints are found to be reliably predicted by an "essential nutrient minimization" approach. After modifying these constraints with the predicted minimal uptake values, a series of unconventional objective functions are applied to minimize each individual non-essential nutrient uptake rate, revealing useful insights about metabolic exchange rates and flows across different cell lines and culture conditions. This unconventional uptake-rate objective functions (UOFs) approach is able to distinguish metabolic differences between three distinct CHO cell lines (CHO-K1, -DG44, and -S) not directly observed using the conventional biomass growth maximization solutions. Further, a comparison of model predictions with experimental data from literature correctly correlates with the specific CHO-DG44-derived cell line used experimentally, and the corresponding dual prices provide fruitful information concerning coupling relationships between nutrients. The UOFs approach is likely to be particularly suited for mammalian cells and other complex organisms which contain multiple distinct essential nutrient inputs, and may offer enhanced applicability for characterizing cell metabolism and physiology as well as media optimization and biomanufacturing control.
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Affiliation(s)
- Yiqun Chen
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Brian O McConnell
- 2Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716 USA
| | - Venkata Gayatri Dhara
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Harnish Mukesh Naik
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Chien-Ting Li
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
| | - Maciek R Antoniewicz
- 2Department of Chemical and Biomolecular Engineering, Metabolic Engineering and Systems Biology Laboratory, University of Delaware, 150 Academy St, Newark, DE 19716 USA
| | - Michael J Betenbaugh
- 1Department of Chemical and Biomolecular Engineering, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD 21218 USA
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43
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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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44
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Abstract
Intensified and accelerated development processes are being demanded by the market, as innovative biopharmaceuticals such as virus-like particles, exosomes, cell and gene therapy, as well as recombinant proteins and peptides will possess no available platform approach. Therefore, methods that are able to accelerate this development are preferred. Especially, physicochemical rigorous process models, based on all relevant effects of fluid dynamics, phase equilibrium, and mass transfer, can be predictive, if the model is verified and distinctly quantitatively validated. In this approach, a macroscopic kinetic model based on Monod kinetics for mammalian cell cultivation is developed and verified according to a general valid model validation workflow. The macroscopic model is verified and validated on the basis of four decision criteria (plausibility, sensitivity, accuracy and precision as well as equality). The process model workflow is subjected to a case study, comprising a Chinese hamster ovary fed-batch cultivation for the production of a monoclonal antibody. By performing the workflow, it was found that, based on design of experiments and Monte Carlo simulation, the maximum growth rate µmax exhibited the greatest influence on model variables such as viable cell concentration XV and product concentration. In addition, partial least squares regressions statistically evaluate the correlations between a higher µmax and a higher cell and product concentration, as well as a higher substrate consumption.
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45
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Wong HE, Huang CJ, Zhang Z. Amino Acid Misincorporation Propensities Revealed through Systematic Amino Acid Starvation. Biochemistry 2018; 57:6767-6779. [DOI: 10.1021/acs.biochem.8b00976] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- H. Edward Wong
- Process Development, Amgen, Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Chung-Jr Huang
- Process Development, Amgen, Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
| | - Zhongqi Zhang
- Process Development, Amgen, Inc., 1 Amgen Center Drive, Thousand Oaks, California 91320, United States
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46
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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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47
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Reinhart D, Damjanovic L, Castan A, Ernst W, Kunert R. Differential gene expression of a feed-spiked super-producing CHO cell line. J Biotechnol 2018; 285:23-37. [PMID: 30157452 DOI: 10.1016/j.jbiotec.2018.08.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 08/15/2018] [Accepted: 08/25/2018] [Indexed: 01/09/2023]
Abstract
Feed supplements are concentrated cell culture media that contain a variety of nutrients, which can be added during a bioprocess. During fed-batch cultivation, feed media are typically added to a growing cell culture to maximize cell and product concentrations. In this study, only a single shot of feed medium was added on day 0 to a basal cell culture medium and compared to non-supplemented basal medium (feed-spiked at day 0 versus control experiments) by cultivation of a recombinant mAb expressing CHO cell line in batch mode under controlled conditions in a bioreactor. Since the feed-spike at day 0 was based on existing medium components without introducing additional supplements, a desirable process with decreased complexity was generated. Unlike cells in basal medium, feed-spiked cultures reached almost 2× higher peak cell concentrations (10 × 106 c/mL vs. 18 × 106 c/mL) and 3× higher antibody concentrations (0.8 g/L vs. 2.4 g/L). Batch process time and the integral over the viable cell count were similar for both process types. Constantly high cell-specific production rates in feed-spiked cultures (70 pg/cell/day) compared to continuously declining rates in basal medium (from 70 to 10 pg/cell/day) were responsible for an overall 70% higher cell-specific production rate and the higher product concentrations. To associate gene expression patterns to different process proceedings, transcriptome analysis was performed using microarrays. Several transcripts that are involved with glutamine de novo synthesis and citric acid cycle were significantly upregulated on several days in feed-spiked cultures. The top identified gene ontology (GO) terms related well to cell cycle and primary metabolism, cellular division as well as nucleobase formation or regulation, which indicated a more active proliferative state for feed-spiked cultures. KEGG biochemical pathway analysis and Gene set enrichment analysis (GSEA) further confirmed these findings from a complementary perspective. Moreover, several interesting gene targets, which have not yet been associated with recombinant protein expression, were identified that related to a higher proliferative state, growth, protein synthesis, cell-size control, metabolism, cell survival as well as genes that are associated with the control of the mammalian target of rapamycin (mTOR) in feed-spiked cultures. Analysis of critical product quality attributes (i.e. glycosylation, charge variants and size distribution) showed that feed-spiking did not change antibody quality.
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Affiliation(s)
- David Reinhart
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
| | - Lukas Damjanovic
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
| | - Andreas Castan
- GE Healthcare Life Sciences AB, Björkgatan 30, 75184, Uppsala, Sweden.
| | - Wolfgang Ernst
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
| | - Renate Kunert
- Department of Biotechnology, University of Natural Resources and Life Sciences, Vienna, Muthgasse 11, 1190 Vienna, Austria.
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48
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Smith RL, Soeters MR, Wüst RCI, Houtkooper RH. Metabolic Flexibility as an Adaptation to Energy Resources and Requirements in Health and Disease. Endocr Rev 2018; 39:489-517. [PMID: 29697773 PMCID: PMC6093334 DOI: 10.1210/er.2017-00211] [Citation(s) in RCA: 341] [Impact Index Per Article: 56.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Accepted: 04/19/2018] [Indexed: 12/15/2022]
Abstract
The ability to efficiently adapt metabolism by substrate sensing, trafficking, storage, and utilization, dependent on availability and requirement, is known as metabolic flexibility. In this review, we discuss the breadth and depth of metabolic flexibility and its impact on health and disease. Metabolic flexibility is essential to maintain energy homeostasis in times of either caloric excess or caloric restriction, and in times of either low or high energy demand, such as during exercise. The liver, adipose tissue, and muscle govern systemic metabolic flexibility and manage nutrient sensing, uptake, transport, storage, and expenditure by communication via endocrine cues. At a molecular level, metabolic flexibility relies on the configuration of metabolic pathways, which are regulated by key metabolic enzymes and transcription factors, many of which interact closely with the mitochondria. Disrupted metabolic flexibility, or metabolic inflexibility, however, is associated with many pathological conditions including metabolic syndrome, type 2 diabetes mellitus, and cancer. Multiple factors such as dietary composition and feeding frequency, exercise training, and use of pharmacological compounds, influence metabolic flexibility and will be discussed here. Last, we outline important advances in metabolic flexibility research and discuss medical horizons and translational aspects.
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Affiliation(s)
- Reuben L Smith
- Laboratory of Genetic Metabolic Diseases, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Gastroenterology and Metabolism, Academic Medical Center, AZ Amsterdam, Netherlands
| | - Maarten R Soeters
- Amsterdam Gastroenterology and Metabolism, Academic Medical Center, AZ Amsterdam, Netherlands.,Department of Endocrinology and Metabolism, Internal Medicine, Academic Medical Center, AZ Amsterdam, Netherlands
| | - Rob C I Wüst
- Laboratory of Genetic Metabolic Diseases, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Cardiovascular Sciences, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Movement Sciences, Academic Medical Center, AZ Amsterdam, Netherlands
| | - Riekelt H Houtkooper
- Laboratory of Genetic Metabolic Diseases, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Gastroenterology and Metabolism, Academic Medical Center, AZ Amsterdam, Netherlands.,Amsterdam Cardiovascular Sciences, Academic Medical Center, AZ Amsterdam, Netherlands
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49
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Zamani L, Lundqvist M, Zhang Y, Aberg M, Edfors F, Bidkhori G, Lindahl A, Mie A, Mardinoglu A, Field R, Turner R, Rockberg J, Chotteau V. High Cell Density Perfusion Culture has a Maintained Exoproteome and Metabolome. Biotechnol J 2018; 13:e1800036. [DOI: 10.1002/biot.201800036] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 06/03/2018] [Indexed: 01/10/2023]
Affiliation(s)
- Leila Zamani
- Department Industrial Biotechnology; School of Engineering Sciences in Chemistry, Biotechnology, and Health; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
| | - Magnus Lundqvist
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Wallenberg Centre for Protein Research; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; AdBIOPRO, Centre for Advanced Bioproduction by Continuous Processing; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
| | - Ye Zhang
- Department Industrial Biotechnology; School of Engineering Sciences in Chemistry, Biotechnology, and Health; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Wallenberg Centre for Protein Research; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
| | - Magnus Aberg
- Department of Analytical Chemistry; Stockholm University; 106 91 Stockholm Sweden
| | - Fredrik Edfors
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Science for Life Laboratory; KTH-Royal Institute of Technology; 171 65 Stockholm Sweden
| | - Gholamreza Bidkhori
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Science for Life Laboratory; KTH-Royal Institute of Technology; 171 65 Stockholm Sweden
| | - Anna Lindahl
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; 171 65 Solna Sweden
| | - Axel Mie
- Department of Clinical Science and Education; Karolinska Institute; 118 83 Solna Sweden
| | - Adil Mardinoglu
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Science for Life Laboratory; KTH-Royal Institute of Technology; 171 65 Stockholm Sweden
| | - Raymond Field
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; 171 65 Solna Sweden
| | - Richard Turner
- Department of Oncology-Pathology; Science for Life Laboratory; Karolinska Institutet; 171 65 Solna Sweden
| | - Johan Rockberg
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Wallenberg Centre for Protein Research; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; AdBIOPRO, Centre for Advanced Bioproduction by Continuous Processing; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
| | - Veronique Chotteau
- Department Industrial Biotechnology; School of Engineering Sciences in Chemistry, Biotechnology, and Health; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; Wallenberg Centre for Protein Research; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- School of Engineering Sciences in Chemistry, Biotechnology, and Health; AdBIOPRO, Centre for Advanced Bioproduction by Continuous Processing; KTH-Royal Institute of Technology; 106 91 Stockholm Sweden
- Biopharmaceutical Development; MedImmune; CB21 6GH Cambridge United Kingdom
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Araki C, Okahashi N, Maeda K, Shimizu H, Matsuda F. Mass Spectrometry-Based Method to Study Inhibitor-Induced Metabolic Redirection in the Central Metabolism of Cancer Cells. Mass Spectrom (Tokyo) 2018; 7:A0067. [PMID: 29922569 PMCID: PMC6002601 DOI: 10.5702/massspectrometry.a0067] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Accepted: 04/24/2018] [Indexed: 11/23/2022] Open
Abstract
Cancer cells often respond to chemotherapeutic inhibitors by redirecting carbon flow in the central metabolism. To understand the metabolic redirections of inhibitor treatment on cancer cells, this study established a 13C-metabolic flux analysis (13C-MFA)-based method to evaluate metabolic redirection in MCF-7 breast cancer cells using mass spectrometry. A metabolic stationary state necessary for accurate 13C-MFA was confirmed during an 8-24 h window using low-dose treatments of various metabolic inhibitors. Further 13C-labeling experiments using [1-13C]glucose and [U-13C]glutamine, combined with gas chromatography-mass spectrometry (GC-MS) analysis of mass isotopomer distributions (MIDs), confirmed that an isotopic stationary state of intracellular metabolites was reached 24 h after treatment with paclitaxel (Taxol), an inhibitor of mitosis used for cancer treatment. Based on these metabolic and isotopic stationary states, metabolic flux distribution in the central metabolism of paclitaxel-treated MCF-7 cells was determined by 13C-MFA. Finally, estimations of the 95% confidence intervals showed that tricarboxylic acid cycle metabolic flux increased after paclitaxel treatment. Conversely, anaerobic glycolysis metabolic flux decreased, revealing metabolic redirections by paclitaxel inhibition. The gap between total regeneration and consumption of ATP in paclitaxel-treated cells was also found to be 1.2 times greater than controls, suggesting ATP demand was increased by paclitaxel treatment, likely due to increased microtubule polymerization. These data confirm that 13C-MFA can be used to investigate inhibitor-induced metabolic redirection in cancer cells. This will contribute to future pharmaceutical developments and understanding variable patient response to treatment.
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Affiliation(s)
- Chie Araki
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Nobuyuki Okahashi
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Kousuke Maeda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Hiroshi Shimizu
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
| | - Fumio Matsuda
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University
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