1
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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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2
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Pellegrini H, Sharpe EH, Liu G, Nishiuchi E, Doerr N, Kipp KR, Chin T, Schimmel MF, Weimbs T. Cleavage fragments of the C-terminal tail of polycystin-1 are regulated by oxidative stress and induce mitochondrial dysfunction. J Biol Chem 2023; 299:105158. [PMID: 37579949 PMCID: PMC10502374 DOI: 10.1016/j.jbc.2023.105158] [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: 03/21/2023] [Revised: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 08/16/2023] Open
Abstract
Mutations in the gene encoding polycystin-1 (PC1) are the most common cause of autosomal dominant polycystic kidney disease (ADPKD). Cysts in ADPKD exhibit a Warburg-like metabolism characterized by dysfunctional mitochondria and aerobic glycolysis. PC1 is an integral membrane protein with a large extracellular domain, a short C-terminal cytoplasmic tail and shares structural and functional similarities with G protein-coupled receptors. Its exact function remains unclear. The C-terminal cytoplasmic tail of PC1 undergoes proteolytic cleavage, generating soluble fragments that are overexpressed in ADPKD kidneys. The regulation, localization, and function of these fragments is poorly understood. Here, we show that a ∼30 kDa cleavage fragment (PC1-p30), comprising the entire C-terminal tail, undergoes rapid proteasomal degradation by a mechanism involving the von Hippel-Lindau tumor suppressor protein. PC1-p30 is stabilized by reactive oxygen species, and the subcellular localization is regulated by reactive oxygen species in a dose-dependent manner. We found that a second, ∼15 kDa fragment (PC1-p15), is generated by caspase cleavage at a conserved site (Asp-4195) on the PC1 C-terminal tail. PC1-p15 is not subject to degradation and constitutively localizes to the mitochondrial matrix. Both cleavage fragments induce mitochondrial fragmentation, and PC1-p15 expression causes impaired fatty acid oxidation and increased lactate production, indicative of a Warburg-like phenotype. Endogenous PC1 tail fragments accumulate in renal cyst-lining cells in a mouse model of PKD. Collectively, these results identify novel mechanisms regarding the regulation and function of PC1 and suggest that C-terminal PC1 fragments may be involved in the mitochondrial and metabolic abnormalities observed in ADPKD.
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Affiliation(s)
- Hannah Pellegrini
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Elizabeth H Sharpe
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Guangyi Liu
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA; Department of Nephrology, Qilu Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Eiko Nishiuchi
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Nicholas Doerr
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Kevin R Kipp
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Tiffany Chin
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Margaret F Schimmel
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA
| | - Thomas Weimbs
- Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, USA.
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3
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Ramos JRC, Bissinger T, Genzel Y, Reichl U. Impact of Influenza A Virus Infection on Growth and Metabolism of Suspension MDCK Cells Using a Dynamic Model. Metabolites 2022; 12:metabo12030239. [PMID: 35323683 PMCID: PMC8950586 DOI: 10.3390/metabo12030239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 11/21/2022] Open
Abstract
Cell cultured-based influenza virus production is a viable option for vaccine manufacturing. In order to achieve a high concentration of viable cells, is requirement to have not only optimal process conditions, but also an active metabolism capable of intracellular synthesis of viral components. Experimental metabolic data collected in such processes are complex and difficult to interpret, for which mathematical models are an appropriate way to simulate and analyze the complex and dynamic interaction between the virus and its host cell. A dynamic model with 35 states was developed in this study to describe growth, metabolism, and influenza A virus production in shake flask cultivations of suspension Madin-Darby Canine Kidney (MDCK) cells. It considers cell growth (concentration of viable cells, mean cell diameters, volume of viable cells), concentrations of key metabolites both at the intracellular and extracellular level and virus titers. Using one set of parameters, the model accurately simulates the dynamics of mock-infected cells and correctly predicts the overall dynamics of virus-infected cells for up to 60 h post infection (hpi). The model clearly suggests that most changes observed after infection are related to cessation of cell growth and the subsequent transition to apoptosis and cell death. However, predictions do not cover late phases of infection, particularly for the extracellular concentrations of glutamate and ammonium after about 12 hpi. Results obtained from additional in silico studies performed indicated that amino acid degradation by extracellular enzymes resulting from cell lysis during late infection stages may contribute to this observed discrepancy.
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Affiliation(s)
- João Rodrigues Correia Ramos
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
- Correspondence:
| | - Thomas Bissinger
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
- Institute of Process Engineering, Faculty of Process & Systems Engineering, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
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4
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Zhu Y, Xu J, Lian S, Zhang R, Hou J, Wang M, Yan X. Difference Analysis Between Canine Adenovirus Types 1 And 2. Front Cell Infect Microbiol 2022; 12:854876. [PMID: 35360116 PMCID: PMC8963759 DOI: 10.3389/fcimb.2022.854876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/21/2022] [Indexed: 11/13/2022] Open
Abstract
Canine adenoviruses (CAdVs) include type 1 (CAdV-1, virulent strain) and type 2 (CAdV-2, attenuated strain). In recent years, the incidences of CAdV infections are increasing. However, they are difficult to distinguish when the symptoms are untypical. It is pivotal to find the differences between the two virus types for scientific, epidemiological, and specific treatment. CAdV-1 (virulent strain) and CAdV-2 (attenuated strain) induced canine hepatitis (ICH) and tracheobronchitis (ITB), respectively, but the clinical symptom is not obvious. CAdV-1 and CAdV-2 have the same genome structure, diameter, morphological features, and cytopathic features, but the same character hinder the diagnose time of the serotypes. CAdV-1 and CAdV-2 have a difference in the genome sequence, coding proteins, viral activity, hemagglutination patterns. After infection, pathogenicity and transmission route are different between the two serotypes. Sequence alignment, PCR, Real time-PCR assay are useful methods to distinguish the two serotypes. The attenuated live CAdV-2 vaccine is currently used to protect against CAdV-1, but it also has a risk. The further research should focus on the pathogenicity mechanism and the useful vaccine for the two serotypes of canine adenovirus.
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Affiliation(s)
- Yanzhu Zhu
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, China
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
- *Correspondence: Yanzhu Zhu,
| | - Jinfeng Xu
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shizhen Lian
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, China
| | - Rui Zhang
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, China
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Jinyu Hou
- College of Traditional Chinese Medicine, Jilin Agricultural University, Changchun, China
| | - Minchun Wang
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, China
| | - Xijun Yan
- Institute of Special Animal and Plant Sciences of Chinese Academy of Agricultural Sciences, Changchun, China
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5
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Sacco SA, Young JD. 13C metabolic flux analysis in cell line and bioprocess development. Curr Opin Chem Eng 2021. [DOI: 10.1016/j.coche.2021.100718] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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6
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Zhu Y, Sun J, Yan M, Lian S, Hu B, Lv S, Li Y, Zhang Y, Yan X. The biological characteristics of the canine adenovirus type 1 from fox and the transcriptome analysis of the infected MDCK cell. Cell Biol Int 2021; 45:936-947. [PMID: 33382191 DOI: 10.1002/cbin.11537] [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: 08/12/2020] [Revised: 12/09/2020] [Accepted: 12/25/2020] [Indexed: 11/09/2022]
Abstract
Canine adenovirus type 1 (CAdV-1) is the etiologic agent of fox encephalitis, and a virus strain from fox encephalitis is isolated and related research are conducted. In this experiment, the results showed that the F1301 strain was confirmed to be the CAdV-1. The whole genome of the CAdV-1 F1301 strain isolated from fox was 30,535 bp and had higher homology to the other reported CAdV-1 strains. After 0, 12, and 36 h of CAdV-1 infection, the difference gene of the 592 long noncoding RNA and 11,215 microRNA were involved in cell responses to CAdV-1 infection through the PI3K-AKT, Wnt, Herpes simplex, hepatitis C, and Epstein-Barr virus infection pathway in Madin-Darby canine kidney cell line (MDCK). The results indicate that the biological characterization of the CAdV-1 and the MDCK cell-CAdV-1 interaction are clarified.
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Affiliation(s)
- Yanzhu Zhu
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Jie Sun
- Pharmaron Beijing Co., Ltd., Beijing, China
| | - Minghao Yan
- Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Shizhen Lian
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Bo Hu
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Shuang Lv
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yali Li
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yufei Zhang
- National Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
| | - Xijun Yan
- Key Laboratory of Special Animal Epidemic Disease, Ministry of Agriculture, Institute of Special Animal and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China.,Sinovet Biopharm. Co., Ltd., Taizhou, China
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7
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Laevskaya A, Borovjagin A, Timashev PS, Lesniak MS, Ulasov I. Metabolome-Driven Regulation of Adenovirus-Induced Cell Death. Int J Mol Sci 2021; 22:ijms22010464. [PMID: 33466472 PMCID: PMC7796492 DOI: 10.3390/ijms22010464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/26/2020] [Accepted: 12/27/2020] [Indexed: 02/06/2023] Open
Abstract
A viral infection that involves virus invasion, protein synthesis, and virion assembly is typically accompanied by sharp fluctuations in the intracellular levels of metabolites. Under certain conditions, dramatic metabolic shifts can result in various types of cell death. Here, we review different types of adenovirus-induced cell death associated with changes in metabolic profiles of the infected cells. As evidenced by experimental data, in most cases changes in the metabolome precede cell death rather than represent its consequence. In our previous study, the induction of autophagic cell death was observed following adenovirus-mediated lactate production, acetyl-CoA accumulation, and ATP release, while apoptosis was demonstrated to be modulated by alterations in acetate and asparagine metabolism. On the other hand, adenovirus-induced ROS production and ATP depletion were demonstrated to play a significant role in the process of necrotic cell death. Interestingly, the accumulation of ceramide compounds was found to contribute to the induction of all the three types of cell death mentioned above. Eventually, the characterization of metabolite analysis could help in uncovering the molecular mechanism of adenovirus-mediated cell death induction and contribute to the development of efficacious oncolytic adenoviral vectors.
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Affiliation(s)
- Anastasia Laevskaya
- Group of Experimental Biotherapy and Diagnostic, Institute for Regenerative Medicine, World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
| | - Anton Borovjagin
- Department of Biomedical Engineering, University of Alabama at Birmingham, Birmingham, AL 35294, USA;
| | - Peter S. Timashev
- Institute for Regenerative Medicine, World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Department of Polymers and Composites, N.N.Semenov Institute of Chemical Physics, 4 Kosygin St., 119991 Moscow, Russia
- Chemistry Department, Lomonosov Moscow State University, Leninskiye Gory 1-3, 119991 Moscow, Russia
| | - Maciej S. Lesniak
- Department of Neurological Surgery, Northwestern University, Chicago, IL 60601, USA;
| | - Ilya Ulasov
- Group of Experimental Biotherapy and Diagnostic, Institute for Regenerative Medicine, World-Class Research Center “Digital Biodesign and Personalized Healthcare”, Sechenov First Moscow State Medical University, 119991 Moscow, Russia;
- Correspondence:
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8
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He ST, Lee DY, Tung CY, Li CY, Wang HC. Glutamine Metabolism in Both the Oxidative and Reductive Directions Is Triggered in Shrimp Immune Cells (Hemocytes) at the WSSV Genome Replication Stage to Benefit Virus Replication. Front Immunol 2019; 10:2102. [PMID: 31555294 PMCID: PMC6737011 DOI: 10.3389/fimmu.2019.02102] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/20/2019] [Indexed: 12/15/2022] Open
Abstract
White spot syndrome virus (WSSV) is the causative agent of a shrimp disease that has caused huge global economic losses. Although its pathogenesis remains poorly understood, it has been reported that in the shrimp immune cells (hemocytes) targeted by WSSV, the virus triggers both the Warburg effect and glutamine metabolism at the WSSV genome replication stage (12 h post infection). Glutamine metabolism follows two pathways: an oxidative pathway mediated by α-KGDH (α-ketoglutarate dehydrogenase) and an alternative reductive pathway mediated by IDH1 and IDH2 (isocitrate dehydrogenase 1 and 2). Here we used isotopically labeled glutamine ([U-13C]glutamine and [1-13C]glutamine) as metabolic tracers to show that, at the replication stage, both the oxidative and reductive glutamine metabolic pathways were activated. We further show that the mRNA expression levels of α-KGDH and IDH1 were increased in WSSV-infected shrimps and that silencing of α-KGDH, IDH1, and IDH2 with their respective dsRNAs led to a decrease in WSSV gene expression and WSSV replication. Taken together, our findings provide new evidence for WSSV-induced metabolic reprogramming in hemocytes and demonstrate its importance in virus replication.
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Affiliation(s)
- Shu-Ting He
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Der-Yen Lee
- Graduate Institute of Integrated Medicine, China Medical University, Taichung, Taiwan
| | - Cheng-Yi Tung
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Chun-Yuan Li
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan
| | - Han-Ching Wang
- Department of Biotechnology and Bioindustry Sciences, College of Biosciences and Biotechnology, National Cheng Kung University, Tainan, Taiwan.,International Center for the Scientific Development of Shrimp Aquaculture, National Cheng Kung University, Tainan, Taiwan
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9
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Correia C, Koshkin A, Duarte P, Hu D, Teixeira A, Domian I, Serra M, Alves PM. Distinct carbon sources affect structural and functional maturation of cardiomyocytes derived from human pluripotent stem cells. Sci Rep 2017; 7:8590. [PMID: 28819274 PMCID: PMC5561128 DOI: 10.1038/s41598-017-08713-4] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 07/12/2017] [Indexed: 12/15/2022] Open
Abstract
The immature phenotype of human pluripotent stem cell derived cardiomyocytes (hPSC-CMs) constrains their potential in cell therapy and drug testing. In this study, we report that shifting hPSC-CMs from glucose-containing to galactose- and fatty acid-containing medium promotes their fast maturation into adult-like CMs with higher oxidative metabolism, transcriptional signatures closer to those of adult ventricular tissue, higher myofibril density and alignment, improved calcium handling, enhanced contractility, and more physiological action potential kinetics. Integrated "-Omics" analyses showed that addition of galactose to culture medium improves total oxidative capacity of the cells and ameliorates fatty acid oxidation avoiding the lipotoxicity that results from cell exposure to high fatty acid levels. This study provides an important link between substrate utilization and functional maturation of hPSC-CMs facilitating the application of this promising cell type in clinical and preclinical applications.
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Affiliation(s)
- Cláudia Correia
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2780-901, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, 2780-157, Portugal
| | - Alexey Koshkin
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2780-901, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, 2780-157, Portugal
| | - Patrícia Duarte
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2780-901, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, 2780-157, Portugal
| | - Dongjian Hu
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA 02115, USA, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Ana Teixeira
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2780-901, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, 2780-157, Portugal
- ETH Zurich, Department of Biosystems Science and Engineering, Mattenstrasse 26, 4058, Basel, Switzerland
| | - Ibrahim Domian
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, 02114, USA
- Harvard Medical School, Boston, MA 02115, USA, Harvard Stem Cell Institute, Cambridge, MA, 02138, USA
| | - Margarida Serra
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2780-901, Portugal.
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, 2780-157, Portugal.
| | - Paula M Alves
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, Oeiras, 2780-901, Portugal.
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB-NOVA), Oeiras, 2780-157, Portugal.
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10
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Carinhas N, Koshkin A, Pais DAM, Alves PM, Teixeira AP. 13 C-metabolic flux analysis of human adenovirus infection: Implications for viral vector production. Biotechnol Bioeng 2016; 114:195-207. [PMID: 27477740 DOI: 10.1002/bit.26063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Revised: 07/24/2016] [Accepted: 07/26/2016] [Indexed: 01/08/2023]
Abstract
Adenoviruses are human pathogens increasingly used as gene therapy and vaccination vectors. However, their impact on cell metabolism is poorly characterized. We performed carbon labeling experiments with [1,2-13 C]glucose or [U-13 C]glutamine to evaluate metabolic alterations in the amniocyte-derived, E1-transformed 1G3 cell line during production of a human adenovirus type 5 vector (AdV5). Nonstationary 13 C-metabolic flux analysis revealed increased fluxes of glycolysis (17%) and markedly PPP (over fourfold) and cytosolic AcCoA formation (nearly twofold) following infection of growing cells. Interestingly, infection of growth-arrested cells increased overall carbon flow even more, including glutamine anaplerosis and TCA cycle activity (both over 1.5-fold), but was unable to stimulate the PPP and was associated with a steep drop in AdV5 replication (almost 80%). Our results underscore the importance of nucleic and fatty acid biosynthesis for adenovirus replication. Overall, we portray a metabolic blueprint of human adenovirus infection, highlighting similarities with other viruses and cancer, and suggest strategies to improve AdV5 production. Biotechnol. Bioeng. 2017;114: 195-207. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Nuno Carinhas
- iBET, Instituto de Biologia Experimental e Tecnológica, Avenida da República, Oeiras, 2781-157, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Oeiras, 2780-157, Portugal
| | - Alexey Koshkin
- iBET, Instituto de Biologia Experimental e Tecnológica, Avenida da República, Oeiras, 2781-157, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Oeiras, 2780-157, Portugal
| | - Daniel A M Pais
- iBET, Instituto de Biologia Experimental e Tecnológica, Avenida da República, Oeiras, 2781-157, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Oeiras, 2780-157, Portugal
| | - Paula M Alves
- iBET, Instituto de Biologia Experimental e Tecnológica, Avenida da República, Oeiras, 2781-157, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Oeiras, 2780-157, Portugal
| | - Ana P Teixeira
- iBET, Instituto de Biologia Experimental e Tecnológica, Avenida da República, Oeiras, 2781-157, Portugal.,Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Avenida da República, Oeiras, 2780-157, Portugal
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11
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Impact of Adenovirus infection in host cell metabolism evaluated by (1)H-NMR spectroscopy. J Biotechnol 2016; 231:16-23. [PMID: 27215342 DOI: 10.1016/j.jbiotec.2016.05.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Revised: 05/12/2016] [Accepted: 05/19/2016] [Indexed: 12/22/2022]
Abstract
Adenovirus-based vectors are powerful vehicles for gene transfer applications in vaccination and gene therapy. Although highly exploited in the clinical setting, key aspects of the adenovirus biology are still not well understood, in particular the subversion of host cell metabolism during viral infection and replication. The aim of this work was to gain insights on the metabolism of two human cell lines (HEK293 and an amniocyte-derived cell line, 1G3) after infection with an adenovirus serotype 5 vector (AdV5). In order to profile metabolic alterations, we used (1)H-NMR spectroscopy, which allowed the quantification of 35 metabolites in cell culture supernatants with low sample preparation and in a relatively short time. Significant differences between both cell lines in non-infected cultures were identified, namely in glutamine and acetate metabolism, as well as by-product secretion. The main response to AdV5 infection was an increase in glucose consumption and lactate production rates. Moreover, cultures performed with or without glutamine supplementation confirmed the exhaustion of this amino acid as one of the main causes of lower AdV5 production at high cell densities (10- and 1.5-fold less specific yields in HEK293 and 1G3 cells, respectively), and highlighted different degrees of glutamine dependency of adenovirus replication in each cell line. The observed metabolic alterations associated with AdV5 infection and specificity of the host cell line can be useful for targeted bioprocess optimization.
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12
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Quantification of Metabolic Rearrangements During Neural Stem Cells Differentiation into Astrocytes by Metabolic Flux Analysis. Neurochem Res 2016; 42:244-253. [DOI: 10.1007/s11064-016-1907-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 03/31/2016] [Accepted: 04/01/2016] [Indexed: 12/27/2022]
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