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Singh R, Fatima E, Thakur L, Singh S, Ratan C, Kumar N. Advancements in CHO metabolomics: techniques, current state and evolving methodologies. Front Bioeng Biotechnol 2024; 12:1347138. [PMID: 38600943 PMCID: PMC11004234 DOI: 10.3389/fbioe.2024.1347138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/28/2024] [Indexed: 04/12/2024] Open
Abstract
Background: Investigating the metabolic behaviour of different cellular phenotypes, i.e., good/bad grower and/or producer, in production culture is important to identify the key metabolite(s)/pathway(s) that regulate cell growth and/or recombinant protein production to improve the overall yield. Currently, LC-MS, GC-MS and NMR are the most used and advanced technologies for investigating the metabolome. Although contributed significantly in the domain, each technique has its own biasness towards specific metabolites or class of metabolites due to various reasons including variability in the concept of working, sample preparation, metabolite-extraction methods, metabolite identification tools, and databases. As a result, the application of appropriate analytical technique(s) is very critical. Purpose and scope: This review provides a state-of-the-art technological insights and overview of metabolic mechanisms involved in regulation of cell growth and/or recombinant protein production for improving yield from CHO cultures. Summary and conclusion: In this review, the advancements in CHO metabolomics over the last 10 years are traced based on a bibliometric analysis of previous publications and discussed. With the technical advancement in the domain of LC-MS, GC-MS and NMR, metabolites of glycolytic and nucleotide biosynthesis pathway (glucose, fructose, pyruvate and phenylalanine, threonine, tryptophan, arginine, valine, asparagine, and serine, etc.) were observed to be upregulated in exponential-phase thereby potentially associated with cell growth regulation, whereas metabolites/intermediates of TCA, oxidative phosphorylation (aspartate, glutamate, succinate, malate, fumarate and citrate), intracellular NAD+/NADH ratio, and glutathione metabolic pathways were observed to be upregulated in stationary-phase and hence potentially associated with increased cell-specific productivity in CHO bioprocess. Moreover, each of technique has its own bias towards metabolite identification, indicating their complementarity, along with a number of critical gaps in the CHO metabolomics pipeline and hence first time discussed here to identify their potential remedies. This knowledge may help in future study designs to improve the metabolomic coverage facilitating identification of the metabolites/pathways which might get missed otherwise and explore the full potential of metabolomics for improving the CHO bioprocess performances.
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Affiliation(s)
- Rita Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Eram Fatima
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Lovnish Thakur
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Sevaram Singh
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Chandra Ratan
- Translational Health Science and Technology Institute, Faridabad, India
- Jawaharlal Nehru University, New Delhi, India
| | - Niraj Kumar
- Translational Health Science and Technology Institute, Faridabad, India
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2
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Tian L, Gao C, Lu J, Liao S, Gong G. Key biological processes and essential genes for Proteus mirabilis biofilm development inhibition by protocatechuic acid. Int J Food Microbiol 2024; 412:110570. [PMID: 38219343 DOI: 10.1016/j.ijfoodmicro.2024.110570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 01/16/2024]
Abstract
Proteus mirabilis is an opportunistic pathogen linked to human urinary tract infections, and is potentially present as a foodborne pathogen within poultry products, including broiler chickens. This report outlines the inhibitory impacts of protocatechuic acid (PCA) on P. mirabilis isolated from a broiler slaughterhouse in China as well as its biofilm. This investigation encompasses assays related to motility and adhesion, bacterial metabolic activity, extracellular polymer (EPS) production, and scavenging capacity. The findings demonstrated that PCA reduced biofilm formation by 61 %. Transcriptomics findings identified that PCA limited the expression of genes like PstS that promote adhesin formation, rbsA and RcsB that alter bacterial chemotaxis, lipopolysaccharide synthesis genes LpxA and EptB, and cell wall synthesis genes MurF and MrdA, and affects the Regulator of Capsule Synthesis (RCS) two-component modulation system. Weighted gene co-expression network analysis (WGCNA) was conducted to identify the core genes. Furthermore, the binding sites of PCA to cytochrome oxidases cydA and cydB, two subunits of ATP synthase atpI and atpH, and ftsZ, which regulate bacterial division, were predicted via molecular docking. Metabolome analysis determined that PCA critically influenced coenzyme A biosynthesis, nucleotide metabolism, alanine, aspartic acid, and glutamate metabolic pathways of P. mirabilis. Therefore, PCA impacts metabolism within bacteria via various pathways, limiting the levels of extracellular polymer and bacterial viability to hinder biofilm formation. Additionally, we prepared an antibacterial plastic film containing protocatechuic acid using PVA as the monomer and CNC as the reinforcing agent. We examined the mechanical and antibacterial properties of this film. When used to wrap chicken, it reduced the total number of colonies, slowed the deterioration of chicken, and maintained the freshness of chicken. In conclusion, the information outlined in this study complements our comprehension of P. mirabilis inhibition by PCA and provides clues for the reduction of foodborne infections associated with P. mirabilis.
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Affiliation(s)
- Lu Tian
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China.
| | - Chang Gao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Jiaxing Lu
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Sichen Liao
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Guoli Gong
- School of Food Science and Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China.
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3
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Martínez VS, Rodriguez K, McCubbin T, Tong J, Mahler S, Shave E, Baker K, Munro TP, Marcellin E. Amino acid degradation pathway inhibitory by-products trigger apoptosis in CHO cells. Biotechnol J 2024; 19:e2300338. [PMID: 38375561 DOI: 10.1002/biot.202300338] [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: 07/12/2023] [Revised: 11/25/2023] [Accepted: 12/13/2023] [Indexed: 02/21/2024]
Abstract
Chinese hamster ovary (CHO) cells are widely used to produce complex biopharmaceuticals. Improving their productivity is necessary to fulfill the growing demand for such products. One way to enhance productivity is by cultivating cells at high densities, but inhibitory by-products, such as metabolite derivatives from amino acid degradation, can hinder achieving high cell densities. This research examines the impact of these inhibitory by-products on high-density cultures. We cultured X1 and X2 CHO cell lines in a small-scale semi-perfusion system and introduced a mix of inhibitory by-products on day 10. The X1 and X2 cell lines were chosen for their varied responses to the by-products; X2 was susceptible, while X1 survived. Proteomics revealed that the X2 cell line presented changes in the proteins linked to apoptosis regulation, cell building block synthesis, cell growth, DNA repair, and energy metabolism. We later used the AB cell line, an apoptosis-resistant cell line, to validate the results. AB behaved similar to X1 under stress. We confirmed the activation of apoptosis in X2 using a caspase assay. This research provides insights into the mechanisms of cell death triggered by inhibitory by-products and can guide the optimization of CHO cell culture for biopharmaceutical manufacturing.
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Affiliation(s)
- Verónica S Martínez
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
| | - Karen Rodriguez
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
| | - Timothy McCubbin
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, St Lucia, Queensland, Australia
| | - Junjie Tong
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
| | - Stephen Mahler
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
| | - Evan Shave
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
- Patheon, by Thermo Fisher Scientific, Woolloongabba, Queensland, Australia
| | - Kym Baker
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
- Patheon, by Thermo Fisher Scientific, Woolloongabba, Queensland, Australia
| | - Trent P Munro
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
- National Biologics Facility, The University of Queensland, St Lucia, Queensland, Australia
| | - Esteban Marcellin
- ARC Training Centre for Biopharmaceutical Innovation (CBI), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, Queensland, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, St Lucia, Queensland, Australia
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4
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Dodia H, Sunder AV, Borkar Y, Wangikar PP. Precision fermentation with mass spectrometry-based spent media analysis. Biotechnol Bioeng 2023; 120:2809-2826. [PMID: 37272489 DOI: 10.1002/bit.28450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/13/2023] [Accepted: 05/15/2023] [Indexed: 06/06/2023]
Abstract
Optimization and monitoring of bioprocesses requires the measurement of several process parameters and quality attributes. Mass spectrometry (MS)-based techniques such as those coupled to gas chromatography (GCMS) and liquid Chromatography (LCMS) enable the simultaneous measurement of hundreds of metabolites with high sensitivity. When applied to spent media, such metabolome analysis can help determine the sequence of substrate uptake and metabolite secretion, consequently facilitating better design of initial media and feeding strategy. Furthermore, the analysis of metabolite diversity and abundance from spent media will aid the determination of metabolic phases of the culture and the identification of metabolites as surrogate markers for product titer and quality. This review covers the recent advances in metabolomics analysis applied to the development and monitoring of bioprocesses. In this regard, we recommend a stepwise workflow and guidelines that a bioprocesses engineer can adopt to develop and optimize a fermentation process using spent media analysis. Finally, we show examples of how the use of MS can revolutionize the design and monitoring of bioprocesses.
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Affiliation(s)
- Hardik Dodia
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
| | | | - Yogen Borkar
- Clarity Bio Systems India Pvt. Ltd., Pune, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, India
- Clarity Bio Systems India Pvt. Ltd., Pune, India
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5
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Masson HO, Karottki KJLC, Tat J, Hefzi H, Lewis NE. From observational to actionable: rethinking omics in biologics production. Trends Biotechnol 2023; 41:1127-1138. [PMID: 37062598 PMCID: PMC10524802 DOI: 10.1016/j.tibtech.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 04/18/2023]
Abstract
As the era of omics continues to expand with increasing ubiquity and success in both academia and industry, omics-based experiments are becoming commonplace in industrial biotechnology, including efforts to develop novel solutions in bioprocess optimization and cell line development. Omic technologies provide particularly valuable 'observational' insights for discovery science, especially in academic research and industrial R&D; however, biomanufacturing requires a different paradigm to unlock 'actionable' insights from omics. Here, we argue the value of omic experiments in biotechnology can be maximized with deliberate selection of omic approaches and forethought about analysis techniques. We describe important considerations when designing and implementing omic-based experiments and discuss how systems biology analysis strategies can enhance efforts to obtain actionable insights in mammalian-based biologics production.
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Affiliation(s)
- Helen O Masson
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | | | - Jasmine Tat
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Amgen Inc., Thousand Oaks, CA, USA
| | | | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
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6
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Cortada-Garcia J, Daly R, Arnold SA, Burgess K. Streamlined identification of strain engineering targets for bioprocess improvement using metabolic pathway enrichment analysis. Sci Rep 2023; 13:12990. [PMID: 37563133 PMCID: PMC10415327 DOI: 10.1038/s41598-023-39661-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 07/28/2023] [Indexed: 08/12/2023] Open
Abstract
Metabolomics is a powerful tool for the identification of genetic targets for bioprocess optimisation. However, in most cases, only the biosynthetic pathway directed to product formation is analysed, limiting the identification of these targets. Some studies have used untargeted metabolomics, allowing a more unbiased approach, but data interpretation using multivariate analysis is usually not straightforward and requires time and effort. Here we show, for the first time, the application of metabolic pathway enrichment analysis using untargeted and targeted metabolomics data to identify genetic targets for bioprocess improvement in a more streamlined way. The analysis of an Escherichia coli succinate production bioprocess with this methodology revealed three significantly modulated pathways during the product formation phase: the pentose phosphate pathway, pantothenate and CoA biosynthesis and ascorbate and aldarate metabolism. From these, the two former pathways are consistent with previous efforts to improve succinate production in Escherichia coli. Furthermore, to the best of our knowledge, ascorbate and aldarate metabolism is a newly identified target that has so far never been explored for improving succinate production in this microorganism. This methodology therefore represents a powerful tool for the streamlined identification of strain engineering targets that can accelerate bioprocess optimisation.
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Affiliation(s)
- Joan Cortada-Garcia
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK
| | - Rónán Daly
- Institute of Infection, Immunity and Inflammation, Glasgow Polyomics, University of Glasgow, Glasgow, G61 1QH, UK
| | - S Alison Arnold
- Ingenza Ltd., Roslin Innovation Centre, Roslin, EH25 9RG, UK
| | - Karl Burgess
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh, EH8 9AB, UK.
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7
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Li M, Zhu J, Liu X, Dong Z, Tang J, Zhang C, Jiao J, Chen J, Yin F, Qiu S, Zhang F, Gao S, Wang Z, Tao X, Yue X, Sun L, Chen W. Chaihu-Guizhi-Ganjiang Decoction is more efficacious in treating irritable bowel syndrome than Dicetel according to metabolomics analysis. Chin Med 2022; 17:139. [DOI: 10.1186/s13020-022-00695-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/30/2022] [Indexed: 12/15/2022] Open
Abstract
Abstract
Background
Chaihu-Guizhi-Ganjiang Decoction (CGGD) is a traditional Chinese medicine (TCM) prescription used to treat viral influenza. There is evidence that CGGD can be used to treat irritable bowel syndrome (IBS) but the potential mechanism of action and metabolites produced upon CGGD treatment remains elusive.
Methods
Patients with IBS were treated with pinaverium bromide (Dicetel™) and then CGGD after a washout period of 1 week. Both treatments lasted for 30 days. The efficacy and changes of metabolites in plasma after the two treatments were compared. Plasma samples were acquired before and after each treatment, and untargeted metabolics analysis was performed.
Results
Efficacy was measured according to the Rome IV criteria and TCM theory. Our results indicated that CGGD showed significantly better efficacy than Dicetel in the treatment of IBS utilizing each criterion. CGGD exerted greater effects on plasma metabolism than Dicetel. Dicetel treatment led to increased tryptophan metabolism (increased levels of 5-Hydroxyindoleacetaldehyde) and increased protein metabolism (increased levels of L-arginine). CGGD treatment significantly (p < 0.05) increased carnitine metabolism, with elevated levels of L-carnitine and acylcarnitine in plasma. Such changes in these metabolites could exert effects against IBS by improving gastrointestinal motility and suppressing pain, depression, and inflammation.
Conclusions
CGGD appeared to be more efficacious than Dicetel for treating patients with IBS. The findings provide a sound support for the underlying biomolecular mechanism of CGGD in the prevention and treatment of IBS.
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8
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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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9
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Lai Z, Choudhury FK, Tang D, Liang X, Dean B, Misaghi S, Sangaraju D. LC-HRMS based Targeted Metabolomics for High-throughput and Quantitative Analysis of 21 Growth Inhibition Related Metabolites in CHO Cell Fed-Batch Cultures. Biomed Chromatogr 2022; 36:e5348. [PMID: 35083760 DOI: 10.1002/bmc.5348] [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: 12/02/2021] [Revised: 01/10/2022] [Accepted: 01/20/2022] [Indexed: 11/08/2022]
Abstract
Chinese hamster ovary (CHO) cells have been widely used in the biopharmaceutical industry for production of therapeutic proteins. CHO cells in fed-batch cultures produce various amino acid-derived intermediate metabolites. These small molecule metabolic byproducts have proven to be critical to cell growth, culture performance, and more interestingly antibody drug productivity. Herein, we developed a liquid chromatography - high resolution mass spectrometry (LC-HRMS) based targeted metabolomics approach for comprehensive quantification of total 21 growth inhibition related metabolites generated from 14 different amino acids in CHO cell fed-batch cultures. High throughput derivatization procedures, matrix-matched calibration curves, stable isotope-labeled internal standards, and accurate mass Full MS scan were utilized in order to achieve our goal for wide scope of metabolite screening as well as validity and reliability of metabolite quantification. We further present a novel analytical strategy for extending the assay's dynamic range by utilizing naturally occurring isotope M+1 ion as a quantification analogue in the circumstances where the principal M ion is beyond its calibration range. The integrated method was qualified for selectivity, sensitivity, linearity, accuracy, precision, isotope analysis and other analytical aspects to demonstrate assay robustness. We then applied this metabolomics approach to characterize metabolites of interest in a CHO cell based monoclonal antibody (mAb) production process with fed-batch bioreactor culture mode. Absolute quantification combined with multivariate statistical analysis illustrated that our target analytes derived from amino acids, especially from branched-chain amino acids, closely correlated with cell viability and significantly differentiated cellular stages in production process.
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Affiliation(s)
- Zijuan Lai
- Drug Metabolism and Pharmacokinetics Department, Genentech Inc., South San Francisco, CA, USA
| | - Feroza K Choudhury
- Drug Metabolism and Pharmacokinetics Department, Genentech Inc., South San Francisco, CA, USA
| | - Danming Tang
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA, USA
| | - Xiaorong Liang
- Drug Metabolism and Pharmacokinetics Department, Genentech Inc., South San Francisco, CA, USA
| | - Brian Dean
- Drug Metabolism and Pharmacokinetics Department, Genentech Inc., South San Francisco, CA, USA
| | - Shahram Misaghi
- Cell Culture and Bioprocess Operations Department, Genentech Inc., South San Francisco, CA, USA
| | - Dewakar Sangaraju
- Drug Metabolism and Pharmacokinetics Department, Genentech Inc., South San Francisco, CA, USA
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A Metabolomics Approach to Increasing Chinese Hamster Ovary (CHO) Cell Productivity. Metabolites 2021; 11:metabo11120823. [PMID: 34940581 PMCID: PMC8704136 DOI: 10.3390/metabo11120823] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 12/12/2022] Open
Abstract
Much progress has been made in improving the viable cell density of bioreactor cultures in monoclonal antibody production from Chinese hamster ovary (CHO) cells; however, specific productivity (qP) has not been increased to the same degree. In this work, we analyzed a library of 24 antibody-expressing CHO cell clones to identify metabolites that positively associate with qP and could be used for clone selection or medium supplementation. An initial library of 12 clones, each producing one of two antibodies, was analyzed using untargeted LC-MS experiments. Metabolic model-based annotation followed by correlation analysis detected 73 metabolites that significantly correlated with growth, qP, or both. Of these, metabolites in the alanine, aspartate, and glutamate metabolism pathway, and the TCA cycle showed the strongest association with qP. To evaluate whether these metabolites could be used as indicators to identify clones with potential for high productivity, we performed targeted LC-MS experiments on a second library of 12 clones expressing a third antibody. These experiments found that aspartate and cystine were positively correlated with qP, confirming the results from untargeted analysis. To investigate whether qP correlated metabolites reflected endogenous metabolic activity beneficial for productivity, several of these metabolites were tested as medium additives during cell culture. Medium supplementation with citrate improved qP by up to 490% and more than doubled the titer. Together, these studies demonstrate the potential for using metabolomics to discover novel metabolite additives that yield higher volumetric productivity in biologics production processes.
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11
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Salim T, Chauhan G, Templeton N, Ling WLW. Using MVDA with stoichiometric balances to optimize amino acid concentrations in chemically defined CHO cell culture medium for improved culture performance. Biotechnol Bioeng 2021; 119:452-469. [PMID: 34811720 DOI: 10.1002/bit.27998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/22/2021] [Accepted: 11/13/2021] [Indexed: 11/07/2022]
Abstract
Chemically defined (CD) media are routinely used in the production of biologics in Chinese hamster ovary (CHO) cell culture and provide enhanced raw material control. Nutrient optimized CD media is an important path to increase cell growth and monoclonal antibody (mAb) productivity in recombinant CHO cell lines. However, nutrient optimization efforts for CD media typically rely on multifactorial and experimental design of experiment approaches or complex mathematical models of cellular metabolism or gene expression systems. Moreover, the majority of these efforts are aimed at amino acids since they constitute essential nutrients in CD media as they directly contribute to biomass and protein production. In this study, we demonstrate the utilization of multivariate data analytics (MVDA) coupled with amino acid stoichiometric balances (SBs) to increased cell growth and mAb productivity in efforts to support CD media development efforts. SBs measure the difference between theoretical demand of amino acids and the empirically measured fluxes to identify various catabolic or anabolic states of the cell. When coupled with MVDA, the statistical models were not only able to highlight key amino acids toward cell growth or productivity, but also provided direction on metabolic favorability of the amino acid. Experimental validation of our approach resulted in a 55% increase in total cell growth and about an 80% increase in total mAb productivity. Increased specific consumption of stoichiometrically balanced amino acids and decreased specific consumption of glucose was also observed in optimized CD media suggesting favorable consumption of desired nutrients and a potential for energy redistribution toward increased cellular growth and mAb productivity.
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Affiliation(s)
- Taha Salim
- Merck & Co. Inc., Kenilworth, New Jersey, USA
- Taha Salim, Regeneron, Tarrytown, New York, USA
| | | | | | - Wai Lam W Ling
- Merck & Co. Inc., Kenilworth, New Jersey, USA
- Wai L. W. Ling, Rocket Pharma, Cranbury, New Jersey, USA
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12
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Samy A, Yamano-Adachi N, Koga Y, Omasa T. Secretion of a low-molecular-weight species of endogenous GRP94 devoid of the KDEL motif during endoplasmic reticulum stress in Chinese hamster ovary cells. Traffic 2021; 22:425-438. [PMID: 34536241 PMCID: PMC9293085 DOI: 10.1111/tra.12818] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 08/02/2021] [Accepted: 09/14/2021] [Indexed: 01/04/2023]
Abstract
GRP94 (glucose‐regulated protein 94) is a well‐studied chaperone with a lysine, aspartic acid, glutamic acid and leucine (KDEL) motif at its C‐terminal, which is responsible for GRP94 localization in the endoplasmic reticulum (ER). GRP94 is upregulated during ER stress to help fold unfolded proteins or direct proteins to ER‐associated degradation. In a previous study, engineered GRP94 without the KDEL motif stimulated a powerful immune response in vaccine cells. In this report, we show that endogenous GRP94 is naturally secreted into the medium in a truncated form that lacks the KDEL motif in Chinese hamster ovary cells. The secretion of the truncated form of GRP94 was stimulated by the induction of ER stress. These truncations prevent GRP94 recognition by KDEL receptors and retention inside the cell. This study sheds light on a potential trafficking phenomenon during the unfolded protein response that may help understand the functional role of GRP94 as a trafficking molecule.
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Affiliation(s)
- Andrew Samy
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan
| | - Noriko Yamano-Adachi
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan.,Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Yuichi Koga
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan.,Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Takeshi Omasa
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Japan.,Industrial Biotechnology Initiative Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
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Characterization of dynamic regulation in Chinese hamster ovary (CHO) cell cultures in the late exponential phase. Biochem Eng J 2021. [DOI: 10.1016/j.bej.2020.107897] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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Special Issue "Metabolic Engineering and Synthetic Biology Volume 2". Metabolites 2021; 11:metabo11010035. [PMID: 33418903 PMCID: PMC7825028 DOI: 10.3390/metabo11010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 01/04/2021] [Indexed: 11/22/2022] Open
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Ho YY, Lu HK, Lim ZFS, Lim HW, Ho YS, Ng SK. Applications and analysis of hydrolysates in animal cell culture. BIORESOUR BIOPROCESS 2021; 8:93. [PMID: 34603939 PMCID: PMC8476327 DOI: 10.1186/s40643-021-00443-w] [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: 06/02/2021] [Accepted: 09/07/2021] [Indexed: 12/19/2022] Open
Abstract
Animal cells are used in the manufacturing of complex biotherapeutic products since the 1980s. From its initial uses in biological research to its current importance in the biopharmaceutical industry, many types of culture media were developed: from serum-based media to serum-free to protein-free chemically defined media. The cultivation of animal cells economically has become the ultimate goal in the field of biomanufacturing. Serum serves as a source of amino acids, lipids, proteins and most importantly growth factors and hormones, which are essential for many cell types. However, the use of serum is unfavorable due to its high price tag, increased lot-to-lot variations and potential risk of microbial contamination. Efforts are progressively being made to replace serum with recombinant proteins such as growth factors, cytokines and hormones, as well as supplementation with lipids, vitamins, trace elements and hydrolysates. While hydrolysates are more complex, they provide a diverse source of nutrients to animal cells, with potential beneficial effects beyond the nutritional value. In this review, we discuss the use of hydrolysates in animal cell culture and briefly cover the composition of hydrolysates, mode of action and potential contaminants with some perspectives on its potential role in animal cell culture media formulations in the future.
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Affiliation(s)
- Yin Ying Ho
- grid.185448.40000 0004 0637 0221Bioprocessing Technology Institute, Agency for Science, Technology, and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668 Singapore
| | - Hao Kim Lu
- grid.185448.40000 0004 0637 0221Bioprocessing Technology Institute, Agency for Science, Technology, and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668 Singapore
| | - Zhi Feng Sherman Lim
- grid.185448.40000 0004 0637 0221Bioprocessing Technology Institute, Agency for Science, Technology, and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668 Singapore
| | - Hao Wei Lim
- grid.185448.40000 0004 0637 0221Bioprocessing Technology Institute, Agency for Science, Technology, and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668 Singapore
| | - Ying Swan Ho
- grid.185448.40000 0004 0637 0221Bioprocessing Technology Institute, Agency for Science, Technology, and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668 Singapore
| | - Say Kong Ng
- grid.185448.40000 0004 0637 0221Bioprocessing Technology Institute, Agency for Science, Technology, and Research (A*STAR), 20 Biopolis Way, #06-01 Centros, Singapore, 138668 Singapore
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