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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Park SY, Choi DH, Song J, Park U, Cho H, Hong BH, Silberberg YR, Lee DY. Debottlenecking and reformulating feed media for improved CHO cell growth and titer by data-driven and model-guided analyses. Biotechnol J 2023; 18:e2300126. [PMID: 37605365 DOI: 10.1002/biot.202300126] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/11/2023] [Accepted: 08/17/2023] [Indexed: 08/23/2023]
Abstract
Designing and selecting cell culture media along with their feeding are a key strategy to maximize culture performance in biopharmaceutical processes. However, the sensitivity of mammalian cells to their culture environment necessitates specific nutritional requirements for their growth and the production of high-quality proteins such as antibodies, depending on the cell lines and operational conditions employed. In this regard, previously we developed a data-driven and in-silico model-guided systematic framework to investigate the effect of growth media on Chinese hamster ovary (CHO) cell culture performance, allowing us to design and reformulate basal media. To expand our exploration for media development research, we evaluated two chemically defined feed media, A and B, using a monoclonal antibody-producing CHO-K1 cell line in ambr15 bioreactor runs. We observed a significant impact of the feed media on various aspects of cell culture, including growth, longevity, viability, productivity, and the production of toxic metabolites. Specifically, the concentrated feed A was inadequate in sustaining prolonged cell culture and achieving high titers when compared to feed B. Within our framework, we systematically investigated the major metabolic bottlenecks in the tricarboxylic acid cycle and relevant amino acid transferase reactions. This analysis identified target components that play a crucial role in alleviating bottlenecks and designing highly productive cell cultures, specifically the addition of glutamate to feed A and asparagine to feed B. Based on our findings, we reformulated the feeds by adjusting the amounts of the targeted amino acids and successfully validated the effectiveness of the strategy in promoting cell growth, life span, and/or titer.
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Affiliation(s)
- Seo-Young Park
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do, Republic of Korea
| | - Dong-Hyuk Choi
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do, Republic of Korea
| | - Jinsung Song
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do, Republic of Korea
| | - Uiseon Park
- Ajinomoto Genexine Co., Ltd., CELLiST Solution Center, Incheon, Republic of Korea
| | - Hyeran Cho
- Ajinomoto Genexine Co., Ltd., CELLiST Solution Center, Incheon, Republic of Korea
| | - Bee Hak Hong
- Ajinomoto Genexine Co., Ltd., CELLiST Solution Center, Incheon, Republic of Korea
| | - Yaron R Silberberg
- Ajinomoto Genexine Co., Ltd., CELLiST Solution Center, Incheon, Republic of Korea
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, Suwon, Gyeonggi-do, Republic of Korea
- Bitwinners Pte. Ltd., Singapore
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Lao T, Farnos O, Bueno A, Alvarez A, Rodríguez E, Palacios J, de la Luz KR, Kamen A, Carpio Y, Estrada MP. Transient Expression in HEK-293 Cells in Suspension Culture as a Rapid and Powerful Tool: SARS-CoV-2 N and Chimeric SARS-CoV-2N-CD154 Proteins as a Case Study. Biomedicines 2023; 11:3050. [PMID: 38002050 PMCID: PMC10669214 DOI: 10.3390/biomedicines11113050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/03/2023] [Accepted: 11/08/2023] [Indexed: 11/26/2023] Open
Abstract
In a previous work, we proposed a vaccine chimeric antigen based on the fusion of the SARS-CoV-2 N protein to the extracellular domain of the human CD40 ligand (CD154). This vaccine antigen was named N-CD protein and its expression was carried out in HEK-293 stably transfected cells, grown in adherent conditions and serum-supplemented medium. The chimeric protein obtained in these conditions presented a consistent pattern of degradation. The immunization of mice and monkeys with this chimeric protein was able to induce a high N-specific IgG response with only two doses in pre-clinical experiments. In order to explore ways to diminish protein degradation, in the present work, the N and N-CD proteins were produced in suspension cultures and serum-free media following transient transfection of the HEK-293 clone 3F6, at different scales, including stirred-tank controlled bioreactors. The results showed negligible or no degradation of the target proteins. Further, clones stably expressing N-CD were obtained and adapted to suspension culture, obtaining similar results to those observed in the transient expression experiments in HEK-293-3F6. The evidence supports transient protein expression in suspension cultures and serum-free media as a powerful tool to produce in a short period of time high levels of complex proteins susceptible to degradation, such as the SARS-CoV-2 N protein.
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Affiliation(s)
- Thailin Lao
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Omar Farnos
- Department of Bioengineering, McGill University, Montreal, QC H3A 0E9, Canada; (O.F.); (A.K.)
| | - Alexi Bueno
- Process Development Department, Center of Molecular Immunology, Havana 11600, Cuba (J.P.); (K.R.d.l.L.)
| | - Anays Alvarez
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Elsa Rodríguez
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Julio Palacios
- Process Development Department, Center of Molecular Immunology, Havana 11600, Cuba (J.P.); (K.R.d.l.L.)
| | - Kathya Rashida de la Luz
- Process Development Department, Center of Molecular Immunology, Havana 11600, Cuba (J.P.); (K.R.d.l.L.)
| | - Amine Kamen
- Department of Bioengineering, McGill University, Montreal, QC H3A 0E9, Canada; (O.F.); (A.K.)
| | - Yamila Carpio
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
| | - Mario Pablo Estrada
- Center for Genetic Engineering and Biotechnology, Animal Biotechnology Department, Havana 10600, Cuba; (T.L.)
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Li WF, Fan ZL, Wang XY, Lin Y, Wang TY. Combination of sodium butyrate and decitabine promotes transgene expression in CHO cells via apoptosis inhibition. N Biotechnol 2022; 69:8-17. [PMID: 35217202 DOI: 10.1016/j.nbt.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/16/2022] [Accepted: 02/19/2022] [Indexed: 12/18/2022]
Abstract
Chinese hamster ovary (CHO) cells are currently the most widely used host cells for production of recombinant therapeutic proteins (RTPs). Small-molecule additives related to cell cycle apoptosis and autophagy regulation have been used to promote RTP production. By combining two small-molecule additives, positive synergistic effects on transgene expression were observed in CHO cells. In the present study, six small-molecule additives were used, including hydrocinnamic acid (HCA), sodium butyrate (NaB), lithium acetate (LiAc), sodium succinate dibasic hexahydrate (SDH), decitabine (DAC), and sodium propionate (SP). Experiments to test the effects of their pairwise combinations on two different recombinant CHO cell lines (rCHO) were designed using Design-Expert 12.0. Different effects of various pairs of small molecules on apoptosis- and autophagy-related protein expression were observed in the rCHOs. The results showed that compared to the control culture, NaB alone increased the volumetric yield and specific productivity (Qp) by 166% and 143%, respectively. The volumetric yield and Qp of NaB combined with DAC (Cg1)-treated cells increased by 178% and 212%, respectively. Cg1 selectively blocked the cells in the G0/G1 cell cycle stage. The relative expression levels of B-cell lymphoma 2 (Bcl-2), Beclin 1, and microtubule-associated protein light chain 3 (LC3B) in Cg1-treated CHO cells were significantly increased, while relative levels of cleaved caspase-3 expression were significantly decreased. In conclusion, Cg1 had the most obvious effect on RTP production and Qp in CHO cells, suggesting the Cg1 combination of small molecules may be used to improve the expression of recombinant protein in CHO cells.
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Affiliation(s)
- Wei-Feng Li
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
| | - Zhen-Lin Fan
- Henan International Joint Laboratory of Recombinant Pharmaceutical Protein Expression System, Xinxiang Medical University, Xinxiang 453003, Henan, China
| | - Xiao-Yin Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
| | - Yan Lin
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China
| | - Tian-Yun Wang
- Department of Biochemistry and Molecular Biology, Xinxiang Medical University, Xinxiang, China; Henan International Joint Laboratory of Recombinant Pharmaceutical Protein Expression System, Xinxiang Medical University, Xinxiang 453003, Henan, China.
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