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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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Shi Y, Wan Y, Sun Y, Yang J, Lu Y, Xie X, Pan J, Wang H, Qu H. Exploring metabolic responses and pathway changes in CHO-K1 cells under varied aeration conditions and copper supplementations using 1 H NMR-based metabolomics. Biotechnol J 2024; 19:e2300495. [PMID: 38403407 DOI: 10.1002/biot.202300495] [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: 09/19/2023] [Revised: 01/13/2024] [Accepted: 01/17/2024] [Indexed: 02/27/2024]
Abstract
The optimization of bioprocess for CHO cell culture involves careful consideration of factors such as nutrient consumption, metabolic byproduct accumulation, cell growth, and monoclonal antibody (mAb) production. Valuable insights can be obtained by understanding cellular physiology to ensure robust and efficient bioprocess. This study aims to improve our understanding of the CHO-K1 cell metabolism using 1 H NMR-based metabolomics. Initially, the variations in culture performance and metabolic profiles under varied aeration conditions and copper supplementations were thoroughly examined. Furthermore, a comprehensive metabolic pathway analysis was performed to assess the impact of these conditions on the implicated pathways. The results revealed substantial alterations in the pyruvate metabolism, histidine metabolism, as well as phenylalanine, tyrosine and tryptophan biosynthesis, which were especially evident in cultures subjected to copper deficiency conditions. Conclusively, significant metabolites governing cell growth and mAb titer were identified through orthogonal partial least square-discriminant analysis (OPLS-DA). Metabolites, including glycerol, alanine, formate, glutamate, phenylalanine, and valine, exhibited strong associations with distinct cell growth phases. Additionally, glycerol, acetate, lactate, formate, glycine, histidine, and aspartate emerged as metabolites influencing cell productivity. This study demonstrates the potential of employing 1 H NMR-based metabolomics technology in bioprocess research. It provides valuable guidance for feed medium development, feeding strategy design, bioprocess parameter adjustments, and ultimately the enhancement of cell proliferation and mAb yield.
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Affiliation(s)
- Yingting Shi
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yuxiang Wan
- Hisun BioPharmaceutical Co., Ltd., Hangzhou, China
| | - Yan Sun
- Hisun BioPharmaceutical Co., Ltd., Hangzhou, China
| | - Jiayu Yang
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Yuting Lu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Xinyuan Xie
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jianyang Pan
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Haibin Wang
- Hisun BioPharmaceutical Co., Ltd., Hangzhou, China
| | - Haibin Qu
- Pharmaceutical Informatics Institute, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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Xiang S, Zhang J, Yu L, Tian J, Tang W, Tang H, Xu K, Wang X, Cui Y, Ren K, Cao W, Su Y, Zhou W. Developing an ultra-intensified fed-batch cell culture process with greatly improved performance and productivity. Biotechnol Bioeng 2024; 121:696-709. [PMID: 37994547 DOI: 10.1002/bit.28605] [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: 08/22/2023] [Revised: 10/31/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
Intensified fed-batch (IFB), a popular cell culture intensification strategy, has been widely used for productivity improvement through high density inoculation followed by fed-batch cultivation. However, such an intensification strategy may counterproductively induce rapidly progressing cell apoptosis and difficult-to-sustain productivity. To improve culture performance, we developed a novel cell culture process intermittent-perfusion fed-batch (IPFB) which incorporates one single or multiple cycles of intermittent perfusion during an IFB process for better sustained cellular and metabolic behaviors and notably improved productivity. Unlike continuous perfusion or other semi-continuous processes such as hybrid perfusion fed-batch with only early-stage perfusion, IPFB applies limited times of intermittent perfusion in the mid-to-late stage of production and still inherits bolus feedings on nonperfusion days as in a fed-batch culture. Compared to IFB, an average titer increase of ~45% was obtained in eight recombinant CHO cell lines studied. Beyond IPFB, ultra-intensified IPFB (UI-IPFB) was designed with a markedly elevated seeding density of 20-80 × 106 cell/mL, achieved through the conventional alternating tangential flow filtration (ATF) perfusion expansion followed with a cell culture concentration step using the same ATF system. With UI-IPFB, up to ~6 folds of traditional fed-batch and ~3 folds of IFB productivity were achieved. Furthermore, the application grounded in these two novel processes showed broad-based feasibility in multiple cell lines and products of interest, and was proven to be effective in cost of goods reduction and readily scalable to a larger scale in existing facilities.
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Affiliation(s)
| | | | - Le Yu
- Process Development, WuXi Biologics, Wuxi, China
| | - Jun Tian
- Process Development, WuXi Biologics, Wuxi, China
| | - Wenxiu Tang
- Process Development, WuXi Biologics, Wuxi, China
| | - Hao Tang
- Process Development, WuXi Biologics, Wuxi, China
| | - Kecui Xu
- Process Development, WuXi Biologics, Wuxi, China
| | - Xin Wang
- Process Development, WuXi Biologics, Wuxi, China
| | - Yanyan Cui
- Process Development, WuXi Biologics, Wuxi, China
| | - Kaidi Ren
- Process Development, WuXi Biologics, Wuxi, China
| | - Weijia Cao
- Process Development, WuXi Biologics, Wuxi, China
| | - Yuning Su
- Process Development, WuXi Biologics, Wuxi, China
| | - Weichang Zhou
- Waigaoqiao Free Trade Zone, WuXi Biologics, Shanghai, China
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Geada I, Roldão A, Betenbaugh MJ, Alves PM. Advanced cell technologies: Making protein, cell, and gene therapies a reality. Biotechnol Bioeng 2023; 120:2385-2388. [PMID: 37534587 DOI: 10.1002/bit.28521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/14/2023] [Accepted: 07/22/2023] [Indexed: 08/04/2023]
Affiliation(s)
- Isabelle Geada
- Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Antonio Roldão
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
| | - Michael J Betenbaugh
- Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Paula M Alves
- Instituto de Biologia Experimental e Tecnológica (iBET), Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Oeiras, Portugal
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