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Lee HM, Kim TH, Park JH, Heo NY, Kim HS, Kim DE, Lee MK, Lee GM, You J, Kim YG. Sialyllactose supplementation enhances sialylation of Fc-fusion glycoprotein in recombinant Chinese hamster ovary cell culture. J Biotechnol 2024; 392:180-189. [PMID: 39038661 DOI: 10.1016/j.jbiotec.2024.07.016] [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: 04/03/2024] [Revised: 07/03/2024] [Accepted: 07/17/2024] [Indexed: 07/24/2024]
Abstract
Sialylation during N-glycosylation plays an important role in the half-life of therapeutic glycoproteins in vivo and has sparked interest in the production of therapeutic proteins using recombinant Chinese hamster ovary (rCHO) cells. To improve the sialylation of therapeutic proteins, we examined the effect of sialyllactose supplementation on sialylation of Fc-fusion glycoproteins produced in rCHO cells. Two enzymatically-synthesized sialyllactoses, 3'-sialyllactose (3'-SL) and 6'-sialyllactose (6'-SL), were administered separately to two rCHO cell lines producing the same Fc-fusion glycoprotein derived from DUKX-B11 and DG44, respectively. Two sialyllactoses successfully increased sialylation of Fc-fusion glycoprotein in both cell lines, as evidenced by isoform distribution, sialylated N-glycan formation, and sialic acid content. Increased sialylation by adding sialyllactose was likely the result of increased amount of intracellular CMP-sialic acid (CMP-SA), the direct nucleotide sugar for sialylation. Furthermore, the degree of sialylation enhanced by sialyllactoses was slightly effective or nearly similar compared with the addition of N-acetylmannosamine (ManNAc), a representative nucleotide sugar precursor, to increase sialylation of glycoproteins. The effectiveness of sialyllactose was also confirmed using three commercially available CHO cell culture media. Taken together, these results suggest that enzymatically-synthesized sialyllactose represents a promising candidate for culture media supplementation to increase sialylation of glycoproteins in rCHO cell culture.
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Affiliation(s)
- Hoon-Min Lee
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Bioprocess Engineering, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea
| | - Tae-Ho Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Plant and Environmental New Resources, Graduate School of Biotechnology, College of Life Science, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do, South Korea
| | - Jong-Ho Park
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Biological Sciences, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Na-Yeong Heo
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Bioprocess Engineering, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea
| | - Hyun-Seung Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Bioprocess Engineering, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea
| | - Dae Eung Kim
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Korea
| | - Mi Kyeong Lee
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, 335 Gwahak-ro, Yuseong-gu, Daejeon, South Korea
| | - Jungmok You
- Department of Plant and Environmental New Resources, Graduate School of Biotechnology, College of Life Science, Kyung Hee University, 1732 Deogyeong-daero, Giheung-gu, Yongin-si, Gyeonggi-do, South Korea.
| | - Yeon-Gu Kim
- Biotherapeutics Translational Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 125 Gwahak-ro, Yuseong-gu, Daejeon, South Korea; Department of Bioprocess Engineering, KRIBB School of Biotechnology, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, South Korea.
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Sukwattananipaat P, Kuroda H, Yamano-Adachi N, Omasa T. Metabolomic characterization of monoclonal antibody-producing Chinese hamster lung (CHL)-YN cells in glucose-controlled serum-free fed-batch operation. Biotechnol Bioeng 2024; 121:2848-2867. [PMID: 39138873 DOI: 10.1002/bit.28777] [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: 03/08/2024] [Revised: 05/31/2024] [Accepted: 06/09/2024] [Indexed: 08/15/2024]
Abstract
The fast-growing Chinese hamster lung (CHL)-YN cell line was recently developed for monoclonal antibody production. In this study, we applied a serum-free fed-batch cultivation process to immunoglobulin (Ig)G1-producing CHL-YN cells, which were then used to design a dynamic glucose supply system to stabilize the extracellular glucose concentration based on glucose consumption. Glucose consumption of the cultures rapidly oscillated following three phases of glutamine metabolism: consumption, production, and re-consumption. Use of the dynamic glucose supply prolonged the viability of the CHL-YN-IgG1 cell cultures and increased IgG1 production. Liquid chromatography with tandem mass spectrometry-based target metabolomics analysis of the extracellular metabolites during the first glutamine shift was conducted to search for depleted compounds. The results suggest that the levels of four amino acids, namely arginine, aspartate, methionine, and serine, were sharply decreased in CHL-YN cells during glutamine production. Supporting evidence from metabolic and gene expression analyses also suggest that CHL-YN cells acquired ornithine- and cystathionine-production abilities that differed from those in Chinese hamster ovary-K1 cells, potentially leading to proline and cysteine biosynthesis.
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Affiliation(s)
| | - Hirotaka Kuroda
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Shimadzu Corp., Kyoto, Japan
- Shimadzu Analytical Innovation Research Laboratories, Osaka, Japan
| | - Noriko Yamano-Adachi
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Manufacturing Technology Association of Biologics (MAB), Hyogo, Japan
| | - Takeshi Omasa
- Graduate School of Engineering, Osaka University, Osaka, Japan
- Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Osaka, Japan
- Manufacturing Technology Association of Biologics (MAB), Hyogo, Japan
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Goraltchouk A, Lourie J, Hollander JM, Grace Rosen H, Fujishiro AA, Luppino F, Zou K, Seregin A. Development and characterization of a first-in-class adjustable-dose gene therapy system. Gene 2024; 919:148500. [PMID: 38663689 DOI: 10.1016/j.gene.2024.148500] [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: 12/27/2023] [Revised: 04/11/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
Abstract
INTRODUCTION Despite significant potential, gene therapy has been relegated to the treatment of rare diseases, due in part to an inability to adjust dosage following initial administration. Other significant constraints include cost, specificity, antigenicity, and systemic toxicity of current generation technologies. To overcome these challenges, we developed a first-in-class adjustable-dose gene therapy system, with optimized biocompatibility, localization, durability, and cost. METHODS A lipid nanoparticle (LNP) delivery system was developed and characterized by dynamic light scattering for size, zeta potential, and polydispersity. Cytocompatibility and transfection efficiency were optimized in vitro using primary human adipocytes and preadipocytes. Durability, immunogenicity, and adjustment of expression were evaluated in C57BL/6 and B6 albino mice using in vivo bioluminescence imaging. Biodistribution was assessed by qPCR and immunohistochemistry; therapeutic protein expression was quantified by ELISA. RESULTS Following LNP optimization, in vitro transfection efficiency of primary human adipocytes reached 81.3 % ± 8.3 % without compromising cytocompatibility. Critical physico-chemical properties of the system (size, zeta potential, polydispersity) remained stable over a broad range of genetic cassette sizes (1,871-6,203 bp). Durable expression was observed in vivo over 6 months, localizing to subcutaneous adipose tissues at the injection site with no detectable transgene in the liver, heart, spleen, or kidney. Gene expression was adjustable using several physical and pharmacological approaches, including cryolipolysis, focused ultrasound, and pharmacologically inducible apoptosis. The ability of transfected adipocytes to express therapeutic transgenes ranging from peptides to antibodies, at potentially clinically relevant levels, was confirmed in vitro and in vivo. CONCLUSION We report the development of a novel, low-cost therapeutic platform, designed to enable the replacement of subcutaneously administered protein treatments with a single-injection, adjustable-dose gene therapy.
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Affiliation(s)
- Alex Goraltchouk
- Remedium Bio, Inc. 1116 Great Plain Ave, Suite 203, Needham, MA 02492, United States of America
| | - Jared Lourie
- Department of Exercise and Health Sciences, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA 02125, United States of America
| | - Judith M Hollander
- Remedium Bio, Inc. 1116 Great Plain Ave, Suite 203, Needham, MA 02492, United States of America
| | - H Grace Rosen
- Department of Biology, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA 02125, United States of America
| | - Atsutaro A Fujishiro
- Department of Exercise and Health Sciences, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA 02125, United States of America
| | - Francesco Luppino
- Remedium Bio, Inc. 1116 Great Plain Ave, Suite 203, Needham, MA 02492, United States of America
| | - Kai Zou
- Department of Exercise and Health Sciences, University of Massachusetts Boston, 100 Morrissey Blvd, Boston, MA 02125, United States of America
| | - Alexey Seregin
- Remedium Bio, Inc. 1116 Great Plain Ave, Suite 203, Needham, MA 02492, United States of America.
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Tsvik L, Zhang S, O'Hare D, Haltrich D, Sützl L. More Than One Enzyme: Exploring Alternative FMN-Dependent L-Lactate Oxidases for Biosensor Development. ACS OMEGA 2024; 9:29442-29452. [PMID: 39005781 PMCID: PMC11238220 DOI: 10.1021/acsomega.4c01897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/05/2024] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
The α-hydroxy acid oxidoreductase (HAOx) family contains a diverse group of enzymes that can be applied in biosensors for L-lactate detection, most prominently lactate oxidase (LOx). The limited availability and a lack of diversity of L-lactate-oxidizing enzymes have currently hindered advancements in L-lactate biosensor development. Until now, the field has mostly relied on a single, commercially available enzyme, namely Aerococcus viridans L-lactate oxidase (AvLOx). In this study, we present newly discovered alternative L-lactate oxidases that exhibit a narrow substrate specificity and varied kinetic efficiencies toward L-lactate, making them suitable for integration into existing biosensor configurations. Some of these FMN-dependent L-lactate oxidases could be obtained in substantial amounts from routine E. coli expression, potentially facilitating commercial production. Using electrochemical characterization with a mediated biosensor setup, we present 7 enzymes that perform comparable or even better than commercial AvLOx. Finally, we show that their electrochemical performance is not directly correlating with their biochemical performance, making predictions of the suitability of enzymes for biosensor applications extremely difficult. Our research emphasizes the significance of expanding the enzyme toolbox of L-lactate oxidases for the development of improved L-lactate biosensors.
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Affiliation(s)
- Lidiia Tsvik
- Laboratory of Food Biotechnology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 11, Wien, Vienna A-1190, Austria
- Doctoral Programme 'Biomolecular Technology of Proteins (BioToP)', University of Natural Resources and Life Sciences, Muthgasse 18, Wien, Vienna A-1190, Austria
| | - Shulin Zhang
- Department of Bioengineering, Imperial College London, London SW72AZ, U.K
| | - Danny O'Hare
- Department of Bioengineering, Imperial College London, London SW72AZ, U.K
| | - Dietmar Haltrich
- Laboratory of Food Biotechnology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 11, Wien, Vienna A-1190, Austria
| | - Leander Sützl
- Laboratory of Food Biotechnology, Department of Food Science and Technology, University of Natural Resources and Life Sciences, Muthgasse 11, Wien, Vienna A-1190, Austria
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Flynn J, Breen L, Narayanan S, Butler M. Measurement and control of foam generation in a mammalian cell culture. Biotechnol Prog 2024; 40:e3450. [PMID: 38476025 DOI: 10.1002/btpr.3450] [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: 12/12/2023] [Revised: 02/13/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024]
Abstract
Foam is generated in mammalian cell cultures by excessive agitation or gas sparging. This occurs particularly in cultures that generate recombinant proteins at high cell concentrations. Three antifoam agents were tested for their compatibility with antibody-producing Chinese hamster ovary (CHO) cells. One agent (antifoam 204) was completely inhibitory to growth at a concentration of 10 ppm, one agent (antifoam C) showed partial inhibition and a third (antifoam SE-15) showed no inhibition at this concentration. A novel foam image analyzer (LabCam) was used to evaluate two antifoams (C and SE-15) for their ability to dissipate foam generated in cell culture media by enhanced agitation. The presence of antifoam in the media reduced significantly the foam layer that was generated and this was shown to be rapidly dissipated in the presence of 10 ppm SE-15. The antifoams were also tested for foam dissipation in cultures of CHO cells at >106 cells/mL. Supplementation of the cultures with SE-15 resulted in dissipation of foam generated by excessive gas sparging within 2 min. Under equivalent conditions 75% of foam dissipated in the presence of antifoam C, within 2 min but there was a residual foam layer up to 25 min. This study showed the value of an optical monitoring system (LabCam) for measuring foam generation and dissipation in a bioreactor to assess the efficiency of antifoam agents to reduce foam in a bioreactor. This has the potential for use as a control system that could be designed for continuous monitoring and foam control in a mammalian cell bioprocess.
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Affiliation(s)
- James Flynn
- National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland
| | - Laura Breen
- National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland
| | - Shankara Narayanan
- National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland
| | - Michael Butler
- National Institute for Bioprocessing Research and Training (NIBRT), Dublin, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin (UCD), Dublin 4, Ireland
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Jarusintanakorn S, Mastrobattista E, Yamabhai M. Ectoine enhances recombinant antibody production in Chinese hamster ovary cells by promoting cell cycle arrest. N Biotechnol 2024; 83:56-65. [PMID: 38945523 DOI: 10.1016/j.nbt.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 06/08/2024] [Accepted: 06/27/2024] [Indexed: 07/02/2024]
Abstract
Chinese hamster ovary (CHO) cells represent the most preferential host cell system for therapeutic monoclonal antibody (mAb) production. Enhancing mAb production in CHO cells can be achieved by adding chemical compounds that regulate the cell cycle and cell survival pathways. This study investigated the impact of ectoine supplementation on mAb production in CHO cells. The results showed that adding ectoine at a concentration of 100 mM on the 3rd day of cultivation improved mAb production by improving cell viability and extending the culture duration. RNA sequencing analysis revealed differentially expressed genes associated with cell cycle regulation, cell proliferation, and cellular homeostasis, in particular promotion of cell cycle arrest, which was then confirmed by flow cytometry analysis. Ectoine-treated CHO cells exhibited an increase in the number of cells in the G0/G1 phase. In addition, the cell diameter was also increased. These findings support the hypothesis that ectoine enhances mAb production in CHO cells through mechanisms involving cell cycle arrest and cellular homeostasis. Overall, this study highlights the potential of ectoine as a promising supplementation strategy to enhance mAb production not only in CHO cells but also in other cell lines.
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Affiliation(s)
- Salinthip Jarusintanakorn
- Utrecht Institute for Pharmaceutical Sciences (UIPS), Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Mahidol University, 447, Sri-Ayuthaya Road, Rachathevi, Bangkok 10400, Thailand
| | - Enrico Mastrobattista
- Utrecht Institute for Pharmaceutical Sciences (UIPS), Department of Pharmaceutics, Faculty of Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, the Netherlands.
| | - Montarop Yamabhai
- Molecular Biotechnology Laboratory, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
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Okamura K, Badr S, Ichida Y, Yamada A, Sugiyama H. Modeling of cell cultivation for monoclonal antibody production processes considering lactate metabolic shifts. Biotechnol Prog 2024:e3486. [PMID: 38924316 DOI: 10.1002/btpr.3486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 05/10/2024] [Accepted: 05/24/2024] [Indexed: 06/28/2024]
Abstract
Demand for monoclonal antibodies (mAbs) is rapidly increasing. To achieve higher productivity, there have been improvements to cell lines, operating modes, media, and cultivation conditions. Representative mathematical models are needed to narrow down the growing number of process alternatives. Previous studies have proposed mechanistic models to depict cell metabolic shifts (e.g., lactate production to consumption). However, the impacts of variations of some operating conditions have not yet been fully incorporated in such models. This paper offers a new mechanistic model considering variations in dissolved oxygen and glutamine depletion on cell metabolism applied to a novel Chinese hamster ovary (CHO) cell line. Expressions for the specific rates of lactate production, glutamine consumption, and mAb production were formulated for stirred and shaken-tank reactors. A deeper understanding of lactate metabolic shifts was obtained under different combinations of experimental conditions. Lactate consumption was more pronounced in conditions with higher DO and low glutamine concentrations. The model offers mechanistic insights that are useful for designing advanced operation strategies. It can be used in design space generation and process optimization for better productivity and product quality.
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Affiliation(s)
- Kozue Okamura
- Department of Chemical System Engineering, The University of Tokyo, Tokyo, Japan
| | - Sara Badr
- Department of Chemical System Engineering, The University of Tokyo, Tokyo, Japan
| | - Yusuke Ichida
- Department of Chemical System Engineering, The University of Tokyo, Tokyo, Japan
| | - Akira Yamada
- Department of Chemical System Engineering, The University of Tokyo, Tokyo, Japan
| | - Hirokazu Sugiyama
- Department of Chemical System Engineering, The University of Tokyo, Tokyo, Japan
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Hammel A, Cucos LM, Caras I, Ionescu I, Tucureanu C, Tofan V, Costache A, Onu A, Hoepfner L, Hippler M, Neupert J, Popescu CI, Stavaru C, Branza-Nichita N, Bock R. The red alga Porphyridium as a host for molecular farming: Efficient production of immunologically active hepatitis C virus glycoprotein. Proc Natl Acad Sci U S A 2024; 121:e2400145121. [PMID: 38833465 PMCID: PMC11181018 DOI: 10.1073/pnas.2400145121] [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: 01/08/2024] [Accepted: 05/03/2024] [Indexed: 06/06/2024] Open
Abstract
Microalgae are promising production platforms for the cost-effective production of recombinant proteins. We have recently established that the red alga Porphyridium purpureum provides superior transgene expression properties, due to the episomal maintenance of transformation vectors as multicopy plasmids in the nucleus. Here, we have explored the potential of Porphyridium to synthesize complex pharmaceutical proteins to high levels. Testing expression constructs for a candidate subunit vaccine against the hepatitis C virus (HCV), we show that the soluble HCV E2 glycoprotein can be produced in transgenic algal cultures to high levels. The antigen undergoes faithful posttranslational modification by N-glycosylation and is recognized by conformationally selective antibodies, suggesting that it adopts a proper antigenic conformation in the endoplasmic reticulum of red algal cells. We also report the experimental determination of the structure of the N-glycan moiety that is attached to glycosylated proteins in Porphyridium. Finally, we demonstrate the immunogenicity of the HCV antigen produced in red algae when administered by injection as pure protein or by feeding of algal biomass.
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Affiliation(s)
- Alexander Hammel
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, D-14476Potsdam-Golm, Germany
| | - Lia-Maria Cucos
- Institute of Biochemistry of the Romanian Academy, Department of Viral Glycoproteins, 060031Bucharest, Romania
| | - Iuliana Caras
- ”Cantacuzino” Medico-Military National Research Institute, 050096Bucharest, Romania
| | - Irina Ionescu
- ”Cantacuzino” Medico-Military National Research Institute, 050096Bucharest, Romania
| | - Catalin Tucureanu
- ”Cantacuzino” Medico-Military National Research Institute, 050096Bucharest, Romania
| | - Vlad Tofan
- ”Cantacuzino” Medico-Military National Research Institute, 050096Bucharest, Romania
| | - Adriana Costache
- ”Cantacuzino” Medico-Military National Research Institute, 050096Bucharest, Romania
| | - Adrian Onu
- ”Cantacuzino” Medico-Military National Research Institute, 050096Bucharest, Romania
| | - Lara Hoepfner
- Institute of Plant Biology and Biotechnology, University of Münster, D-48143Münster, Germany
| | - Michael Hippler
- Institute of Plant Biology and Biotechnology, University of Münster, D-48143Münster, Germany
- Institute of Plant Science and Resources, Okayama University, Kurashiki710-0046, Japan
| | - Juliane Neupert
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, D-14476Potsdam-Golm, Germany
| | - Costin-Ioan Popescu
- Institute of Biochemistry of the Romanian Academy, Department of Viral Glycoproteins, 060031Bucharest, Romania
| | - Crina Stavaru
- ”Cantacuzino” Medico-Military National Research Institute, 050096Bucharest, Romania
| | - Norica Branza-Nichita
- Institute of Biochemistry of the Romanian Academy, Department of Viral Glycoproteins, 060031Bucharest, Romania
| | - Ralph Bock
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Department of Organelle Biology, Biotechnology and Molecular Ecophysiology, D-14476Potsdam-Golm, Germany
- NIBIO, Norwegian Institute of Bioeconomy Research, NO-1431 Ås, Norway
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González-Hernández Y, Perré P. Building blocks needed for mechanistic modeling of bioprocesses: A critical review based on protein production by CHO cells. Metab Eng Commun 2024; 18:e00232. [PMID: 38501051 PMCID: PMC10945193 DOI: 10.1016/j.mec.2024.e00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/12/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
This paper reviews the key building blocks needed to develop a mechanistic model for use as an operational production tool. The Chinese Hamster Ovary (CHO) cell, one of the most widely used hosts for antibody production in the pharmaceutical industry, is considered as a case study. CHO cell metabolism is characterized by two main phases, exponential growth followed by a stationary phase with strong protein production. This process presents an appropriate degree of complexity to outline the modeling strategy. The paper is organized into four main steps: (1) CHO systems and data collection; (2) metabolic analysis; (3) formulation of the mathematical model; and finally, (4) numerical solution, calibration, and validation. The overall approach can build a predictive model of target variables. According to the literature, one of the main current modeling challenges lies in understanding and predicting the spontaneous metabolic shift. Possible candidates for the trigger of the metabolic shift include the concentration of lactate and carbon dioxide. In our opinion, ammonium, which is also an inhibiting product, should be further investigated. Finally, the expected progress in the emerging field of hybrid modeling, which combines the best of mechanistic modeling and machine learning, is presented as a fascinating breakthrough. Note that the modeling strategy discussed here is a general framework that can be applied to any bioprocess.
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Affiliation(s)
- Yusmel González-Hernández
- Université Paris-Saclay, CentraleSupélec, Laboratoire de Génie des Procédés et Matériaux, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), 3 Rue des Rouges Terres, 51110, Pomacle, France
| | - Patrick Perré
- Université Paris-Saclay, CentraleSupélec, Laboratoire de Génie des Procédés et Matériaux, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), 3 Rue des Rouges Terres, 51110, Pomacle, France
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10
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Yamaguchi T, Ishikawa H, Fukuda M, Sugita Y, Furuie M, Nagano R, Suzawa T, Yamamoto K, Wakamatsu K. Catechins prevent monoclonal antibody fragmentation during production via fed-batch culture of Chinese hamster ovary cells. Biotechnol Prog 2024; 40:e3447. [PMID: 38415979 DOI: 10.1002/btpr.3447] [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: 12/10/2023] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/29/2024]
Abstract
Chinese hamster ovary (CHO) cells are widely used for the industrial production of therapeutic monoclonal antibodies (mAbs). To meet the increasing market demands, high productivity, and quality are required in cell culture. One of the critical attributes of mAbs, from a safety perspective, is mAb fragmentation. However, methods for preventing mAbs fragmentation in CHO cell culture are limited. In this study, we observed that the antibody fragment content increased with increasing titers in fed-batch cultures for all three cell lines expressing recombinant antibodies. Adding copper sulfate to the culture medium further increased the fragment content, suggesting the involvement of reactive oxygen species (ROS) in the fragmentation process. Though antioxidants may be helpful to scavenge ROS, several antioxidants are reported to decrease the productivity of CHO cells. Among the antioxidants examined, we observed that the addition of catechin or (-)-epigallocatechin gallate to the culture medium prevented fragmentation content by about 20% and increased viable cell density and titer by 30% and 10%, respectively. Thus, the addition of catechins or compounds of equivalent function would be beneficial for manufacturing therapeutic mAbs with a balance between high titers and good quality.
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Affiliation(s)
- Tsuyoshi Yamaguchi
- Graduate School of Science and Technology, Gunma University, Gunma, Japan
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., Takasaki, Gunma, Japan
| | - Hiroko Ishikawa
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., Takasaki, Gunma, Japan
| | - Mie Fukuda
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., Takasaki, Gunma, Japan
| | - Yumi Sugita
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., Takasaki, Gunma, Japan
| | - Misaki Furuie
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., Takasaki, Gunma, Japan
| | - Ryuma Nagano
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., Takasaki, Gunma, Japan
| | | | - Koichi Yamamoto
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., Takasaki, Gunma, Japan
| | - Kaori Wakamatsu
- Graduate School of Science and Technology, Gunma University, Gunma, Japan
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11
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Pandey U, Madhugiri I, Gadgil C, Gadgil M. Leveraging machine learning to dissect role of combinations of amino acids in modulating the effect of zinc on mammalian cell growth. Biotechnol Prog 2024; 40:e3436. [PMID: 38357841 DOI: 10.1002/btpr.3436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/04/2024] [Accepted: 01/14/2024] [Indexed: 02/16/2024]
Abstract
Although the contributions of individual components of cell culture media are largely known, their combinatorial effects are far less understood. Experiments varying one component at a time cannot identify combinatorial effects, and analysis of the large number of experiments required to decipher such effects is challenging. Machine learning algorithms can help in the analysis of such datasets to identify multi-component interactions. Zinc toxicity in vitro is known to change depending on amino acid concentration in the extracellular medium. Multiple amino acids are known to be involved in this protection. Thirty-two amino acid compositions were formulated to evaluate their effect on the growth of CHO cells under high zinc conditions. A sequential machine learning analysis methodology was used, which led to the identification of a set of amino acids (threonine, proline, glutamate, aspartate, asparagine, and tryptophan) contributing to protection from zinc. Our results suggest that a decrease in availability of these set of amino acids due to consumption may affect cell growth in media formulated with high zinc concentrations, and in contrast, normal levels of these amino acids are associated with better tolerance to high zinc concentration. Our sequential analysis method may be similarly employed for high throughput medium design and optimization experiments to identify interactions among a large number of cell culture medium components.
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Affiliation(s)
- Ujjiti Pandey
- Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Indrani Madhugiri
- Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Chetan Gadgil
- Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Mugdha Gadgil
- Chemical Engineering and Process Development, CSIR-National Chemical Laboratory, Pune, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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12
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Gangwar N, Balraj K, Rathore AS. Explainable AI for CHO cell culture media optimization and prediction of critical quality attribute. Appl Microbiol Biotechnol 2024; 108:308. [PMID: 38656382 PMCID: PMC11043154 DOI: 10.1007/s00253-024-13147-w] [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: 12/22/2023] [Revised: 03/28/2024] [Accepted: 04/11/2024] [Indexed: 04/26/2024]
Abstract
Cell culture media play a critical role in cell growth and propagation by providing a substrate; media components can also modulate the critical quality attributes (CQAs). However, the inherent complexity of the cell culture media makes unraveling the impact of the various media components on cell growth and CQAs non-trivial. In this study, we demonstrate an end-to-end machine learning framework for media component selection and prediction of CQAs. The preliminary dataset for feature selection was generated by performing CHO-GS (-/-) cell culture in media formulations with varying metal ion concentrations. Acidic and basic charge variant composition of the innovator product (24.97 ± 0.54% acidic and 11.41 ± 1.44% basic) was chosen as the target variable to evaluate the media formulations. Pearson's correlation coefficient and random forest-based techniques were used for feature ranking and feature selection for the prediction of acidic and basic charge variants. Furthermore, a global interpretation analysis using SHapley Additive exPlanations was utilized to select optimal features by evaluating the contributions of each feature in the extracted vectors. Finally, the medium combinations were predicted by employing fifteen different regression models and utilizing a grid search and random search cross-validation for hyperparameter optimization. Experimental results demonstrate that Fe and Zn significantly impact the charge variant profile. This study aims to offer insights that are pertinent to both innovators seeking to establish a complete pipeline for media development and optimization and biosimilar-based manufacturers who strive to demonstrate the analytical and functional biosimilarity of their products to the innovator. KEY POINTS: • Developed a framework for optimizing media components and prediction of CQA. • SHAP enhances global interpretability, aiding informed decision-making. • Fifteen regression models were employed to predict medium combinations.
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Affiliation(s)
- Neelesh Gangwar
- School of Interdisciplinary Research, Indian Institute of Technology, Delhi, New Delhi, 110016, India
| | - Keerthiveena Balraj
- Yardi School of Artificial Intelligence, Indian Institute of Technology, Delhi, New Delhi, 110016, India
| | - Anurag S Rathore
- Yardi School of Artificial Intelligence, Indian Institute of Technology, Delhi, New Delhi, 110016, India.
- Department of Chemical Engineering, Indian Institute of Technology, Delhi, New Delhi, 110016, India.
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13
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Balam S, Miura K, Ayadi I, Konaté D, Incandela NC, Agnolon V, Guindo MA, Diakité SA, Olugbile S, Nebie I, Herrera SM, Long C, Kajava AV, Diakité M, Corradin G, Herrera S, Herrera MA. Cross-reactivity of r Pvs48/45, a recombinant Plasmodium vivax protein, with sera from Plasmodium falciparum endemic areas of Africa. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.10.588966. [PMID: 38659832 PMCID: PMC11042229 DOI: 10.1101/2024.04.10.588966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
Background Ps48/45, a Plasmodium gametocyte surface protein, is a promising candidate for malaria transmission-blocking (TB) vaccine. Due to its relevance for a multispecies vaccine, we explored the cross-reactivity and TB activity of a recombinant P. vivax Ps48/45 protein (rPvs48/45) with sera from P. falciparum-exposed African donors. Methods rPvs48/45 was produced in Chinese hamster ovary cell lines and tested by ELISA for its cross-reactivity with sera from Burkina Faso, Tanzania, Mali, and Nigeria - In addition, BALB/c mice were immunized with the rPvs48/45 protein formulated in Montanide ISA-51 and inoculated with a crude extract of P. falciparum NF-54 gametocytes to evaluate the parasite-boosting effect on rPvs48/45 antibody titers. Specific anti-rPvs48/45 IgG purified from African sera was used to evaluate the ex vivo TB activity on P. falciparum, using standard mosquito membrane feeding assays (SMFA). Results rPvs48/45 protein showed cross-reactivity with sera of individuals from all four African countries, in proportions ranging from 94% (Tanzania) to 40% (Nigeria). Also, the level of cross-reactive antibodies varied significantly between countries (p<0.0001), with a higher antibody level in Mali and the lowest in Nigeria. In addition, antibody levels were higher in adults (≥ 17 years) than young children (≤ 5 years) in both Mali and Tanzania, with a higher proportion of responders in adults (90%) than in children (61%) (p<0.0001) in Mali, where male (75%) and female (80%) displayed similar antibody responses. Furthermore, immunization of mice with P. falciparum gametocytes boosted anti-Pvs48/45 antibody responses, recognizing P. falciparum gametocytes in indirect immunofluorescence antibody test. Notably, rPvs48/45 affinity-purified African IgG exhibited a TB activity of 61% against P. falciparum in SMFA. Conclusion African sera (exposed only to P. falciparum) cross-recognized the rPvs48/45 protein. This, together with the functional activity of IgG, warrants further studies for the potential development of a P. vivax and P. falciparum cross-protective TB vaccine.
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Affiliation(s)
- Saidou Balam
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Kazutoyo Miura
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Imen Ayadi
- Immunobiology Department, University of Lausanne, Lausanne, Switzerland
| | - Drissa Konaté
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Valentina Agnolon
- Division of Immunology and Allergy, Centre Hospitalier Universitaire Vaudois (CHUV), Lausanne, Switzerland aaaa
| | - Merepen A Guindo
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Seidina A.S. Diakité
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | - Sope Olugbile
- Immunobiology Department, University of Lausanne, Lausanne, Switzerland
| | - Issa Nebie
- Groupe de Recherche Action Santé (GRAS), Burkina Faso, West Africa
| | | | - Carole Long
- Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, MD 20852, USA
| | - Andrey V. Kajava
- Montpellier Cell Biology Research Center (CRBM), University of Montpellier, CNRS, France
| | - Mahamadou Diakité
- International Center for Excellence in Research (ICER-Mali), University of Sciences, Techniques and Technologies of Bamako (USTTB), Bamako, Mali
| | | | - Socrates Herrera
- Caucaseco Scientific Research Center, Cali, Colombia
- Malaria Vaccine and Drug Development Center, Cali, Colombia
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14
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Sanchez-Martinez ZV, Alpuche-Lazcano SP, Stuible M, Durocher Y. CHO cells for virus-like particle and subunit vaccine manufacturing. Vaccine 2024; 42:2530-2542. [PMID: 38503664 DOI: 10.1016/j.vaccine.2024.03.034] [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: 01/14/2024] [Revised: 02/27/2024] [Accepted: 03/13/2024] [Indexed: 03/21/2024]
Abstract
Chinese Hamster Ovary (CHO) cells, employed primarily for manufacturing monoclonal antibodies and other recombinant protein (r-protein) therapeutics, are emerging as a promising host for vaccine antigen production. This is exemplified by the recently approved CHO cell-derived subunit vaccines (SUV) against respiratory syncytial virus (RSV) and varicella-zoster virus (VZV), as well as the enveloped virus-like particle (eVLP) vaccine against hepatitis B virus (HBV). Here, we summarize the design, production, and immunogenicity features of these vaccine and review the most recent progress of other CHO-derived vaccines in pre-clinical and clinical development. We also discuss the challenges associated with vaccine production in CHO cells, with a focus on ensuring viral clearance for eVLP products.
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Affiliation(s)
- Zalma V Sanchez-Martinez
- Human Health Therapeutics Research Centre, National Research Council of Canada, Montreal, QC H4P 2R2, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada
| | - Sergio P Alpuche-Lazcano
- Human Health Therapeutics Research Centre, National Research Council of Canada, Montreal, QC H4P 2R2, Canada
| | - Matthew Stuible
- Human Health Therapeutics Research Centre, National Research Council of Canada, Montreal, QC H4P 2R2, Canada
| | - Yves Durocher
- Human Health Therapeutics Research Centre, National Research Council of Canada, Montreal, QC H4P 2R2, Canada; Department of Biochemistry and Molecular Medicine, University of Montreal, Montreal, QC H3T 1J4, Canada; PROTEO: The Quebec Network for Research on Protein Function, Structure, and Engineering, Université du Québec à Montréal, 201 Avenue du Président Kennedy, Montréal, QC H2X 3Y7, Canada.
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15
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Hirsch E, Bornemissza Z, Nagy ZK, Marosi GJ, Farkas A. Quantitative and qualitative analysis of cell culture media powders for mammalian cells by Raman microscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 310:123906. [PMID: 38277781 DOI: 10.1016/j.saa.2024.123906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 11/23/2023] [Accepted: 01/15/2024] [Indexed: 01/28/2024]
Abstract
Cell culture media are essential for large-scale recombinant protein production using mammalian cell cultures. The composition and quality of media significantly impact cell growth and product formation. Analyzing media poses challenges due to complex compositions and undisclosed exact compositions. Traditional methods like NMR and chromatography offer sensitivity but require time-consuming sample preparation and lack spatial information. Raman chemical mapping characterizes solids, but its use in cell culture media analysis is limited so far. We present a chemometric evaluation for Raman maps to qualify and quantify media components, evaluate powder homogeneity, and perform lot-to-lot comparisons. Three lots of a marketed cell culture media powder were measured with Raman mapping technique. Chemometrics techniques have outlined a strategy to extract information from complex data. First, a spectral library has been structured. In addition to the 23 spectra for presumed ingredients, we obtained another 9 pure components with Multivariate Curve Resolution-Alternating Least Squares (MCR-ALS). Then the Spectral Angle Mapper-Orthogonal Projection (SAM-OP) algorithm revealed whether references actually occur in the mapped media powders. Finally, a quantification was provided by Classical Least Squares (CLS) modelling. Quantities of 18 significant amino acids mostly correlated with the reference method. The proposed method can be generally applied even for such complicated samples. Leveraging Raman mapping and innovative chemometric methods enhance recombinant protein production by improving the understanding of the spatial distribution and composition of cell culture media in mammalian cell cultivations.
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Affiliation(s)
- Edit Hirsch
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Zsuzsanna Bornemissza
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Zsombor K Nagy
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
| | - György J Marosi
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Attila Farkas
- Department of Organic Chemistry and Technology, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Müegyetem rkp. 3., H-1111 Budapest, Hungary.
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16
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Nöbel M, Barry C, MacDonald MA, Baker K, Shave E, Mahler S, Munro T, Martínez VS, Nielsen LK, Marcellin E. Harnessing metabolic plasticity in CHO cells for enhanced perfusion cultivation. Biotechnol Bioeng 2024; 121:1371-1383. [PMID: 38079117 DOI: 10.1002/bit.28613] [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: 08/27/2023] [Revised: 10/25/2023] [Accepted: 11/19/2023] [Indexed: 04/01/2024]
Abstract
Chinese Hamster Ovary (CHO) cells have rapidly become a cornerstone in biopharmaceutical production. Recently, a reinvigoration of perfusion culture mode in CHO cell cultivation has been observed. However, most cell lines currently in use have been engineered and adapted for fed-batch culture methods, and may not perform optimally under perfusion conditions. To improve the cell's resilience and viability during perfusion culture, we cultured a triple knockout CHO cell line, deficient in three apoptosis related genes BAX, BAK, and BOK in a perfusion system. After 20 days of culture, the cells exhibited a halt in cell proliferation. Interestingly, following this phase of growth arrest, the cells entered a second growth phase. During this phase, the cell numbers nearly doubled, but cell specific productivity decreased. We performed a proteomics investigation, elucidating a distinct correlation between growth arrest and cell cycle arrest and showing an upregulation of the central carbon metabolism and oxidative phosphorylation. The upregulation was partially reverted during the second growth phase, likely caused by intragenerational adaptations to stresses encountered. A phase-dependent response to oxidative stress was noted, indicating glutathione has only a secondary role during cell cycle arrest. Our data provides evidence of metabolic regulation under high cell density culturing conditions and demonstrates that cell growth arrest can be overcome. The acquired insights have the potential to not only enhance our understanding of cellular metabolism but also contribute to the development of superior cell lines for perfusion cultivation.
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Affiliation(s)
- Matthias Nöbel
- Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, Australia
| | - Craig Barry
- Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, St. Lucia, Australia
| | - Michael A MacDonald
- Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, Australia
| | - Kym Baker
- Thermo Fisher Scientific, Woolloongabba, Australia
| | - Evan Shave
- Thermo Fisher Scientific, Woolloongabba, Australia
| | - Stephen Mahler
- Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, Australia
| | - Trent Munro
- Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, Australia
| | - Verónica S Martínez
- Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, Australia
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, St. Lucia, Australia
- The Novo Nordisk Foundation Centre for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, St. Lucia, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology, ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, St. Lucia, Australia
- ARC Centre of Excellence in Synthetic Biology (COESB), The University of Queensland, St. Lucia, Australia
- Queensland Metabolomics and Proteomics (Q-MAP), The University of Queensland, St. Lucia, Australia
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17
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Hall D. Equations describing semi-confluent cell growth (I) Analytical approximations. Biophys Chem 2024; 307:107173. [PMID: 38241828 DOI: 10.1016/j.bpc.2024.107173] [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: 08/24/2023] [Revised: 12/27/2023] [Accepted: 01/05/2024] [Indexed: 01/21/2024]
Abstract
A set of differential equations with analytical solutions are presented that can quantitatively account for variable degrees of contact inhibition on cell growth in two- and three-dimensional cultures. The developed equations can be used for comparative purposes when assessing contribution of higher-order effects, such as culture geometry and nutrient depletion, on mean cell growth rate. These equations also offer experimentalists the opportunity to characterize cell culture experiments using a single reductive parameter.
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Affiliation(s)
- Damien Hall
- WPI Nano Life Science Institute, Kanazawa University, Kakumamachi, Kanazawa, Ishikawa 920-1164, Japan.
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18
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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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Eisenhut P, Marx N, Borsi G, Papež M, Ruggeri C, Baumann M, Borth N. Manipulating gene expression levels in mammalian cell factories: An outline of synthetic molecular toolboxes to achieve multiplexed control. N Biotechnol 2024; 79:1-19. [PMID: 38040288 DOI: 10.1016/j.nbt.2023.11.003] [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: 10/02/2023] [Revised: 11/06/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023]
Abstract
Mammalian cells have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell's phenotype. Modulating cellular phenotypes is of major interest to study their role in disease or to reprogram cells for the manufacturing of recombinant products, such as biopharmaceuticals. Cells of mammalian origin, for example Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Early genetic engineering approaches to alter their phenotype have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, highlight that rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much more precision than such "uncontrolled" approaches. To this end, synthetic biology tools have been generated that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools used in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.
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Affiliation(s)
- Peter Eisenhut
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicolas Marx
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
| | - Giulia Borsi
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Maja Papež
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Caterina Ruggeri
- BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria
| | - Martina Baumann
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria
| | - Nicole Borth
- Austrian Centre of Industrial Biotechnology (acib GmbH), Muthgasse 11, 1190 Vienna, Austria; BOKU University of Natural Resources and Life Sciences, Institute of Animal Cell Technology and Systems Biology, Muthgasse 18, 1190 Vienna, Austria.
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20
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Cheng J, Zhang Y, Tian Y, Cao L, Liu X, Miao S, Zhao L, Ye Q, Zhou Y, Tan WS. Development of a novel tyrosine-based selection system for generation of recombinant Chinese hamster ovary cells. J Biosci Bioeng 2024; 137:221-229. [PMID: 38220502 DOI: 10.1016/j.jbiosc.2023.12.013] [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: 09/17/2023] [Revised: 12/18/2023] [Accepted: 12/18/2023] [Indexed: 01/16/2024]
Abstract
Efficiently expanding Chinese hamster ovary (CHO) cells, which serve as the primary host cells for recombinant protein production, have gained increasing industrial significance. A significant hurdle in stable cell line development is the low efficiency of the target gene integrated into the host genome, implying the necessity for an effective screening and selection procedure to separate these stable cells. In this study, the genes of phenylalanine hydroxylase (PAH) and pterin 4 alpha carbinolamine dehydratase 1 (PCBD1), which are key enzymes in the tyrosine synthesis pathway, were utilized as selection markers and transduced into host cells together with the target genes. This research investigated the enrichment effect of this system and advanced further in understanding its benefits for cell line development and rCHO cell culture. A novel tyrosine-based selection system that only used PCBD1 as a selection marker was designed to promote the enrichment effect. Post 9 days of starvation, positive transductants in the cell pool approached 100%. Applied the novel tyrosine-based selection system, rCHO cells expressing E2 protein were generated and named CHO TS cells. It could continue to grow, and the yield of E2 achieved 95.95 mg/L in a tyrosine-free and chemically-defined (CD) medium. Herein, we introduced an alternative to antibiotic-based selections for the establishment of CHO cell lines and provided useful insights for the design and development of CD medium.
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Affiliation(s)
- Jun Cheng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yanmin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Yuan Tian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Lei Cao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Xuping Liu
- Shanghai BioEngine Sci-Tech Co., Ltd, Shanghai 201203, China
| | - Shiwei Miao
- Hangzhou Sumgen Biotech Co., Ltd., Hangzhou 310051, China
| | - Liang Zhao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Qian Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Yan Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Wen-Song Tan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China
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21
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Olin M, Wolnick N, Crittenden H, Quach A, Russell B, Hendrick S, Armstrong J, Webster T, Hadley B, Dickson M, Hodgkins J, Busa K, Connolly R, Downey B. An automated high inoculation density fed-batch bioreactor, enabled through N-1 perfusion, accommodates clonal diversity and doubles titers. Biotechnol Prog 2024; 40:e3410. [PMID: 38013663 DOI: 10.1002/btpr.3410] [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: 01/12/2023] [Revised: 10/04/2023] [Accepted: 11/01/2023] [Indexed: 11/29/2023]
Abstract
An important consideration for biopharmaceutical processes is the cost of goods (CoGs) of biotherapeutics manufacturing. CoGs can be reduced by dramatically increasing the productivity of the bioreactor process. In this study, we demonstrate that an intensified process which couples a perfused N-1 seed reactor and a fully automated high inoculation density (HID) N stage reactor substantially increases the bioreactor productivity as compared to a low inoculation density (LID) control fed-batch process. A panel of six CHOK1SV GS-KO® CHO cell lines expressing three different monoclonal antibodies was evaluated in this intensified process, achieving an average 85% titer increase and 132% space-time yield (STY) increase was demonstrated when comparing the 12-day HID process to a 15-day LID control process. These productivity increases were enabled by automated nutrient feeding in both the N-1 and N stage bioreactors using in-line process analytical technologies (PAT) and feedback control. The N-1 bioreactor utilized in-line capacitance to automatically feed the bioreactor based on a capacitance-specific perfusion rate (CapSPR). The N-stage bioreactor utilized in-line Raman spectroscopy to estimate real-time concentrations of glucose, phenylalanine, and methionine, which are held to target set points using automatic feed additions. These automated feeding methodologies were shown to be generalizable across six cell lines with diverse feed requirements. We show this new process can accommodate clonal diversity and reproducibly achieve substantial titer uplifts compared to traditional cell culture processes, thereby establishing a baseline technology platform upon which further increases bioreactor productivity and CoGs reduction can be achieved.
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Affiliation(s)
- Mikayla Olin
- Research and Development, Lonza Biologics, Bend, Oregon, USA
| | - Nicolas Wolnick
- Research and Development, Lonza Biologics, Bend, Oregon, USA
| | | | - Anthony Quach
- Research and Development, Lonza Biologics, Bend, Oregon, USA
| | - Brian Russell
- Research and Development, Lonza Biologics, Bend, Oregon, USA
| | | | - Julia Armstrong
- Research and Development, Lonza Biologics, Bend, Oregon, USA
| | - Thaddaeus Webster
- Research and Development, Lonza Biologics, Portsmouth, New Hampshire, USA
| | - Brian Hadley
- Research and Development, Lonza Biologics, Portsmouth, New Hampshire, USA
| | - Marissa Dickson
- Research and Development, Lonza Biologics, Portsmouth, New Hampshire, USA
| | - Jessica Hodgkins
- Research and Development, Lonza Biologics, Portsmouth, New Hampshire, USA
| | - Kevin Busa
- Research and Development, Lonza Biologics, Portsmouth, New Hampshire, USA
| | - Roger Connolly
- Research and Development, Lonza Biologics, Portsmouth, New Hampshire, USA
| | - Brandon Downey
- Research and Development, Lonza Biologics, Bend, Oregon, USA
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22
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Ababneh R, Telfah A, Al Bataineh QM, Tolstik E, Dierks J, Hergenröder R. 1H, 31P NMR, Raman and FTIR spectroscopies for investigating phosphoric acid dissociation to understand phosphate ion kinetics in body fluids. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 307:123594. [PMID: 37976576 DOI: 10.1016/j.saa.2023.123594] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 10/17/2023] [Accepted: 10/29/2023] [Indexed: 11/19/2023]
Abstract
The study investigates the formation and transportation of ionic charge carriers in phosphoric acid-water system. This investigation encompasses an analysis of 1H and 31P NMR chemical shifts, self-diffusion coefficients, spin-lattice relaxation rates, spin-spin relaxation rates, activation energies, dissociation constants, electrical conductivity, and Raman shifts, along with FTIR spectra across various water concentrations. Significantly, the maxima observed in these curves at around 0.8 water molar fraction predominantly from the unique molecular arrangement between phosphoric acid and water molecules, influenced by a hydrogen bonding network. These findings yield valuable insights into phosphate ion kinetics within body fluids, covering essential aspects like hydrogen bonding networks, ionization processes, and the energy kinetics of phosphoric dissociation. A customized semiempirical model is applied to calculate dissociated species (water, phosphoric acid, and hydronium ion) at different water contents within a wide range of water mole fraction. Furthermore, this investigation extends to the dissociation of phosphoric acid in DMEM cell culture media, offering a more precise model for phosphate ionic kinetics within body fluids, especially at nominal phosphate concentrations of approximately 1:700μL.
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Affiliation(s)
- Riad Ababneh
- Department of Physics, Yarmouk University (YU), Irbid 21163, Jordan
| | - Ahmad Telfah
- Department of Physics, Yarmouk University (YU), Irbid 21163, Jordan; Nanotechnology Center, The University of Jordan, 11942 Amman, Jordan; Department of Physics, University of Nebraska at Omaha, Omaha, NE 68182, USA.
| | - Qais M Al Bataineh
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany; Experimental Physics, TU Dortmund University, 44227 Dortmund, Germany
| | - Elen Tolstik
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Johann Dierks
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
| | - Roland Hergenröder
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e.V., 44139 Dortmund, Germany
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23
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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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24
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Hashizume T, Ying BW. Challenges in developing cell culture media using machine learning. Biotechnol Adv 2024; 70:108293. [PMID: 37984683 DOI: 10.1016/j.biotechadv.2023.108293] [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: 07/01/2023] [Revised: 10/17/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
Microbial and mammalian cells are widely used in the food, pharmaceutical, and medical industries. Developing or optimizing culture media is essential to improve cell culture performance as a critical technology in cell culture engineering. Methodologies for media optimization have been developed to a great extent, such as the approaches of one-factor-at-a-time (OFAT) and response surface methodology (RSM). The present review introduces the emerging machine learning (ML) technology in cell culture engineering by combining high-throughput experimental technologies to develop highly efficient and effective culture media. The commonly used ML algorithms and the successful applications of employing ML in medium optimization are summarized. This review highlights the benefits of ML-assisted medium development and guides the selection of the media optimization method appropriate for various cell culture purposes.
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Affiliation(s)
- Takamasa Hashizume
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan
| | - Bei-Wen Ying
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572 Ibaraki, Japan.
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25
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Zhang K, Barbieri E, LeBarre J, Rameez S, Mostafa S, Menegatti S. Peptonics: A new family of cell-protecting surfactants for the recombinant expression of therapeutic proteins in mammalian cell cultures. Biotechnol J 2024; 19:e2300261. [PMID: 37844203 DOI: 10.1002/biot.202300261] [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: 06/02/2023] [Revised: 08/08/2023] [Accepted: 10/05/2023] [Indexed: 10/18/2023]
Abstract
Polymer surfactants are key components of cell culture media as they prevent mechanical damage during fermentation in stirred bioreactors. Among cell-protecting surfactants, Pluronics are widely utilized in biomanufacturing to ensure high cell viability and productivity. Monodispersity of monomer sequence and length is critical for the effectiveness of Pluronics-since minor deviations can damage the cells-but is challenging to achieve due to the stochastic nature of polymerization. Responding to this challenge, this study introduces Peptonics, a novel family of peptide and peptoid surfactants whose monomer composition and sequence are designed to achieve high cell viability and productivity at a fraction of chain length and cost of Pluronics. A designed ensemble of Peptonics was initially characterized via light scattering and tensiometry to select sequences whose phase behavior and tensioactivity align with those of Pluronics. Selected sequences were evaluated as cell-protecting surfactants using Chinese hamster ovary (CHO) cells expressing therapeutic monoclonal antibodies (mAb). Peptonics IH-T1010, ih-T1010, and ih-T1020 afforded high cell density (up to 3 × 107 cells mL-1 ) and viability (up to 95% within 10 days of culture), while reducing the accumulation of ammonia (a toxic metabolite) by ≈10% compared to Pluronic F-68. Improved cell viability afforded high mAb titer (up to 5.5 mg mL-1 ) and extended the production window beyond 14 days; notably, Peptonic IH-T1020 decreased mAb fragmentation and aggregation ≈5%, and lowered the titer of host cell proteins by 16% compared to Pluronic F-68. These features can improve significantly the purification of mAbs, thus increasing their availability at a lower cost to patients.
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Affiliation(s)
- Ka Zhang
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- KBI Biopharma, Durham, North Carolina, USA
| | - Eduardo Barbieri
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- LigaTrap Technologies LLC, Raleigh, North Carolina, USA
| | - Jacob LeBarre
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
| | | | | | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, USA
- LigaTrap Technologies LLC, Raleigh, North Carolina, USA
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina, USA
- North Carolina Viral Vector Initiative in Research and Learning (NC-VVIRAL), North Carolina State University, Raleigh, North Carolina, USA
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26
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Liu H, Zhang W, Xie L, Hu Y. Identification of a New Integration Site and Study on Site-Specific Integration in CHO-K1 Cells. Pharmaceuticals (Basel) 2023; 17:8. [PMID: 38275994 PMCID: PMC10819697 DOI: 10.3390/ph17010008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/15/2023] [Accepted: 12/18/2023] [Indexed: 01/27/2024] Open
Abstract
Site-specific integration is an important approach used to address the problem of unstable cell lines in industry. In this study, we observed a reduction in the gene copy number and antibody production in a CHOK1 cell line BA03 capable of high antibody expression. We identified a new integration site named locus 7 in the intron region of the parva gene through sequencing, FISH, and genome walking. We demonstrate that the integration of the exogenous gene at this locus does not affect the transcription of the parva and, therefore, has a minimal impact on cell growth. We designed sgRNA and donor vectors to integrate the etanercept-coding gene into locus 7 and obtained a cell line, SSI-4. We performed a passaged stability study on SSI-4 and proved the possibility of the stable, site-specific integration of exogenous genes at this locus in terms of integration site, copy number, expression level, and cell growth. In summary, our study has identified a new integration site suitable for site-specific integration, which lays the foundation for the subsequent development of site-specific integration cell lines.
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Affiliation(s)
| | | | - Liping Xie
- Department of Biology, China State Institute of Pharmaceutical Industry, Shanghai 201203, China; (H.L.); (W.Z.)
| | - Youjia Hu
- Department of Biology, China State Institute of Pharmaceutical Industry, Shanghai 201203, China; (H.L.); (W.Z.)
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27
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Tanemura H, Kitamura R, Yamada Y, Hoshino M, Kakihara H, Nonaka K. Comprehensive modeling of cell culture profile using Raman spectroscopy and machine learning. Sci Rep 2023; 13:21805. [PMID: 38071246 PMCID: PMC10710501 DOI: 10.1038/s41598-023-49257-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Accepted: 12/06/2023] [Indexed: 12/18/2023] Open
Abstract
Chinese hamster ovary (CHO) cells are widely utilized in the production of antibody drugs. To ensure the production of large quantities of antibodies that meet the required specifications, it is crucial to monitor and control the levels of metabolites comprehensively during CHO cell culture. In recent years, continuous analysis methods employing on-line/in-line techniques using Raman spectroscopy have attracted attention. While these analytical methods can nondestructively monitor culture data, constructing a highly accurate measurement model for numerous components is time-consuming, making it challenging to implement in the rapid research and development of pharmaceutical manufacturing processes. In this study, we developed a comprehensive, simple, and automated method for constructing a Raman model of various components measured by LC-MS and other techniques using machine learning with Python. Preprocessing and spectral-range optimization of data for model construction (partial least square (PLS) regression) were automated and accelerated using Bayes optimization. Subsequently, models were constructed for each component using various model construction techniques, including linear regression, ridge regression, XGBoost, and neural network. This enabled the model accuracy to be improved compared with PLS regression. This automated approach allows continuous monitoring of various parameters for over 100 components, facilitating process optimization and process monitoring of CHO cells.
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Affiliation(s)
- Hiroki Tanemura
- Biologics Technology Research Laboratories I, Biologics Division, Daiichi Sankyo Co., Ltd., 2716-1, Aza Kurakake, Oaza Akaiwa, Chiyoda-Machi, Oura-Gun, Gunma, 370-0503, Japan.
| | - Ryunosuke Kitamura
- Biologics Technology Research Laboratories I, Biologics Division, Daiichi Sankyo Co., Ltd., 2716-1, Aza Kurakake, Oaza Akaiwa, Chiyoda-Machi, Oura-Gun, Gunma, 370-0503, Japan
| | - Yasuko Yamada
- Analytical & Quality Evaluation Research Laboratories, Pharmaceutical Technology Division, Daiichi Sankyo Co., Ltd., 1-12-1, Shinomiya, Hiratsuka, Kanagawa, 254-0014, Japan
| | - Masato Hoshino
- Biologics Technology Research Laboratories I, Biologics Division, Daiichi Sankyo Co., Ltd., 2716-1, Aza Kurakake, Oaza Akaiwa, Chiyoda-Machi, Oura-Gun, Gunma, 370-0503, Japan
| | - Hirofumi Kakihara
- Biologics Technology Research Laboratories I, Biologics Division, Daiichi Sankyo Co., Ltd., 2716-1, Aza Kurakake, Oaza Akaiwa, Chiyoda-Machi, Oura-Gun, Gunma, 370-0503, Japan
| | - Koichi Nonaka
- Biologics Division, Daiichi Sankyo Co., Ltd., 2716-1, Aza Kurakake, Oaza Akaiwa, Chiyoda-Machi, Oura-Gun, Gunma, 370-0503, Japan
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28
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Wysor SK, Marcus RK. Quantitative Recoveries of Exosomes and Monoclonal Antibodies from Chinese Hamster Ovary Cell Cultures by Use of a Single, Integrated Two-Dimensional Liquid Chromatography Method. Anal Chem 2023; 95:17886-17893. [PMID: 37995145 PMCID: PMC11095952 DOI: 10.1021/acs.analchem.3c04044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Cultured cell lines are very commonly used for the mass production of therapeutic proteins, such as monoclonal antibodies (mAbs). In particular, Chinese hamster ovary (CHO) cell lines are widely employed due to their high tolerance to variations in experimental conditions and their ability to grow in suspension or serum free media. CHO cell lines are known for their ability to produce high titers of biotherapeutic products such as immunoglobulin G (IgG). An emergent alternative means of treating diseases, such as cancer, is the use of gene therapies, wherein genetic cargo is "packaged" in nanosized vesicular structures, referred to as "vectors". One particularly attractive vector option is extracellular vesicles (EVs), of which exosomes are of greatest interest. While exosomes can be harvested from virtually any human body fluid, bovine milk, or even plants, their production in cell cultures is an attractive commercial approach. In fact, the same CHO cell types employed for mAb production also produce exosomes as a natural byproduct. Here, we describe a single integrated 2D liquid chromatography (2DLC) method for the quantitative recovery of both exosomes and antibodies from a singular sample aliquot. At the heart of the method is the use of polyester capillary-channeled polymer (C-CP) fibers as the first dimension column, wherein exosomes/EVs are captured from the supernatant sample and subsequently determined by multiangle light scattering (MALS), while the mAbs are captured, eluted, and quantified using a protein A-modified C-CP fiber column in the second dimension, all in a 10 min workflow. These efforts demonstrate the versatility of the C-CP fiber phases with the capacity to harvest both forms of therapeutics from a single bioreactor, suggesting an appreciable potential impact in the field of biotherapeutics production.
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Affiliation(s)
- Sarah K Wysor
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, South Carolina 29634-0973, United States
| | - R Kenneth Marcus
- Department of Chemistry, Biosystems Research Complex, Clemson University, Clemson, South Carolina 29634-0973, United States
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29
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Yarinich LA, Ogienko AA, Pindyurin AV, Omelina ES. Analysis of the transcriptional activity of model piggyBac transgenes stably integrated into different loci of the genome of CHO cells in the absence of selection pressure. Vavilovskii Zhurnal Genet Selektsii 2023; 27:906-915. [PMID: 38213697 PMCID: PMC10777298 DOI: 10.18699/vjgb-23-105] [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: 09/03/2023] [Revised: 09/21/2023] [Accepted: 09/27/2023] [Indexed: 01/13/2024] Open
Abstract
CHO cells are most commonly used for the synthesis of recombinant proteins in biopharmaceutical production. When stable producer cell lines are obtained, the locus of transgene integration into the genome has a great influence on the level of its expression. Therefore, the identification of genomic loci ensuring a high level of protein production is very important. Here, we used the TRIP assay to study the influence of the local chromatin environment on the activity of transgenes in CHO cells. For this purpose, reporter constructs encoding eGFP under the control of four promoters were stably integrated into the genome of CHO cells using the piggyBac transposon. Each individual transgene contained a unique tag, a DNA barcode, and the resulting polyclonal cell population was cultured for almost a month without any selection. Next, using the high-throughput sequencing, genomic localizations of barcodes, as well as their abundances in the population and transcriptional activities were identified. In total, ~640 transgenes more or less evenly distributed across all chromosomes of CHO cells were characterized. More than half of the transgenes were completely silent. The most active transgenes were identified to be inserted in gene promoters and 5' UTRs. Transgenes carrying Chinese hamster full-length promoter of the EF-1α gene showed the highest activity. Transgenes with a truncated version of the same promoter and with the mouse PGK gene promoter were on average 10 and 19 times less active, respectively. In total, combinations of genomic loci of CHO cells and transgene promoters that together provide different levels of transcriptional activity of the model reporter construct were described.
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Affiliation(s)
- L A Yarinich
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A A Ogienko
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - A V Pindyurin
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - E S Omelina
- Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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30
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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] [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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31
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Vitharana S, Stillahn JM, Katayama DS, Henry CS, Manning MC. Application of Formulation Principles to Stability Issues Encountered During Processing, Manufacturing, and Storage of Drug Substance and Drug Product Protein Therapeutics. J Pharm Sci 2023; 112:2724-2751. [PMID: 37572779 DOI: 10.1016/j.xphs.2023.08.003] [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: 10/14/2022] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/14/2023]
Abstract
The field of formulation and stabilization of protein therapeutics has become rather extensive. However, most of the focus has been on stabilization of the final drug product. Yet, proteins experience stress and degradation through the manufacturing process, starting with fermentaition. This review describes how formulation principles can be applied to stabilize biopharmaceutical proteins during bioprocessing and manufacturing, considering each unit operation involved in prepration of the drug substance. In addition, the impact of the container on stabilty is discussed as well.
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Affiliation(s)
| | - Joshua M Stillahn
- Legacy BioDesign LLC, Johnstown, CO 80534, USA; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA
| | - Mark Cornell Manning
- Legacy BioDesign LLC, Johnstown, CO 80534, USA; Department of Chemistry, Colorado State University, Fort Collins, CO 80523, USA.
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32
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Tian J, Yang Y, Xu W, Du X, Ye Y, Zhu B, Huang Y, Zhao Y, Li Y. Effects of β-1,3-glucan on growth, immune responses, and intestinal microflora of the river prawn (Macrobrachium nipponense) and its resistance against Vibrio parahaemolyticus. FISH & SHELLFISH IMMUNOLOGY 2023; 142:109142. [PMID: 37805111 DOI: 10.1016/j.fsi.2023.109142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/01/2023] [Accepted: 10/04/2023] [Indexed: 10/09/2023]
Abstract
In this study, we investigated the impact of β-1,3-glucan on the immune responses and gut microbiota of the river prawn (Macrobrachium nipponense) in the presence of Vibrio parahaemolyticus stress. Shrimps were fed one of the following diets: control (G1), 0.2% curdlan (G2), 0.1% β-1,3-glucan (G3), 0.2% β-1,3-glucan (G4), or 1.0% β-1,3-glucan (G5) for 6 weeks and then challenged with V. parahaemolyticus for 96 h. Under Vibrio stress, shrimps in G4 exhibited the highest length gain rate, weight gain rate, and survival rate. They also showed increased intestinal muscle thickness and villus thickness compared to the control and 0.2% curdlan groups. The apoptosis rate was lower in G4 than in the control group, and the digestive enzyme activities (pepsin, trypsin, amylase, and lipase), immune enzyme activities (acid phosphatase, alkaline phosphatase, lysozyme, and phenoxidase), and energy metabolism (triglyceride, cholesterol, glycogen, and lactate dehydrogenase) were enhanced. Expression levels of growth-related genes (ecdysone receptor, calmodulin-dependent protein kinase I, chitin synthase, and retinoid X receptor) and immune-related genes (toll-like receptor 3, myeloid differentiation primary response 88, mitogen-activated protein kinase 7, and mitogen-activated protein kinase 14) were higher in G4 than in the control. Microbiota analysis indicated higher bacterial abundance in shrimps fed β-1,3-glucan, as evidenced by Sob, Chao1, and ACE indices. Moreover, 0.2% β-1,3-glucan increased the relative abundances of Bacteroidota and Firmicutes while reducing those of Corynebacteriales and Lactobacillales. In summary, β-1,3-glucan enhances immune enzyme activities, alters immune-related gene expression, and impacts gut microbial diversity in shrimp. These findings provide valuable insights into the mechanisms underlying β-1,3 glucan's immune-enhancing effects.
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Affiliation(s)
- Jiangtao Tian
- School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Ying Yang
- School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Wenyue Xu
- School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Xinglin Du
- School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Yucong Ye
- School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Bihong Zhu
- School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Yizhou Huang
- School of Life Science, East China Normal University, Shanghai, 200241, China
| | - Yunlong Zhao
- School of Life Science, East China Normal University, Shanghai, 200241, China.
| | - Yiming Li
- Fishery Machinery and Instrument Research Institute, Chinese Academy of Fisheries Sciences, Shanghai, 200092, China.
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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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Yamaguchi T, Fukuda M, Matsumoto Y, Mori T, Kikuchi S, Nagano R, Yamamoto K, Wakamatsu K. New high-throughput screening method for Chinese hamster ovary cell lines expressing low reduced monoclonal antibody levels: application of a system controlling the gas phase over cell lysates in miniature bioreactors and facilitating multiple sample setup. Cytotechnology 2023; 75:421-433. [PMID: 37655271 PMCID: PMC10465464 DOI: 10.1007/s10616-023-00587-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 06/29/2023] [Indexed: 09/02/2023] Open
Abstract
Interchain disulfide bonds in monoclonal antibodies may be reduced during large-scale mAb production using Chinese hamster ovary (CHO) cells. This reaction lowers the mAb product yield and purity; however, it may be prevented by screening cell lines that are unsusceptible to reduction and using them in mAb production. Antibody reduction susceptibility may be cell line-dependent. To the best of our knowledge, however, an efficient method of screening reduction-unsusceptible CHO cell lines has not been previously reported. Here, we report a novel screening method that can simultaneously detect and identify mAb reduction susceptibility in lysates containing ≤ 48 CHO cell lines. This evaluation system was equally effective and generated similar results at all culture scales, including 250 mL, 3 L, and 1000 L. Furthermore, we discovered that reduction-susceptible cell lines contained higher total intracellular nicotinamide adenine dinucleotide phosphate (NADPH) and NADP+ concentrations than reduction-unsusceptible cell lines, regardless of whether they expressed immunoglobulin (Ig)G4 or IgG1. NADPH or NADP+ supplementation in the lysate of reduction-unsusceptible cells resulted in mAb reduction. Application of the innovative CHO cell line screening approach could mitigate or prevent reductions in large-scale mAb generation from CHO cells.
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Affiliation(s)
- Tsuyoshi Yamaguchi
- Graduate School of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma 376-8515 Japan
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., 100-1, Hagiwara, Takasaki, Gunma 370-0013 Japan
| | - Mie Fukuda
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., 100-1, Hagiwara, Takasaki, Gunma 370-0013 Japan
| | - Yuichi Matsumoto
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., 100-1, Hagiwara, Takasaki, Gunma 370-0013 Japan
| | - Takaaki Mori
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., 100-1, Hagiwara, Takasaki, Gunma 370-0013 Japan
| | - Shinsuke Kikuchi
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., 100-1, Hagiwara, Takasaki, Gunma 370-0013 Japan
| | - Ryuma Nagano
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., 100-1, Hagiwara, Takasaki, Gunma 370-0013 Japan
| | - Koichi Yamamoto
- Bio Process Research and Development Laboratories, Production Division, Kyowa Kirin Co. Ltd., 100-1, Hagiwara, Takasaki, Gunma 370-0013 Japan
| | - Kaori Wakamatsu
- Graduate School of Science and Technology, Gunma University, 1-5-1, Tenjin-cho, Kiryu, Gunma 376-8515 Japan
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35
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van der Burg D, Wätzig H, Sänger-van de Griend CE. Design of experiments for micellar electrokinetic chromatography method development for the monitoring of water-soluble vitamins in cell culture medium. Electrophoresis 2023; 44:1548-1558. [PMID: 37732546 DOI: 10.1002/elps.202300032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 07/05/2023] [Accepted: 07/18/2023] [Indexed: 09/22/2023]
Abstract
Biopharmaceutical production takes place in complex processes which should be thoroughly understood. Therefore, the iConsensus project focuses on developing a monitoring platform integrating several process analytical technology tools for integrated, automated monitoring of the biopharmaceutical process. Water-soluble vitamin monitoring using (microchip) capillary electrophoresis (CE) is part of this platform. This work comprises the development of conventional CE methods as the first part towards integrated vitamin monitoring. The vitamins were divided based on their physical-chemical properties to develop two robust methods. Previously, a method for the analysis of cationic vitamins (pyridoxine, pyridoxal, pyridoxamine, thiamine and nicotinamide) in cell culture medium was developed. This work focused on the development of a micellar electrokinetic chromatography method for anionic and neutral vitamins (riboflavin, d-calcium pantothenate, biotin, folic acid, cyanocobalamin and ascorbic acid). By employing multivariate design of experiments, the background electrolyte (BGE) could be optimised within one experiment testing only 11 BGEs. The optimised BGE conditions were 200 mM borate with 77 mM sodium dodecyl sulphate at a pH of 8.6. Using this BGE, all above-mentioned cationic, anionic and neutral vitamins could be separated in clean samples. In cell culture medium, most anionic and neutral vitamins could be separated. Combining the two methods allows for analysis of cationic, anionic and neutral vitamins in cell culture medium samples. The next step towards integrated vitamin monitoring includes transfer to microchip CE. Due to the lack of fast and reliable methods for vitamin monitoring, the developed capillary methods could be valuable as stand-alone at-line process analytical technology solutions as well.
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Affiliation(s)
- Debbie van der Burg
- Kantisto BV, Baarn, The Netherlands
- TU Braunschweig, Institute of Medicinal and Pharmaceutical Chemistry, Braunschweig, Germany
| | - Hermann Wätzig
- TU Braunschweig, Institute of Medicinal and Pharmaceutical Chemistry, Braunschweig, Germany
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Zhang D, Qiu J, Niu QT, Liu T, Gu R, Zhang X, Luo S. Effects of various pine needle extracts on Chinese hamster ovary cell growth and monoclonal antibody quality. Prep Biochem Biotechnol 2023; 53:1081-1091. [PMID: 36756987 DOI: 10.1080/10826068.2023.2166959] [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] [Indexed: 02/10/2023]
Abstract
Chinese hamster ovary (CHO) cells are commonly used as "bio-machines" to pro-duce monoclonal antibodies (mAb) because of their ability to produce very complex proteins. In this study, we evaluated the effects of pine needle water extract (PNWE), pine needle ethanol extract (PNEE), and pine needle polysaccharide extract (PNPE) on the CHO cell growth, mAb production and quality using a Fed-batch culture process. PNPE maintained high VCD and viability, and the titer increase was correlated with its concentration. Three extracts effectively reduced the acidic charge variant and modulated mAb glycosylation. PNPE had the most profound effect, with G0F decreasing by 8.7% and G1Fa increasing by 6.7%. The change in the glycoform was also closely related to the PNPE concentration. This study demonstrated that PNPE could facilitate CHO cell growth, increase the mAb production, decrease acidic charge variants, and regulate mAb glycoforms. To identify the components responsible for the above changes, the sugar and flavonoid contents in the extracts were determined, and the chemical compounds were identified by LC-MS, resulting in 38 compounds identified from PNPE. Rich in sugars and flavonoids in these three extracts may be related to increased CHO cell growth and productivity, and changes in glycoforms.
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Affiliation(s)
- Dingyue Zhang
- Anhui University of Chinese Medicine, Hefei, China
- Yangtze Delta Drug Advanced Research Institute, Nantong, China
| | - Jinshu Qiu
- Thousand Oaks Biopharmaceuticals Co., Ltd., Nantong, China
| | - Qing-Tian Niu
- Thousand Oaks Biopharmaceuticals Co., Ltd., Nantong, China
| | - Tingting Liu
- Thousand Oaks Biopharmaceuticals Co., Ltd., Nantong, China
| | - Rulin Gu
- Thousand Oaks Biopharmaceuticals Co., Ltd., Nantong, China
| | - Xiaoying Zhang
- Thousand Oaks Biopharmaceuticals Co., Ltd., Nantong, China
| | - Shun Luo
- Anhui University of Chinese Medicine, Hefei, China
- Thousand Oaks Biopharmaceuticals Co., Ltd., Nantong, China
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37
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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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38
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Sun M, Gao AX, Liu X, Yang Y, Ledesma-Amaro R, Bai Z. High-throughput process development from gene cloning to protein production. Microb Cell Fact 2023; 22:182. [PMID: 37715258 PMCID: PMC10503041 DOI: 10.1186/s12934-023-02184-1] [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: 05/24/2023] [Accepted: 08/19/2023] [Indexed: 09/17/2023] Open
Abstract
In the post-genomic era, the demand for faster and more efficient protein production has increased, both in public laboratories and industry. In addition, with the expansion of protein sequences in databases, the range of possible enzymes of interest for a given application is also increasing. Faced with peer competition, budgetary, and time constraints, companies and laboratories must find ways to develop a robust manufacturing process for recombinant protein production. In this review, we explore high-throughput technologies for recombinant protein expression and present a holistic high-throughput process development strategy that spans from genes to proteins. We discuss the challenges that come with this task, the limitations of previous studies, and future research directions.
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Affiliation(s)
- Manman Sun
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Alex Xiong Gao
- Division of Life Science, The Hong Kong University of Science and Technology, Hong Kong, China
| | - Xiuxia Liu
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Yankun Yang
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK.
| | - Zhonghu Bai
- National Engineering Research Center of Cereal Fermentation and Food Biomanufacturing, Jiangnan University, Wuxi, 214112, China.
- Key Laboratory of Industrial Biotechnology, School of Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, Wuxi, 214122, China.
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Ladiwala P, Dhara VG, Jenkins J, Kuang B, Hoang D, Yoon S, Betenbaugh MJ. Addressing amino acid-derived inhibitory metabolites and enhancing CHO cell culture performance through DOE-guided media modifications. Biotechnol Bioeng 2023; 120:2542-2558. [PMID: 37096798 DOI: 10.1002/bit.28403] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 04/26/2023]
Abstract
Previously, we identified six inhibitory metabolites (IMs) accumulating in Chinese hamster ovary (CHO) cultures using AMBIC 1.0 community reference medium that negatively impacted culture performance. The goal of the current study was to modify the medium to control IM accumulation through design of experiments (DOE). Initial over-supplementation of precursor amino acids (AAs) by 100% to 200% in the culture medium revealed positive correlations between initial AA concentrations and IM levels. A screening design identified 5 AA targets, Lys, Ile, Trp, Leu, Arg, as key contributors to IMs. Response surface design analysis was used to reduce initial AA levels between 13% and 33%, and these were then evaluated in batch and fed-batch cultures. Lowering AAs in basal and feed medium and reducing feed rate from 10% to 5% reduced inhibitory metabolites HICA and NAP by up to 50%, MSA by 30%, and CMP by 15%. These reductions were accompanied by a 13% to 40% improvement in peak viable cell densities and 7% to 50% enhancement in IgG production in batch and fed-batch processes, respectively. This study demonstrates the value of tuning specific AA levels in reference basal and feed media using statistical design methodologies to lower problematic IMs.
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Affiliation(s)
- Pranay Ladiwala
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Venkata Gayatri Dhara
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jackson Jenkins
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Bingyu Kuang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Duc Hoang
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, USA
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40
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Schwarz H, Lee K, Castan A, Chotteau V. Optimization of medium with perfusion microbioreactors for high density CHO cell cultures at very low renewal rate aided by design of experiments. Biotechnol Bioeng 2023; 120:2523-2541. [PMID: 37079436 DOI: 10.1002/bit.28397] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/15/2023] [Accepted: 04/01/2023] [Indexed: 04/21/2023]
Abstract
A novel approach of design of experiment (DoE) is developed for the optimization of key substrates of the culture medium, amino acids, and sugars, by utilizing perfusion microbioreactors with 2 mL working volume, operated in high cell density continuous mode, to explore the design space. A mixture DoE based on a simplex-centroid is proposed to test multiple medium blends in parallel perfusion runs, where the amino acids concentrations are selected based on the culture behavior in presence of different amino acid mixtures, and using targeted specific consumption rates. An optimized medium is identified with models predicting the culture parameters and product quality attributes (G0 and G1 level N-glycans) as a function of the medium composition. It is then validated in runs performed in perfusion microbioreactor in comparison with stirred-tank bioreactors equipped with alternating tangential flow filtration (ATF) or with tangential flow filtration (TFF) for cell separation, showing overall a similar process performance and N-glycosylation profile of the produced antibody. These results demonstrate that the present development strategy generates a perfusion medium with optimized performance for stable Chinese hamster ovary (CHO) cell cultures operated with very high cell densities of 60 × 106 and 120 × 106 cells/mL and a low cell-specific perfusion rate of 17 pL/cell/day, which is among the lowest reported and is in line with the framework recently published by the industry.
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Affiliation(s)
- Hubert Schwarz
- Cell Technology Group, Department of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- AdBIOPRO, Competence Centre for Advanced BioProduction by Continuous Processing, Stockholm, Sweden
| | | | | | - Veronique Chotteau
- Cell Technology Group, Department of Industrial Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
- AdBIOPRO, Competence Centre for Advanced BioProduction by Continuous Processing, Stockholm, Sweden
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Becker L, Sturm J, Eiden F, Holtmann D. Analyzing and understanding the robustness of bioprocesses. Trends Biotechnol 2023; 41:1013-1026. [PMID: 36959084 DOI: 10.1016/j.tibtech.2023.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 03/25/2023]
Abstract
The robustness of bioprocesses is becoming increasingly important. The main driving forces of this development are, in particular, increasing demands on product purities as well as economic aspects. In general, bioprocesses exhibit extremely high complexity and variability. Biological systems often have a much higher intrinsic variability compared with chemical processes, which makes the development and characterization of robust processes tedious task. To predict and control robustness, a clear understanding of interactions between input and output variables is necessary. Robust bioprocesses can be realized, for example, by using advanced control strategies for the different unit operations. In this review, we discuss the different biological, technical, and mathematical tools for the analysis and control of bioprocess robustness.
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Affiliation(s)
- Lucas Becker
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany
| | - Jonathan Sturm
- Bioprozesstechnik Group, Westfälische Hochschule, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany; iAMB - Institute of Applied Microbiology, ABBt - Aachen Biology and Biotechnology, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Frank Eiden
- Bioprozesstechnik Group, Westfälische Hochschule, August-Schmidt-Ring 10, 45665 Recklinghausen, Germany
| | - Dirk Holtmann
- Institute of Bioprocess Engineering and Pharmaceutical Technology, University of Applied Sciences Mittelhessen, Wiesenstrasse 14, 35390 Giessen, Germany.
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Gomez Romero S, Boyle N. Systems biology and metabolic modeling for cultivated meat: A promising approach for cell culture media optimization and cost reduction. Compr Rev Food Sci Food Saf 2023; 22:3422-3443. [PMID: 37306528 DOI: 10.1111/1541-4337.13193] [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: 02/10/2023] [Revised: 05/07/2023] [Accepted: 05/22/2023] [Indexed: 06/13/2023]
Abstract
The cultivated meat industry, also known as cell-based meat, cultured meat, lab-grown meat, or meat alternatives, is a growing field that aims to generate animal tissues ex-vivo in a cost-effective manner that achieves price parity with traditional agricultural products. However, cell culture media costs account for 55%-90% of production costs. To address this issue, efforts are aimed at optimizing media composition. Systems biology-driven approaches have been successfully used to improve the biomass and productivity of multiple bioproduction platforms, like Chinese hamster ovary cells, by accelerating the development of cell line-specific media and reducing research and development and production costs related to cell media and its optimization. In this review, we summarize systems biology modeling approaches, methods for cell culture media and bioprocess optimization, and metabolic studies done in animals of interest to the cultivated meat industry. More importantly, we identify current gaps in knowledge that prevent the identification of metabolic bottlenecks. These include the lack of genome-scale metabolic models for some species (pigs and ducks), a lack of accurate biomass composition studies for different growth conditions, and 13 C-metabolic flux analysis (MFA) studies for many of the species of interest for the cultivated meat industry (only shrimp and duck cells have been subjected to 13 C-MFA). We also highlight the importance of characterizing the metabolic requirements of cells at the organism, breed, and cell line-specific levels, and we outline future steps that this nascent field needs to take to achieve price parity and production efficiency similar to those of other bioproduction platforms. Practical Application: Our article summarizes systems biology techniques for cell culture media design and bioprocess optimization, which may be used to significantly reduce cell-based meat production costs. We also present the results of experimental studies done on some of the species of interest to the cultivated meat industry and highlight why modeling approaches are required for multiple species, cell-types, and cell lines.
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Affiliation(s)
- Sandra Gomez Romero
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, Colorado, USA
| | - Nanette Boyle
- Chemical and Biological Engineering, Colorado School of Mines, Golden, Colorado, USA
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Forte T, Grinnell C, Zhang A, Polilli B, Leshinski J, Khattak S. Methods for identifying precipitates and improving stability of chemically defined highly concentrated cell culture media. Biotechnol Prog 2023; 39:e3345. [PMID: 37062873 DOI: 10.1002/btpr.3345] [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: 11/18/2022] [Revised: 03/10/2023] [Accepted: 03/26/2023] [Indexed: 04/18/2023]
Abstract
Currently, within the biopharmaceutical industry, media development is a key area of development as the ratios and concentrations of media components such as amino acids, metals, vitamins, sugars, salts, and buffering agents play arguably the largest role in cellular productivity and product quality. However, optimizing media for these targets often conflicts with solubility limitations and slow-rate chemical reactions that result in precipitation formation. Here we present methods such as inductively coupled plasma mass spectrometry (ICP-MS), X-ray fluorescence (XRF), colorimetry, and turbidity to identify multiple likely components of a complex precipitate that was observed in preparations of a custom nutrient feed medium across all storage conditions evaluated. Using these analytical methods, as well as adjustments to the formulation pH, increasing the pyruvate concentration, and removing sodium bicarbonate, we were able to extend the media shelf life from approximately 10 days to over 28 days. Alternatively, copper, selenium, and magnesium sources were removed from the media and no precipitation was observed until 32 days after prep, pointing to key metals as the probable root cause of precipitation. By analytically quantifying the precipitate using the methods above, instead of visual inspection, which is the current industry standard for media precipitation observation, we were better able to compare conditions to one another and relate them to the onset of precipitation. Cell culture performance and product quality remained comparable to the historical process despite the media formulation changes.
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Affiliation(s)
- Taylor Forte
- Cell Culture Development, Biogen, Cambridge, Massachusetts, USA
| | | | - An Zhang
- Cell Culture Development, Biogen, Durham, North Carolina, USA
| | - Brian Polilli
- API Proteins, Janssen R&D, Malvern, Pennsylvania, USA
| | | | - Sarwat Khattak
- Cell Culture Development, Biogen, Durham, North Carolina, USA
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44
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Hashizume T, Ozawa Y, Ying BW. Employing active learning in the optimization of culture medium for mammalian cells. NPJ Syst Biol Appl 2023; 9:20. [PMID: 37253825 DOI: 10.1038/s41540-023-00284-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/18/2023] [Indexed: 06/01/2023] Open
Abstract
Medium optimization is a crucial step during cell culture for biopharmaceutics and regenerative medicine; however, this step remains challenging, as both media and cells are highly complex systems. Here, we addressed this issue by employing active learning. Specifically, we introduced machine learning to cell culture experiments to optimize culture medium. The cell line HeLa-S3 and the gradient-boosting decision tree algorithm were used to find optimized media as pilot studies. To acquire the training data, cell culture was performed in a large variety of medium combinations. The cellular NAD(P)H abundance, represented as A450, was used to indicate the goodness of culture media. In active learning, regular and time-saving modes were developed using culture data at 168 h and 96 h, respectively. Both modes successfully fine-tuned 29 components to generate a medium for improved cell culture. Intriguingly, the two modes provided different predictions for the concentrations of vitamins and amino acids, and a significant decrease was commonly predicted for fetal bovine serum (FBS) compared to the commercial medium. In addition, active learning-assisted medium optimization significantly increased the cellular concentration of NAD(P)H, an active chemical with a constant abundance in living cells. Our study demonstrated the efficiency and practicality of active learning for medium optimization and provided valuable information for employing machine learning technology in cell biology experiments.
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Affiliation(s)
- Takamasa Hashizume
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Ibaraki, Japan
| | - Yuki Ozawa
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Ibaraki, Japan
| | - Bei-Wen Ying
- School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, 305-8572, Ibaraki, Japan.
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45
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Zhou T, Reji R, Kairon RS, Chiam KH. A review of algorithmic approaches for cell culture media optimization. Front Bioeng Biotechnol 2023; 11:1195294. [PMID: 37251567 PMCID: PMC10213948 DOI: 10.3389/fbioe.2023.1195294] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023] Open
Abstract
Cell culture media composition and culture conditions play a crucial role in product yield, quality and cost of production. Culture media optimization is the technique of improving media composition and culture conditions to achieve desired product outcomes. To achieve this, there have been many algorithmic methods proposed and used for culture media optimization in the literature. To help readers evaluate and decide on a method that best suits their specific application, we carried out a systematic review of the different methods from an algorithmic perspective that classifies, explains and compares the available methods. We also examine the trends and new developments in the area. This review provides recommendations to researchers regarding the suitable media optimization algorithm for their applications and we hope to also promote the development of new cell culture media optimization methods that are better suited to existing and upcoming challenges in this biotechnology field, which will be essential for more efficient production of various cell culture products.
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Affiliation(s)
- Tianxun Zhou
- Bioinformatics Institute, Cellular Image Informatics Division, A*STAR, Singapore, Singapore
| | - Rinta Reji
- Bioinformatics Institute, Cellular Image Informatics Division, A*STAR, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Ryanjit Singh Kairon
- Bioinformatics Institute, Cellular Image Informatics Division, A*STAR, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Keng Hwee Chiam
- Bioinformatics Institute, Cellular Image Informatics Division, A*STAR, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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46
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Duarte AC, Costa EC, Filipe HAL, Saraiva SM, Jacinto T, Miguel SP, Ribeiro MP, Coutinho P. Animal-derived products in science and current alternatives. BIOMATERIALS ADVANCES 2023; 151:213428. [PMID: 37146527 DOI: 10.1016/j.bioadv.2023.213428] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/08/2023] [Accepted: 04/11/2023] [Indexed: 05/07/2023]
Abstract
More than fifty years after the 3Rs definition and despite the continuous implementation of regulatory measures, animals continue to be widely used in basic research. Their use comprises not only in vivo experiments with animal models, but also the production of a variety of supplements and products of animal origin for cell and tissue culture, cell-based assays, and therapeutics. The animal-derived products most used in basic research are fetal bovine serum (FBS), extracellular matrix proteins such as Matrigel™, and antibodies. However, their production raises several ethical issues regarding animal welfare. Additionally, their biological origin is associated with a high risk of contamination, resulting, frequently, in poor scientific data for clinical translation. These issues support the search for new animal-free products able to replace FBS, Matrigel™, and antibodies in basic research. In addition, in silico methodologies play an important role in the reduction of animal use in research by refining the data previously to in vitro and in vivo experiments. In this review, we depicted the current available animal-free alternatives in in vitro research.
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Affiliation(s)
- Ana C Duarte
- CPIRN/IPG - Centro de Potencial e Inovação em Recursos Naturais, Instituto Politécnico da Guarda (CPIRN/IPG), 6300-559 Guarda, Portugal; CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6200-506 Covilhã, Portugal
| | - Elisabete C Costa
- CPIRN/IPG - Centro de Potencial e Inovação em Recursos Naturais, Instituto Politécnico da Guarda (CPIRN/IPG), 6300-559 Guarda, Portugal
| | - Hugo A L Filipe
- CPIRN/IPG - Centro de Potencial e Inovação em Recursos Naturais, Instituto Politécnico da Guarda (CPIRN/IPG), 6300-559 Guarda, Portugal
| | - Sofia M Saraiva
- CPIRN/IPG - Centro de Potencial e Inovação em Recursos Naturais, Instituto Politécnico da Guarda (CPIRN/IPG), 6300-559 Guarda, Portugal
| | - Telma Jacinto
- CPIRN/IPG - Centro de Potencial e Inovação em Recursos Naturais, Instituto Politécnico da Guarda (CPIRN/IPG), 6300-559 Guarda, Portugal
| | - Sónia P Miguel
- CPIRN/IPG - Centro de Potencial e Inovação em Recursos Naturais, Instituto Politécnico da Guarda (CPIRN/IPG), 6300-559 Guarda, Portugal; CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6200-506 Covilhã, Portugal
| | - Maximiano P Ribeiro
- CPIRN/IPG - Centro de Potencial e Inovação em Recursos Naturais, Instituto Politécnico da Guarda (CPIRN/IPG), 6300-559 Guarda, Portugal; CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6200-506 Covilhã, Portugal
| | - Paula Coutinho
- CPIRN/IPG - Centro de Potencial e Inovação em Recursos Naturais, Instituto Politécnico da Guarda (CPIRN/IPG), 6300-559 Guarda, Portugal; CICS-UBI - Centro de Investigação em Ciências da Saúde, Universidade da Beira Interior, 6200-506 Covilhã, Portugal.
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47
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Reichstein IS, König M, Wojtysiak N, Escher BI, Henneberger L, Behnisch P, Besselink H, Thalmann B, Colas J, Hörchner S, Hollert H, Schiwy A. Replacing animal-derived components in in vitro test guidelines OECD 455 and 487. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161454. [PMID: 36638987 DOI: 10.1016/j.scitotenv.2023.161454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 12/23/2022] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
The evaluation of single substances or environmental samples for their genotoxic or estrogenic potential is highly relevant for human- and environment-related risk assessment. To examine the effects on a mechanism-specific level, standardized cell-based in vitro methods are widely applied. However, these methods include animal-derived components like fetal bovine serum (FBS) or rat-derived liver homogenate fractions (S9-mixes), which are a source of variability, reduced assay reproducibility and ethical concerns. In our study, we evaluated the adaptation of the cell-based in vitro OECD test guidelines TG 487 (assessment of genotoxicity) and TG 455 (detection of estrogenic activity) to an animal-component-free methodology. Firstly, the human cell lines A549 (for OECD TG 487), ERα-CALUX® and GeneBLAzer™ ERα-UAS-bla GripTite™ (for OECD TG 455) were investigated for growth in a chemically defined medium without the addition of FBS. Secondly, the biotechnological S9-mix ewoS9R was implemented in comparison to the induced rat liver S9 to simulate in vivo metabolism capacities in both OECD test guidelines. As a model compound, Benzo[a]pyrene was used due to its increased genotoxicity and endocrine activity after metabolization. The metabolization of Benzo[a]Pyrene by S9-mixes was examined via chemical analysis. All cell lines (A549, ERα-CALUX® and GeneBLAzer™ Erα-UAS-bla GripTite™) were successfully cultivated in chemically defined media without FBS. The micronucleus assay could not be conducted in chemically defined medium due to formation of cell clusters. The methods for endocrine activity assessment could be conducted in chemically defined media or reduced FBS content, but with decreased assay sensitivity. The biotechnological ewoS9R showed potential to replace rat liver S9 in the micronucleus in FBS-medium with A549 cells and in the ERα-CALUX® assay in FBS- and chemically defined medium. Our study showed promising steps towards an animal-component free toxicity testing. After further improvements, the new methodology could lead to more reproducible and reliable results for risk assessment.
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Affiliation(s)
- Inska S Reichstein
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Maria König
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Niklas Wojtysiak
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | - Beate I Escher
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research, Leipzig, Germany; Environmental Toxicology, Center for Applied Geosciences, Eberhard Karls University Tübingen, Germany
| | - Luise Henneberger
- Department of Cell Toxicology, Helmholtz Centre for Environmental Research, Leipzig, Germany
| | | | | | | | - Julien Colas
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Sarah Hörchner
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Henner Hollert
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany; Department Environmental Media Related Ecotoxicology, Fraunhofer IME, Schmallenberg, Germany.
| | - Andreas Schiwy
- Department of Evolutionary Ecology and Environmental Toxicology, Goethe University Frankfurt, Frankfurt am Main, Germany; Department Environmental Media Related Ecotoxicology, Fraunhofer IME, Schmallenberg, Germany.
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48
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Krumm TL, Ehsani A, Schaub J, Stiefel F. An Investigation into the Metabolic Differences between Conventional and High Seeding Density Fed-Batch Cell Cultures by Applying a Segmented Modeling Approach. Processes (Basel) 2023. [DOI: 10.3390/pr11041094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023] Open
Abstract
The conventional fed-batch process characterized by a low titer currently challenges pharmaceutical development. Process optimization by applying a perfusion process in the pre-stage and subsequent production phase at a high seeding density (HSD) can meet this challenge. In this study, we employed a simplified approach based on measured experiments, namely segmented modeling, to systematically analyze an HSD fed-batch process compared to a standard process. A comparison indicated that the metabolic phases of HSD processes are not only shifted in time, but metabolite trends show an altered metabolism. In an extended study, we integrated the intracellular fluxes determined by a metabolic flux analysis into the segmented modeling approach. Compared to using only extracellular rates, similar phases are identified, and this highlights the reliability of phase identification modeling using extracellular rates only. Furthermore, the segmented linear regression approach is used to create a model that describes cellular behavior and that can be used to predict potential improvements in the feeding strategy and in harvest viability. Here, overfeeding was eliminated and a significantly higher titer was achieved. This work provides insights into the overall metabolic changes in the HSD process and paves the way towards the optimization of the feeding regime.
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Affiliation(s)
- Teresa Laura Krumm
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Biologicals Germany, Birkendorfer Strasse 65, D-88397 Biberach an der Riß, Germany
| | - Alireza Ehsani
- Boehringer Ingelheim Pharma GmbH & Co.KG, Biopharmaceuticals Germany, Birkendorfer Strasse 65, D-88397 Biberach an der Riß, Germany
| | - Jochen Schaub
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Biologicals Germany, Birkendorfer Strasse 65, D-88397 Biberach an der Riß, Germany
| | - Fabian Stiefel
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Biologicals Germany, Birkendorfer Strasse 65, D-88397 Biberach an der Riß, Germany
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49
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Zhang Q, Mi C, Wang T. Effects and mechanism of small molecule additives on recombinant protein in CHO cells. Appl Microbiol Biotechnol 2023; 107:2771-2781. [PMID: 36971794 DOI: 10.1007/s00253-023-12486-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Chinese hamster ovary (CHO) cells can produce proteins with complex structures and post-translational modifications which are similar to human-derived cells, and they have been the ideal host cells for the production of recombinant therapy proteins (RTPs). Nearly 70% of approved RTPs are produced by CHO cells. In recent years, a series of measures have been developed to increase the expression of RTPs to achieve the lower production cost during the process of large-scale industrial production of recombinant protein in CHO cells. Among of them, the addition of small molecule additives in the culture medium can improve the expression and production efficiency of recombinant proteins, and has become an effective and simple method. In this paper, the characteristics of CHO cells, the effect and mechanism of small molecule additives are reviewed. KEY POINTS: • Small molecular additives on the expression of RTPs in CHO cells are reviewed • Small molecular additives improve the yield of RTPs • Small molecular additives provide methods for the optimization of serum-free medium.
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Affiliation(s)
- Qiuli Zhang
- School of Pharmacy, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Chunliu Mi
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China
| | - Tianyun Wang
- International Joint Research Laboratory for Recombinant Pharmaceutical Protein Expression System of Henan, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, 453003, Henan, China.
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50
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Kang DE, An YB, Kim Y, Ahn S, Kim YJ, Lim JS, Ryu SH, Choi H, Yoo J, You WK, Lee DY, Park J, Hong M, Lee GM, Baik JY, Hong JK. Enhanced cell growth, production, and mAb quality produced in Chinese hamster ovary-K1 cells by supplementing polyamine in the media. Appl Microbiol Biotechnol 2023; 107:2855-2870. [PMID: 36947192 DOI: 10.1007/s00253-023-12459-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 02/22/2023] [Accepted: 02/26/2023] [Indexed: 03/23/2023]
Abstract
Polyamines such as putrescine (PUT), spermidine (SPD), and spermine (SPM) are amine group-containing biomolecules that regulate multiple intracellular functions such as proliferation, differentiation, and stress response in mammalian cells. Although these biomolecules can be generated intracellularly, lack of polyamine-synthesizing activity has occasionally been reported in a few mammalian cell lines such as Chinese hamster ovary (CHO)-K1; thus, polyamine supplementation in serum-free media is required to support cell growth and production. In the present study, the effects of biogenic polyamines PUT, SPD, and SPM in media on cell growth, production, metabolism, and antibody quality were explored in cultures of antibody-producing CHO-K1 cells. Polyamine withdrawal from media significantly suppressed cell growth and production. On the other hand, enhanced culture performance was achieved in polyamine-containing media conditions in a dose-dependent manner regardless of polyamine type. In addition, in polyamine-deprived medium, distinguishing metabolic features, such as enriched glycolysis and suppressed amino acid consumption, were observed and accompanied by higher heterogeneity of antibody quality compared with the optimal concentration of polyamines. Furthermore, an excessive concentration of polyamines negatively affected culture performance as well as antibody quality. Hence, the results suggest that polyamine-related metabolism needs to be further investigated and polyamines in cell growth media should be optimized as a controllable parameter in CHO cell culture bioprocessing. KEY POINTS: • Polyamine supplementation enhanced cell growth and production in a dose-dependent manner • Polyamine type and concentration in the media affected mAb quality • Optimizing polyamines in the media is suggested in CHO cell bioprocessing.
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Affiliation(s)
- Da Eun Kang
- Division of Biological Science and Technology, Yonsei University, 1 Yonseidae-Gil, Gangwon-Do, Wonju-Si, 26493, South Korea
| | - Yeong Bin An
- Division of Biological Science and Technology, Yonsei University, 1 Yonseidae-Gil, Gangwon-Do, Wonju-Si, 26493, South Korea
| | - Yeunju Kim
- R&D Center, ABL Bio Inc, 16 Daewangpangyo-Ro, 712 Beon-Gil, Bundang-GuGyeonggi-Do 13488, 2F, Seongnam-Si, South Korea
| | - Seawon Ahn
- R&D Center, ABL Bio Inc, 16 Daewangpangyo-Ro, 712 Beon-Gil, Bundang-GuGyeonggi-Do 13488, 2F, Seongnam-Si, South Korea
| | - Young Jin Kim
- Division of Biological Science and Technology, Yonsei University, 1 Yonseidae-Gil, Gangwon-Do, Wonju-Si, 26493, South Korea
| | - Jung Soo Lim
- Division of Biological Science and Technology, Yonsei University, 1 Yonseidae-Gil, Gangwon-Do, Wonju-Si, 26493, South Korea
| | - Soo Hyun Ryu
- Division of Biological Science and Technology, Yonsei University, 1 Yonseidae-Gil, Gangwon-Do, Wonju-Si, 26493, South Korea
| | - Hyoju Choi
- R&D Center, ABL Bio Inc, 16 Daewangpangyo-Ro, 712 Beon-Gil, Bundang-GuGyeonggi-Do 13488, 2F, Seongnam-Si, South Korea
| | - Jiseon Yoo
- R&D Center, ABL Bio Inc, 16 Daewangpangyo-Ro, 712 Beon-Gil, Bundang-GuGyeonggi-Do 13488, 2F, Seongnam-Si, South Korea
| | - Weon-Kyoo You
- R&D Center, ABL Bio Inc, 16 Daewangpangyo-Ro, 712 Beon-Gil, Bundang-GuGyeonggi-Do 13488, 2F, Seongnam-Si, South Korea
| | - Dong-Yup Lee
- School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-Ro, Jangan-Gu, Suwon, Gyeonggi-Do, 16419, South Korea
| | - Junsoo Park
- Division of Biological Science and Technology, Yonsei University, 1 Yonseidae-Gil, Gangwon-Do, Wonju-Si, 26493, South Korea
| | - Minsun Hong
- Division of Biological Science and Technology, Yonsei University, 1 Yonseidae-Gil, Gangwon-Do, Wonju-Si, 26493, South Korea
| | - Gyun Min Lee
- Department of Biological Sciences, KAIST, 291 Daehak-Ro, Yuseong-Gu, Daejeon, 34141, South Korea
| | - Jong Youn Baik
- Department of Biological Engineering, Inha University, Incheon, 22212, South Korea.
| | - Jong Kwang Hong
- Division of Biological Science and Technology, Yonsei University, 1 Yonseidae-Gil, Gangwon-Do, Wonju-Si, 26493, South Korea.
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