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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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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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Grenier J, David B, Journé C, Cicha I, Letourneur D, Duval H. Perfusion of MC3T3E1 Preosteoblast Spheroids within Polysaccharide-Based Hydrogel Scaffolds: An Experimental and Numerical Study at the Bioreactor Scale. Bioengineering (Basel) 2023; 10:849. [PMID: 37508876 PMCID: PMC10376891 DOI: 10.3390/bioengineering10070849] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/08/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The traditional 3D culture systems in vitro lack the biological and mechanical spatiotemporal stimuli characteristic to native tissue development. In our study, we combined porous polysaccharide-based hydrogel scaffolds with a bioreactor-type perfusion device that generates favorable mechanical stresses while enhancing nutrient transfers. MC3T3E1 mouse osteoblasts were seeded in the scaffolds and cultivated for 3 weeks under dynamic conditions at a perfusion rate of 10 mL min-1. The spatial distribution of the cells labeled with superparamagnetic iron oxide nanoparticles was visualized by MRI. Confocal microscopy was used to assess cell numbers, their distribution inside the scaffolds, cell viability, and proliferation. The oxygen diffusion coefficient in the hydrogel was measured experimentally. Numerical simulations of the flow and oxygen transport within the bioreactor were performed using a lattice Boltzmann method with a two-relaxation time scheme. Last, the influence of cell density and spheroid size on cell oxygenation was investigated. The cells spontaneously organized into spheroids with a diameter of 30-100 μm. Cell viability remained unchanged under dynamic conditions but decreased under static culture. The cell proliferation (Ki67 expression) in spheroids was not observed. The flow simulation showed that the local fluid velocity reached 27 mm s-1 at the height where the cross-sectional area of the flow was the smallest. The shear stress exerted by the fluid on the scaffolds may locally rise to 100 mPa, compared with the average value of 25 mPa. The oxygen diffusion coefficient in the hydrogel was 1.6×10-9 m2 s-1. The simulation of oxygen transport and consumption confirmed that the cells in spheroids did not suffer from hypoxia when the bioreactor was perfused at 10 mL min-1, and suggested the existence of optimal spheroid size and spacing for appropriate oxygenation. Collectively, these findings enabled us to define the optimal conditions inside the bioreactor for an efficient in vitro cell organization and survival in spheroids, which are paramount to future applications with organoids.
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Affiliation(s)
- Jérôme Grenier
- Laboratoire de Génie des Procédés et Matériaux, CentraleSupélec, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- Laboratoire de Mécanique Paris-Saclay, CNRS, CentraleSupélec, ENS Paris-Saclay, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
- Laboratoire de Recherche Vasculaire Translationnelle (LVTS), INSERM U 1148, Université Paris Cité, Université Sorbonne Paris Nord, Hôpital Bichat, 75018 Paris, France
| | - Bertrand David
- Laboratoire de Mécanique Paris-Saclay, CNRS, CentraleSupélec, ENS Paris-Saclay, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
| | - Clément Journé
- Laboratoire de Recherche Vasculaire Translationnelle (LVTS), INSERM U 1148, Université Paris Cité, Université Sorbonne Paris Nord, Hôpital Bichat, 75018 Paris, France
| | - Iwona Cicha
- Department of Otorhinolaryngology, Head and Neck Surgery, Section of Experimental Oncology und Nanomedicine (SEON), Friedrich-Alexander Universität Erlangen-Nürnberg, Universitätsklinikum Erlangen, 91054 Erlangen, Germany
| | - Didier Letourneur
- Laboratoire de Recherche Vasculaire Translationnelle (LVTS), INSERM U 1148, Université Paris Cité, Université Sorbonne Paris Nord, Hôpital Bichat, 75018 Paris, France
| | - Hervé Duval
- Laboratoire de Génie des Procédés et Matériaux, CentraleSupélec, Université Paris-Saclay, 91190 Gif-sur-Yvette, France
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Rekena A, Livkisa D, Kamolins E, Vanags J, Loca D. Biopharmaceutical-Type Chinese Hamster Ovary Cell Cultivation Under Static Magnetic Field Exposure: A Study of Genotoxic Effect. Front Bioeng Biotechnol 2021; 9:751538. [PMID: 34900956 PMCID: PMC8656418 DOI: 10.3389/fbioe.2021.751538] [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: 08/01/2021] [Accepted: 10/28/2021] [Indexed: 12/04/2022] Open
Abstract
The lack of a sufficient research base is the reason for the ongoing discussion regarding the genotoxic effect of magnetic field (MF) exposure on mammalian cell cultures. Chinese hamster ovary (CHO) suspension-type cells, which are widely used for biopharmaceutical production, are potentially subjected to an increased MF when cultivated in bioreactors equipped with bottom-placed magnetically coupled stirring mechanisms. The main challenge for conducting research in this field remains the availability of a suitable experimental setup that generates an appropriate MF for the raised research question. In the present study, a simple and cost-effective experimental setup was developed that generated a static MF, similar to what has been modeled in large-scale bioreactors and, at the same time, was suitable for experimental cell cultivation in laboratory conditions. The measured maximum magnetic flux density to which the cells were exposed was 0.66 T. To assess the possible genotoxic effect, cells were continuously subcultivated in laboratory petri dishes for a period of 14 days, corresponding to a typical duration of a biopharmaceutical production process in a conventional fed-batch regime. The genotoxic effect was assessed using the cytokinesis-block micronucleus assay with fluorescent staining. Results showed that a 0.66-T static MF exposure had no significant long-term effect on cell viability and chromosomal damage but demonstrated a short-term effect on cell apoptosis. Significant increase in nuclear bud formation was observed. These findings may encourage other researchers in future studies investigating cellular responses to MF exposure and contribute relevant data for comparison.
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Affiliation(s)
- Alina Rekena
- Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre of RTU, Faculty of Materials Science and Applied Chemistry, Institute of General Chemical Engineering, Riga Technical University, Riga, Latvia
| | - Dora Livkisa
- Department of Microbiology and Biotechnology, Faculty of Biology, University of Latvia, Riga, Latvia
| | - Edmunds Kamolins
- Institute of Physical Energetics, Riga, Latvia.,Institute of Industrial Electronics and Electrical Engineering, Riga Technical University, Riga, Latvia
| | - Juris Vanags
- Bioengineering Laboratory, Latvian State Institute of Wood Chemistry, Riga, Latvia
| | - Dagnija Loca
- Rudolfs Cimdins Riga Biomaterials Innovations and Development Centre of RTU, Faculty of Materials Science and Applied Chemistry, Institute of General Chemical Engineering, Riga Technical University, Riga, Latvia.,Baltic Biomaterials Centre of Excellence, Headquarters at Riga Technical University, Riga, Latvia
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Kotidis P, Pappas I, Avraamidou S, Pistikopoulos EN, Kontoravdi C, Papathanasiou MM. DigiGlyc: A hybrid tool for reactive scheduling in cell culture systems. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2021.107460] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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Jeynes-Smith C, Araujo RP. Ultrasensitivity and bistability in covalent-modification cycles with positive autoregulation. Proc Math Phys Eng Sci 2021; 477:20210069. [PMID: 35153570 PMCID: PMC8331239 DOI: 10.1098/rspa.2021.0069] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 07/02/2021] [Indexed: 12/17/2022] Open
Abstract
Switch-like behaviours in biochemical networks are of fundamental significance in biological signal processing, and exist as two distinct types: ultra-sensitivity and bistability. Here we propose two new models of a reversible covalent-modification cycle with positive autoregulation (PAR), a motif structure that is thought to be capable of both ultrasensitivity and bistability in different parameter regimes. These new models appeal to a modelling framework that we call complex-complete, which accounts fully for the molecular complexities of the underlying signalling mechanisms. Each of the two new models encodes a specific molecular mechanism for PAR. We demonstrate that the modelling simplifications for PAR models that have been used in previous work, which rely on Michaelian approximations, are unable to accurately recapitulate the qualitative signalling responses supported by our detailed models. Strikingly, we show that complex-complete PAR models are capable of new qualitative responses such as one-way switches and a 'prozone' effect, depending on the specific PAR-encoding mechanism, which are not supported by Michaelian simplifications. Our results highlight the critical importance of accurately representing the molecular details of biochemical signalling mechanisms, and strongly suggest that the Michaelian approximation is inadequate for predictive models of enzyme-mediated chemical reactions with added regulations such as PAR.
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Affiliation(s)
- Cailan Jeynes-Smith
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
- Institute of Health and Biomedical Innovation (IHBI), Brisbane, Australia
| | - Robyn P. Araujo
- School of Mathematical Sciences, Queensland University of Technology, Brisbane, Australia
- Institute of Health and Biomedical Innovation (IHBI), Brisbane, Australia
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Bezjak L, Erklavec Zajec V, Baebler Š, Stare T, Gruden K, Pohar A, Novak U, Likozar B. Incorporating RNA-Seq transcriptomics into glycosylation-integrating metabolic network modelling kinetics: Multiomic Chinese hamster ovary (CHO) cell bioreactors. Biotechnol Bioeng 2021; 118:1476-1490. [PMID: 33399226 DOI: 10.1002/bit.27660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 09/10/2020] [Accepted: 11/16/2020] [Indexed: 12/23/2022]
Abstract
In this work, the kinetic model based on the previously developed metabolic and glycan reaction networks of the ovarian cells of the Chinese hamster ovary (CHO) cell line was improved by the inclusion of transcriptomic data that took into account the values of the RPKM gene (Reads per Kilobase of Exon per Million Reads Mapped). The transcriptomic (RNASeq) data were obtained together with metabolic and glycan data from the literature, and the concentrations with RPKM values were collected at several points in time from two fed-batch processes. First, the fluxes were determined by regression analysis of the metabolic data, then these fluxes were corrected by using the fold change in gene expression as a measure of enzyme concentrations. Next, the corrected fluxes in the kinetic model were used to calculate the concentration profiles of the metabolites, and literature data were used to evaluate the predicted results of the model. Compared to other studies where the concentration profiles of CHO cell metabolites were described using a kinetic model without consideration of RNA-Seq data to correct the fluxes, this model is unique. The additional integration of transcriptomic data led to better predictions of metabolic concentrations in the fed-batch process, which is a significant improvement of the modelling technique used.
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Affiliation(s)
- Lara Bezjak
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
| | - Vivian Erklavec Zajec
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
| | - Špela Baebler
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Tjaša Stare
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Andrej Pohar
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
| | - Uroš Novak
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
| | - Blaž Likozar
- Department of Catalysis and Chemical Reaction Engineering, National Institute of Chemistry, Ljubljana, Slovenia
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