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Claes E, Heck T, Coddens K, Sonnaert M, Schrooten J, Verwaeren J. Bayesian cell therapy process optimization. Biotechnol Bioeng 2024; 121:1569-1582. [PMID: 38372656 DOI: 10.1002/bit.28669] [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: 05/31/2023] [Revised: 11/17/2023] [Accepted: 01/22/2024] [Indexed: 02/20/2024]
Abstract
Optimizing complex bioprocesses poses a significant challenge in several fields, particularly in cell therapy manufacturing. The development of customized, closed, and automated processes is crucial for their industrial translation and for addressing large patient populations at a sustainable price. Limited understanding of the underlying biological mechanisms, coupled with highly resource-intensive experimentation, are two contributing factors that make the development of these next-generation processes challenging. Bayesian optimization (BO) is an iterative experimental design methodology that addresses these challenges, but has not been extensively tested in situations that require parallel experimentation with significant experimental variability. In this study, we present an evaluation of noisy, parallel BO for increasing noise levels and parallel batch sizes on two in silico bioprocesses, and compare it to the industry state-of-the-art. As an in vitro showcase, we apply the method to the optimization of a monocyte purification unit operation. The in silico results show that BO significantly outperforms the state-of-the-art, requiring approximately 50% fewer experiments on average. This study highlights the potential of noisy, parallel BO as valuable tool for cell therapy process development and optimization.
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Affiliation(s)
- Evan Claes
- Antleron, Leuven, Belgium
- Biovism, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
| | | | | | | | | | - Jan Verwaeren
- Biovism, Department of Data Analysis and Mathematical Modelling, Faculty of Bioscience Engineering, Ghent University, Gent, Belgium
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Weber T, Wiest J, Oredsson S, Bieback K. Case Studies Exemplifying the Transition to Animal Component-free Cell Culture. Altern Lab Anim 2022; 50:330-338. [PMID: 35983799 DOI: 10.1177/02611929221117999] [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: 11/15/2022]
Abstract
Cell culture techniques are strongly connected with modern scientific laboratories and production facilities. Thus, choosing the most suitable medium for the cells involved is vital, not only directly to optimise cell viability but also indirectly to maximise the reliability of the experiments performed with the cells. Fetal bovine or calf serum (FBS or FCS, respectively) is the most commonly used cell culture medium supplement, providing various nutritional factors and macromolecules essential for cell growth. Yet, the use of FBS encompasses a number of disadvantages. Scientifically, one of the most severe disadvantages is the lot-to-lot variability of animal sera that hampers reproducibility. Therefore, transitioning from the use of these ill-defined, component-variable, inconsistent, xenogenic, ethically questionable and even potentially infectious media supplements, is key to achieving better data reproducibility and thus better science. To demonstrate that the transition to animal component-free cell culture is possible and achievable, we highlight three different scenarios and provide some case studies of each, namely: i) the adaptation of single cell lines to animal component-free culture conditions by the replacement of FBS and trypsin; ii) the adaptation of multicellular models to FBS-free conditions; and (iii) the replacement of FBS with human platelet lysate (hPL) for the generation of primary stem/stromal cell cultures for clinical purposes. By highlighting these examples, we aim to foster and support the global movement towards more consistent science and provide evidence that it is indeed possible to step out of the currently smouldering scientific reproducibility crisis.
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Affiliation(s)
- Tilo Weber
- 84510Animal Welfare Academy of the German Animal Welfare Federation, Neubiberg, Germany
| | | | - Stina Oredsson
- Department of Biology, 5193Lund University, Lund, Sweden
| | - Karen Bieback
- Institute of Transfusion Medicine and Immunology, German Red Cross Blood Donor Service Baden-Württemberg-Hessen, Medical Faculty Mannheim, 99045Heidelberg University, Mannheim, Germany
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3
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Kasemiire A, Avohou HT, De Bleye C, Sacre PY, Dumont E, Hubert P, Ziemons E. Design of experiments and design space approaches in the pharmaceutical bioprocess optimization. Eur J Pharm Biopharm 2021; 166:144-154. [PMID: 34147574 DOI: 10.1016/j.ejpb.2021.06.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Revised: 06/10/2021] [Accepted: 06/11/2021] [Indexed: 01/04/2023]
Abstract
The optimization of pharmaceutical bioprocesses suffers from several challenges like complexity, upscaling costs, regulatory approval, leading to the risk of delivering substandard drugs to patients. Bioprocess is very complex and requires the evaluation of multiple components that need to be monitored and controlled in order to attain the desired state when the process ends. Statistical design of experiments (DoE) is a powerful tool for optimizing bioprocesses because it plays a critical role in the quality by design strategy as it is useful in exploring the experimental domain and providing statistics of interest that enable scientists to understand the impact of critical process parameters on the critical quality attributes. This review summarizes selected publications in which DoE methodology was used to optimize bioprocess. The main objective of the critical review was to clearly demonstrate potential benefits of using the DoE and design space methodologies in bioprocess optimization.
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Affiliation(s)
- Alice Kasemiire
- University of Liege (ULiege), CIRM, ViBra-Sante Hub, Department of Pharmacy, Pharmaceutical Analytical Chemistry, Avenue Hippocrate 15, 4000 Liege, Belgium.
| | - Hermane T Avohou
- University of Liege (ULiege), CIRM, ViBra-Sante Hub, Department of Pharmacy, Pharmaceutical Analytical Chemistry, Avenue Hippocrate 15, 4000 Liege, Belgium
| | - Charlotte De Bleye
- University of Liege (ULiege), CIRM, ViBra-Sante Hub, Department of Pharmacy, Pharmaceutical Analytical Chemistry, Avenue Hippocrate 15, 4000 Liege, Belgium
| | - Pierre-Yves Sacre
- University of Liege (ULiege), CIRM, ViBra-Sante Hub, Department of Pharmacy, Pharmaceutical Analytical Chemistry, Avenue Hippocrate 15, 4000 Liege, Belgium
| | - Elodie Dumont
- University of Liege (ULiege), CIRM, ViBra-Sante Hub, Department of Pharmacy, Pharmaceutical Analytical Chemistry, Avenue Hippocrate 15, 4000 Liege, Belgium
| | - Philippe Hubert
- University of Liege (ULiege), CIRM, ViBra-Sante Hub, Department of Pharmacy, Pharmaceutical Analytical Chemistry, Avenue Hippocrate 15, 4000 Liege, Belgium
| | - Eric Ziemons
- University of Liege (ULiege), CIRM, ViBra-Sante Hub, Department of Pharmacy, Pharmaceutical Analytical Chemistry, Avenue Hippocrate 15, 4000 Liege, Belgium
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A serum-free medium suitable for maintaining cell morphology and liver-specific function in induced human hepatocytes. Cytotechnology 2019; 71:329-344. [PMID: 30603919 DOI: 10.1007/s10616-018-0289-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 12/05/2018] [Indexed: 12/15/2022] Open
Abstract
hiHep is a new type of hepatocyte-like cell that is predicted to be a potential unlimited source of hepatocytes for a bioartificial liver. However, hiHep cannot currently be used in clinical settings because serum must be added during the culture process. Thus, a defined medium is required. Because serum is complex, an efficient statistical approach based on the Plackett-Burman design was used. In this manner, an original medium and several significant cell growth factors were identified. These factors include insulin, VH, and VE, and the original medium was optimized based on these significant factors. Additionally, hiHep liver-specific functions and metabolism in the optimized serum-free medium were measured. Results showed that hiHep functions, such as glycogen storage, albumin secretion, and urea production, were well maintained in our optimized serum-free medium. In summary, we created a chemically defined, serum-free medium in which cell growth, proliferation, metabolism, and function were well maintained. This medium has the potential to support the clinical use of hiHep.
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Liu CH, Liu YX, Wu WC. Facile development of medium optimization for antibody production: implementation in spinner flask and hollow fiber reactor. Cytotechnology 2018; 70:1631-1642. [PMID: 30284074 DOI: 10.1007/s10616-018-0255-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 09/08/2018] [Indexed: 12/22/2022] Open
Abstract
Most bio-industrial mammalian cells are cultured in serum-free media to achieve advantages, such as batch consistency, suspended growth, and simplified purification. The successful development of a serum-free medium could contribute to a reduction in the experimental variation, enhance cell productivity, and facilitate biopharmaceuticals production using the cell culture process. Commercial serum-free media are also becoming more and more popular. However, the cell line secrets its own recombinant product and has special nutritional requirements. How can the composition of the proprietary medium be adjusted to support the specific cell's metabolism and recombinant protein? This article uses statistical strategies to modify the commercial medium. A design of experiments is adopted to optimize the medium composition for the hybridoma cell in a serum-free condition. The supplements of peptone, ferric citrate, and trace elements were chosen to study their impact on hybridoma growth and antibody production using the response surface methodology. The stimulatory effect of the developed formulation on hybridoma growth was confirmed by the steepest ascent path. The optimal medium stimulated the hybridoma growth and antibody production in three diverse systems: a static plate, an agitated spinner flask, and a hollow fiber reactor. The cells in the developed serum-free medium had a better antibody production as compared to that in the commercial medium in the hollow fiber reactor. Our results demonstrated that the facile optimization for medium and antibody production was successfully accomplished in the hybridoma cells.
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Affiliation(s)
- Chi-Hsien Liu
- Department of Chemical and Materials Engineering, Chang Gung University, 259, Wen-Hwa First Road, Kwei-Shan, Taoyuan, 333, Taiwan. .,Research Center for Chinese Herbal Medicine and Research Center for Food and Cosmetic Safety, College of Human Ecology, Chang Gung University of Science and Technology, 261, Wen-Hwa First Road, Taoyuan, Taiwan. .,Department of Chemical Engineering, Ming Chi University of Technology, 84, Gung-Juan Road, New Taipei City, Taiwan. .,Department of Ophthalmology, Chang Gung Memorial Hospital, 5, Fu-Hsing Street, Taoyuan, Taiwan.
| | - Yi-Xin Liu
- Graduate Institute of Biochemical and Biomedical Engineering, Chang Gung University, 259, Wen-Hwa First Road, Kwei-Shan, Taoyuan, 333, Taiwan
| | - Wei-Chi Wu
- Department of Ophthalmology, Chang Gung Memorial Hospital, 5, Fu-Hsing Street, Taoyuan, Taiwan.,College of Medicine, Chang Gung University, 259, Wen-Hwa First Road, Taoyuan, Taiwan
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Vieira MS, Santos AK, Vasconcellos R, Goulart VAM, Parreira RC, Kihara AH, Ulrich H, Resende RR. Neural stem cell differentiation into mature neurons: Mechanisms of regulation and biotechnological applications. Biotechnol Adv 2018; 36:1946-1970. [PMID: 30077716 DOI: 10.1016/j.biotechadv.2018.08.002] [Citation(s) in RCA: 105] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 07/31/2018] [Accepted: 08/01/2018] [Indexed: 02/07/2023]
Abstract
The abilities of stem cells to self-renew and form different mature cells expand the possibilities of applications in cell-based therapies such as tissue recomposition in regenerative medicine, drug screening, and treatment of neurodegenerative diseases. In addition to stem cells found in the embryo, various adult organs and tissues have niches of stem cells in an undifferentiated state. In the central nervous system of adult mammals, neurogenesis occurs in two regions: the subventricular zone and the dentate gyrus in the hippocampus. The generation of the different neural lines originates in adult neural stem cells that can self-renew or differentiate into astrocytes, oligodendrocytes, or neurons in response to specific stimuli. The regulation of the fate of neural stem cells is a finely controlled process relying on a complex regulatory network that extends from the epigenetic to the translational level and involves extracellular matrix components. Thus, a better understanding of the mechanisms underlying how the process of neurogenesis is induced, regulated, and maintained will provide elues for development of novel for strategies for neurodegenerative therapies. In this review, we focus on describing the mechanisms underlying the regulation of the neuronal differentiation process by transcription factors, microRNAs, and extracellular matrix components.
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Affiliation(s)
- Mariana S Vieira
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Instituto Nanocell, Divinopólis, MG, Brazil
| | - Anderson K Santos
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Rebecca Vasconcellos
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Instituto Nanocell, Divinopólis, MG, Brazil
| | - Vânia A M Goulart
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
| | - Ricardo C Parreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Instituto Nanocell, Divinopólis, MG, Brazil
| | - Alexandre H Kihara
- Centro de Matemática, Computação e Cognição, Universidade Federal do ABC, São Bernardo do Campo, SP, Brazil
| | - Henning Ulrich
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil.
| | - Rodrigo R Resende
- Departamento de Bioquímica e Imunologia, Instituto de Ciência Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Instituto Nanocell, Divinopólis, MG, Brazil.
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Overexpression and purification of human myosins from transiently and stably transfected suspension adapted HEK293SF-3F6 cells. Anal Biochem 2018; 558:19-27. [PMID: 30075102 DOI: 10.1016/j.ab.2018.07.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/30/2018] [Accepted: 07/30/2018] [Indexed: 12/11/2022]
Abstract
The myosin family of motor proteins is an attractive target of therapeutic small-molecule protein inhibitors and modulators. Milligrams of protein quantities are required to conduct proper biophysical and biochemical studies to understand myosin functions. Myosin protein expression and purification represent a critical starting point towards this goal. Established utilization of Dictyostelium discoideum, Drosophila melanogaster, insect and mouse cells for myosin expression and purification is limited, cost, labor and time inefficient particularly for (full-length) human myosins. Here we are presenting detailed protocols for production of several difficult-to-purify recombinant human myosins in efficient quantities up to 1 mg of protein per liter of cell culture. This is the first time that myosins have been purified in large scales from suspension adapted transiently and stably expressing human cells. The method is also useful for expressing other human proteins in quantities sufficient to perform extensive biochemical and biophysical characterization.
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Cloning, expression, and purification of a synthetic human growth hormone in Escherichia coli using response surface methodology. Mol Biotechnol 2015; 57:241-50. [PMID: 25380986 DOI: 10.1007/s12033-014-9818-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The aim of this study was to achieve high-level production of the human growth hormone (hGH) in the prokaryotic expression system. In this regard, we performed cloning, expression, and purification of a synthetic hGH gene in BL21 (DE3) strain of E. coli. The hGH production was determined by SDS-PAGE and western blotting techniques, and then the protein concentration was determined by the Bradford assay. To gain insight into the effect of different nutrients on the growth of E. coli and hGH production, in a preliminary assessment nine different types of the basal medium were analyzed. The highest growth of E. coli and hGH production were observed in TB and SOB media. Accordingly, design of experiments was employed for screening the most significant nutrients, and central composite face design was applied for the optimization. The optimum medium consisted of yeast extract (10 g/L), tryptone (10 g/L), and K2HPO4 (2 g/L). The optimum hGH concentration was 391 mg/L, which was 3-fold higher than the hGH concentration in the LB basal medium (119 mg/L). This production rate is the highest hGH concentration reported in the IPTG-inducible expression systems.
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Zhang H, Wang H, Liu M, Zhang T, Zhang J, Wang X, Xiang W. Rational development of a serum-free medium and fed-batch process for a GS-CHO cell line expressing recombinant antibody. Cytotechnology 2012; 65:363-78. [PMID: 22907508 DOI: 10.1007/s10616-012-9488-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2012] [Accepted: 07/17/2012] [Indexed: 11/28/2022] Open
Abstract
A serum-free medium (CHO-SFM) together with a fed-batch process was developed for the cultivation of a recombinant GS-CHO cell line producing TNFR-Fc. According to the metabolic characteristics of GS-CHO cell, a basal medium was prepared by supplementing DMEM:F12:RPMI1640 (2:1:1) with amino acids, insulin, transferrin, Pluronic F68 and some other ingredients. Statistical optimization approaches based on Plackett-Burman and central composite designs were then adopted to identify additional positive determinants and determine their optimal concentrations, which resulted in the final CHO-SFM medium formulations. The maximum antibody titer reached was 90.95 mg/l in the developed CHO-SFM, which was a 18 % and 10 fold higher than that observed in the commercial EX-CELL™ 302 medium (76.95 mg/l) and basal medium (8.28 mg/l), respectively. Subsequently, a reliable, reproducible and robust fed-batch strategy was designed according to the offline measurement of glucose, giving a final antibody yield of 378 mg/l, which was a threefold improvement over that in conventional batch culture (122 mg/l) using CHO-SFM. In conclusion, the use of design of experiment (DoE) method facilitated the development of CHO-SFM medium and fed-batch process for the production of recombinant antibody using GS-CHO cells.
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Affiliation(s)
- Huifeng Zhang
- School of Life Science, Northeast Agricultural University, Harbin, 150030, China
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Bora N, Bawa Z, Bill RM, Wilks MDB. The implementation of a design of experiments strategy to increase recombinant protein yields in yeast (review). Methods Mol Biol 2012; 866:115-127. [PMID: 22454119 DOI: 10.1007/978-1-61779-770-5_11] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Biological processes are subject to the influence of numerous factors and their interactions, which may be non-linear in nature. In a recombinant protein production experiment, understanding the relative importance of these factors, and their influence on the yield and quality of the recombinant protein being produced, is an essential part of its optimisation. In many cases, implementing a design of experiments (DoE) approach has delivered this understanding. This chapter aims to provide the reader with useful pointers in applying a DoE strategy to improve the yields of recombinant yeast cultures.
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Affiliation(s)
- Nagamani Bora
- School of Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Birmingham, UK
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Poster Presentations. Regen Med 2011. [DOI: 10.2217/rme.12.16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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