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Grilo AL, Mantalaris A. Apoptosis: A mammalian cell bioprocessing perspective. Biotechnol Adv 2019; 37:459-475. [PMID: 30797096 DOI: 10.1016/j.biotechadv.2019.02.012] [Citation(s) in RCA: 98] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/08/2019] [Accepted: 02/19/2019] [Indexed: 02/07/2023]
Abstract
Apoptosis is a form of programmed and controlled cell death that accounts for the majority of cellular death in bioprocesses. Cell death affects culture longevity and product quality; it is instigated by several stresses experienced by the cells within a bioreactor. Understanding the factors that cause apoptosis as well as developing strategies that can protect cells is crucial for robust bioprocess development. This review aims to a) address apoptosis from a bioprocess perspective; b) describe the significant apoptotic mechanisms linking them to the most relevant stresses encountered in bioreactors; c) discuss the design of operating conditions in order to avoid cell death; d) focus on industrially relevant cell lines; and e) present anti-apoptosis strategies including cell engineering and model-based optimization of bioprocesses. In addition, the importance of apoptosis in quality-by-design bioprocess development from clone screening to production scale are highlighted.
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Affiliation(s)
- Antonio L Grilo
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom.
| | - Athanasios Mantalaris
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom.
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2
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Sequential Parameter Estimation for Mammalian Cell Model Based on In Silico Design of Experiments. Processes (Basel) 2018. [DOI: 10.3390/pr6080100] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Due to the complicated metabolism of mammalian cells, the corresponding dynamic mathematical models usually consist of large sets of differential and algebraic equations with a large number of parameters to be estimated. On the other hand, the measured data for estimating the model parameters are limited. Consequently, the parameter estimates may converge to a local minimum far from the optimal ones, especially when the initial guesses of the parameter values are poor. The methodology presented in this paper provides a systematic way for estimating parameters sequentially that generates better initial guesses for parameter estimation and improves the accuracy of the obtained metabolic model. The model parameters are first classified into four subsets of decreasing importance, based on the sensitivity of the model’s predictions on the parameters’ assumed values. The parameters in the most sensitive subset, typically a small fraction of the total, are estimated first. When estimating the remaining parameters with next most sensitive subset, the subsets of parameters with higher sensitivities are estimated again using their previously obtained optimal values as the initial guesses. The power of this sequential estimation approach is illustrated through a case study on the estimation of parameters in a dynamic model of CHO cell metabolism in fed-batch culture. We show that the sequential parameter estimation approach improves model accuracy and that using limited data to estimate low-sensitivity parameters can worsen model performance.
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Kyriakopoulos S, Ang KS, Lakshmanan M, Huang Z, Yoon S, Gunawan R, Lee DY. Kinetic Modeling of Mammalian Cell Culture Bioprocessing: The Quest to Advance Biomanufacturing. Biotechnol J 2017; 13:e1700229. [DOI: 10.1002/biot.201700229] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2017] [Revised: 09/27/2017] [Accepted: 10/11/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Sarantos Kyriakopoulos
- Bioprocessing Technology Institute, Agency for Science; Technology and Research (A*STAR); Singapore
| | - Kok Siong Ang
- Bioprocessing Technology Institute, Agency for Science; Technology and Research (A*STAR); Singapore
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science; Technology and Research (A*STAR); Singapore
| | - Zhuangrong Huang
- Department of Chemical Engineering; University of Massachusetts Lowell; Lowell MA USA
| | - Seongkyu Yoon
- Department of Chemical Engineering; University of Massachusetts Lowell; Lowell MA USA
| | - Rudiyanto Gunawan
- Institute for Chemical and Bioengineering; ETH Zurich; Zurich Switzerland
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science; Technology and Research (A*STAR); Singapore
- Department of Chemical and Biomolecular Engineering; National University of Singapore; Singapore
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Dynamic Optimization of the Production of Monoclonal Antibodies in Semi-batch Operation. ACTA ACUST UNITED AC 2017. [DOI: 10.1016/b978-0-444-63965-3.50362-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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López-Meza J, Araíz-Hernández D, Carrillo-Cocom LM, López-Pacheco F, Rocha-Pizaña MDR, Alvarez MM. Using simple models to describe the kinetics of growth, glucose consumption, and monoclonal antibody formation in naive and infliximab producer CHO cells. Cytotechnology 2016; 68:1287-300. [PMID: 26091615 PMCID: PMC4960177 DOI: 10.1007/s10616-015-9889-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 05/13/2015] [Indexed: 12/12/2022] Open
Abstract
Despite their practical and commercial relevance, there are few reports on the kinetics of growth and production of Chinese hamster ovary (CHO) cells-the most frequently used host for the industrial production of therapeutic proteins. We characterize the kinetics of cell growth, substrate consumption, and product formation in naive and monoclonal antibody (mAb) producing recombinant CHO cells. Culture experiments were performed in 125 mL shake flasks on commercial culture medium (CD Opti CHO™ Invitrogen, Carlsbad, CA, USA) diluted to different glucose concentrations (1.2-4.8 g/L). The time evolution of cell, glucose, lactic acid concentration and monoclonal antibody concentrations was monitored on a daily basis for mAb-producing cultures and their naive counterparts. The time series were differentiated to calculate the corresponding kinetic rates (rx = d[X]/dt; rs = d[S]/dt; rp = d[mAb]/dt). Results showed that these cell lines could be modeled by Monod-like kinetics if a threshold substrate concentration value of [S]t = 0.58 g/L (for recombinant cells) and [S]t = 0.96 g/L (for naïve cells), below which growth is not observed, was considered. A set of values for μmax, and Ks was determined for naive and recombinant cell cultures cultured at 33 and 37 °C. The yield coefficient (Yx/s) was observed to be a function of substrate concentration, with values in the range of 0.27-1.08 × 10(7) cell/mL and 0.72-2.79 × 10(6) cells/mL for naive and recombinant cultures, respectively. The kinetics of mAb production can be described by a Luedeking-Piret model (d[mAb]/dt = αd[X]/dt + β[X]) with values of α = 7.65 × 10(-7) µg/cell and β = 7.68 × 10(-8) µg/cell/h for cultures conducted in batch-agitated flasks and batch and instrumented bioreactors operated in batch and fed-batch mode.
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Affiliation(s)
- Julián López-Meza
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico
| | - Diana Araíz-Hernández
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico
| | - Leydi Maribel Carrillo-Cocom
- Facultad de Ingeniería Química, Universidad Autónoma de Yucatán, Periférico Norte kilómetro 33.5, C.P. 97203, Mérida, Yucatán, Mexico
| | - Felipe López-Pacheco
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico
| | - María Del Refugio Rocha-Pizaña
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico
| | - Mario Moisés Alvarez
- Centro de Biotecnología-FEMSA, Tecnológico de Monterrey at Monterrey, Ave. Eugenio Garza Sada 2501 Sur, C.P. 64849, Monterrey, Nuevo León, Mexico.
- Biomaterials Innovation Research Center, Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02139, USA.
- Harvard-Massachusetts Institute of Technology Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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Impact of aeration strategies on fed-batch cell culture kinetics in a single-use 24-well miniature bioreactor. Biochem Eng J 2014. [DOI: 10.1016/j.bej.2013.11.010] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Analysis of Chinese hamster ovary cell metabolism through a combined computational and experimental approach. Cytotechnology 2013; 66:945-66. [PMID: 24292563 DOI: 10.1007/s10616-013-9648-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2013] [Accepted: 09/20/2013] [Indexed: 01/22/2023] Open
Abstract
Optimization of cell culture processes can benefit from the systematic analysis of experimental data and their organization in mathematical models, which can be used to decipher the effect of individual process variables on multiple outputs of interest. Towards this goal, a kinetic model of cytosolic glucose metabolism coupled with a population-level model of Chinese hamster ovary cells was used to analyse metabolic behavior under batch and fed-batch cell culture conditions. The model was parameterized using experimental data for cell growth dynamics, extracellular and intracellular metabolite profiles. The results highlight significant differences between the two culture conditions in terms of metabolic efficiency and motivate the exploration of lactate as a secondary carbon source. Finally, the application of global sensitivity analysis to the model parameters highlights the need for additional experimental information on cell cycle distribution to complement metabolomic analyses with a view to parameterize kinetic models.
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Chen L, Tian Y, Cao C, Zhang S, Zhang S. Sensitivity and uncertainty analyses of an extended ASM3-SMP model describing membrane bioreactor operation. J Memb Sci 2012. [DOI: 10.1016/j.memsci.2011.10.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Ho Y, Kiparissides A, Pistikopoulos EN, Mantalaris A. Computational approach for understanding and improving GS-NS0 antibody production under hyperosmotic conditions. J Biosci Bioeng 2012; 113:88-98. [DOI: 10.1016/j.jbiosc.2011.08.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Revised: 08/21/2011] [Accepted: 08/22/2011] [Indexed: 02/02/2023]
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Pfeffer M, Maurer M, Köllensperger G, Hann S, Graf AB, Mattanovich D. Modeling and measuring intracellular fluxes of secreted recombinant protein in Pichia pastoris with a novel 34S labeling procedure. Microb Cell Fact 2011; 10:47. [PMID: 21703020 PMCID: PMC3147017 DOI: 10.1186/1475-2859-10-47] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2011] [Accepted: 06/26/2011] [Indexed: 12/24/2022] Open
Abstract
Background The budding yeast Pichia pastoris is widely used for protein production. To determine the best suitable strategy for strain improvement, especially for high secretion, quantitative data of intracellular fluxes of recombinant protein are very important. Especially the balance between intracellular protein formation, degradation and secretion defines the major bottleneck of the production system. Because these parameters are different for unlimited growth (shake flask) and carbon-limited growth (bioreactor) conditions, they should be determined under "production like" conditions. Thus labeling procedures must be compatible with minimal production media and the usage of bioreactors. The inorganic and non-radioactive 34S labeled sodium sulfate meets both demands. Results We used a novel labeling method with the stable sulfur isotope 34S, administered as sodium sulfate, which is performed during chemostat culivations. The intra- and extracellular sulfur 32 to 34 ratios of purified recombinant protein, the antibody fragment Fab3H6, are measured by HPLC-ICP-MS. The kinetic model described here is necessary to calculate the kinetic parameters from sulfur ratios of consecutive samples as well as for sensitivity analysis. From the total amount of protein produced intracellularly (143.1 μg g-1 h-1 protein per yeast dry mass and time) about 58% are degraded within the cell, 35% are secreted to the exterior and 7% are inherited to the daughter cells. Conclusions A novel 34S labeling procedure that enables in vivo quantification of intracellular fluxes of recombinant protein under "production like" conditions is described. Subsequent sensitivity analysis of the fluxes by using MATLAB, indicate the most promising approaches for strain improvement towards increased secretion.
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Affiliation(s)
- Martin Pfeffer
- University of Natural Resources and Life Sciences, Department of Biotechnology, Muthgasse 18, Vienna, Austria
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Naderi S, Meshram M, Wei C, McConkey B, Ingalls B, Budman H, Scharer J. Development of a mathematical model for evaluating the dynamics of normal and apoptotic Chinese hamster ovary cells. Biotechnol Prog 2011; 27:1197-205. [DOI: 10.1002/btpr.647] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2010] [Revised: 01/24/2011] [Indexed: 12/18/2022]
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McLeod J, O'Callaghan PM, Pybus LP, Wilkinson SJ, Root T, Racher AJ, James DC. An empirical modeling platform to evaluate the relative control discrete CHO cell synthetic processes exert over recombinant monoclonal antibody production process titer. Biotechnol Bioeng 2011; 108:2193-204. [PMID: 21445882 DOI: 10.1002/bit.23146] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2010] [Revised: 01/31/2011] [Accepted: 03/14/2011] [Indexed: 12/16/2022]
Abstract
In this study we have combined empirically derived mathematical models of intracellular Mab synthesis to quantitatively compare the degree to which individual cellular processes limit recombinant IgG(4) monoclonal antibody production by GS-CHO cells throughout a state-of-the-art industrial fed-batch culture process. Based on the calculation of a production process control coefficient for each stage of the intracellular Mab synthesis and secretion pathway, we identified the major cellular restrictions on Mab production throughout the entire culture process to be recombinant heavy chain gene transcription and heavy chain mRNA translation. Surprisingly, despite a substantial decline in the rate of cellular biomass synthesis during culture, with a concomitant decline in the calculated rate constants for energy-intensive Mab synthetic processes (Mab folding/assembly and secretion), these did not exert significant control of Mab synthesis at any stage of production. Instead, cell-specific Mab production was maintained by increased Mab gene transcription which offset the decline in cellular biosynthetic rates. Importantly, this study shows that application of this whole-process predictive modeling strategy should rationally precede and inform cell engineering approaches to increase production of a recombinant protein by a mammalian host cell--where control of productivity is inherently protein product and cell line specific.
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Affiliation(s)
- Jane McLeod
- Department of Chemical and Biological Engineering, University of Sheffield, Mappin St., Sheffield S1 3JD, UK
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O'Callaghan PM, McLeod J, Pybus LP, Lovelady CS, Wilkinson SJ, Racher AJ, Porter A, James DC. Cell line-specific control of recombinant monoclonal antibody production by CHO cells. Biotechnol Bioeng 2010; 106:938-51. [DOI: 10.1002/bit.22769] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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15
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Towards energy-based dynamic optimization of monoclonal antibody producing GS-NS0 Cultures. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/s1570-7946(10)28099-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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Long-term prediction of fish growth under varying ambient temperature using a multiscale dynamic model. BMC SYSTEMS BIOLOGY 2009; 3:107. [PMID: 19903354 PMCID: PMC2786910 DOI: 10.1186/1752-0509-3-107] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2009] [Accepted: 11/10/2009] [Indexed: 11/10/2022]
Abstract
Background Feed composition has a large impact on the growth of animals, particularly marine fish. We have developed a quantitative dynamic model that can predict the growth and body composition of marine fish for a given feed composition over a timespan of several months. The model takes into consideration the effects of environmental factors, particularly temperature, on growth, and it incorporates detailed kinetics describing the main metabolic processes (protein, lipid, and central metabolism) known to play major roles in growth and body composition. Results For validation, we compared our model's predictions with the results of several experimental studies. We showed that the model gives reliable predictions of growth, nutrient utilization (including amino acid retention), and body composition over a timespan of several months, longer than most of the previously developed predictive models. Conclusion We demonstrate that, despite the difficulties involved, multiscale models in biology can yield reasonable and useful results. The model predictions are reliable over several timescales and in the presence of strong temperature fluctuations, which are crucial factors for modeling marine organism growth. The model provides important improvements over existing models.
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Kiparissides A, Kucherenko SS, Mantalaris A, Pistikopoulos EN. Global Sensitivity Analysis Challenges in Biological Systems Modeling. Ind Eng Chem Res 2009. [DOI: 10.1021/ie900139x] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Kiparissides
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - S. S. Kucherenko
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - A. Mantalaris
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
| | - E. N. Pistikopoulos
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London SW7 2AZ, U.K
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Engineering Mammalian Cells for Recombinant Monoclonal Antibody Production. CELL ENGINEERING 2009. [DOI: 10.1007/978-90-481-2245-5_8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Franceschini G, Macchietto S. Model-based design of experiments for parameter precision: State of the art. Chem Eng Sci 2008. [DOI: 10.1016/j.ces.2007.11.034] [Citation(s) in RCA: 297] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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