1
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Gopalakrishnan S, Johnson W, Valderrama-Gomez MA, Icten E, Tat J, Ingram M, Fung Shek C, Chan PK, Schlegel F, Rolandi P, Kontoravdi C, Lewis NE. COSMIC-dFBA: A novel multi-scale hybrid framework for bioprocess modeling. Metab Eng 2024; 82:183-192. [PMID: 38387677 DOI: 10.1016/j.ymben.2024.02.012] [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: 09/13/2023] [Revised: 02/01/2024] [Accepted: 02/19/2024] [Indexed: 02/24/2024]
Abstract
Metabolism governs cell performance in biomanufacturing, as it fuels growth and productivity. However, even in well-controlled culture systems, metabolism is dynamic, with shifting objectives and resources, thus limiting the predictive capability of mechanistic models for process design and optimization. Here, we present Cellular Objectives and State Modulation In bioreaCtors (COSMIC)-dFBA, a hybrid multi-scale modeling paradigm that accurately predicts cell density, antibody titer, and bioreactor metabolite concentration profiles. Using machine-learning, COSMIC-dFBA decomposes the instantaneous metabolite uptake and secretion rates in a bioreactor into weighted contributions from each cell state (growth or antibody-producing state) and integrates these with a genome-scale metabolic model. A major strength of COSMIC-dFBA is that it can be parameterized with only metabolite concentrations from spent media, although constraining the metabolic model with other omics data can further improve its capabilities. Using COSMIC-dFBA, we can predict the final cell density and antibody titer to within 10% of the measured data, and compared to a standard dFBA model, we found the framework showed a 90% and 72% improvement in cell density and antibody titer prediction, respectively. Thus, we demonstrate our hybrid modeling framework effectively captures cellular metabolism and expands the applicability of dFBA to model the dynamic conditions in a bioreactor.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, UK
| | - Nathan E Lewis
- Department of Pediatrics, University of California San Diego, USA; Department of Bioengineering, University of California San Diego, USA.
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2
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Ben Yahia B, Piednoir A, Dahomais T, Eggermont S, Paul W. "Organized stress" for robust scale-up of intensified production process with fed-batch seed bioreactor. Biotechnol Bioeng 2023; 120:2509-2522. [PMID: 37027375 DOI: 10.1002/bit.28396] [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: 11/30/2022] [Revised: 03/17/2023] [Accepted: 03/27/2023] [Indexed: 04/08/2023]
Abstract
Process intensification has been widely used for many years in the mammalian biomanufacturing industry to increase productivity, agility and flexibility while reducing production costs. The most commonly used intensified processes are operated using a perfusion or fed-batch seed bioreactor enabling a higher than usual seeding density in the fed-batch production bioreactor. Hence, as part of the growth phase is shifted to the seed bioreactor, there is a lower split ratio, which increases the criticality of the seed bioreactor and could impact production performance. Therefore, such intensified processes should be designed and characterized for robust process scale-up. This research work is focused on intensified processes with high seeding density inoculated from seed bioreactor in fed-batch mode. The impact of the feeding strategy and specific power input (P/V) in the seed bioreactor and on the production step with two different cell lines (CL1 and CL2) producing two different monoclonal antibodies was investigated. Cell culture performance in the production bioreactor has been improved due to more stressful conditions for the cells in the seed bioreactor and the impact of the production bioreactor P/V on the production performance was limited. This is the first reported study highlighting a positive impact of cellular stress in seed bioreactors on intensified production bioreactor with the introduction of the "organized stress" concept.
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Affiliation(s)
- Bassem Ben Yahia
- Biologics Process Sciences, Biotech Sciences, UCB Pharma S.A., Avenue de l'Industrie, Brussels, Braine l'Alleud, Belgium
| | - Antoine Piednoir
- Biologics Process Sciences, Biotech Sciences, UCB Pharma S.A., Avenue de l'Industrie, Brussels, Braine l'Alleud, Belgium
| | - Thomas Dahomais
- Biologics Process Sciences, Biotech Sciences, UCB Pharma S.A., Avenue de l'Industrie, Brussels, Braine l'Alleud, Belgium
| | - Stefanie Eggermont
- Biologics Process Sciences, Biotech Sciences, UCB Pharma S.A., Avenue de l'Industrie, Brussels, Braine l'Alleud, Belgium
| | - Wolfgang Paul
- Biologics Process Sciences, Biotech Sciences, UCB Pharma S.A., Avenue de l'Industrie, Brussels, Braine l'Alleud, Belgium
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3
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Rathore AS, Thakur G, Kateja N. Continuous integrated manufacturing for biopharmaceuticals: A new paradigm or an empty promise? Biotechnol Bioeng 2023; 120:333-351. [PMID: 36111450 DOI: 10.1002/bit.28235] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/09/2022] [Accepted: 09/11/2022] [Indexed: 01/13/2023]
Abstract
Continuous integrated bioprocessing has elicited considerable interest from the biopharma industry for the many purported benefits it promises. Today many major biopharma manufacturers around the world are engaged in the development of continuous process platforms for their products. In spite of great potential, the path toward continuous integrated bioprocessing remains unclear for the biologics industry due to legacy infrastructure, process integration challenges, vague regulatory guidelines, and a diverging focus toward novel therapies. In this article, we present a review and perspective on this topic. We explore the status of the implementation of continuous integrated bioprocessing among biopharmaceutical manufacturers. We also present some of the key hurdles that manufacturers are likely to face during this implementation. Finally, we hypothesize that the real impact of continuous manufacturing is likely to come when the cost of manufacturing is a substantial portion of the cost of product development, such as in the case of biosimilar manufacturing and emerging economies.
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Affiliation(s)
- Anurag S Rathore
- Department of Chemical Engineering, Indian Institute of Technology, New Delhi, India
| | - Garima Thakur
- Department of Chemical Engineering, Indian Institute of Technology, New Delhi, India
| | - Nikhil Kateja
- Department of Chemical Engineering, Indian Institute of Technology, New Delhi, India
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4
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Mutaf T, Oncel SS. Bubble column and airlift bioreactor systems for animal cell culture applications. ASIA-PAC J CHEM ENG 2022. [DOI: 10.1002/apj.2872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Tugce Mutaf
- Department of Bioengineering,Faculty of Engineering Ege University Izmir Turkey
- Department of Bioengineering, Faculty of Engineering Manisa Celal Bayar University Manisa Turkey
| | - Suphi S. Oncel
- Department of Bioengineering,Faculty of Engineering Ege University Izmir Turkey
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5
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Wang J, Dowling AW. Pyomo.
DOE
: An
Open‐Source
Package for
Model‐Based
Design of Experiments in Python. AIChE J 2022. [DOI: 10.1002/aic.17813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jialu Wang
- Department of Chemical and Biomolecular Engineering University of Notre Dame Notre Dame IN
| | - Alexander W. Dowling
- Department of Chemical and Biomolecular Engineering University of Notre Dame Notre Dame IN
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6
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Ramos JRC, Bissinger T, Genzel Y, Reichl U. Impact of Influenza A Virus Infection on Growth and Metabolism of Suspension MDCK Cells Using a Dynamic Model. Metabolites 2022; 12:metabo12030239. [PMID: 35323683 PMCID: PMC8950586 DOI: 10.3390/metabo12030239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/04/2022] [Accepted: 03/09/2022] [Indexed: 11/21/2022] Open
Abstract
Cell cultured-based influenza virus production is a viable option for vaccine manufacturing. In order to achieve a high concentration of viable cells, is requirement to have not only optimal process conditions, but also an active metabolism capable of intracellular synthesis of viral components. Experimental metabolic data collected in such processes are complex and difficult to interpret, for which mathematical models are an appropriate way to simulate and analyze the complex and dynamic interaction between the virus and its host cell. A dynamic model with 35 states was developed in this study to describe growth, metabolism, and influenza A virus production in shake flask cultivations of suspension Madin-Darby Canine Kidney (MDCK) cells. It considers cell growth (concentration of viable cells, mean cell diameters, volume of viable cells), concentrations of key metabolites both at the intracellular and extracellular level and virus titers. Using one set of parameters, the model accurately simulates the dynamics of mock-infected cells and correctly predicts the overall dynamics of virus-infected cells for up to 60 h post infection (hpi). The model clearly suggests that most changes observed after infection are related to cessation of cell growth and the subsequent transition to apoptosis and cell death. However, predictions do not cover late phases of infection, particularly for the extracellular concentrations of glutamate and ammonium after about 12 hpi. Results obtained from additional in silico studies performed indicated that amino acid degradation by extracellular enzymes resulting from cell lysis during late infection stages may contribute to this observed discrepancy.
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Affiliation(s)
- João Rodrigues Correia Ramos
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
- Correspondence:
| | - Thomas Bissinger
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Sandtorstrasse 1, 39106 Magdeburg, Germany; (T.B.); (Y.G.); (U.R.)
- Institute of Process Engineering, Faculty of Process & Systems Engineering, Otto-von-Guericke University, Universitätsplatz 2, 39106 Magdeburg, Germany
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7
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8
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Ramos JRC, Rath AG, Genzel Y, Sandig V, Reichl U. A dynamic model linking cell growth to intracellular metabolism and extracellular by-product accumulation. Biotechnol Bioeng 2020; 117:1533-1553. [PMID: 32022250 DOI: 10.1002/bit.27288] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2019] [Revised: 12/12/2019] [Accepted: 01/26/2020] [Indexed: 12/16/2022]
Abstract
Mathematical modeling of animal cell growth and metabolism is essential for the understanding and improvement of the production of biopharmaceuticals. Models can explain the dynamic behavior of cell growth and product formation, support the identification of the most relevant parameters for process design, and significantly reduce the number of experiments to be performed for process optimization. Few dynamic models have been established that describe both extracellular and intracellular dynamics of growth and metabolism of animal cells. In this study, a model was developed, which comprises a set of 33 ordinary differential equations to describe batch cultivations of suspension AGE1.HN.AAT cells considered for the production of α1-antitrypsin. This model combines a segregated cell growth model with a structured model of intracellular metabolism. Overall, it considers the viable cell concentration, mean cell diameter, viable cell volume, concentration of extracellular substrates, and intracellular concentrations of key metabolites from the central carbon metabolism. Furthermore, the release of metabolic by-products such as lactate and ammonium was estimated directly from the intracellular reactions. Based on the same set of parameters, this model simulates well the dynamics of four independent batch cultivations. Analysis of the simulated intracellular rates revealed at least two distinct cellular physiological states. The first physiological state was characterized by a high glycolytic rate and high lactate production. Whereas the second state was characterized by efficient adenosine triphosphate production, a low glycolytic rate, and reactions of the TCA cycle running in the reverse direction from α-ketoglutarate to citrate. Finally, we show possible applications of the model for cell line engineering and media optimization with two case studies.
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Affiliation(s)
- João R C Ramos
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Alexander G Rath
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Bioprocess Engineering, AMINO GmbH, Frellstedt, Germany
| | - Yvonne Genzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
| | - Volker Sandig
- Bioprocess Engineering, ProBioGen AG, Berlin, Germany
| | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany
- Bioprocess Engineering, Otto von Guericke University Magdeburg, Chair of Bioprocess Engineering, Magdeburg, Germany
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9
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Abbate T, Fernandes de Sousa S, Dewasme L, Bastin G, Vande Wouwer A. Inference of dynamic macroscopic models of cell metabolism based on elementary flux modes analysis. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.107325] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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10
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Combes R, Balls M, Illing P, Bhogal N, Dale J, Duvé G, Feron V, Grindon C, Gülden M, Loizou G, Priston R, Westmoreland C. Possibilities for a New Approach to Chemicals Risk Assessment — The Report of a FRAME Workshop. Altern Lab Anim 2019; 34:621-49. [PMID: 17266394 DOI: 10.1177/026119290603400606] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Robert Combes
- FRAME, Russell & Burch House, 96-98 North Sherwood Street, Nottingham, NG1 4EE, UK.
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11
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Prieto P, Baird AW, Blaauboer BJ, Castell Ripoll JV, Corvi R, Dekant W, Dietl P, Gennari A, Gribaldo L, Griffin JL, Hartung T, Heindel JJ, Hoet P, Jennings P, Marocchio L, Noraberg J, Pazos P, Westmoreland C, Wolf A, Wright J, Pfaller W. The Assessment of Repeated Dose ToxicityIn Vitro: A Proposed Approach. Altern Lab Anim 2019; 34:315-41. [PMID: 16831063 DOI: 10.1177/026119290603400307] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- Pilar Prieto
- ECVAM, Institute for Health & Consumer Protection, European Joint Research Centre, 21020 Ispra (VA), Italy
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12
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Joseph JA, Akkermans S, Nimmegeers P, Van Impe JFM. Bioproduction of the Recombinant Sweet Protein Thaumatin: Current State of the Art and Perspectives. Front Microbiol 2019; 10:695. [PMID: 31024485 PMCID: PMC6463758 DOI: 10.3389/fmicb.2019.00695] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Accepted: 03/19/2019] [Indexed: 12/12/2022] Open
Abstract
There is currently a worldwide trend to reduce sugar consumption. This trend is mostly met by the use of artificial non-nutritive sweeteners. However, these sweeteners have also been proven to have adverse health effects such as dizziness, headaches, gastrointestinal issues, and mood changes for aspartame. One of the solutions lies in the commercialization of sweet proteins, which are not associated with adverse health effects. Of these proteins, thaumatin is one of the most studied and most promising alternatives for sugars and artificial sweeteners. Since the natural production of these proteins is often too expensive, biochemical production methods are currently under investigation. With these methods, recombinant DNA technology is used for the production of sweet proteins in a host organism. The most promising host known today is the methylotrophic yeast, Pichia pastoris. This yeast has a tightly regulated methanol-induced promotor, allowing a good control over the recombinant protein production. Great efforts have been undertaken for improving the yields and purities of thaumatin productions, but a further optimization is still desired. This review focuses on (i) the motivation for using and producing sweet proteins, (ii) the properties and history of thaumatin, (iii) the production of recombinant sweet proteins, and (iv) future possibilities for process optimization based on a systems biology approach.
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Affiliation(s)
- Jewel Ann Joseph
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
- Optimization in Engineering Center-of-Excellence, KU Leuven, Leuven, Belgium
- CPMF, Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
| | - Simen Akkermans
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
- Optimization in Engineering Center-of-Excellence, KU Leuven, Leuven, Belgium
- CPMF, Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
| | - Philippe Nimmegeers
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
- Optimization in Engineering Center-of-Excellence, KU Leuven, Leuven, Belgium
- CPMF, Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
| | - Jan F. M. Van Impe
- BioTeC+, Chemical and Biochemical Process Technology and Control, Department of Chemical Engineering, KU Leuven, Leuven, Belgium
- Optimization in Engineering Center-of-Excellence, KU Leuven, Leuven, Belgium
- CPMF, Flemish Cluster Predictive Microbiology in Foods, Leuven, Belgium
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13
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Abstract
Intensified and accelerated development processes are being demanded by the market, as innovative biopharmaceuticals such as virus-like particles, exosomes, cell and gene therapy, as well as recombinant proteins and peptides will possess no available platform approach. Therefore, methods that are able to accelerate this development are preferred. Especially, physicochemical rigorous process models, based on all relevant effects of fluid dynamics, phase equilibrium, and mass transfer, can be predictive, if the model is verified and distinctly quantitatively validated. In this approach, a macroscopic kinetic model based on Monod kinetics for mammalian cell cultivation is developed and verified according to a general valid model validation workflow. The macroscopic model is verified and validated on the basis of four decision criteria (plausibility, sensitivity, accuracy and precision as well as equality). The process model workflow is subjected to a case study, comprising a Chinese hamster ovary fed-batch cultivation for the production of a monoclonal antibody. By performing the workflow, it was found that, based on design of experiments and Monte Carlo simulation, the maximum growth rate µmax exhibited the greatest influence on model variables such as viable cell concentration XV and product concentration. In addition, partial least squares regressions statistically evaluate the correlations between a higher µmax and a higher cell and product concentration, as well as a higher substrate consumption.
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14
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Sha S, Huang Z, Wang Z, Yoon S. Mechanistic modeling and applications for CHO cell culture development and production. Curr Opin Chem Eng 2018. [DOI: 10.1016/j.coche.2018.08.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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15
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Kim JH, Lee JM. Successive complementary model-based experimental designs for parameter estimation of fed-batch bioreactors. Bioprocess Biosyst Eng 2018; 41:1767-1777. [PMID: 30099622 DOI: 10.1007/s00449-018-1999-8] [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: 06/18/2018] [Accepted: 08/07/2018] [Indexed: 10/28/2022]
Abstract
When a dynamic model is used for the description of (fed-)batch bioreactors, it is typical that the model parameters are highly correlated to each other. In this case, it is important to keep the parameter correlation as small as possible to obtain a reliable set of parameter estimates. In this study, we propose an anticorrelation parameter estimation scheme that can be best utilized when a number of different batch experiments are sequentially processed. The scheme iteratively performs parameter estimation and model-based design of experiment (MBDOE) at the beginning and between the batches. The important difference from the existing approaches is that the MBDOE objective is defined according to the system analysis performed a priori, so that each new batch supplements what is lacking from the previous batches combined, in terms of information. The use of the scheme is illustrated on a fed-batch bioreactor model.
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Affiliation(s)
- Jung Hun Kim
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Jong Min Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
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16
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Kappatou CD, Mhamdi A, Campano AQ, Mantalaris A, Mitsos A. Model-Based Dynamic Optimization of Monoclonal Antibodies Production in Semibatch Operation—Use of Reformulation Techniques. Ind Eng Chem Res 2018. [DOI: 10.1021/acs.iecr.7b05357] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Chrysoula D. Kappatou
- RWTH Aachen University, Aachener Verfahrenstechnik-Process Systems Engineering, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Adel Mhamdi
- RWTH Aachen University, Aachener Verfahrenstechnik-Process Systems Engineering, Forckenbeckstraße 51, 52074 Aachen, Germany
| | - Ana Quiroga Campano
- Department of Chemical Engineering, Centre for Process Systems Engineering (CPSE), Imperial College London SW7 2AZ, London, U.K
| | - Athanasios Mantalaris
- Department of Chemical Engineering, Centre for Process Systems Engineering (CPSE), Imperial College London SW7 2AZ, London, U.K
| | - Alexander Mitsos
- RWTH Aachen University, Aachener Verfahrenstechnik-Process Systems Engineering, Forckenbeckstraße 51, 52074 Aachen, Germany
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17
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Stacey AJ, Cheeseman EA, Glen KE, Moore RL, Thomas RJ. Experimentally integrated dynamic modelling for intuitive optimisation of cell based processes and manufacture. Biochem Eng J 2018. [DOI: 10.1016/j.bej.2018.01.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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18
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Process Analytical Technology for Advanced Process Control in Biologics Manufacturing with the Aid of Macroscopic Kinetic Modeling. Bioengineering (Basel) 2018; 5:bioengineering5010025. [PMID: 29547557 PMCID: PMC5874891 DOI: 10.3390/bioengineering5010025] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 11/20/2022] Open
Abstract
Productivity improvements of mammalian cell culture in the production of recombinant proteins have been made by optimizing cell lines, media, and process operation. This led to enhanced titers and process robustness without increasing the cost of the upstream processing (USP); however, a downstream bottleneck remains. In terms of process control improvement, the process analytical technology (PAT) initiative, initiated by the American Food and Drug Administration (FDA), aims to measure, analyze, monitor, and ultimately control all important attributes of a bioprocess. Especially, spectroscopic methods such as Raman or near-infrared spectroscopy enable one to meet these analytical requirements, preferably in-situ. In combination with chemometric techniques like partial least square (PLS) or principal component analysis (PCA), it is possible to generate soft sensors, which estimate process variables based on process and measurement models for the enhanced control of bioprocesses. Macroscopic kinetic models can be used to simulate cell metabolism. These models are able to enhance the process understanding by predicting the dynamic of cells during cultivation. In this article, in-situ turbidity (transmission, 880 nm) and ex-situ Raman spectroscopy (785 nm) measurements are combined with an offline macroscopic Monod kinetic model in order to predict substrate concentrations. Experimental data of Chinese hamster ovary cultivations in bioreactors show a sufficiently linear correlation (R2 ≥ 0.97) between turbidity and total cell concentration. PLS regression of Raman spectra generates a prediction model, which was validated via offline viable cell concentration measurement (RMSE ≤ 13.82, R2 ≥ 0.92). Based on these measurements, the macroscopic Monod model can be used to determine different process attributes, e.g., glucose concentration. In consequence, it is possible to approximately calculate (R2 ≥ 0.96) glucose concentration based on online cell concentration measurements using turbidity or Raman spectroscopy. Future approaches will use these online substrate concentration measurements with turbidity and Raman measurements, in combination with the kinetic model, in order to control the bioprocess in terms of feeding strategies, by employing an open platform communication (OPC) network—either in fed-batch or perfusion mode, integrated into a continuous operation of upstream and downstream.
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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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20
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Ben Yahia B, Gourevitch B, Malphettes L, Heinzle E. Segmented linear modeling of CHO fed-batch culture and its application to large scale production. Biotechnol Bioeng 2016; 114:785-797. [PMID: 27869296 PMCID: PMC5324675 DOI: 10.1002/bit.26214] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 08/16/2016] [Accepted: 11/02/2016] [Indexed: 12/21/2022]
Abstract
We describe a systematic approach to model CHO metabolism during biopharmaceutical production across a wide range of cell culture conditions. To this end, we applied the metabolic steady state concept. We analyzed and modeled the production rates of metabolites as a function of the specific growth rate. First, the total number of metabolic steady state phases and the location of the breakpoints were determined by recursive partitioning. For this, the smoothed derivative of the metabolic rates with respect to the growth rate were used followed by hierarchical clustering of the obtained partition. We then applied a piecewise regression to the metabolic rates with the previously determined number of phases. This allowed identifying the growth rates at which the cells underwent a metabolic shift. The resulting model with piecewise linear relationships between metabolic rates and the growth rate did well describe cellular metabolism in the fed‐batch cultures. Using the model structure and parameter values from a small‐scale cell culture (2 L) training dataset, it was possible to predict metabolic rates of new fed‐batch cultures just using the experimental specific growth rates. Such prediction was successful both at the laboratory scale with 2 L bioreactors but also at the production scale of 2000 L. This type of modeling provides a flexible framework to set a solid foundation for metabolic flux analysis and mechanistic type of modeling. Biotechnol. Bioeng. 2017;114: 785–797. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Bassem Ben Yahia
- Biochemical Engineering InstituteSaarland UniversityCampus A1.5, D‐66123 SaarbrückenGermany
- Upstream Process Sciences Biotech SciencesUCB Pharma S.A.Avenue de l'Industrie, Braine l'Alleud B‐1420Belgium
| | - Boris Gourevitch
- Institut de NeuroScience Paris‐Saclay (NeuroPSI)UMR CNRS 9197
- Université Paris‐SudOrsay Cedex 91405France
| | - Laetitia Malphettes
- Upstream Process Sciences Biotech SciencesUCB Pharma S.A.Avenue de l'Industrie, Braine l'Alleud B‐1420Belgium
| | - Elmar Heinzle
- Biochemical Engineering InstituteSaarland UniversityCampus A1.5, D‐66123 SaarbrückenGermany
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21
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Nikdel A, Budman H. Identification of active constraints in dynamic flux balance analysis. Biotechnol Prog 2016; 33:26-36. [PMID: 27790866 DOI: 10.1002/btpr.2388] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 08/23/2016] [Indexed: 12/24/2022]
Abstract
This study deals with the calibration of dynamic metabolic flux models that are formulated as the maximization of an objective subject to constraints. Two approaches were applied for identifying the constraints from data. In the first approach a minimal active number of limiting constraints is found based on data that are assumed to be bounded within sets whereas, in the second approach, the limiting constraints are found based on parametric sensitivity analysis. The ability of these approaches to finding the active limiting constraints was verified through their application to two case studies: an in-silico (simulated) data-based study describing the growth of E. coli and an experimental data-based study for Bordetella pertussis (B. pertussis). © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 33:26-36, 2017.
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Affiliation(s)
- Ali Nikdel
- Dept. of Chemical Engineering, University of Waterloo, Waterloo, ON, Canada
| | - Hector Budman
- Dept. of Chemical Engineering, University of Waterloo, Waterloo, ON, Canada
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22
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Weegman BP, Essawy A, Nash P, Carlson AL, Voltzke KJ, Geng Z, Jahani M, Becker BB, Papas KK, Firpo MT. Nutrient Regulation by Continuous Feeding for Large-scale Expansion of Mammalian Cells in Spheroids. J Vis Exp 2016:52224. [PMID: 27768027 PMCID: PMC5092061 DOI: 10.3791/52224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In this demonstration, spheroids formed from the β-TC6 insulinoma cell line were cultured as a model of manufacturing a mammalian islet cell product to demonstrate how regulating nutrient levels can improve cell yields. In previous studies, bioreactors facilitated increased culture volumes over static cultures, but no increase in cell yields were observed. Limitations in key nutrients such as glucose, which were consumed between batch feedings, can lead to limitations in cell expansion. Large fluctuations in glucose levels were observed, despite the increase in glucose concentrations in the media. The use of continuous feeding systems eliminated fluctuations in glucose levels, and improved cell growth rates when compared with batch fed static and SSB culture methods. Additional increases in growth rates were observed by adjusting the feed rate based on calculated nutrient consumption, which allowed the maintenance of physiological glucose over three weeks in culture. This method can also be adapted for other cell types.
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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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Shirsat N, Avesh M, English NJ, Glennon B, Al-Rubeai M. Verhulst and stochastic models for comparing mechanisms of MAb productivity in six CHO cell lines. Cytotechnology 2016; 68:1499-511. [PMID: 26307674 PMCID: PMC4960197 DOI: 10.1007/s10616-015-9910-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 08/04/2015] [Indexed: 12/12/2022] Open
Abstract
The present study validates previously published methodologies-stochastic and Verhulst-for modelling the growth and MAb productivity of six CHO cell lines grown in batch cultures. Cytometric and biochemical data were used to model growth and productivity. The stochastic explanatory models were developed to improve our understanding of the underlying mechanisms of growth and productivity, whereas the Verhulst mechanistic models were developed for their predictability. The parameters of the two sets of models were compared for their biological significance. The stochastic models, based on the cytometric data, indicated that the productivity mechanism is cell specific. However, as shown before, the modelling results indicated that G2 + ER indicate high productivity, while G1 + ER indicate low productivity, where G1 and G2 are the cell cycle phases and ER is Endoplasmic Reticulum. In all cell lines, growth proved to be inversely proportional to the cumulative G1 time (CG1T) for the G1 phase, whereas productivity was directly proportional to ER. Verhulst's rule, "the lower the intrinsic growth factor (r), the higher the growth (K)," did not hold for growth across all cell lines but held good for the cell lines with the same growth mechanism-i.e., r is cell specific. However, the Verhulst productivity rule, that productivity is inversely proportional to the intrinsic productivity factor (r x ), held well across all cell lines in spite of differences in their mechanisms for productivity-that is, r x is not cell specific. The productivity profile, as described by Verhulst's logistic model, is very similar to the Michaelis-Menten enzyme kinetic equation, suggesting that productivity is more likely enzymatic in nature. Comparison of the stochastic and Verhulst models indicated that CG1T in the cytometric data has the same significance as r, the intrinsic growth factor in the Verhulst models. The stochastic explanatory and the Verhulst logistic models can explain the differences in the productivity of the six clones.
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Affiliation(s)
- Nishikant Shirsat
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mohd Avesh
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Niall J English
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Brian Glennon
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland
| | - Mohamed Al-Rubeai
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, Ireland.
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25
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Vozzi G, Lucarini G, Dicarlo M, Andreoni C, Salvolini E, Ferretti C, Mattioli-Belmonte M. In vitro lifespan and senescent behaviour of human periosteal derived stem cells. Bone 2016; 88:1-12. [PMID: 27102545 DOI: 10.1016/j.bone.2016.04.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 03/08/2016] [Accepted: 04/06/2016] [Indexed: 01/26/2023]
Abstract
Periosteum derived progenitor cells (PDPCs) represent promising mesenchymal stem cells (MSCs) for skeletal regeneration and to test bone cell based tissue engineering strategies. Most of regenerative medicine approaches based on MSCs require a noteworthy amount of cells that must be expanded in vitro prior to their use. As culture expansion method may impact on cell behaviour, we assessed the replicative and metabolic capacity (nitric oxide production and glucose consumption), senescence hallmarks of PDPCs serially passaged as well as the expression of selected genes specifically related to early osteoblastic differentiation, bone remodelling and stemness during PDPC sequential passaging. We also scouted a Systems Biology approach to examine and elucidate the experimental results through mathematical modelling and in silico simulations. PDPC subculture led to a progressive proliferative decline but, despite this, PDPCs maintained almost constant their metabolic activity. In vitro, senescent PDPCs displayed the typical "replicative senescence" features, involving p16 and not p53 in the regulation of this phenomenon. Gene expression analysis evidenced the tendency of sub-cultured PDPCs to increase the expression of genes involved in bone resorption. The mathematical analysis of the experimental results showed a strict similarity between replicative senescence and age-related changes, enabling the definition of an in silico model mimicking PDPC behaviour in terms of nitric oxide (NO) production. The relationship between NO production and subculture passages could represent a cutting edge "replicative senescence index". Overall, our findings suggest the possibility to use early-passage PDPCs for bone regenerative approaches based on the local recruitment of stem cells, whilst the later cell passages could be a suitable in vitro tool to validate scaffolds intended for bone regeneration in elderly subjects.
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Affiliation(s)
- Giovanni Vozzi
- Research Centre "E. Piaggio", Faculty of Engineering, University of Pisa, Largo Lucio Lazzarino, 2, 56126 Pisa, Italy
| | - Guendalina Lucarini
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - Manuela Dicarlo
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - Chiara Andreoni
- Research Centre "E. Piaggio", Faculty of Engineering, University of Pisa, Largo Lucio Lazzarino, 2, 56126 Pisa, Italy
| | - Eleonora Salvolini
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - Concetta Ferretti
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy
| | - Monica Mattioli-Belmonte
- Department of Clinical and Molecular Sciences, Università Politecnica delle Marche, Via Tronto 10/a, 60126 Ancona, Italy.
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26
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Groh A, Kohr H, Louis AK. Numerical rate function determination in partial differential equations modeling cell population dynamics. J Math Biol 2016; 74:533-565. [PMID: 27295108 DOI: 10.1007/s00285-016-1032-2] [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: 08/18/2014] [Revised: 08/23/2015] [Indexed: 10/21/2022]
Abstract
This paper introduces a method to solve the inverse problem of determining an unknown rate function in a partial differential equation (PDE) based on discrete measurements of the modeled quantity. The focus is put on a size-structured population balance equation (PBE) predicting the evolution of the number distribution of a single cell population as a function of the size variable. Since the inverse problem at hand is ill-posed, an adequate regularization scheme is required to avoid amplification of measurement errors in the solution method. The technique developed in this work to determine a rate function in a PBE is based on the approximate inverse method, a pointwise regularization scheme, which employs two key ideas. Firstly, the mollification in the directions of time and size variables are separated. Secondly, instable numerical data derivatives are circumvented by shifting the differentiation to an analytically given function. To examine the performance of the introduced scheme, adapted test scenarios have been designed with different levels of data disturbance simulating the model and measurement errors in practice. The success of the method is substantiated by visualizing the results of these numerical experiments.
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Affiliation(s)
- Andreas Groh
- Hexagon Metrology PTS, Walter-Zapp-Strasse 4, 35578, Wetzlar, Germany.
| | - Holger Kohr
- Royal Institute of Technology (KTH), Lindstedtsvägen 25, 10044, Stockholm, Sweden
| | - Alfred K Louis
- Saarland University, POB: 151150, 66041, Saarbrücken, Germany
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27
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A Predictive Model for Energy Metabolism and ATP Balance in Mammalian Cells: Towards the Energy-Based Optimization of mAb Production. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/b978-0-444-63428-3.50268-x] [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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28
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Ben Yahia B, Malphettes L, Heinzle E. Macroscopic modeling of mammalian cell growth and metabolism. Appl Microbiol Biotechnol 2015; 99:7009-24. [PMID: 26198881 PMCID: PMC4536272 DOI: 10.1007/s00253-015-6743-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Revised: 05/28/2015] [Accepted: 05/30/2015] [Indexed: 12/24/2022]
Abstract
We review major modeling strategies and methods to understand and simulate the macroscopic behavior of mammalian cells. These strategies comprise two important steps: the first step is to identify stoichiometric relationships for the cultured cells connecting the extracellular inputs and outputs. In a second step, macroscopic kinetic models are introduced. These relationships together with bioreactor and metabolite balances provide a complete description of a system in the form of a set of differential equations. These can be used for the simulation of cell culture performance and further for optimization of production.
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Affiliation(s)
- Bassem Ben Yahia
- />Biochemical Engineering Institute, Saarland University, Campus A1.5, D-66123 Saarbruecken, Germany
- />Upstream Process Sciences Biotech Sciences, UCB Pharma S.A., Avenue de l’Industrie, B-1420, Braine l’Alleud, Belgium
| | - Laetitia Malphettes
- />Upstream Process Sciences Biotech Sciences, UCB Pharma S.A., Avenue de l’Industrie, B-1420, Braine l’Alleud, Belgium
| | - Elmar Heinzle
- />Biochemical Engineering Institute, Saarland University, Campus A1.5, D-66123 Saarbruecken, Germany
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29
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Klein T, Heinzel N, Kroll P, Brunner M, Herwig C, Neutsch L. Quantification of cell lysis during CHO bioprocesses: Impact on cell count, growth kinetics and productivity. J Biotechnol 2015; 207:67-76. [DOI: 10.1016/j.jbiotec.2015.04.021] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 04/18/2015] [Accepted: 04/27/2015] [Indexed: 02/02/2023]
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30
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Castillo Salvador AE, Fuge G, Jandt U, Zeng AP. Growth kinetics and validation of near-physiologically synchronized HEK293S Cultures. Eng Life Sci 2015. [DOI: 10.1002/elsc.201400224] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
| | - Grischa Fuge
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Hamburg Germany
| | - Uwe Jandt
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Hamburg Germany
| | - An-Ping Zeng
- Institute of Bioprocess and Biosystems Engineering; Hamburg University of Technology; Hamburg Germany
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31
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García Münzer DG, Kostoglou M, Georgiadis MC, Pistikopoulos EN, Mantalaris A. Cyclin and DNA distributed cell cycle model for GS-NS0 cells. PLoS Comput Biol 2015; 11:e1004062. [PMID: 25723523 PMCID: PMC4344234 DOI: 10.1371/journal.pcbi.1004062] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Accepted: 11/26/2014] [Indexed: 01/10/2023] Open
Abstract
Mammalian cell cultures are intrinsically heterogeneous at different scales (molecular to bioreactor). The cell cycle is at the centre of capturing heterogeneity since it plays a critical role in the growth, death, and productivity of mammalian cell cultures. Current cell cycle models use biological variables (mass/volume/age) that are non-mechanistic, and difficult to experimentally determine, to describe cell cycle transition and capture culture heterogeneity. To address this problem, cyclins-key molecules that regulate cell cycle transition-have been utilized. Herein, a novel integrated experimental-modelling platform is presented whereby experimental quantification of key cell cycle metrics (cell cycle timings, cell cycle fractions, and cyclin expression determined by flow cytometry) is used to develop a cyclin and DNA distributed model for the industrially relevant cell line, GS-NS0. Cyclins/DNA synthesis rates were linked to stimulatory/inhibitory factors in the culture medium, which ultimately affect cell growth. Cell antibody productivity was characterized using cell cycle-specific production rates. The solution method delivered fast computational time that renders the model's use suitable for model-based applications. Model structure was studied by global sensitivity analysis (GSA), which identified parameters with a significant effect on the model output, followed by re-estimation of its significant parameters from a control set of batch experiments. A good model fit to the experimental data, both at the cell cycle and viable cell density levels, was observed. The cell population heterogeneity of disturbed (after cell arrest) and undisturbed cell growth was captured proving the versatility of the modelling approach. Cell cycle models able to capture population heterogeneity facilitate in depth understanding of these complex systems and enable systematic formulation of culture strategies to improve growth and productivity. It is envisaged that this modelling approach will pave the model-based development of industrial cell lines and clinical studies.
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Affiliation(s)
- David G. García Münzer
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Margaritis Kostoglou
- Department of Chemistry, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Michael C. Georgiadis
- Department of Chemical Engineering, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Efstratios N. Pistikopoulos
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, United Kingdom
| | - Athanasios Mantalaris
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, United Kingdom
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32
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Mammalian cell culture process for monoclonal antibody production: nonlinear modelling and parameter estimation. BIOMED RESEARCH INTERNATIONAL 2015; 2015:598721. [PMID: 25685797 PMCID: PMC4313526 DOI: 10.1155/2015/598721] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Revised: 12/05/2014] [Accepted: 12/07/2014] [Indexed: 11/17/2022]
Abstract
Monoclonal antibodies (mAbs) are at present one of the fastest growing products of pharmaceutical industry, with widespread applications in biochemistry, biology, and medicine. The operation of mAbs production processes is predominantly based on empirical knowledge, the improvements being achieved by using trial-and-error experiments and precedent practices. The nonlinearity of these processes and the absence of suitable instrumentation require an enhanced modelling effort and modern kinetic parameter estimation strategies. The present work is dedicated to nonlinear dynamic modelling and parameter estimation for a mammalian cell culture process used for mAb production. By using a dynamical model of such kind of processes, an optimization-based technique for estimation of kinetic parameters in the model of mammalian cell culture process is developed. The estimation is achieved as a result of minimizing an error function by a particle swarm optimization (PSO) algorithm. The proposed estimation approach is analyzed in this work by using a particular model of mammalian cell culture, as a case study, but is generic for this class of bioprocesses. The presented case study shows that the proposed parameter estimation technique provides a more accurate simulation of the experimentally observed process behaviour than reported in previous studies.
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33
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García Münzer D, Ivarsson M, Usaku C, Habicher T, Soos M, Morbidelli M, Pistikopoulos E, Mantalaris A. An unstructured model of metabolic and temperature dependent cell cycle arrest in hybridoma batch and fed-batch cultures. Biochem Eng J 2015. [DOI: 10.1016/j.bej.2014.10.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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34
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Andreoni C, Orsi G, De Maria C, Montemurro F, Vozzi G. In silico models for dynamic connected cell cultures mimicking hepatocyte-endothelial cell-adipocyte interaction circle. PLoS One 2014; 9:e111946. [PMID: 25502576 PMCID: PMC4266517 DOI: 10.1371/journal.pone.0111946] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 10/09/2014] [Indexed: 01/12/2023] Open
Abstract
The biochemistry of a system made up of three kinds of cell is virtually impossible to work out without the use of in silico models. Here, we deal with homeostatic balance phenomena from a metabolic point of view and we present a new computational model merging three single-cell models, already available from our research group: the first model reproduced the metabolic behaviour of a hepatocyte, the second one represented an endothelial cell, and the third one described an adipocyte. Multiple interconnections were created among these three models in order to mimic the main physiological interactions that are known for the examined cell phenotypes. The ultimate aim was to recreate the accomplishment of the homeostatic balance as it was observed for an in vitro connected three-culture system concerning glucose and lipid metabolism in the presence of the medium flow. The whole model was based on a modular approach and on a set of nonlinear differential equations implemented in Simulink, applying Michaelis-Menten kinetic laws and some energy balance considerations to the studied metabolic pathways. Our in silico model was then validated against experimental datasets coming from literature about the cited in vitro model. The agreement between simulated and experimental results was good and the behaviour of the connected culture system was reproduced through an adequate parameter evaluation. The developed model may help other researchers to investigate further about integrated metabolism and the regulation mechanisms underlying the physiological homeostasis.
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Affiliation(s)
- Chiara Andreoni
- Research Center “E. Piaggio”, University of Pisa, Pisa, Italy
- * E-mail:
| | - Gianni Orsi
- Research Center “E. Piaggio”, University of Pisa, Pisa, Italy
| | - Carmelo De Maria
- Research Center “E. Piaggio”, University of Pisa, Pisa, Italy
- Department of Information Engineering, University of Pisa, Pisa, Italy
| | | | - Giovanni Vozzi
- Research Center “E. Piaggio”, University of Pisa, Pisa, Italy
- Department of Information Engineering, University of Pisa, Pisa, Italy
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35
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Naderi S, Nikdel A, Meshram M, McConkey B, Ingalls B, Budman H, Scharer J. Modeling of cell culture damage and recovery leads to increased antibody and biomass productivity in CHO cell cultures. Biotechnol J 2014; 9:1152-63. [DOI: 10.1002/biot.201300287] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Revised: 04/01/2014] [Accepted: 05/18/2014] [Indexed: 12/12/2022]
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36
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Approach toward an efficient inoculum preparation stage for suspension BHK-21 cell culture. Cytotechnology 2014; 68:95-104. [PMID: 24942228 DOI: 10.1007/s10616-014-9756-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 06/07/2014] [Indexed: 10/25/2022] Open
Abstract
Mammalian cells are the most frequently used hosts for biopharmaceutical proteins manufacturing. Inoculum quality is a key element for establishing an efficient bioconversion process. The main objective in inoculation expansion process is to generate large volume of viable cells in the shortest time. The aim of this paper was to optimize the inoculum preparation stage of baby hamster kidney (BHK)-21 cells for suspension cultures in benchtop bioreactors, by means of a combination of static and agitated culture systems. Critical parameters for static (liquid column height: 5, 10, 15 mm) and agitated (working volume: 35, 50, 65 mL, inoculum volume percentage: 10, 30 % and agitation speed: 25, 60 rpm) cultures were study in T-flask and spinner flask, respectively. The optimal liquid column height was 5 mm for static culture. The maximum viable cell concentration in spinner flask cultures was reached with 50 mL working volume and the inoculum volume percentage was not significant in the range under study (10-30 %) at 25 rpm agitation. Agitation speed at 60 rpm did not change the main kinetic parameters with respect to those observed for 25 rpm. These results allowed for a schedule to produce more than 4 × 10(9) BHK-21 cells from 4 × 10(6) cells in 13 day with 1,051 mL culture medium.
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Abstract
Population balance modeling is undergoing phenomenal growth in its applications, and this growth is accompanied by multifarious reviews. This review aims to fortify the model's fundamental base, as well as point to a variety of new applications, including modeling of crystal morphology, cell growth and differentiation, gene regulatory processes, and transfer of drug resistance. This is accomplished by presenting the many faces of population balance equations that arise in the foregoing applications.
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Affiliation(s)
| | - Meenesh R. Singh
- School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94704
- Joint Center for Artificial Photosynthesis, Lawrence Berkeley National Laboratory, Berkeley, California 94720
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Kontoravdi C. Systematic methodology for the development of mathematical models for biological processes. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2014; 1073:177-90. [PMID: 23996448 DOI: 10.1007/978-1-62703-625-2_15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Synthetic biology gives researchers the opportunity to rationally (re-)design cellular activities to achieve a desired function. The design of networks of pathways towards accomplishing this calls for the application of engineering principles, often using model-based tools. Success heavily depends on model reliability. Herein, we present a systematic methodology for developing predictive models comprising model formulation considerations, global sensitivity analysis, model reduction (for highly complex models or where experimental data are limited), optimal experimental design for parameter estimation, and predictive capability checking. Its efficacy and validity are demonstrated using an example from bioprocessing. This approach systematizes the process of developing reliable mathematical models at a minimum experimental cost, enabling in silico simulation and optimization.
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Affiliation(s)
- Cleo Kontoravdi
- Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, London, UK
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García Münzer D, Kostoglou M, Georgiadis M, Pistikopoulos E, Mantalaris A. Developing a cyclin blueprint as a tool for mapping the cell cycle in GS-NS0. Biochem Eng J 2013. [DOI: 10.1016/j.bej.2013.10.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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40
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Weegman BP, Nash P, Carlson AL, Voltzke KJ, Geng Z, Jahani M, Becker BB, Papas KK, Firpo MT. Nutrient regulation by continuous feeding removes limitations on cell yield in the large-scale expansion of Mammalian cell spheroids. PLoS One 2013; 8:e76611. [PMID: 24204645 PMCID: PMC3799778 DOI: 10.1371/journal.pone.0076611] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 08/25/2013] [Indexed: 02/06/2023] Open
Abstract
Cellular therapies are emerging as a standard approach for the treatment of several diseases. However, realizing the promise of cellular therapies across the full range of treatable disorders will require large-scale, controlled, reproducible culture methods. Bioreactor systems offer the scale-up and monitoring needed, but standard stirred bioreactor cultures do not allow for the real-time regulation of key nutrients in the medium. In this study, β-TC6 insulinoma cells were aggregated and cultured for 3 weeks as a model of manufacturing a mammalian cell product. Cell expansion rates and medium nutrient levels were compared in static, stirred suspension bioreactors (SSB), and continuously fed (CF) SSB. While SSB cultures facilitated increased culture volumes, no increase in cell yields were observed, partly due to limitations in key nutrients, which were consumed by the cultures between feedings, such as glucose. Even when glucose levels were increased to prevent depletion between feedings, dramatic fluctuations in glucose levels were observed. Continuous feeding eliminated fluctuations and improved cell expansion when compared with both static and SSB culture methods. Further improvements in growth rates were observed after adjusting the feed rate based on calculated nutrient depletion, which maintained physiological glucose levels for the duration of the expansion. Adjusting the feed rate in a continuous medium replacement system can maintain the consistent nutrient levels required for the large-scale application of many cell products. Continuously fed bioreactor systems combined with nutrient regulation can be used to improve the yield and reproducibility of mammalian cells for biological products and cellular therapies and will facilitate the translation of cell culture from the research lab to clinical applications.
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Affiliation(s)
- Bradley P. Weegman
- Stem Cell Institute, Division of Endocrinology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Peter Nash
- Stem Cell Institute, Division of Endocrinology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Alexandra L. Carlson
- Stem Cell Institute, Division of Endocrinology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Kristin J. Voltzke
- Stem Cell Institute, Division of Endocrinology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Zhaohui Geng
- Stem Cell Institute, Division of Endocrinology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Marjan Jahani
- Stem Cell Institute, Division of Endocrinology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Benjamin B. Becker
- Stem Cell Institute, Division of Endocrinology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
| | - Klearchos K. Papas
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
- Institute for Cellular Transplantation, Department of Surgery, University of Arizona, Tucson, Arizona, United States of America
| | - Meri T. Firpo
- Stem Cell Institute, Division of Endocrinology, Department of Medicine, University of Minnesota, Minneapolis, Minnesota, United States of America
- Schulze Diabetes Institute, Department of Surgery, University of Minnesota, Minneapolis, Minnesota, United States of America
- * E-mail:
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Shirsat N, Avesh M, English NJ, Glennon B, Al-Rubeai M. Application of statistical techniques for elucidating flow cytometric data of batch and fed-batch cultures. Biotechnol Appl Biochem 2013; 60:536-45. [PMID: 23826910 DOI: 10.1002/bab.1138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2013] [Accepted: 06/23/2013] [Indexed: 12/21/2022]
Abstract
The objective of this work is to develop structured, segregated stochastic models for bioprocesses using time-series flow cytometric (FC) data. To this end, mammalian CHO cells were grown in both batch and fed-batch cultures, and their viable cell numbers (VCDs), monoclonal antibody (MAb), cell cycle phases, mitochondria membrane potential/mitochondria mass, Golgi apparatus, and endoplasmic reticulum (ER) were analyzed. For the fed-batch mode, soy hydrolysate was introduced at 24-H intervals. The cytometric data were analyzed for early indicators of growth and productivity by multiple linear regression analysis, which involved taking into account multicollinearity diagnostics, Durbin-Watson statistics, and Houston tests to determine and refine statistically significant correlations between categorical variables (FC parameters) and response variables (yield parameters). The results indicate that the percentage of G1 cells and ER was significantly correlated with VCD and MAb in the case of batch culture, whereas for fed-batch culture, the percentage of G2 cells and ER was correlated significantly. There was a significant difference between cells in the batch and fed-batch cultures in their ER content, suggesting that the increase in protein synthesis as reflected by the ER content and consequent increase in growth rate and MAb productivity both can be monitored at the cellular level by FC analysis of ER content.
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Affiliation(s)
- Nishikant Shirsat
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin, Ireland
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Hoang MD, Barz T, Merchan VA, Biegler LT, Arellano-Garcia H. Simultaneous solution approach to model-based experimental design. AIChE J 2013. [DOI: 10.1002/aic.14145] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- M. D. Hoang
- Chair of Process Dynamics and Operation, Sekr. KWT-9; Berlin Institute of Technology; Str. des 17 Juni 135, D-10623; Berlin; Germany
| | - T. Barz
- Chair of Process Dynamics and Operation, Sekr. KWT-9; Berlin Institute of Technology; Str. des 17 Juni 135, D-10623; Berlin; Germany
| | - V. A. Merchan
- Chair of Process Dynamics and Operation, Sekr. KWT-9; Berlin Institute of Technology; Str. des 17 Juni 135, D-10623; Berlin; Germany
| | - L. T. Biegler
- Dept. of Chemical Engineering; Carnegie Mellon University; 5000 Forbes Avenue; Pittsburgh; PA; 15213
| | - H. Arellano-Garcia
- School of Design, Engineering and Technology; University of Bradford; Richmond Road; Bradford; BD7 1DP; U.K
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Geng J, Bi J, Zeng A, Yuan J. Application of hybrid cybernetic model in simulating myeloma cell culture co-consuming glucose and glutamine with mixed consumption patterns. Process Biochem 2013. [DOI: 10.1016/j.procbio.2013.03.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Gétaz D, Butté A, Morbidelli M. Model-based design space determination of peptide chromatographic purification processes. J Chromatogr A 2013; 1284:80-7. [PMID: 23466201 DOI: 10.1016/j.chroma.2013.01.117] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2012] [Revised: 01/30/2013] [Accepted: 01/31/2013] [Indexed: 11/30/2022]
Abstract
Operating a chemical process at fixed operating conditions often leads to suboptimal process performances. It is important in fact to be able to vary the process operating conditions depending upon possible changes in feed composition, products requirements or economics. This flexibility in the manufacturing process was facilitated by the publication of the PAT initiative from the U.S. FDA [1]. In this work, the implementation of Quality-by-design in the development of a chromatographic purification process is discussed. A procedure to determine the design space of the process using chromatographic modeling is presented. Moreover, the risk of batch failure and the critical process parameters (CPP) are assessed by modeling. The ideal cut strategy is adopted and therefore only yield and productivity are considered as critical quality attributes (CQA). The general trends in CQA variations within the design space are discussed. The effect of process disturbances is also considered. It is shown that process disturbances significantly decrease the design space and that only simultaneous and specific changes in multiple process parameters (i.e. critical process parameters (CPP) lead to batch failure. The reliability of the obtained results is proven by comparing the model predictions to suitable experimental data. The case study presented in this work proves the reliability of process development using a model-based approach.
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Affiliation(s)
- David Gétaz
- Department of Chemistry and Applied Bioscience, Institute for Chemical and Bioengineering, ETH Zurich, CH-8093 Zurich, Switzerland
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Chakrabarty A, Buzzard GT, Rundell AE. Model-based design of experiments for cellular processes. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE 2013; 5:181-203. [PMID: 23293047 DOI: 10.1002/wsbm.1204] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Ankush Chakrabarty
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN, USA
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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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47
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Lencastre Fernandes R, Bodla VK, Carlquist M, Heins AL, Eliasson Lantz A, Sin G, Gernaey KV. Applying Mechanistic Models in Bioprocess Development. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 132:137-66. [DOI: 10.1007/10_2012_166] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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48
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Gerdtzen ZP. Modeling metabolic networks for mammalian cell systems: general considerations, modeling strategies, and available tools. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2012; 127:71-108. [PMID: 21984615 DOI: 10.1007/10_2011_120] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Over the past decades, the availability of large amounts of information regarding cellular processes and reaction rates, along with increasing knowledge about the complex mechanisms involved in these processes, has changed the way we approach the understanding of cellular processes. We can no longer rely only on our intuition for interpreting experimental data and evaluating new hypotheses, as the information to analyze is becoming increasingly complex. The paradigm for the analysis of cellular systems has shifted from a focus on individual processes to comprehensive global mathematical descriptions that consider the interactions of metabolic, genomic, and signaling networks. Analysis and simulations are used to test our knowledge by refuting or validating new hypotheses regarding a complex system, which can result in predictive capabilities that lead to better experimental design. Different types of models can be used for this purpose, depending on the type and amount of information available for the specific system. Stoichiometric models are based on the metabolic structure of the system and allow explorations of steady state distributions in the network. Detailed kinetic models provide a description of the dynamics of the system, they involve a large number of reactions with varied kinetic characteristics and require a large number of parameters. Models based on statistical information provide a description of the system without information regarding structure and interactions of the networks involved. The development of detailed models for mammalian cell metabolism has only recently started to grow more strongly, due to the intrinsic complexities of mammalian systems, and the limited availability of experimental information and adequate modeling tools. In this work we review the strategies, tools, current advances, and recent models of mammalian cells, focusing mainly on metabolism, but discussing the methodology applied to other types of networks as well.
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Affiliation(s)
- Ziomara P Gerdtzen
- Department of Chemical Engineering and Biotechnology, Millennium Institute for Cell Dynamics and Biotechnology: a Centre for Systems Biology, University of Chile, Beauchef 850, Santiago, Chile,
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Abstract
In this feature, leading researchers in the field of microbial biotechnology speculate on the technical and conceptual developments that will drive innovative research and open new vistas over the next few years.
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