1
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Dewasme L, Mäkinen M, Chotteau V. Practical data-driven modeling and robust predictive control of mammalian cell fed-batch process. Comput Chem Eng 2023. [DOI: 10.1016/j.compchemeng.2023.108164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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2
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van der Burg D, Josefsson L, Mikkonen S, Chotteau V, Emmer Å, Wätzig H, Sänger-van de Griend CE. Method development for mono- and disaccharides monitoring in cell culture medium by capillary and microchip electrophoresis. Electrophoresis 2021; 43:922-929. [PMID: 34510488 DOI: 10.1002/elps.202100213] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/12/2021] [Accepted: 09/01/2021] [Indexed: 12/19/2022]
Abstract
The rapidly growing, competitive biopharmaceutical market requires tight bioprocess monitoring. An integrated, automated platform for the routine online/at-line monitoring of key factors in the cell culture medium could greatly improve process monitoring. Mono- and disaccharides, as the main energy and carbon source, are one of these key factors. A CE-LIF method was developed for the analysis of several mono- and disaccharides, considering requirements and restrictions for analysis in an integrated, automated monitoring platform, such as the possibility for miniaturization to microchip electrophoresis. Analysis was performed after fluorescent derivatization with 8-aminopyrene-1,3,6-trisulfonic acid. The derivatisation reaction and the separation BGE were optimized using design of experiments. The developed method is applicable to the complex matrix of cell culture medium and proved transferable to microchip electrophoresis.
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Affiliation(s)
- Debbie van der Burg
- Kantisto BV, Baarn, The Netherlands.,Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Leila Josefsson
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Saara Mikkonen
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Véronique Chotteau
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Åsa Emmer
- Department of Chemistry, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hermann Wätzig
- Institute of Medicinal and Pharmaceutical Chemistry, TU Braunschweig, Braunschweig, Germany
| | - Cari E Sänger-van de Griend
- Kantisto BV, Baarn, The Netherlands.,Department of Medicinal Chemistry, Faculty of Pharmacy, Uppsala University, Uppsala, Sweden
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3
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Brechmann NA, Schwarz H, Eriksson P, Eriksson K, Shokri A, Chotteau V. Back Cover Image, Volume 118, Number 9, September 2021. Biotechnol Bioeng 2021. [DOI: 10.1002/bit.27922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Nils A. Brechmann
- AdBIOPRO VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing Stockholm Sweden
- Cell Technology Group (CETEG), Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Hubert Schwarz
- AdBIOPRO VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing Stockholm Sweden
- Cell Technology Group (CETEG), Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | | | - Kristofer Eriksson
- AdBIOPRO VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing Stockholm Sweden
- R&D MAGic Bioprocessing Uppsala Sweden
| | - Atefeh Shokri
- AdBIOPRO VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing Stockholm Sweden
- Cell Technology Group (CETEG), Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Véronique Chotteau
- AdBIOPRO VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing Stockholm Sweden
- Cell Technology Group (CETEG), Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
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4
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Rodrigues D, Abdalmoaty MR, Jacobsen EW, Chotteau V, Hjalmarsson H. An integrated approach for modeling and identification of perfusion bioreactors via basis flux modes. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2021.107238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Brechmann NA, Schwarz H, Eriksson PO, Eriksson K, Shokri A, Chotteau V. Antibody capture process based on magnetic beads from very high cell density suspension. Biotechnol Bioeng 2021; 118:3499-3510. [PMID: 33811659 DOI: 10.1002/bit.27776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 03/03/2021] [Accepted: 03/25/2021] [Indexed: 11/09/2022]
Abstract
Cell clarification represents a major challenge for the intensification through very high cell density in the production of biopharmaceuticals such as monoclonal antibodies (mAbs). The present report proposes a solution to this challenge in a streamlined process where cell clarification and mAb capture are performed in a single step using magnetic beads coupled with protein A. Capture of mAb from non-clarified CHO cell suspension showed promising results; however, it has not been demonstrated that it can handle the challenge of very high cell density as observed in intensified fed-batch cultures. The performances of magnetic bead-based mAb capture on non-clarified cell suspension from intensified fed-batch culture were studied. Capture from a culture at density larger than 100 × 106 cells/ml provided an adsorption efficiency of 99% and an overall yield of 93% with a logarithmic host cell protein (HCP) clearance of ≈2-3 and a resulting HCP concentration ≤≈5 ppm. These results show that direct capture from very high cell density cell suspension is possible without prior processing. This technology, which brings significant benefits in terms of operational cost reduction and performance improvements such as low HCP, can be a powerful tool alleviating the challenge of process intensification.
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Affiliation(s)
- Nils A Brechmann
- AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, Stockholm, Sweden.,Cell Technology Group (CETEG), Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hubert Schwarz
- AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, Stockholm, Sweden.,Cell Technology Group (CETEG), Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | | | - Kristofer Eriksson
- AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, Stockholm, Sweden.,R&D, MAGic Bioprocessing, Uppsala, Sweden
| | - Atefeh Shokri
- AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, Stockholm, Sweden.,Cell Technology Group (CETEG), Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Véronique Chotteau
- AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, Stockholm, Sweden.,Cell Technology Group (CETEG), Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
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6
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Gomis‐Fons J, Schwarz H, Zhang L, Andersson N, Nilsson B, Castan A, Solbrand A, Stevenson J, Chotteau V. Model‐based design and control of a small‐scale integrated continuous end‐to‐end
mAb
platform. Biotechnol Prog 2020; 36:e2995. [DOI: 10.1002/btpr.2995] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 03/08/2020] [Accepted: 03/23/2020] [Indexed: 12/14/2022]
Affiliation(s)
| | - Hubert Schwarz
- Department of Industrial Biotechnology School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology Stockholm Sweden
| | - Liang Zhang
- Department of Industrial Biotechnology School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology Stockholm Sweden
| | | | - Bernt Nilsson
- Department of Chemical Engineering Lund University Lund Sweden
| | | | | | | | - Véronique Chotteau
- Department of Industrial Biotechnology School of Engineering Sciences in Chemistry, Biotechnology and Health, Royal Institute of Technology Stockholm Sweden
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7
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Schwarz H, Zhang Y, Zhan C, Malm M, Field R, Turner R, Sellick C, Varley P, Rockberg J, Chotteau V. Small-scale bioreactor supports high density HEK293 cell perfusion culture for the production of recombinant Erythropoietin. J Biotechnol 2020; 309:44-52. [DOI: 10.1016/j.jbiotec.2019.12.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 12/11/2019] [Accepted: 12/26/2019] [Indexed: 12/26/2022]
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8
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Wang M, Risuleo RS, Jacobsen EW, Chotteau V, Hjalmarsson H. Identification of nonlinear kinetics of macroscopic bio-reactions using multilinear Gaussian processes. Comput Chem Eng 2020. [DOI: 10.1016/j.compchemeng.2019.106671] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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9
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Brechmann NA, Eriksson PO, Eriksson K, Oscarsson S, Buijs J, Shokri A, Hjälm G, Chotteau V. Pilot-scale process for magnetic bead purification of antibodies directly from non-clarified CHO cell culture. Biotechnol Prog 2019; 35:e2775. [PMID: 30629859 PMCID: PMC6617771 DOI: 10.1002/btpr.2775] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/31/2018] [Accepted: 12/31/2018] [Indexed: 11/20/2022]
Abstract
High capacity magnetic protein A agarose beads, LOABeads PrtA, were used in the development of a new process for affinity purification of monoclonal antibodies (mAbs) from non‐clarified CHO cell broth using a pilot‐scale magnetic separator. The LOABeads had a maximum binding capacity of 65 mg/mL and an adsorption capacity of 25–42 mg IgG/mL bead in suspension for an IgG concentration of 1 to 8 g/L. Pilot‐scale separation was initially tested in a mAb capture step from 26 L clarified harvest. Small‐scale experiments showed that similar mAb adsorptions were obtained in cell broth containing 40 × 106 cells/mL as in clarified supernatant. Two pilot‐scale purification runs were then performed on non‐clarified cell broth from fed‐batch runs of 16 L, where a rapid mAb adsorption ≥96.6% was observed after 1 h. This process using 1 L of magnetic beads had an overall mAb yield of 86% and 16 times concentration factor. After this single protein A capture step, the mAb purity was similar to the one obtained by column chromatography, while the host cell protein content was very low, <10 ppm. Our results showed that this magnetic bead mAb purification process, using a dedicated pilot‐scale separation device, was a highly efficient single step, which directly connected the culture to the downstream process without cell clarification. Purification of mAb directly from non‐clarified cell broth without cell separation can provide significant savings in terms of resources, operation time, and equipment, compared to legacy procedure of cell separation followed by column chromatography step. © 2019 American Institute of Chemical Engineers Biotechnol. Prog., 35: e2775, 2019.
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Affiliation(s)
- Nils A Brechmann
- AdBIOPRO, VINNOVA Competence Centre for Advanced BioProduction by Continuous Processing, Stockholm, Sweden.,Cell Technology Group (CETEG), Dept. of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Inst. of Technology, Stockholm, Sweden
| | | | - Kristofer Eriksson
- AdBIOPRO, VINNOVA Competence Centre for Advanced BioProduction by Continuous Processing, Stockholm, Sweden.,Lab-on-a-Bead AB, Uppsala, Sweden
| | - Sven Oscarsson
- Dept. of Organic Chemistry, Stockholm University, Stockholm, Sweden
| | - Jos Buijs
- Dept. of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Atefeh Shokri
- AdBIOPRO, VINNOVA Competence Centre for Advanced BioProduction by Continuous Processing, Stockholm, Sweden.,Cell Technology Group (CETEG), Dept. of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Inst. of Technology, Stockholm, Sweden
| | - Göran Hjälm
- AdBIOPRO, VINNOVA Competence Centre for Advanced BioProduction by Continuous Processing, Stockholm, Sweden.,Lab-on-a-Bead AB, Uppsala, Sweden
| | - Véronique Chotteau
- AdBIOPRO, VINNOVA Competence Centre for Advanced BioProduction by Continuous Processing, Stockholm, Sweden.,Cell Technology Group (CETEG), Dept. of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Inst. of Technology, Stockholm, Sweden
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10
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Hagrot E, Oddsdóttir HÆ, Mäkinen M, Forsgren A, Chotteau V. Novel column generation-based optimization approach for poly-pathway kinetic model applied to CHO cell culture. Metab Eng Commun 2018; 8:e00083. [PMID: 30809468 PMCID: PMC6376161 DOI: 10.1016/j.mec.2018.e00083] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 10/30/2018] [Accepted: 12/08/2018] [Indexed: 11/26/2022] Open
Abstract
Mathematical modelling can provide precious tools for bioprocess simulation, prediction, control and optimization of mammalian cell-based cultures. In this paper we present a novel method to generate kinetic models of such cultures, rendering complex metabolic networks in a poly-pathway kinetic model. The model is based on subsets of elementary flux modes (EFMs) to generate macro-reactions. Thanks to our column generation-based optimization algorithm, the experimental data are used to identify the EFMs, which are relevant to the data. Here the systematic enumeration of all the EFMs is eliminated and a network including a large number of reactions can be considered. In particular, the poly-pathway model can simulate multiple metabolic behaviors in response to changes in the culture conditions. We apply the method to a network of 126 metabolic reactions describing cultures of antibody-producing Chinese hamster ovary cells, and generate a poly-pathway model that simulates multiple experimental conditions obtained in response to variations in amino acid availability. A good fit between simulated and experimental data is obtained, rendering the variations in the growth, product, and metabolite uptake/secretion rates. The intracellular reaction fluxes simulated by the model are explored, linking variations in metabolic behavior to adaptations of the intracellular metabolism. Novel method to model multiple states by a poly-pathway kinetic model. EFMs relevant to data identified by column generation (CG)-based optimization. CG optimization enables use of networks much larger than systematic enumeration. A kinetic model simulates changes in metabolic rates linked to available amino acids. The flux distribution of each metabolic state is visualized in the original network.
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Affiliation(s)
- Erika Hagrot
- Cell Technology Group, Department of Industrial Biotechnology/Bioprocess Design, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, Sweden
| | - Hildur Æsa Oddsdóttir
- Department of Mathematics, Division of Optimization and Systems Theory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Meeri Mäkinen
- Cell Technology Group, Department of Industrial Biotechnology/Bioprocess Design, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, Sweden
| | - Anders Forsgren
- Department of Mathematics, Division of Optimization and Systems Theory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Véronique Chotteau
- Cell Technology Group, Department of Industrial Biotechnology/Bioprocess Design, School of Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden.,AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, Sweden.,WCPR, Wallenberg Centre for Protein Research, Sweden
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11
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Hagrot E, Oddsdóttir HÆ, Hosta JG, Jacobsen EW, Chotteau V. Retraction notice to "Poly-pathway model, a novel approach to simulate multiple metabolic states by reaction network-based model - Application to amino acid depletion in CHO cell culture". J Biotechnol 2018; 265:127. [PMID: 29274652 DOI: 10.1016/j.jbiotec.2017.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Erika Hagrot
- Cell Technology Group, Department of Industrial Biotechnology/Bioprocess Design, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Hildur Æsa Oddsdóttir
- Department of Mathematics, Division of Optimization and Systems Theory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Joan Gonzalez Hosta
- Cell Technology Group, Department of Industrial Biotechnology/Bioprocess Design, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Elling W Jacobsen
- Department of Automatic Control, School of Electrical Engineering, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Véronique Chotteau
- Cell Technology Group, Department of Industrial Biotechnology/Bioprocess Design, School of Biotechnology, KTH Royal Institute of Technology, Stockholm, Sweden
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12
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Leino M, Astrand C, Hughes-Brittain N, Robb B, McKean R, Chotteau V. Human embryonic stem cell dispersion in electrospun PCL fiber scaffolds by coating with laminin-521 and E-cadherin-Fc. J Biomed Mater Res B Appl Biomater 2017; 106:1226-1236. [PMID: 28577328 DOI: 10.1002/jbm.b.33928] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 04/21/2017] [Accepted: 05/12/2017] [Indexed: 12/14/2022]
Abstract
Advances in human pluripotent cell cultivation and differentiation protocols have led to production of stem cell-derived progenitors as a promising cell source for replacement therapy. Three-dimensional (3-D) culture is a better mimic of the natural niche for stem cells and is widely used for disease modeling. Here, we describe a nonaggregate culture system of human embryonic stem cells inside electrospun polycaprolactone (PCL) fiber scaffolds combined with defined extracellular proteins naturally occurring in the stem cell niche. PCL fiber scaffolds coated with recombinant human laminin-521 readily supported initial stem cell attachment and growth from a single-cell suspension. The combination of recombinant E-cadherin-Fc and laminin-521 further improved cell dispersion rendering a uniform cell population. Finally, we showed that the cells cultured in E-cadherin-Fc- and laminin-521-coated PCL scaffolds could differentiate into all three germ layers. Importantly, we provided a chemically defined 3-D system in which pluripotent stem cells grown and differentiated avoiding the formation of cell aggregates. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 1226-1236, 2018.
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Affiliation(s)
- Mattias Leino
- School of Biotechnology, Cell Technology Group (CETEG), KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Carolina Astrand
- School of Biotechnology, Cell Technology Group (CETEG), KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Nanayaa Hughes-Brittain
- The Electrospinning Company Ltd, R70 Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, OX11 0QX, UK
| | - Brendan Robb
- The Electrospinning Company Ltd, R70 Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, OX11 0QX, UK
| | - Robert McKean
- The Electrospinning Company Ltd, R70 Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, OX11 0QX, UK
| | - Véronique Chotteau
- School of Biotechnology, Cell Technology Group (CETEG), KTH - Royal Institute of Technology, Stockholm, Sweden.,AdBIOPRO, Competence Centre for Advanced Bioproduction by Continuous Bioprocessing, KTH, Stockholm, Sweden
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13
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Ravichandran R, Astrand C, Patra HK, Turner APF, Chotteau V, Phopase J. Intelligent ECM mimetic injectable scaffolds based on functional collagen building blocks for tissue engineering and biomedical applications. RSC Adv 2017. [DOI: 10.1039/c7ra02927f] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A one-pot approach to fabricate in situ-gellable, thermo- and pH-responsive, hydrogels based on covalently crosslinked networks of collagen-I and thermo-responsive polymer.
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Affiliation(s)
- R. Ravichandran
- Division of Molecular Physics
- Department of Physics, Chemistry and Biology (IFM)
- Linköping University
- Linköping
- Sweden
| | - C. Astrand
- School of Biotechnology
- KTH-Royal Institute of Technology
- Stockholm
- Sweden
| | - H. K. Patra
- Biosensors and Bioelectronics Centre
- Department of Physics
- Chemistry and Biology (IFM)
- Linköping University
- Linköping
| | - Anthony P. F. Turner
- Biosensors and Bioelectronics Centre
- Department of Physics
- Chemistry and Biology (IFM)
- Linköping University
- Linköping
| | - V. Chotteau
- School of Biotechnology
- KTH-Royal Institute of Technology
- Stockholm
- Sweden
| | - J. Phopase
- Division of Molecular Physics
- Department of Physics, Chemistry and Biology (IFM)
- Linköping University
- Linköping
- Sweden
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14
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Hagrot E, Oddsdóttir HÆ, Hosta JG, Jacobsen EW, Chotteau V. RETRACTED: Poly-pathway model, a novel approach to simulate multiple metabolic states by reaction network-based model – Application to amino acid depletion in CHO cell culture. J Biotechnol 2016; 228:37-49. [DOI: 10.1016/j.jbiotec.2016.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Revised: 03/03/2016] [Accepted: 03/09/2016] [Indexed: 12/20/2022]
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15
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Oddsdóttir HÆ, Hagrot E, Chotteau V, Forsgren A. Robustness analysis of elementary flux modes generated by column generation. Math Biosci 2015; 273:45-56. [PMID: 26748294 DOI: 10.1016/j.mbs.2015.12.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 12/05/2015] [Accepted: 12/22/2015] [Indexed: 10/22/2022]
Abstract
Elementary flux modes (EFMs) are vectors defined from a metabolic reaction network, giving the connections between substrates and products. EFMs-based metabolic flux analysis (MFA) estimates the flux over each EFM from external flux measurements through least-squares data fitting. The measurements used in the data fitting are subject to errors. A robust optimization problem includes information on errors and gives a way to examine the sensitivity of the solution of the EFMs-based MFA to these errors. In general, formulating a robust optimization problem may make the problem significantly harder. We show that in the case of the EFMs-based MFA, when the errors are only in measurements and bounded by an interval, the robust problem can be stated as a convex quadratic programming (QP) problem. We have previously shown how the data fitting problem may be solved in a column-generation framework. In this paper, we show how column generation may be applied also to the robust problem, thereby avoiding explicit enumeration of EFMs. Furthermore, the option to indicate intervals on metabolites that are not measured is introduced in this column generation framework. The robustness of the data is evaluated in a case-study, which indicates that the solutions of our non-robust problems are in fact near-optimal also when robustness is considered, implying that the errors in measurement do not have a large impact on the optimal solution. Furthermore, we showed that the addition of intervals on unmeasured metabolites resulted in a change in the optimal solution.
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Affiliation(s)
- Hildur Æsa Oddsdóttir
- Department of Mathematics, Optimization and Systems Theory, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden.
| | - Erika Hagrot
- Division of Industrial Biotechnology/Bioprocess Design, KTH Royal Institute of Technology, Albanova Center, Stockholm SE-106 91, Sweden
| | - Véronique Chotteau
- Division of Industrial Biotechnology/Bioprocess Design, KTH Royal Institute of Technology, Albanova Center, Stockholm SE-106 91, Sweden
| | - Anders Forsgren
- Department of Mathematics, Optimization and Systems Theory, KTH Royal Institute of Technology, Stockholm SE-100 44, Sweden
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16
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Zhang Y, Chotteau V. Observation of Chinese Hamster Ovary Cells retained inside the non-woven fiber matrix of the CellTank bioreactor. Data Brief 2015; 5:586-8. [PMID: 26958613 PMCID: PMC4773380 DOI: 10.1016/j.dib.2015.10.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/02/2015] [Accepted: 10/07/2015] [Indexed: 11/15/2022] Open
Abstract
This data article shows how the recombinant Chinese Hamster Ovary (CHO) cells are located in the interstices of the matrix fibers of a CellTank bioreactor after completion of a perfusion culture, supporting the article entitled "Very high cell density perfusion of CHO cells anchored in a non-woven matrix-based bioreactor" by Zhang et al. [1]. It provides a visualization of the cell distribution in the non-woven fiber matrix in a deeper view.
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Affiliation(s)
- Ye Zhang
- School of Biotechnology, Department Industrial Biotechnology/Bioprocess Design, Cell Technology Group (CETEG), Royal Institute of Technology, KTH, SE-10691 Stockholm, Sweden
| | - Véronique Chotteau
- School of Biotechnology, Department Industrial Biotechnology/Bioprocess Design, Cell Technology Group (CETEG), Royal Institute of Technology, KTH, SE-10691 Stockholm, Sweden
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17
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18
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Oddsdóttir HÆ, Hagrot E, Chotteau V, Forsgren A. On dynamically generating relevant elementary flux modes in a metabolic network using optimization. J Math Biol 2014; 71:903-20. [PMID: 25323319 DOI: 10.1007/s00285-014-0844-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2014] [Revised: 10/06/2014] [Indexed: 11/24/2022]
Abstract
Elementary flux modes (EFMs) are pathways through a metabolic reaction network that connect external substrates to products. Using EFMs, a metabolic network can be transformed into its macroscopic counterpart, in which the internal metabolites have been eliminated and only external metabolites remain. In EFMs-based metabolic flux analysis (MFA) experimentally determined external fluxes are used to estimate the flux of each EFM. It is in general prohibitive to enumerate all EFMs for complex networks, since the number of EFMs increases rapidly with network complexity. In this work we present an optimization-based method that dynamically generates a subset of EFMs and solves the EFMs-based MFA problem simultaneously. The obtained subset contains EFMs that contribute to the optimal solution of the EFMs-based MFA problem. The usefulness of our method was examined in a case-study using data from a Chinese hamster ovary cell culture and two networks of varied complexity. It was demonstrated that the EFMs-based MFA problem could be solved at a low computational cost, even for the more complex network. Additionally, only a fraction of the total number of EFMs was needed to compute the optimal solution.
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Affiliation(s)
- Hildur Æsa Oddsdóttir
- Department of Mathematics, Optimization and Systems Theory, KTH Royal Institute of Technology, SE-100 44, Stockholm, Sweden,
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Clincke MF, Mölleryd C, Samani PK, Lindskog E, Fäldt E, Walsh K, Chotteau V. Very high density of Chinese hamster ovary cells in perfusion by alternating tangential flow or tangential flow filtration in WAVE Bioreactor™-part II: Applications for antibody production and cryopreservation. Biotechnol Prog 2013; 29:768-77. [PMID: 23436783 PMCID: PMC3752935 DOI: 10.1002/btpr.1703] [Citation(s) in RCA: 100] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 02/11/2013] [Indexed: 01/20/2023]
Abstract
A high cell density perfusion process of monoclonal antibody (MAb) producing Chinese hamster ovary (CHO) cells was developed in disposable WAVE Bioreactor™ using external hollow fiber (HF) filter as cell separation device. Tangential flow filtration (TFF) and alternating tangential flow (ATF) systems were compared and process applications of high cell density perfusion were studied here: MAb production and cryopreservation. Operations by perfusion using microfiltration (MF) or ultrafiltration (UF) with ATF or TFF and by fed-batch were compared. Cell densities higher than 108 cells/mL were obtained using UF TFF or UF ATF. The cells produced comparable amounts of MAb in perfusion by ATF or TFF, MF or UF. MAbs were partially retained by the MF using ATF or TFF but more severely using TFF. Consequently, MAbs were lost when cell broth was discarded from the bioreactor in the daily bleeds. The MAb cell-specific productivity was comparable at cell densities up to 1.3 × 108 cells/mL in perfusion and was comparable or lower in fed-batch. After 12 days, six times more MAbs were harvested using perfusion by ATF or TFF with MF or UF, compared to fed-batch and 28× more in a 1-month perfusion at 108 cells/mL density. Pumping at a recirculation rate up to 2.75 L/min did not damage the cells with the present TFF settings with HF short circuited. Cell cryopreservation at 0.5 × 108 and 108 cells/mL was performed using cells from a perfusion run at 108 cells/mL density. Cell resuscitation was very successful, showing that this system was a reliable process for cell bank manufacturing. © 2013 American Institute of Chemical Engineers Biotechnol. Prog., 29:768–777, 2013
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Affiliation(s)
- Marie-Françoise Clincke
- School of Biotechnology, Cell Technology Group, KTH (Royal Institute of Technology), Stockholm, SE-10691, Sweden
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Clincke MF, Mölleryd C, Zhang Y, Lindskog E, Walsh K, Chotteau V. Very high density of CHO cells in perfusion by ATF or TFF in WAVE bioreactor™. Part I. Effect of the cell density on the process. Biotechnol Prog 2013; 29:754-67. [PMID: 23436789 PMCID: PMC3752962 DOI: 10.1002/btpr.1704] [Citation(s) in RCA: 155] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Revised: 02/11/2013] [Indexed: 11/20/2022]
Abstract
High cell density perfusion process of antibody producing CHO cells was developed in disposable WAVE Bioreactor™ using external hollow fiber filter as cell separation device. Both "classical" tangential flow filtration (TFF) and alternating tangential flow system (ATF) equipment were used and compared. Consistency of both TFF- and ATF-based cultures was shown at 20-35 × 10(6) cells/mL density stabilized by cell bleeds. To minimize the nutrients deprivation and by-product accumulation, a perfusion rate correlated to the cell density was applied. The cells were maintained by cell bleeds at density 0.9-1.3 × 10(8) cells/mL in growing state and at high viability for more than 2 weeks. Finally, with the present settings, maximal cell densities of 2.14 × 10(8) cells/mL, achieved for the first time in a wave-induced bioreactor, and 1.32 × 10(8) cells/mL were reached using TFF and ATF systems, respectively. Using TFF, the cell density was limited by the membrane capacity for the encountered high viscosity and by the pCO2 level. Using ATF, the cell density was limited by the vacuum capacity failing to pull the highly viscous fluid. Thus, the TFF system allowed reaching higher cell densities. The TFF inlet pressure was highly correlated to the viscosity leading to the development of a model of this pressure, which is a useful tool for hollow fiber design of TFF and ATF. At very high cell density, the viscosity introduced physical limitations. This led us to recommend cell densities under 1.46 × 10(8) cell/mL based on the analysis of the theoretical distance between the cells for the present cell line.
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Affiliation(s)
- Marie-Françoise Clincke
- School of Biotechnology, Cell Technology Group, KTH (Royal Institute of Technology), SE-106 91, Stockholm, Sweden
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Clincke MF, Mölleryd C, Zhang Y, Lindskog E, Walsh K, Chotteau V. Study of a recombinant CHO cell line producing a monoclonal antibody by ATF or TFF external filter perfusion in a WAVE Bioreactor™. BMC Proc 2011; 5 Suppl 8:P105. [PMID: 22373105 PMCID: PMC3285023 DOI: 10.1186/1753-6561-5-s8-p105] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Affiliation(s)
- Marie-Françoise Clincke
- School of Biotechnology, Animal Cell Technology Group, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden
| | - Carin Mölleryd
- School of Biotechnology, Animal Cell Technology Group, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden
| | - Ye Zhang
- School of Biotechnology, Animal Cell Technology Group, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden
| | - Eva Lindskog
- GE Healthcare Bio-Sciences AB, Björkgatan 30, SE-75184 Uppsala, Sweden
| | - Kieron Walsh
- GE Healthcare Bio-Sciences Corp, 14 Walk Up Drive, Westborough MA, 01581, USA
| | - Véronique Chotteau
- School of Biotechnology, Animal Cell Technology Group, Royal Institute of Technology (KTH), SE-106 91 Stockholm, Sweden
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