1
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Destro F, Wu W, Srinivasan P, Joseph J, Bal V, Neufeld C, Wolfrum JM, Manalis SR, Sinskey AJ, Springs SL, Barone PW, Braatz RD. The state of technological advancement to address challenges in the manufacture of rAAV gene therapies. Biotechnol Adv 2024; 76:108433. [PMID: 39168354 DOI: 10.1016/j.biotechadv.2024.108433] [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: 03/13/2024] [Revised: 07/04/2024] [Accepted: 08/17/2024] [Indexed: 08/23/2024]
Abstract
Current processes for the production of recombinant adeno-associated virus (rAAV) are inadequate to meet the surging demand for rAAV-based gene therapies. This article reviews recent advances that hold the potential to address current limitations in rAAV manufacturing. A multidisciplinary perspective on technological progress in rAAV production is presented, underscoring the necessity to move beyond incremental refinements and adopt a holistic strategy to address existing challenges. Since several recent reviews have thoroughly covered advancements in upstream technology, this article provides only a concise overview of these developments before moving to pivotal areas of rAAV manufacturing not well covered in other reviews, including analytical technologies for rapid and high-throughput measurement of rAAV quality attributes, mathematical modeling for platform and process optimization, and downstream approaches to maximize efficiency and rAAV yield. Novel technologies that have the potential to address the current gaps in rAAV manufacturing are highlighted. Implementation challenges and future research directions are critically discussed.
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Affiliation(s)
- Francesco Destro
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Weida Wu
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Prasanna Srinivasan
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - John Joseph
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Vivekananda Bal
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Caleb Neufeld
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Jacqueline M Wolfrum
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Scott R Manalis
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Anthony J Sinskey
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Stacy L Springs
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Paul W Barone
- Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Richard D Braatz
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA; Center for Biomedical Innovation, Massachusetts Institute of Technology, Cambridge, MA, USA.
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2
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González-Hernández Y, Perré P. Building blocks needed for mechanistic modeling of bioprocesses: A critical review based on protein production by CHO cells. Metab Eng Commun 2024; 18:e00232. [PMID: 38501051 PMCID: PMC10945193 DOI: 10.1016/j.mec.2024.e00232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 02/12/2024] [Accepted: 02/23/2024] [Indexed: 03/20/2024] Open
Abstract
This paper reviews the key building blocks needed to develop a mechanistic model for use as an operational production tool. The Chinese Hamster Ovary (CHO) cell, one of the most widely used hosts for antibody production in the pharmaceutical industry, is considered as a case study. CHO cell metabolism is characterized by two main phases, exponential growth followed by a stationary phase with strong protein production. This process presents an appropriate degree of complexity to outline the modeling strategy. The paper is organized into four main steps: (1) CHO systems and data collection; (2) metabolic analysis; (3) formulation of the mathematical model; and finally, (4) numerical solution, calibration, and validation. The overall approach can build a predictive model of target variables. According to the literature, one of the main current modeling challenges lies in understanding and predicting the spontaneous metabolic shift. Possible candidates for the trigger of the metabolic shift include the concentration of lactate and carbon dioxide. In our opinion, ammonium, which is also an inhibiting product, should be further investigated. Finally, the expected progress in the emerging field of hybrid modeling, which combines the best of mechanistic modeling and machine learning, is presented as a fascinating breakthrough. Note that the modeling strategy discussed here is a general framework that can be applied to any bioprocess.
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Affiliation(s)
- Yusmel González-Hernández
- Université Paris-Saclay, CentraleSupélec, Laboratoire de Génie des Procédés et Matériaux, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), 3 Rue des Rouges Terres, 51110, Pomacle, France
| | - Patrick Perré
- Université Paris-Saclay, CentraleSupélec, Laboratoire de Génie des Procédés et Matériaux, Centre Européen de Biotechnologie et de Bioéconomie (CEBB), 3 Rue des Rouges Terres, 51110, Pomacle, France
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3
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Bokelmann C, Ehsani A, Schaub J, Stiefel F. Deciphering Metabolic Pathways in High-Seeding-Density Fed-Batch Processes for Monoclonal Antibody Production: A Computational Modeling Perspective. Bioengineering (Basel) 2024; 11:331. [PMID: 38671753 PMCID: PMC11048072 DOI: 10.3390/bioengineering11040331] [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: 02/23/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Due to their high specificity, monoclonal antibodies (mAbs) have garnered significant attention in recent decades, with advancements in production processes, such as high-seeding-density (HSD) strategies, contributing to improved titers. This study provides a thorough investigation of high seeding processes for mAb production in Chinese hamster ovary (CHO) cells, focused on identifying significant metabolites and their interactions. We observed high glycolytic fluxes, the depletion of asparagine, and a shift from lactate production to consumption. Using a metabolic network and flux analysis, we compared the standard fed-batch (STD FB) with HSD cultivations, exploring supplementary lactate and cysteine, and a bolus medium enriched with amino acids. We reconstructed a metabolic network and kinetic models based on the observations and explored the effects of different feeding strategies on CHO cell metabolism. Our findings revealed that the addition of a bolus medium (BM) containing asparagine improved final titers. However, increasing the asparagine concentration in the feed further prevented the lactate shift, indicating a need to find a balance between increased asparagine to counteract limitations and lower asparagine to preserve the shift in lactate metabolism.
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Affiliation(s)
- Carolin Bokelmann
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Alireza Ehsani
- Boehringer Ingelheim Pharma GmbH & Co.KG, Launch & Innovation, 88400 Biberach an der Riß, Germany
| | - Jochen Schaub
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Biologicals Germany, 88400 Biberach an der Riß, Germany
| | - Fabian Stiefel
- Boehringer Ingelheim Pharma GmbH & Co.KG, Development Sciences Germany, 88400 Biberach an der Riß, Germany
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4
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Fu Q, Polanco A, Lee YS, Yoon S. Critical challenges and advances in recombinant adeno-associated virus (rAAV) biomanufacturing. Biotechnol Bioeng 2023; 120:2601-2621. [PMID: 37126355 DOI: 10.1002/bit.28412] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 03/27/2023] [Accepted: 04/19/2023] [Indexed: 05/02/2023]
Abstract
Gene therapy is a promising therapeutic approach for genetic and acquired diseases nowadays. Among DNA delivery vectors, recombinant adeno-associated virus (rAAV) is one of the most effective and safest vectors used in commercial drugs and clinical trials. However, the current yield of rAAV biomanufacturing lags behind the necessary dosages for clinical and commercial use, which embodies a concentrated reflection of low productivity of rAAV from host cells, difficult scalability of the rAAV-producing bioprocess, and high levels of impurities materialized during production. Those issues directly impact the price of gene therapy medicine in the market, limiting most patients' access to gene therapy. In this context, the current practices and several critical challenges associated with rAAV gene therapy bioprocesses are reviewed, followed by a discussion of recent advances in rAAV-mediated gene therapy and other therapeutic biological fields that could improve biomanufacturing if these advances are integrated effectively into the current systems. This review aims to provide the current state-of-the-art technology and perspectives to enhance the productivity of rAAV while reducing impurities during production of rAAV.
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Affiliation(s)
- Qiang Fu
- Department of Biomedical Engineering and Biotechnology, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Ashli Polanco
- Department of Chemical Engineering, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Yong Suk Lee
- Department of Pharmaceutical Sciences, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
| | - Seongkyu Yoon
- Department of Chemical Engineering, The University of Massachusetts Lowell, Lowell, Massachusetts, USA
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5
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Monteiro M, Fadda S, Kontoravdi C. Towards advanced bioprocess optimization: A multiscale modelling approach. Comput Struct Biotechnol J 2023; 21:3639-3655. [PMID: 37520284 PMCID: PMC10371800 DOI: 10.1016/j.csbj.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 06/30/2023] [Accepted: 07/01/2023] [Indexed: 08/01/2023] Open
Abstract
Mammalian cells produce up to 80 % of the commercially available therapeutic proteins, with Chinese Hamster Ovary (CHO) cells being the primary production host. Manufacturing involves a train of reactors, the last of which is typically run in fed-batch mode, where cells grow and produce the required protein. The feeding strategy is decided a priori, from either past operations or the design of experiments and rarely considers the current state of the process. This work proposes a Model Predictive Control (MPC) formulation based on a hybrid kinetic-stoichiometric reactor model to provide optimal feeding policies in real-time, which is agnostic to the culture, hence transferable across CHO cell culture systems. The benefits of the proposed controller formulation are demonstrated through a comparison between an open-loop simulation and closed-loop optimization, using a digital twin as an emulator of the process.
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6
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González-Arrué N, Inostroza I, Conejeros R, Rivas-Astroza M. Phenotype-specific estimation of metabolic fluxes using gene expression data. iScience 2023; 26:106201. [PMID: 36915687 PMCID: PMC10006673 DOI: 10.1016/j.isci.2023.106201] [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: 09/22/2022] [Revised: 11/30/2022] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
A cell's genome influences its metabolism via the expression of enzyme-related genes, but transcriptome and fluxome are not perfectly correlated as post-transcriptional mechanisms also regulate reaction's kinetics. Here, we addressed the question: given a transcriptome, how unobserved mechanisms of reaction kinetics should be systematically accounted for when inferring the fluxome? To infer the most likely and least biased fluxome, we present Pheflux, a constraint-based model maximizing Shannon's entropy of fluxes per mRNA. Benchmarked against 13C fluxes of yeast and bacteria, Pheflux accurately estimates the carbon core metabolism. We applied Pheflux to thousands of normal and tumor cell transcriptomes obtained from The Cancer Genome Atlas. Pheflux showed statistically significantly higher glucose yields on lactate in breast, kidney, and bronchus-lung tumoral cells than their normal counterparts. Results are consistent with the Warburg effect, a hallmark of cancer metabolism, suggesting that Pheflux can be efficiently used to study the metabolism of eukaryotic cells.
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Affiliation(s)
- Nicolás González-Arrué
- Universidad Tecnológica Metropolitana, Departamento de Biotecnología, Ñuñoa, Santiago 7800003, Chile
| | - Isidora Inostroza
- Universidad Tecnológica Metropolitana, Departamento de Biotecnología, Ñuñoa, Santiago 7800003, Chile
| | - Raúl Conejeros
- Pontificia Universidad Católica de Valparaíso, Escuela de Ingeniería Bioquímica, Valparaíso, 2362803, Chile
| | - Marcelo Rivas-Astroza
- Universidad Tecnológica Metropolitana, Departamento de Biotecnología, Ñuñoa, Santiago 7800003, Chile
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7
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Coulet M, Kepp O, Kroemer G, Basmaciogullari S. Metabolic Profiling of CHO Cells during the Production of Biotherapeutics. Cells 2022; 11:cells11121929. [PMID: 35741058 PMCID: PMC9221972 DOI: 10.3390/cells11121929] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/02/2022] [Accepted: 06/13/2022] [Indexed: 01/08/2023] Open
Abstract
As indicated by an ever-increasing number of FDA approvals, biotherapeutics constitute powerful tools for the treatment of various diseases, with monoclonal antibodies (mAbs) accounting for more than 50% of newly approved drugs between 2014 and 2018 (Walsh, 2018). The pharmaceutical industry has made great progress in developing reliable and efficient bioproduction processes to meet the demand for recombinant mAbs. Mammalian cell lines are preferred for the production of functional, complex recombinant proteins including mAbs, with Chinese hamster ovary (CHO) cells being used in most instances. Despite significant advances in cell growth control for biologics manufacturing, cellular responses to environmental changes need to be understood in order to further improve productivity. Metabolomics offers a promising approach for developing suitable strategies to unlock the full potential of cellular production. This review summarizes key findings on catabolism and anabolism for each phase of cell growth (exponential growth, the stationary phase and decline) with a focus on the principal metabolic pathways (glycolysis, the pentose phosphate pathway and the tricarboxylic acid cycle) and the families of biomolecules that impact these circuities (nucleotides, amino acids, lipids and energy-rich metabolites).
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Affiliation(s)
- Mathilde Coulet
- Sanofi R&D, 94400 Vitry-sur-Seine, France;
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France;
| | - Oliver Kepp
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France;
- Institut Universitaire de France, Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, 75006 Paris, France
| | - Guido Kroemer
- Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Center, 94800 Villejuif, France;
- Institut Universitaire de France, Centre de Recherche des Cordeliers, Equipe Labellisée par la Ligue Contre le Cancer, Université de Paris Cité, Sorbonne Université, Inserm U1138, 75006 Paris, France
- Department of Biology, Institut du Cancer Paris CARPEM, Hôpital Européen Georges Pompidou, AP-HP, 75015 Paris, France
- Correspondence: (G.K.); (S.B.)
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8
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Joiner J, Huang Z, McHugh K, Stebbins M, Aron K, Borys M, Khetan A. Process modeling of recombinant adeno-associated virus production in HEK293 cells. Curr Opin Chem Eng 2022. [DOI: 10.1016/j.coche.2022.100823] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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9
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Park JU, Han HJ, Baik JY. Energy metabolism in Chinese hamster ovary (CHO) cells: Productivity and beyond. KOREAN J CHEM ENG 2022. [DOI: 10.1007/s11814-022-1062-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Combe M, Sokolenko S. Quantifying the impact of cell culture media on CHO cell growth and protein production. Biotechnol Adv 2021; 50:107761. [PMID: 33945850 DOI: 10.1016/j.biotechadv.2021.107761] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 04/22/2021] [Accepted: 04/24/2021] [Indexed: 10/21/2022]
Abstract
In recombinant protein production, cell culture media development and optimization is typically seen as a useful strategy to increase titer and cell density, reduce by-products, as well as improve product quality (with cell density and titer often serving as the primary reported outcome of media studies). However, despite the large number of media optimization studies, there have been few attempts to comprehensively assess the overall effectiveness of media additives. The aim of this review is therefore both to document published media optimization studies over the last twenty years (in the context of Chinese hamster ovary cell recombinant production) and quantitatively estimate the impact of this media optimization on cell culture performance. In considering 78 studies, we have identified 238 unique media components that have been supplemented over the last 20 years. Among these additives, trace elements stood out as having a positive impact on cell density while nucleotides show potential for increasing titer, with commercial supplements benefiting both. However, we also identified that the impact of specific additives is far more variable than often perceived. With relatively few media studies considering multiple cell lines or multiple basal media, teasing out consistent and general trends becomes a considerable challenge. By extracting cell density and titer values from all of the reviewed studies, we were able to build a mixed-effect model capable of estimating the relative impact of additives, cell line, product type, basal medium, cultivation method (flask or reactor), and feeding strategy (batch or fed-batch). Overall, additives only accounted for 3% of the variation in cell density and 1% of the variation in titer. Similarly, the impact of basal media was also relatively modest, at 10% for cell density and 0% for titer. Cell line, product type, and feeding strategy were all found to have more impact. These results emphasize the need for media studies to consider more factors to ensure that reported observations can be generalized and further developed.
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Affiliation(s)
- Michelle Combe
- Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington St., PO Box 15000, Halifax, NS B3H 4R2, Canada
| | - Stanislav Sokolenko
- Department of Process Engineering and Applied Science, Dalhousie University, 1360 Barrington St., PO Box 15000, Halifax, NS B3H 4R2, Canada.
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11
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Schinn SM, Morrison C, Wei W, Zhang L, Lewis NE. Systematic evaluation of parameters for genome-scale metabolic models of cultured mammalian cells. Metab Eng 2021; 66:21-30. [PMID: 33771719 DOI: 10.1016/j.ymben.2021.03.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 11/25/2020] [Accepted: 03/17/2021] [Indexed: 10/21/2022]
Abstract
Genome-scale metabolic models describe cellular metabolism with mechanistic detail. Given their high complexity, such models need to be parameterized correctly to yield accurate predictions and avoid overfitting. Effective parameterization has been well-studied for microbial models, but it remains unclear for higher eukaryotes, including mammalian cells. To address this, we enumerated model parameters that describe key features of cultured mammalian cells - including cellular composition, bioprocess performance metrics, mammalian-specific pathways, and biological assumptions behind model formulation approaches. We tested these parameters by building thousands of metabolic models and evaluating their ability to predict the growth rates of a panel of phenotypically diverse Chinese Hamster Ovary cell clones. We found the following considerations to be most critical for accurate parameterization: (1) cells limit metabolic activity to maintain homeostasis, (2) cell morphology and viability change dynamically during a growth curve, and (3) cellular biomass has a particular macromolecular composition. Depending on parameterization, models predicted different metabolic phenotypes, including contrasting mechanisms of nutrient utilization and energy generation, leading to varying accuracies of growth rate predictions. Notably, accurate parameter values broadly agreed with experimental measurements. These insights will guide future investigations of mammalian metabolism.
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Affiliation(s)
- Song-Min Schinn
- Department of Pediatrics, University of California, San Diego, USA
| | - Carly Morrison
- Pfizer, Biotherapeutics Pharmaceutical Sciences, Andover, MA, USA
| | - Wei Wei
- Pfizer, Biotherapeutics Pharmaceutical Sciences, Andover, MA, USA
| | - Lin Zhang
- Pfizer, Biotherapeutics Pharmaceutical Sciences, Andover, MA, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California, San Diego, USA; Department of Bioengineering, University of California, San Diego, USA; Novo Nordisk Foundation Center for Biosustainability at UC, San Diego, USA.
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12
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Mack SG, Sriram G. NetFlow: A tool for isolating carbon flows in genome-scale metabolic networks. Metab Eng Commun 2021; 12:e00154. [PMID: 33489751 PMCID: PMC7807149 DOI: 10.1016/j.mec.2020.e00154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/11/2020] [Accepted: 11/21/2020] [Indexed: 01/04/2023] Open
Abstract
Genome-scale stoichiometric models (GSMs) have been widely utilized to predict and understand cellular metabolism. GSMs and the flux predictions resulting from them have proven indispensable to fields ranging from metabolic engineering to human disease. Nonetheless, it is challenging to parse these flux predictions due to the inherent size and complexity of the GSMs. Several previous approaches have reduced this complexity by identifying key pathways contained within the genome-scale flux predictions. However, a reduction method that overlays carbon atom transitions on stoichiometry and flux predictions is lacking. To fill this gap, we developed NetFlow, an algorithm that leverages genome-scale carbon mapping to extract and quantitatively distinguish biologically relevant metabolic pathways from a given genome-scale flux prediction. NetFlow extends prior approaches by utilizing both full carbon mapping and context-specific flux predictions. Thus, NetFlow is uniquely able to quantitatively distinguish between biologically relevant pathways of carbon flow within the given flux map. NetFlow simulates 13C isotope labeling experiments to calculate the extent of carbon exchange, or carbon yield, between every metabolite in the given GSM. Based on the carbon yield, the carbon flow to or from any metabolite or between any pair of metabolites of interest can be isolated and readily visualized. The resulting pathways are much easier to interpret, which enables an in-depth mechanistic understanding of the metabolic phenotype of interest. Here, we first demonstrate NetFlow with a simple network. We then depict the utility of NetFlow on a model of central carbon metabolism in E. coli. Specifically, we isolated the production pathway for succinate synthesis in this model and the metabolic mechanism driving the predicted increase in succinate yield in a double knockout of E. coli. Finally, we describe the application of NetFlow to a GSM of lycopene-producing E. coli, which enabled the rapid identification of the mechanisms behind the measured increases in lycopene production following single, double, and triple knockouts.
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Affiliation(s)
- Sean G Mack
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
| | - Ganesh Sriram
- Department of Chemical and Biomolecular Engineering, University of Maryland, College Park, MD, USA
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13
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Vijayakumar S, Rahman PK, Angione C. A Hybrid Flux Balance Analysis and Machine Learning Pipeline Elucidates Metabolic Adaptation in Cyanobacteria. iScience 2020; 23:101818. [PMID: 33354660 PMCID: PMC7744713 DOI: 10.1016/j.isci.2020.101818] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/23/2020] [Accepted: 11/13/2020] [Indexed: 01/20/2023] Open
Abstract
Machine learning has recently emerged as a promising tool for inferring multi-omic relationships in biological systems. At the same time, genome-scale metabolic models (GSMMs) can be integrated with such multi-omic data to refine phenotypic predictions. In this work, we use a multi-omic machine learning pipeline to analyze a GSMM of Synechococcus sp. PCC 7002, a cyanobacterium with large potential to produce renewable biofuels. We use regularized flux balance analysis to observe flux response between conditions across photosynthesis and energy metabolism. We then incorporate principal-component analysis, k-means clustering, and LASSO regularization to reduce dimensionality and extract key cross-omic features. Our results suggest that combining metabolic modeling with machine learning elucidates mechanisms used by cyanobacteria to cope with fluctuations in light intensity and salinity that cannot be detected using transcriptomics alone. Furthermore, GSMMs introduce critical mechanistic details that improve the performance of omic-based machine learning methods.
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Affiliation(s)
- Supreeta Vijayakumar
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
| | - Pattanathu K.S.M. Rahman
- Centre for Enzyme Innovation, Institute of Biological and Biomedical Sciences, School of Biological Sciences, University of Portsmouth, Portsmouth, Hampshire PO1 2UP, UK
- Tara Biologics, Woking, Surrey GU21 6BP, UK
| | - Claudio Angione
- Department of Computer Science and Information Systems, Teesside University, Middlesbrough, North Yorkshire TS1 3BX, UK
- Centre for Digital Innovation, Teesside University, Middlesbrough TS1 3BX, UK
- Healthcare Innovation Centre, Teesside University, Middlesbrough TS1 3BX, UK
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14
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O’Brien SA, Hu WS. Cell culture bioprocessing - the road taken and the path forward. Curr Opin Chem Eng 2020; 30:100663. [PMID: 33391982 PMCID: PMC7773285 DOI: 10.1016/j.coche.2020.100663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Cell culture processes are used to produce the vast majority of protein therapeutics, valued at over US$180 billion per annum worldwide. For more than a decade now, these processes have become highly productive. To further enhance capital efficiency, there has been an increase in the adoption of disposable apparatus and continuous processing, as well as a greater exploration of in-line sensing, various -omic tools, and cell engineering to enhance process controllability and product quality consistency. These feats in cell culture processing for protein biologics will help accelerate the bioprocess advancements for virus and cell therapy applications.
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Affiliation(s)
- Sofie A. O’Brien
- Department of Biomedical Engineering and Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455-0132 USA
| | - Wei-Shou Hu
- Department of Biomedical Engineering and Department of Chemical Engineering and Materials Science, University of Minnesota, Minneapolis, MN 55455-0132 USA
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15
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Zhang L, Schwarz H, Wang M, Castan A, Hjalmarsson H, Chotteau V. Control of IgG glycosylation in CHO cell perfusion cultures by GReBA mathematical model supported by a novel targeted feed, TAFE. Metab Eng 2020; 65:135-145. [PMID: 33161144 DOI: 10.1016/j.ymben.2020.11.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/15/2020] [Accepted: 11/02/2020] [Indexed: 10/23/2022]
Abstract
The N-linked glycosylation pattern is an important quality attribute of therapeutic glycoproteins. It has been reported by our group and by others that different carbon sources, such as glucose, mannose and galactose, can differently impact the glycosylation profile of glycoproteins in mammalian cell culture. Acting on the sugar feeding is thus an attractive strategy to tune the glycan pattern. However, in case of feeding of more than one carbon source simultaneously, the cells give priority to the one with the highest uptake rate, which limits the usage of this tuning, e.g. the cells favor consuming glucose in comparison to galactose. We present here a new feeding strategy (named 'TAFE' for targeted feeding) for perfusion culture to adjust the concentrations of fed sugars influencing the glycosylation. The strategy consists in setting the sugar feeding such that the cells are forced to consume these substrates at a target cell specific consumption rate decided by the operator and taking into account the cell specific perfusion rate (CSPR). This strategy is applied in perfusion cultures of Chinese hamster ovary (CHO) cells, illustrated by ten different regimes of sugar feeding, including glucose, galactose and mannose. Applying the TAFE strategy, different glycan profiles were obtained using the different feeding regimes. Furthermore, we successfully forced the cells to consume higher proportions of non-glucose sugars, which have lower transport rates than glucose in presence of this latter, in a controlled way. In previous work, a mathematical model named Glycan Residues Balance Analysis (GReBA) was developed to model the glycosylation profile based on the fed carbon sources. The present data were applied to the GReBA to design a feeding regime targeting a given glycosylation profile. The ability of the model to achieve this objective was confirmed by a multi-round of leave-one-out cross-validation (LOOCV), leading to the conclusion that the GReBA model can be used to design the feeding regime of a perfusion cell culture to obtain a desired glycosylation profile.
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Affiliation(s)
- Liang Zhang
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Sweden; AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, KTH, Sweden
| | - Hubert Schwarz
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Sweden; AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, KTH, Sweden
| | - Mingliang Wang
- AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, KTH, Sweden; Division of Decision and Control System, School of Electrical Engineering and Computer Science, KTH-Royal Institute of Technology, Sweden
| | | | - Håkan Hjalmarsson
- AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, KTH, Sweden; Division of Decision and Control System, School of Electrical Engineering and Computer Science, KTH-Royal Institute of Technology, Sweden
| | - Veronique Chotteau
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH-Royal Institute of Technology, Sweden; AdBIOPRO, VINNOVA Competence Centre for Advanced Bioproduction by Continuous Processing, KTH, Sweden.
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16
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Hoang Anh N, Min JE, Kim SJ, Phuoc Long N. Biotherapeutic Products, Cellular Factories, and Multiomics Integration in Metabolic Engineering. ACTA ACUST UNITED AC 2020; 24:621-633. [DOI: 10.1089/omi.2020.0112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nguyen Hoang Anh
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Jung Eun Min
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Sun Jo Kim
- College of Pharmacy, Seoul National University, Seoul, South Korea
| | - Nguyen Phuoc Long
- Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, South Korea
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17
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Huang Z, Xu J, Yongky A, Morris CS, Polanco AL, Reily M, Borys MC, Li ZJ, Yoon S. CHO cell productivity improvement by genome-scale modeling and pathway analysis: Application to feed supplements. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107638] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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18
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Identifying metabolic features and engineering targets for productivity improvement in CHO cells by integrated transcriptomics and genome-scale metabolic model. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107624] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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19
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Yeo HC, Hong J, Lakshmanan M, Lee DY. Enzyme capacity-based genome scale modelling of CHO cells. Metab Eng 2020; 60:138-147. [PMID: 32330653 DOI: 10.1016/j.ymben.2020.04.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/21/2020] [Accepted: 04/14/2020] [Indexed: 10/24/2022]
Abstract
Chinese hamster ovary (CHO) cells are most prevalently used for producing recombinant therapeutics in biomanufacturing. Recently, more rational and systems approaches have been increasingly exploited to identify key metabolic bottlenecks and engineering targets for cell line engineering and process development based on the CHO genome-scale metabolic model which mechanistically characterizes cell culture behaviours. However, it is still challenging to quantify plausible intracellular fluxes and discern metabolic pathway usages considering various clonal traits and bioprocessing conditions. Thus, we newly incorporated enzyme kinetic information into the updated CHO genome-scale model (iCHO2291) and added enzyme capacity constraints within the flux balance analysis framework (ecFBA) to significantly reduce the flux variability in biologically meaningful manner, as such improving the accuracy of intracellular flux prediction. Interestingly, ecFBA could capture the overflow metabolism under the glucose excess condition where the usage of oxidative phosphorylation is limited by the enzyme capacity. In addition, its applicability was successfully demonstrated via a case study where the clone- and media-specific lactate metabolism was deciphered, suggesting that the lactate-pyruvate cycling could be beneficial for CHO cells to efficiently utilize the mitochondrial redox capacity. In summary, iCHO2296 with ecFBA can be used to confidently elucidate cell cultures and effectively identify key engineering targets, thus guiding bioprocess optimization and cell engineering efforts as a part of digital twin model for advanced biomanufacturing in future.
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Affiliation(s)
- Hock Chuan Yeo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, 138668, Singapore; Department of Chemical and Biomolecular Engineering, National University of Singapore, 4 Engineering Drive 4, 117585, Singapore
| | - Jongkwang Hong
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, 138668, Singapore
| | - Meiyappan Lakshmanan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, 138668, Singapore.
| | - Dong-Yup Lee
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (A*STAR), 20 Biopolis Way, #06-01, 138668, Singapore; School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do, 16419, Republic of Korea.
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20
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Integration of Time-Series Transcriptomic Data with Genome-Scale CHO Metabolic Models for mAb Engineering. Processes (Basel) 2020. [DOI: 10.3390/pr8030331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Chinese hamster ovary (CHO) cells are the most commonly used cell lines in biopharmaceutical manufacturing. Genome-scale metabolic models have become a valuable tool to study cellular metabolism. Despite the presence of reference global genome-scale CHO model, context-specific metabolic models may still be required for specific cell lines (for example, CHO-K1, CHO-S, and CHO-DG44), and for specific process conditions. Many integration algorithms have been available to reconstruct specific genome-scale models. These methods are mainly based on integrating omics data (i.e., transcriptomics, proteomics, and metabolomics) into reference genome-scale models. In the present study, we aimed to investigate the impact of time points of transcriptomics integration on the genome-scale CHO model by assessing the prediction of growth rates with each reconstructed model. We also evaluated the feasibility of applying extracted models to different cell lines (generated from the same parental cell line). Our findings illustrate that gene expression at various stages of culture slightly impacts the reconstructed models. However, the prediction capability is robust enough on cell growth prediction not only across different growth phases but also in expansion to other cell lines.
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21
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Tang P, Xu J, Louey A, Tan Z, Yongky A, Liang S, Li ZJ, Weng Y, Liu S. Kinetic modeling of Chinese hamster ovary cell culture: factors and principles. Crit Rev Biotechnol 2020; 40:265-281. [DOI: 10.1080/07388551.2019.1711015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Peifeng Tang
- Department of Paper and Bioprocess Engineering, SUNY-ESF, Syracuse, NY, USA
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Jianlin Xu
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Alastair Louey
- Elpiscience Biopharma, Cayman Islands George Town, Grand Cayman, UK
| | - Zhijun Tan
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Andrew Yongky
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Shaoyan Liang
- Department of Molecular Biophysics & Biochemistry, Yale University, New Haven, CT, USA
| | - Zheng Jian Li
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Yongyan Weng
- Department of Civil Engineering, University of Nottingham, Nottingham, UK
| | - Shijie Liu
- Department of Paper and Bioprocess Engineering, SUNY-ESF, Syracuse, NY, USA
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22
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Systems biology approach in the formulation of chemically defined media for recombinant protein overproduction. Appl Microbiol Biotechnol 2019; 103:8315-8326. [PMID: 31418052 DOI: 10.1007/s00253-019-10048-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/16/2019] [Accepted: 07/23/2019] [Indexed: 02/06/2023]
Abstract
The cell culture medium is an intricate mixture of components which has a tremendous effect on cell growth and recombinant protein production. Regular cell culture medium includes various components, and the decision about which component should be included in the formulation and its optimum amount is an underlying issue in biotechnology industries. Applying conventional techniques to design an optimal medium for the production of a recombinant protein requires meticulous and immense research. Moreover, since the medium formulation for the production of one protein could not be the best choice for another protein, hence, the most suitable media should be determined for each recombinant cell line. Accordingly, medium formulation becomes a laborious, time-consuming, and costly process in biomanufacturing of recombinant protein, and finding alternative strategies for medium development seems to be crucial. In silico modeling is an attractive concept to be adapted for medium formulation due to its high potential to supersede laboratory examinations. By emerging the high-throughput datasets, scientists can disclose the knowledge about the effect of medium components on cell growth and metabolism, and via applying this information through systems biology approach, medium formulation optimization could be accomplished in silico with no need of significant amount of experimentation. This review demonstrates some of the applications of systems biology as a powerful tool for medium development and illustrates the effect of medium optimization with system-level analysis on the production of recombinant proteins in different host cells.
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23
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24
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Grilo AL, Mantalaris A. Apoptosis: A mammalian cell bioprocessing perspective. Biotechnol Adv 2019; 37:459-475. [PMID: 30797096 DOI: 10.1016/j.biotechadv.2019.02.012] [Citation(s) in RCA: 108] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 02/08/2019] [Accepted: 02/19/2019] [Indexed: 02/07/2023]
Abstract
Apoptosis is a form of programmed and controlled cell death that accounts for the majority of cellular death in bioprocesses. Cell death affects culture longevity and product quality; it is instigated by several stresses experienced by the cells within a bioreactor. Understanding the factors that cause apoptosis as well as developing strategies that can protect cells is crucial for robust bioprocess development. This review aims to a) address apoptosis from a bioprocess perspective; b) describe the significant apoptotic mechanisms linking them to the most relevant stresses encountered in bioreactors; c) discuss the design of operating conditions in order to avoid cell death; d) focus on industrially relevant cell lines; and e) present anti-apoptosis strategies including cell engineering and model-based optimization of bioprocesses. In addition, the importance of apoptosis in quality-by-design bioprocess development from clone screening to production scale are highlighted.
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Affiliation(s)
- Antonio L Grilo
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom.
| | - Athanasios Mantalaris
- Biological Systems Engineering Laboratory, Centre for Process Systems Engineering, Department of Chemical Engineering, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom.
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25
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Prediction of N-linked Glycoform Profiles of Monoclonal Antibody with Extracellular Metabolites and Two-Step Intracellular Models. Processes (Basel) 2019. [DOI: 10.3390/pr7040227] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Monoclonal antibodies (mAbs) are commonly glycosylated and show varying levels of galactose attachment. A set of experiments in our work showed that the galactosylation level of mAbs was altered by the culture conditions of hybridoma cells. The uridine diphosphate galactose (UDP-Gal) is one of the substrates of galactosylation. Based on that, we proposed a two-step model to predict N-linked glycoform profiles by solely using extracellular metabolites from cell culture. At the first step, the flux level of UDP-Gal in each culture was estimated based on a computational flux balance analysis (FBA); its level was found to be linear with the galactosylation degree on mAbs. At the second step, the glycoform profiles especially for G0F (agalactosylated), G1F (monogalactosylated) and G2F (digalactosylated) were predicted by a kinetic model. The model outputs well matched with the experimental data. Our study demonstrated that the integrated mathematical approach combining FBA and kinetic model is a promising strategy to predict glycoform profiles for mAbs during cell culture processes.
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26
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Becker M, Junghans L, Teleki A, Bechmann J, Takors R. The Less the Better: How Suppressed Base Addition Boosts Production of Monoclonal Antibodies With Chinese Hamster Ovary Cells. Front Bioeng Biotechnol 2019; 7:76. [PMID: 31032253 PMCID: PMC6470187 DOI: 10.3389/fbioe.2019.00076] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 03/25/2019] [Indexed: 11/30/2022] Open
Abstract
Biopharmaceutical production processes strive for the optimization of economic efficiency. Among others, the maximization of volumetric productivity is a key criterion. Typical parameters such as partial pressure of CO2 (pCO2) and pH are known to influence the performance although reasons are not yet fully elucidated. In this study the effects of pCO2 and pH shifts on the phenotypic performance were linked to metabolic and energetic changes. Short peak performance of qmAb (23 pg/cell/day) was achieved by early pCO2 shifts up to 200 mbar but followed by declining intracellular ATP levels to 2.5 fmol/cell and 80% increase of qLac. On the contrary, steadily rising qmAb could be installed by slight pH down-shifts ensuring constant cell specific ATP production (qATP) of 27 pmol/cell/day and high intracellular ATP levels of about 4 fmol/cell. As a result, maximum productivity was achieved combining highest qmAb (20 pg/cell/day) with maximum cell density and no lactate formation. Our results indicate that the energy availability in form of intracellular ATP is crucial for maintaining antibody synthesis and reacts sensitive to pCO2 and pH-process parameters typically responsible for inhomogeneities after scaling up.
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Affiliation(s)
- Max Becker
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Lisa Junghans
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
| | - Jan Bechmann
- Boehringer Ingelheim Pharma GmbH & Co. KG, Biberach an der Riss, Germany
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Stuttgart, Germany
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27
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Ma Y, Ma Q, Cui Y, Du L, Xie X, Chen N. Transcriptomic and metabolomics analyses reveal metabolic characteristics of L-leucine- and L-valine-producing Corynebacterium glutamicum mutants. ANN MICROBIOL 2019. [DOI: 10.1007/s13213-018-1431-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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28
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Xu J, Tang P, Yongky A, Drew B, Borys MC, Liu S, Li ZJ. Systematic development of temperature shift strategies for Chinese hamster ovary cells based on short duration cultures and kinetic modeling. MAbs 2019; 11:191-204. [PMID: 30230966 PMCID: PMC6343780 DOI: 10.1080/19420862.2018.1525262] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2018] [Revised: 09/02/2018] [Accepted: 09/13/2018] [Indexed: 10/28/2022] Open
Abstract
Temperature shift (TS) to a hypothermic condition has been widely used during protein production processes that use Chinese hamster ovary (CHO) cells. The effect of temperature on cell growth, metabolites, protein titer and quality depends on cell line, product, and other bioreactor conditions. Due to the large numbers of experiments, which typically last 2-3 weeks each, limited systematic TS studies have been reported with multiple shift temperatures and steps at different times. Here, we systematically studied the effect of temperature on cell culture performance for the production of two monoclonal antibodies by industrial GS and DG44 CHO cell lines. Three 2-8 day short-duration methods were developed and validated for researching the effect of many different temperatures on CHO cell culture and quality attributes. We found that minor temperature differences (1-1.5 °C) affected cell culture performance. The kinetic parameters extracted from the short duration data were subsequently used to compute and predict cell culture performance in extended duration of 10-14 days with multiple TS conditions for both CHO cell lines. These short-duration culture methods with kinetic modeling tools may be used for effective TS optimization to achieve the best profiles for cell growth, metabolites, titer and quality attributes. Although only three short-duration methods were developed with two CHO cell lines, similar short-duration methods with kinetic modeling may be applied for different hosts, including both microbial and other mammalian cells.
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Affiliation(s)
- Jianlin Xu
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Peifeng Tang
- Department of Paper and Bioprocess Engineering, SUNY-ESF, Syracuse, NY, USA
| | - Andrew Yongky
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Barry Drew
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Michael C. Borys
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
| | - Shijie Liu
- Department of Paper and Bioprocess Engineering, SUNY-ESF, Syracuse, NY, USA
| | - Zheng Jian Li
- Global Product Development and Supply, Bristol-Myers Squibb Company, Devens, MA, USA
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29
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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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30
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Sha S, Bhatia H, Yoon S. An RNA-seq based transcriptomic investigation into the productivity and growth variants with Chinese hamster ovary cells. J Biotechnol 2018; 271:37-46. [DOI: 10.1016/j.jbiotec.2018.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 01/26/2018] [Accepted: 02/19/2018] [Indexed: 02/06/2023]
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31
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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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